From 87413117cb02565757c06d16edba707e9079b40b Mon Sep 17 00:00:00 2001 From: jeanrjc <jean.cury@normalesup.org> Date: Thu, 14 Sep 2023 18:05:48 +0200 Subject: [PATCH] Remove all backslashes --- content/2.defense-systems/abi2.md | 6 +- content/2.defense-systems/abia.md | 8 +- content/2.defense-systems/abib.md | 6 +- content/2.defense-systems/abic.md | 12 +-- content/2.defense-systems/abid.md | 6 +- content/2.defense-systems/abie.md | 8 +- content/2.defense-systems/abig.md | 6 +- content/2.defense-systems/abih.md | 6 +- content/2.defense-systems/abii.md | 6 +- content/2.defense-systems/abij.md | 6 +- content/2.defense-systems/abik.md | 6 +- content/2.defense-systems/abil.md | 6 +- content/2.defense-systems/abin.md | 6 +- content/2.defense-systems/abio.md | 6 +- content/2.defense-systems/abip2.md | 8 +- content/2.defense-systems/abiq.md | 6 +- content/2.defense-systems/abir.md | 6 +- content/2.defense-systems/abit.md | 6 +- content/2.defense-systems/abiu.md | 6 +- 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content/2.defense-systems/menshen.md | 10 +-- content/2.defense-systems/mok_hok_sok.md | 12 +-- content/2.defense-systems/mokosh.md | 10 +-- content/2.defense-systems/mqsrac.md | 4 +- content/2.defense-systems/nhi.md | 14 ++-- content/2.defense-systems/nixi.md | 6 +- content/2.defense-systems/nlr.md | 24 +++--- content/2.defense-systems/old_exonuclease.md | 14 ++-- content/2.defense-systems/olokun.md | 6 +- content/2.defense-systems/pago.md | 24 +++--- content/2.defense-systems/pd-lambda-1.md | 6 +- content/2.defense-systems/pd-lambda-2.md | 8 +- content/2.defense-systems/pd-lambda-3.md | 8 +- content/2.defense-systems/pd-lambda-4.md | 8 +- content/2.defense-systems/pd-lambda-5.md | 8 +- content/2.defense-systems/pd-lambda-6.md | 6 +- content/2.defense-systems/pd-t4-1.md | 6 +- content/2.defense-systems/pd-t4-10.md | 8 +- content/2.defense-systems/pd-t4-2.md | 8 +- content/2.defense-systems/pd-t4-3.md | 6 +- content/2.defense-systems/pd-t4-4.md | 8 +- 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content/2.defense-systems/rst_2tm_1tm_tir.md | 8 +- content/2.defense-systems/rst_3hp.md | 12 +-- content/2.defense-systems/rst_duf4238.md | 12 +-- content/2.defense-systems/rst_gop_beta_cll.md | 12 +-- .../2.defense-systems/rst_helicaseduf2290.md | 12 +-- .../2.defense-systems/rst_hydrolase-3tm.md | 12 +-- content/2.defense-systems/rst_paris.md | 22 +++--- .../2.defense-systems/rst_rt-nitrilase-tm.md | 12 +-- content/2.defense-systems/rst_tir-nlr.md | 12 +-- content/2.defense-systems/sanata.md | 6 +- content/2.defense-systems/sefir.md | 12 +-- content/2.defense-systems/septu.md | 8 +- content/2.defense-systems/shango.md | 14 ++-- content/2.defense-systems/shedu.md | 6 +- content/2.defense-systems/shosta.md | 8 +- content/2.defense-systems/sofic.md | 6 +- content/2.defense-systems/spbk.md | 6 +- content/2.defense-systems/sspbcde.md | 12 +-- content/2.defense-systems/stk2.md | 8 +- content/2.defense-systems/thoeris.md | 12 +-- content/2.defense-systems/tiamat.md | 8 +- content/2.defense-systems/uzume.md | 8 +- content/2.defense-systems/viperin.md | 42 +++++------ content/2.defense-systems/wadjet.md | 8 +- content/2.defense-systems/zorya.md | 12 +-- 130 files changed, 707 insertions(+), 707 deletions(-) diff --git a/content/2.defense-systems/abi2.md b/content/2.defense-systems/abi2.md index 2a2c25fe..b709fb52 100644 --- a/content/2.defense-systems/abi2.md +++ b/content/2.defense-systems/abi2.md @@ -2,13 +2,13 @@ title: Abi2 --- -The Abi2 system is composed of one protein: Abi\_2. +The Abi2 system is composed of one protein: Abi_2. Here is an example found in the RefSeq database:  -Abi2 system in the genome of \*Clostridium butyricum\* (GCF\\_014131795.1) is composed of 1 protein: Abi\\_2 (WP\\_035763709.1). +Abi2 system in the genome of *Clostridium butyricum* (GCF_014131795.1) is composed of 1 protein: Abi_2 (WP_035763709.1). ## Distribution of the system among prokaryotes @@ -18,7 +18,7 @@ Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes  -\*Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/abia.md b/content/2.defense-systems/abia.md index 330be5b1..4329f7f6 100644 --- a/content/2.defense-systems/abia.md +++ b/content/2.defense-systems/abia.md @@ -8,11 +8,11 @@ Here is some example found in the RefSeq database:  -AbiA\\_large subsystem in the genome of \*Lactobacillus amylovorus\* (GCF\\_002706375.1) is composed of 1 protein: AbiA\\_large (WP\\_056940268.1). +AbiA_large subsystem in the genome of *Lactobacillus amylovorus* (GCF_002706375.1) is composed of 1 protein: AbiA_large (WP_056940268.1).  -AbiA\\_small subsystem in the genome of \*Mesobacillus foraminis\* (GCF\\_003667765.1) is composed of 2 proteins: AbiA\\_small (WP\\_121614402.1)and, AbiA\\_SLATT (WP\\_121614403.1). +AbiA_small subsystem in the genome of *Mesobacillus foraminis* (GCF_003667765.1) is composed of 2 proteins: AbiA_small (WP_121614402.1)and, AbiA_SLATT (WP_121614403.1). ## Distribution of the system among prokaryotes @@ -22,13 +22,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 50 genomes (  -\*Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation AbiA systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abib.md b/content/2.defense-systems/abib.md index bc399c55..99b008dd 100644 --- a/content/2.defense-systems/abib.md +++ b/content/2.defense-systems/abib.md @@ -8,7 +8,7 @@ Here is an example found in the RefSeq database:  -AbiB system in the genome of \*Lactococcus lactis\* (GCF\\_020221755.1) is composed of 1 protein: AbiB (WP\\_047687114.1). +AbiB system in the genome of *Lactococcus lactis* (GCF_020221755.1) is composed of 1 protein: AbiB (WP_047687114.1). ## Distribution of the system among prokaryotes @@ -18,13 +18,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 13 genomes (  -\*Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiB systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abic.md b/content/2.defense-systems/abic.md index 8cf4a7dc..c75c585b 100644 --- a/content/2.defense-systems/abic.md +++ b/content/2.defense-systems/abic.md @@ -8,7 +8,7 @@ Here is an example found in the RefSeq database:  -AbiC system in the genome of \*Enterococcus faecium\* (GCF\\_012933295.2) is composed of 1 protein: AbiC (WP\\_098388098.1). +AbiC system in the genome of *Enterococcus faecium* (GCF_012933295.2) is composed of 1 protein: AbiC (WP_098388098.1). ## Distribution of the system among prokaryotes @@ -18,19 +18,19 @@ Among the 22k complete genomes of RefSeq, this system is present in 196 genomes  -\*Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiC systems were experimentally validated using: -A system from \*Klebsiella pneumoniae's PICI (KpCIFDAARGOS\_1313)\* in \*Escherichia coli\* has an anti-phage effect against T5, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022) +A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Escherichia coli* has an anti-phage effect against T5, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022) -A system from \*Klebsiella pneumoniae's PICI (KpCIFDAARGOS\_1313)\* in \*Salmonella enterica\* has an anti-phage effect against P22, BTP1, ES18 (Fillol-Salom et al., 2022) +A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Salmonella enterica* has an anti-phage effect against P22, BTP1, ES18 (Fillol-Salom et al., 2022) -A system from \*Klebsiella pneumoniae's PICI (KpCIFDAARGOS\_1313)\* in \*Klebsiella pneumoniae\* has an anti-phage effect against Pokey, Raw, Eggy (Fillol-Salom et al., 2022) +A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Klebsiella pneumoniae* has an anti-phage effect against Pokey, Raw, Eggy (Fillol-Salom et al., 2022) -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, P335 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, P335 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abid.md b/content/2.defense-systems/abid.md index 94d81ae8..b475fd0b 100644 --- a/content/2.defense-systems/abid.md +++ b/content/2.defense-systems/abid.md @@ -8,7 +8,7 @@ Here is an example found in the RefSeq database:  -AbiD system in the genome of \*Lachnospira eligens\* (GCF\\_020735745.1) is composed of 1 protein: AbiD (WP\\_041688924.1). +AbiD system in the genome of *Lachnospira eligens* (GCF_020735745.1) is composed of 1 protein: AbiD (WP_041688924.1). ## Distribution of the system among prokaryotes @@ -18,13 +18,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 2748 genomes  -\*Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiD systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abie.md b/content/2.defense-systems/abie.md index 08281992..6589b00a 100644 --- a/content/2.defense-systems/abie.md +++ b/content/2.defense-systems/abie.md @@ -14,13 +14,13 @@ Based on this mechanisms, AbiE systems are classified as Type IV Toxin-Antitoxin ## Example of genomic structure -The AbiE system is composed of 2 proteins: AbiEi\_1 and, AbiEii. +The AbiE system is composed of 2 proteins: AbiEi_1 and, AbiEii. Here is an example found in the RefSeq database:  -AbiE system in the genome of \*Desulfuromonas versatilis\* (GCF\\_019704135.1) is composed of 2 proteins: AbiEi\\_1 (WP\\_221251730.1)and, AbiEii (WP\\_221251731.1). +AbiE system in the genome of *Desulfuromonas versatilis* (GCF_019704135.1) is composed of 2 proteins: AbiEi_1 (WP_221251730.1)and, AbiEii (WP_221251731.1). ## Distribution of the system among prokaryotes @@ -30,13 +30,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 3742 genomes  -\*Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiE systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abig.md b/content/2.defense-systems/abig.md index 6212ea72..1ecd3d72 100644 --- a/content/2.defense-systems/abig.md +++ b/content/2.defense-systems/abig.md @@ -8,7 +8,7 @@ Here is an example found in the RefSeq database:  -AbiG system in the genome of \*Streptococcus mutans\* (GCF\\_009738105.1) is composed of 2 proteins: AbiGi (WP\\_002266883.1)and, AbiGii (WP\\_002266884.1). +AbiG system in the genome of *Streptococcus mutans* (GCF_009738105.1) is composed of 2 proteins: AbiGi (WP_002266883.1)and, AbiGii (WP_002266884.1). ## Distribution of the system among prokaryotes @@ -18,13 +18,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 33 genomes (  -\*Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiG systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abih.md b/content/2.defense-systems/abih.md index 390f36ef..6176dc12 100644 --- a/content/2.defense-systems/abih.md +++ b/content/2.defense-systems/abih.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiH system in the genome of \*Agrobacterium tumefaciens\* (GCF\\_005221405.1) is composed of 1 protein: AbiH (WP\\_045021548.1). +AbiH system in the genome of *Agrobacterium tumefaciens* (GCF_005221405.1) is composed of 1 protein: AbiH (WP_045021548.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1277 genomes  -\*Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiH systems were experimentally validated using: -A system from \*lactococci\* in \*lactococci\* has an anti-phage effect against 936, c2 (Chopin et al., 2005) +A system from *lactococci* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abii.md b/content/2.defense-systems/abii.md index 74dccabc..057825ba 100644 --- a/content/2.defense-systems/abii.md +++ b/content/2.defense-systems/abii.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiI system in the genome of \*Enterococcus faecalis\* (GCF\\_002814115.1) is composed of 1 protein: AbiI (WP\\_002367720.1). +AbiI system in the genome of *Enterococcus faecalis* (GCF_002814115.1) is composed of 1 protein: AbiI (WP_002367720.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 8 genomes (0  -\*Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiI systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abij.md b/content/2.defense-systems/abij.md index e11da1a3..245dc812 100644 --- a/content/2.defense-systems/abij.md +++ b/content/2.defense-systems/abij.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiJ system in the genome of \*Loigolactobacillus backii\* (GCF\\_001663735.1) is composed of 1 protein: AbiJ (WP\\_068377534.1). +AbiJ system in the genome of *Loigolactobacillus backii* (GCF_001663735.1) is composed of 1 protein: AbiJ (WP_068377534.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 807 genomes  -\*Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiJ systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abik.md b/content/2.defense-systems/abik.md index e54df0e1..e8715841 100644 --- a/content/2.defense-systems/abik.md +++ b/content/2.defense-systems/abik.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiK system in the genome of \*Lactococcus lactis\* (GCF\\_002078995.2) is composed of 1 protein: AbiK (WP\\_081199340.1). +AbiK system in the genome of *Lactococcus lactis* (GCF_002078995.2) is composed of 1 protein: AbiK (WP_081199340.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 107 genomes  -\*Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiK systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abil.md b/content/2.defense-systems/abil.md index 48bc2166..90521fc9 100644 --- a/content/2.defense-systems/abil.md +++ b/content/2.defense-systems/abil.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiL system in the genome of \*Fusobacterium nucleatum\* (GCF\\_003019785.1) is composed of 2 proteins: AbiLii2 (WP\\_005903821.1)and, AbiLi2 (WP\\_005903823.1). +AbiL system in the genome of *Fusobacterium nucleatum* (GCF_003019785.1) is composed of 2 proteins: AbiLii2 (WP_005903821.1)and, AbiLi2 (WP_005903823.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 783 genomes  -\*Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiL systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abin.md b/content/2.defense-systems/abin.md index ea2c042b..5e732ecb 100644 --- a/content/2.defense-systems/abin.md +++ b/content/2.defense-systems/abin.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiN system in the genome of \*Enterococcus faecalis\* (GCF\\_016743895.1) is composed of 1 protein: AbiN (WP\\_002384355.1). +AbiN system in the genome of *Enterococcus faecalis* (GCF_016743895.1) is composed of 1 protein: AbiN (WP_002384355.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 167 genomes  -\*Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiN systems were experimentally validated using: -A system from \*lactococcal prophage\* in \*lactococci\* has an anti-phage effect against 936, c2 (Chopin et al., 2005) +A system from *lactococcal prophage* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abio.md b/content/2.defense-systems/abio.md index 377fb61e..db17b2c3 100644 --- a/content/2.defense-systems/abio.md +++ b/content/2.defense-systems/abio.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiO system in the genome of \*Pasteurella multocida\* (GCF\\_016313205.1) is composed of 1 protein: AbiO (WP\\_005752771.1). +AbiO system in the genome of *Pasteurella multocida* (GCF_016313205.1) is composed of 1 protein: AbiO (WP_005752771.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 109 genomes  -\*Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiO systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abip2.md b/content/2.defense-systems/abip2.md index c51303e9..b9410413 100644 --- a/content/2.defense-systems/abip2.md +++ b/content/2.defense-systems/abip2.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiP2 system in the genome of \*Casimicrobium huifangae\* (GCF\\_009746125.1) is composed of 1 protein: AbiP2 (WP\\_156862066.1). +AbiP2 system in the genome of *Casimicrobium huifangae* (GCF_009746125.1) is composed of 1 protein: AbiP2 (WP_156862066.1). ## Distribution of the system among prokaryotes @@ -20,15 +20,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 299 genomes  -\*Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiP2 systems were experimentally validated using: -Subsystem RT-Abi-P2 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5 (Gao et al., 2020) +Subsystem RT-Abi-P2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Gao et al., 2020) -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abiq.md b/content/2.defense-systems/abiq.md index 14cd8c8c..c8aba6b6 100644 --- a/content/2.defense-systems/abiq.md +++ b/content/2.defense-systems/abiq.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiQ system in the genome of \*Enterococcus sp.\* (GCF\\_003812305.1) is composed of 1 protein: AbiQ (WP\\_123866849.1). +AbiQ system in the genome of *Enterococcus sp.* (GCF_003812305.1) is composed of 1 protein: AbiQ (WP_123866849.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 262 genomes  -\*Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiQ systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abir.md b/content/2.defense-systems/abir.md index 03fbabdd..8b1da27a 100644 --- a/content/2.defense-systems/abir.md +++ b/content/2.defense-systems/abir.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiR system in the genome of \*Pediococcus pentosaceus\* (GCF\\_019614475.1) is composed of 3 proteins: AbiRa (WP\\_220689027.1), AbiRb (WP\\_011673124.1)and, AbiRc (WP\\_011673125.1). +AbiR system in the genome of *Pediococcus pentosaceus* (GCF_019614475.1) is composed of 3 proteins: AbiRa (WP_220689027.1), AbiRb (WP_011673124.1)and, AbiRc (WP_011673125.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 56 genomes (  -\*Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiR systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against c2 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against c2 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abit.md b/content/2.defense-systems/abit.md index 54cedcc9..c38be058 100644 --- a/content/2.defense-systems/abit.md +++ b/content/2.defense-systems/abit.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiT system in the genome of \*Sphaerochaeta associata\* (GCF\\_022869165.1) is composed of 2 proteins: AbiTi (WP\\_244771454.1)and, AbiTii (WP\\_244771455.1). +AbiT system in the genome of *Sphaerochaeta associata* (GCF_022869165.1) is composed of 2 proteins: AbiTi (WP_244771454.1)and, AbiTii (WP_244771455.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 8 genomes (0  -\*Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiT systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, P335 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, P335 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abiu.md b/content/2.defense-systems/abiu.md index 43cb5dbb..8425bb0f 100644 --- a/content/2.defense-systems/abiu.md +++ b/content/2.defense-systems/abiu.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiU system in the genome of \*Fulvivirga lutea\* (GCF\\_017068455.1) is composed of 1 protein: AbiU (WP\\_205721428.1). +AbiU system in the genome of *Fulvivirga lutea* (GCF_017068455.1) is composed of 1 protein: AbiU (WP_205721428.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1017 genomes  -\*Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiU systems were experimentally validated using: -A system from \*lactococcal plasmid\* in \*lactococci\* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) +A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005) ## Relevant abstracts diff --git a/content/2.defense-systems/abiv.md b/content/2.defense-systems/abiv.md index 89db7fa2..e8367561 100644 --- a/content/2.defense-systems/abiv.md +++ b/content/2.defense-systems/abiv.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiV system in the genome of \*Lactococcus cremoris\* (GCF\\_017376415.1) is composed of 1 protein: AbiV (WP\\_011834704.1). +AbiV system in the genome of *Lactococcus cremoris* (GCF_017376415.1) is composed of 1 protein: AbiV (WP_011834704.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 126 genomes  -\*Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiV systems were experimentally validated using: -A system from \*Lactococcus lactis\* in \*Lactococcus lactis\* has an anti-phage effect against sk1, p2, jj50, P008, bIL170, c2, bIL67, ml3, eb1 (Haaber et al., 2008) +A system from *Lactococcus lactis* in *Lactococcus lactis* has an anti-phage effect against sk1, p2, jj50, P008, bIL170, c2, bIL67, ml3, eb1 (Haaber et al., 2008) ## Relevant abstracts diff --git a/content/2.defense-systems/abiz.md b/content/2.defense-systems/abiz.md index 78081068..62682716 100644 --- a/content/2.defense-systems/abiz.md +++ b/content/2.defense-systems/abiz.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -AbiZ system in the genome of \*Streptococcus oralis\* (GCF\\_019334565.1) is composed of 1 protein: AbiZ (WP\\_215804505.1). +AbiZ system in the genome of *Streptococcus oralis* (GCF_019334565.1) is composed of 1 protein: AbiZ (WP_215804505.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 831 genomes  -\*Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation AbiZ systems were experimentally validated using: -A system from \*Lactococcus lactis\* in \*Lactococcus lactis\* has an anti-phage effect against Phi31.2, ul36, phi31, phi48, phi31.1, Q30, Q36, Q33, phi50, phi48 (Durmaz et al., 2007) +A system from *Lactococcus lactis* in *Lactococcus lactis* has an anti-phage effect against Phi31.2, ul36, phi31, phi48, phi31.1, Q30, Q36, Q33, phi50, phi48 (Durmaz et al., 2007) ## Relevant abstracts diff --git a/content/2.defense-systems/aditi.md b/content/2.defense-systems/aditi.md index bb174371..35d19052 100644 --- a/content/2.defense-systems/aditi.md +++ b/content/2.defense-systems/aditi.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Aditi system in the genome of \*Fusobacterium hwasookii\* (GCF\\_001455105.1) is composed of 2 proteins: DitB (WP\\_029491896.1)and, DitA (WP\\_029491897.1). +Aditi system in the genome of *Fusobacterium hwasookii* (GCF_001455105.1) is composed of 2 proteins: DitB (WP_029491896.1)and, DitA (WP_029491897.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 40 genomes (  -\*Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Aditi systems were experimentally validated using: -A system from \*Saccharibacillus kuerlensis\* in \*Bacillus subtilis\* has an anti-phage effect against phi105, Rho14, SPP1 (Millman et al., 2022) +A system from *Saccharibacillus kuerlensis* in *Bacillus subtilis* has an anti-phage effect against phi105, Rho14, SPP1 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/avast.md b/content/2.defense-systems/avast.md index adb0fc47..a21de140 100644 --- a/content/2.defense-systems/avast.md +++ b/content/2.defense-systems/avast.md @@ -17,23 +17,23 @@ Here is some example found in the RefSeq database:  -AVAST\\_I subsystem in the genome of \*Vibrio sp.\* (GCF\\_905175355.1) is composed of 3 proteins: Avs1A (WP\\_208445041.1), Avs1B (WP\\_208445042.1)and, Avs1C (WP\\_108173272.1). +AVAST_I subsystem in the genome of *Vibrio sp.* (GCF_905175355.1) is composed of 3 proteins: Avs1A (WP_208445041.1), Avs1B (WP_208445042.1)and, Avs1C (WP_108173272.1).  -AVAST\\_II subsystem in the genome of \*Escherichia coli\* (GCF\\_018884505.1) is composed of 1 protein: Avs2A (WP\\_032199984.1). +AVAST_II subsystem in the genome of *Escherichia coli* (GCF_018884505.1) is composed of 1 protein: Avs2A (WP_032199984.1).  -AVAST\\_III subsystem in the genome of \*Enterobacter cancerogenus\* (GCF\\_002850575.1) is composed of 2 proteins: Avs3B (WP\\_199559884.1)and, Avs3A (WP\\_101737373.1). +AVAST_III subsystem in the genome of *Enterobacter cancerogenus* (GCF_002850575.1) is composed of 2 proteins: Avs3B (WP_199559884.1)and, Avs3A (WP_101737373.1).  -AVAST\\_IV subsystem in the genome of \*Escherichia coli\* (GCF\\_016903595.1) is composed of 1 protein: Avs4A (WP\\_000240574.1). +AVAST_IV subsystem in the genome of *Escherichia coli* (GCF_016903595.1) is composed of 1 protein: Avs4A (WP_000240574.1).  -AVAST\\_V subsystem in the genome of \*Leclercia adecarboxylata\* (GCF\\_006171285.1) is composed of 1 protein: Avs5A (WP\\_139565349.1). +AVAST_V subsystem in the genome of *Leclercia adecarboxylata* (GCF_006171285.1) is composed of 1 protein: Avs5A (WP_139565349.1). ## Distribution of the system among prokaryotes @@ -43,49 +43,49 @@ Among the 22k complete genomes of RefSeq, this system is present in 1046 genomes  -\*Proportion of genome encoding the AVAST system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the AVAST system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation AVAST systems were experimentally validated using: -Subsystem SIR2-STAND with a system from \*Escherichia fergusonii's PICI (EfCIRHB19-C05)\* in \*Escherichia coli\* has an anti-phage effect against T4, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022) +Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Escherichia coli* has an anti-phage effect against T4, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022) -Subsystem SIR2-STAND with a system from \*Escherichia fergusonii's PICI (EfCIRHB19-C05)\* in \*Salmonella enterica \* has an anti-phage effect against P22, BTP1, ES18, det7 (Fillol-Salom et al., 2022) +Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Salmonella enterica * has an anti-phage effect against P22, BTP1, ES18, det7 (Fillol-Salom et al., 2022) -Subsystem SIR2-STAND with a system from \*Escherichia fergusonii's PICI (EfCIRHB19-C05)\* in \*Klebsiella pneumoniae \* has an anti-phage effect against Pokey (Fillol-Salom et al., 2022) +Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Klebsiella pneumoniae * has an anti-phage effect against Pokey (Fillol-Salom et al., 2022) -Subsystem Metallo beta-lactamase + protease + STAND (Type 1) with a system from \*Erwinia piriflorinigrans\* in \*Escherichia coli\* has an anti-phage effect against P1 (Gao et al., 2020) +Subsystem Metallo beta-lactamase + protease + STAND (Type 1) with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2020) -Subsystem STAND (Type 2) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4, P1 (Gao et al., 2020) +Subsystem STAND (Type 2) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, P1 (Gao et al., 2020) -Subsystem DUF4297-STAND (Type 3) with a system from \*Salmonella enterica\* in \*Escherichia coli\* has an anti-phage effect against T2, T3, T7, PhiV-1 (Gao et al., 2020) +Subsystem DUF4297-STAND (Type 3) with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T2, T3, T7, PhiV-1 (Gao et al., 2020) -Subsystem Mrr-STAND (Type 4) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020) +Subsystem Mrr-STAND (Type 4) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020) -Subsystem SIR2-STAND (Type 5) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2 (Gao et al., 2020) +Subsystem SIR2-STAND (Type 5) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2 (Gao et al., 2020) -Subsystem SeAvs1 with a system from \*Salmonella enterica\* in \*Escherichia coli\* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022) +Subsystem SeAvs1 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022) -Subsystem EcAcs1 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against ZL-19 (Gao et al., 2022) +Subsystem EcAcs1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022) -Subsystem EpAvs1 with a system from \*Erwinia piriflorinigrans\* in \*Escherichia coli\* has an anti-phage effect against P1, Lambda, , ZL-19 (Gao et al., 2022) +Subsystem EpAvs1 with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1, Lambda, , ZL-19 (Gao et al., 2022) -Subsystem SeAvs3 with a system from \*Salmonella enterica\* in \*Escherichia coli\* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022) +Subsystem SeAvs3 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022) -Subsystem KvAvs3 with a system from \*Klebsiella variicola\* in \*Escherichia coli\* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022) +Subsystem KvAvs3 with a system from *Klebsiella variicola* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022) -Subsystem EcAvs2 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T7, PhiV-1, P1, T4, T5, ZL-19 (Gao et al., 2022) +Subsystem EcAvs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, P1, T4, T5, ZL-19 (Gao et al., 2022) -Subsystem Ec2Avs2 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against P1 (Gao et al., 2022) +Subsystem Ec2Avs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2022) -Subsystem EcAvs4 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022) +Subsystem EcAvs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022) -Subsystem Ec2Avs4 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022) +Subsystem Ec2Avs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022) -Subsystem KpAvs4 with a system from \*Klebsiella pneumoniae\* in \*Escherichia coli\* has an anti-phage effect against ZL-19 (Gao et al., 2022) +Subsystem KpAvs4 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022) -Subsystem CcAvs4 with a system from \*Corallococcus coralloides\* in \*Escherichia coli\* has an anti-phage effect against T7 (Gao et al., 2022) +Subsystem CcAvs4 with a system from *Corallococcus coralloides* in *Escherichia coli* has an anti-phage effect against T7 (Gao et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/azaca.md b/content/2.defense-systems/azaca.md index b8c75a27..bc9e7429 100644 --- a/content/2.defense-systems/azaca.md +++ b/content/2.defense-systems/azaca.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Azaca system in the genome of \*Ornithinimicrobium sp.\* (GCF\\_023923205.1) is composed of 3 proteins: ZacA (WP\\_252620090.1), ZacB (WP\\_252620091.1)and, ZacC (WP\\_252620092.1). +Azaca system in the genome of *Ornithinimicrobium sp.* (GCF_023923205.1) is composed of 3 proteins: ZacA (WP_252620090.1), ZacB (WP_252620091.1)and, ZacC (WP_252620092.1). ## Distribution of the system among prokaryotes @@ -20,15 +20,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 206 genomes  -\*Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Azaca systems were experimentally validated using: -A system from \*Bacillus massilioanorexius\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022) +A system from *Bacillus massilioanorexius* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022) -A system from \*Bacillus massilioanorexius\* in \*Bacillus subtilis\* has an anti-phage effect against SBSphiC (Millman et al., 2022) +A system from *Bacillus massilioanorexius* in *Bacillus subtilis* has an anti-phage effect against SBSphiC (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/borvo.md b/content/2.defense-systems/borvo.md index 6ec5f4c1..a1109c98 100644 --- a/content/2.defense-systems/borvo.md +++ b/content/2.defense-systems/borvo.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Borvo system in the genome of \*Brevundimonas sp.\* (GCF\\_002002865.1) is composed of 1 protein: BovA\\_addition (WP\\_077354142.1). +Borvo system in the genome of *Brevundimonas sp.* (GCF_002002865.1) is composed of 1 protein: BovA_addition (WP_077354142.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 650 genomes  -\*Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Borvo systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18 (Millman et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/brex.md b/content/2.defense-systems/brex.md index 43ce575f..cd6dc538 100644 --- a/content/2.defense-systems/brex.md +++ b/content/2.defense-systems/brex.md @@ -4,13 +4,13 @@ title: BREX ## Description -BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/list\_defense\_systems/RM)\-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1). +BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/list_defense_systems/RM)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1). BREX systems can be divided into six subtypes, and are encoded by 4 to 8 genes, some of these genes being mandatory while others are subtype-specific (1). ## Molecular mechanism -\*B. cereus\* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/list\_defense\_systems/RM) systems. +*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/list_defense_systems/RM) systems. However, the mechanism through which BREX Type 1 systems defend against phages is distinct from RM systems, and does not seem to degrade phage nucleic acids (1). @@ -23,21 +23,21 @@ The BREX system have been describe in a total of 6 subsystems. BREX systems necessarily include the pglZ gene (encoding for a putative alkaline phosphatase), which is accompanied by either brxC or pglY. These two genes share only a distant homology but have been hypothesized to fulfill the same function among the different BREX subtypes (1). -Goldfarb and colleagues reported a 6-gene cassette from \*Bacillus cereus\* as being the model for BREX Type 1. BREX Type 1 are the most widespread BREX systems, and present two core genes (pglZ and brxC).  Four other genes  are associated with BREX Type 1 : \*pglX (\*encoding for a putative methyltransferase),  \*brxA (\*encoding an RNA-binding anti-termination protein)\*, brxB (\*unknown functio\*n), brxC (\*encoding for a protein with ATP-binding domain) and \*brxL\* (encoding for a putative protease) (1,2). +Goldfarb and colleagues reported a 6-gene cassette from *Bacillus cereus* as being the model for BREX Type 1. BREX Type 1 are the most widespread BREX systems, and present two core genes (pglZ and brxC).  Four other genes  are associated with BREX Type 1 : *pglX (*encoding for a putative methyltransferase),  *brxA (*encoding an RNA-binding anti-termination protein)*, brxB (*unknown functio*n), brxC (*encoding for a protein with ATP-binding domain) and *brxL* (encoding for a putative protease) (1,2). Type 2 BREX systems include the system formerly known as Pgl , which is comprised of four genes  (pglW, X, Y, and Z) (3), to which Goldfarb and colleagues found often associated two additional genes (brxD, and brxHI). -Although 4 additional BREX subtypes have been proposed, BREX Type 1 and Type 2 remain the only ones to be experimentally validated. A detailed description of the other subtypes can be found in Goldfarb \*et al\*., 2015. +Although 4 additional BREX subtypes have been proposed, BREX Type 1 and Type 2 remain the only ones to be experimentally validated. A detailed description of the other subtypes can be found in Goldfarb *et al*., 2015. Here is some example found in the RefSeq database:  -BREX\\_I subsystem in the genome of \*Kaistella sp.\* (GCF\\_020410745.1) is composed of 6 proteins: brxL (WP\\_226063319.1), pglZA (WP\\_226063320.1), pglX1 (WP\\_226063321.1), brxC (WP\\_226063322.1), brxB\\_DUF1788 (WP\\_226063323.1)and, brxA\\_DUF1819 (WP\\_226063324.1). +BREX_I subsystem in the genome of *Kaistella sp.* (GCF_020410745.1) is composed of 6 proteins: brxL (WP_226063319.1), pglZA (WP_226063320.1), pglX1 (WP_226063321.1), brxC (WP_226063322.1), brxB_DUF1788 (WP_226063323.1)and, brxA_DUF1819 (WP_226063324.1).  -BREX\\_II subsystem in the genome of \*Streptomyces hygroscopicus\* (GCF\\_001447075.1) is composed of 5 proteins: brxD (WP\\_058082289.1), pglZ2 (WP\\_058082290.1), pglY (WP\\_058082291.1), pglX2 (WP\\_058082292.1)and, pglW (WP\\_237280966.1). +BREX_II subsystem in the genome of *Streptomyces hygroscopicus* (GCF_001447075.1) is composed of 5 proteins: brxD (WP_058082289.1), pglZ2 (WP_058082290.1), pglY (WP_058082291.1), pglX2 (WP_058082292.1)and, pglW (WP_237280966.1). ## Distribution of the system among prokaryotes @@ -47,15 +47,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 1612 genomes  -\*Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation BREX systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against Lambda (Gao et al., 2020 ; Gordeeva et al., 2017) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda (Gao et al., 2020 ; Gordeeva et al., 2017) -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against SPbeta, SP16, Zeta, phi3T, SPO2, SPO1, SP82G (Goldfarb et al., 2015) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SPbeta, SP16, Zeta, phi3T, SPO2, SPO1, SP82G (Goldfarb et al., 2015) ## Relevant abstracts @@ -72,8 +72,8 @@ items: ## References -\*\*1\. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S, Charpak-Amikam Y, Afik S, Ofir G, Sorek R. BREX is a novel phage resistance system widespread in microbial genomes. EMBO J. 2015 Jan 13;34(2):169-83. doi: 10.15252/embj.201489455. Epub 2014 Dec 1. PMID: 25452498; PMCID: PMC4337064.\*\* +**1. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S, Charpak-Amikam Y, Afik S, Ofir G, Sorek R. BREX is a novel phage resistance system widespread in microbial genomes. EMBO J. 2015 Jan 13;34(2):169-83. doi: 10.15252/embj.201489455. Epub 2014 Dec 1. PMID: 25452498; PMCID: PMC4337064.** -\*\*2\. Nunes-Alves C. Bacterial physiology: putting the 'BREX' on phage replication. Nat Rev Microbiol. 2015 Mar;13(3):129. doi: 10.1038/nrmicro3437. Epub 2015 Feb 2. PMID: 25639679.\*\* +**2. Nunes-Alves C. Bacterial physiology: putting the 'BREX' on phage replication. Nat Rev Microbiol. 2015 Mar;13(3):129. doi: 10.1038/nrmicro3437. Epub 2015 Feb 2. PMID: 25639679.** -\*\*3\. Sumby P, Smith MC. Phase variation in the phage growth limitation system of Streptomyces coelicolor A3(2). J Bacteriol. 2003;185(15):4558-4563. doi:10.1128/JB.185.15.4558-4563.2003\*\* +**3. Sumby P, Smith MC. Phase variation in the phage growth limitation system of Streptomyces coelicolor A3(2). J Bacteriol. 2003;185(15):4558-4563. doi:10.1128/JB.185.15.4558-4563.2003** diff --git a/content/2.defense-systems/bsta.md b/content/2.defense-systems/bsta.md index b132981b..4e98cec7 100644 --- a/content/2.defense-systems/bsta.md +++ b/content/2.defense-systems/bsta.md @@ -4,13 +4,13 @@ title: BstA ## Description -BstA is a family of defense systems. BtsA systems from \*Salmonella enterica subsp. enterica\*, \*Klebsiella pneumoniae\* and \*Escherichia coli\* have been shown to provide resistance against a large diversity of phages when expressed in a \*S. enterica\* or \*E.coli\* host (1). +BstA is a family of defense systems. BtsA systems from *Salmonella enterica subsp. enterica*, *Klebsiella pneumoniae* and *Escherichia coli* have been shown to provide resistance against a large diversity of phages when expressed in a *S. enterica* or *E.coli* host (1). The majority of BstA systems appear to be prophage-encoded, as 79% of BstA homologs found in a set of Gram-negative bacterial genomes were associted with phage genes (1). The defense mechanism encoded by BstA remains to be elucidated. Experimental observation suggest that BtsA could act through an abortive infection mechanism. Fluorescence microscopy experiments suggest that the BstA protein colocalizes with phage DNA. The BstA protein appears to inhibit phage DNA replication during lytic phage infection cycles (1). -Interestingly, part of the BstA locus appears to encode an anti-BstA genetic element (\*aba\*), which prevents auto-immunity for prophages encoding the BstA locus. The aba element appears to be specific to a given BstA locus, as replacing the aba element from a BstA locus with the aba element from an other BstA system does not prevent auto-immunity (1). +Interestingly, part of the BstA locus appears to encode an anti-BstA genetic element (*aba*), which prevents auto-immunity for prophages encoding the BstA locus. The aba element appears to be specific to a given BstA locus, as replacing the aba element from a BstA locus with the aba element from an other BstA system does not prevent auto-immunity (1). ## Example of genomic structure @@ -20,7 +20,7 @@ Here is an example found in the RefSeq database:  -BstA system in the genome of \*Providencia rustigianii\* (GCF\\_900635875.1) is composed of 1 protein: BstA (WP\\_126437212.1). +BstA system in the genome of *Providencia rustigianii* (GCF_900635875.1) is composed of 1 protein: BstA (WP_126437212.1). ## Distribution of the system among prokaryotes @@ -30,21 +30,21 @@ Among the 22k complete genomes of RefSeq, this system is present in 236 genomes  -\*Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation BstA systems were experimentally validated using: -A system from \*Salmonella Typhimurium's BTP1 prophage\* in \*Salmonella Typhimurium\* has an anti-phage effect against P22, ES18, 9NA (Owen et al., 2021) +A system from *Salmonella Typhimurium's BTP1 prophage* in *Salmonella Typhimurium* has an anti-phage effect against P22, ES18, 9NA (Owen et al., 2021) -A system from \*Salmonella Typhimurium's BTP1 prophage\* in \*Escherichia coli\* has an anti-phage effect against P22, ES18, 9NA (Owen et al., 2021) +A system from *Salmonella Typhimurium's BTP1 prophage* in *Escherichia coli* has an anti-phage effect against P22, ES18, 9NA (Owen et al., 2021) -A system from \*Klebsiella pneumoniae\* in \*Salmonella Typhimurium\* has an anti-phage effect against BTP1, P22, ES18, P22 HT, 9NA, Felix O1 (Owen et al., 2021) +A system from *Klebsiella pneumoniae* in *Salmonella Typhimurium* has an anti-phage effect against BTP1, P22, ES18, P22 HT, 9NA, Felix O1 (Owen et al., 2021) -A system from \*Escherichia coli\* in \*Salmonella Typhimurium\* has an anti-phage effect against BTP1, P22, ES18, P22 HT, 9NA (Owen et al., 2021) +A system from *Escherichia coli* in *Salmonella Typhimurium* has an anti-phage effect against BTP1, P22, ES18, P22 HT, 9NA (Owen et al., 2021) -A system from \*Salmonella Typhimurium's BTP1\* in \*Escherichia coli\* has an anti-phage effect against Lambda, Phi80, P1vir, T7 (Owen et al., 2021) +A system from *Salmonella Typhimurium's BTP1* in *Escherichia coli* has an anti-phage effect against Lambda, Phi80, P1vir, T7 (Owen et al., 2021) ## Relevant abstracts @@ -59,4 +59,4 @@ items: ## References -1\. Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8. doi: 10.1016/j.chom.2021.09.002. Epub 2021 Sep 30. PMID: 34597593; PMCID: PMC8585504. +1. Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8. doi: 10.1016/j.chom.2021.09.002. Epub 2021 Sep 30. PMID: 34597593; PMCID: PMC8585504. diff --git a/content/2.defense-systems/bunzi.md b/content/2.defense-systems/bunzi.md index 94ec25e4..fa084df8 100644 --- a/content/2.defense-systems/bunzi.md +++ b/content/2.defense-systems/bunzi.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Bunzi system in the genome of \*Mammaliicoccus lentus\* (GCF\\_014070215.1) is composed of 2 proteins: BnzB (WP\\_107556517.1)and, BnzA (WP\\_107556516.1). +Bunzi system in the genome of *Mammaliicoccus lentus* (GCF_014070215.1) is composed of 2 proteins: BnzB (WP_107556517.1)and, BnzA (WP_107556516.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 286 genomes  -\*Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Bunzi systems were experimentally validated using: -A system from \*Ligilactobacillus animalis\* in \*Bacillus subtilis\* has an anti-phage effect against AR9 (Jumbo), PBS1 (Jumbo) (Millman et al., 2022) +A system from *Ligilactobacillus animalis* in *Bacillus subtilis* has an anti-phage effect against AR9 (Jumbo), PBS1 (Jumbo) (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/caprel.md b/content/2.defense-systems/caprel.md index ac155b30..2a563ff8 100644 --- a/content/2.defense-systems/caprel.md +++ b/content/2.defense-systems/caprel.md @@ -4,7 +4,7 @@ title: CapRel ## Description -CapRel is a fused toxin–antitoxin system that is active against diverse phages when expressed in \*Escherichia coli\*. CapRel belongs to the family of toxSAS toxin–antitoxin systems. CapRel is an Abortive infection system which is found in Cyanobacteria, Actinobacteria, and Proteobacteria, Spirochetes, Bacteroidetes, and Firmicutes, as well as in some temperate phages. +CapRel is a fused toxin–antitoxin system that is active against diverse phages when expressed in *Escherichia coli*. CapRel belongs to the family of toxSAS toxin–antitoxin systems. CapRel is an Abortive infection system which is found in Cyanobacteria, Actinobacteria, and Proteobacteria, Spirochetes, Bacteroidetes, and Firmicutes, as well as in some temperate phages. ## Molecular mechanism @@ -22,7 +22,7 @@ Here is an example found in the RefSeq database:  -CapRel system in the genome of \*Escherichia coli\* (GCF\\_003856995.1) is composed of 1 protein: CapRel (WP\\_000526244.1). +CapRel system in the genome of *Escherichia coli* (GCF_003856995.1) is composed of 1 protein: CapRel (WP_000526244.1). ## Distribution of the system among prokaryotes @@ -32,17 +32,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 407 genomes  -\*Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation CapRel systems were experimentally validated using: -A system from \*Salmonella phage SJ46\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, RB69, SECphi27 (Zhang et al., 2022) +A system from *Salmonella phage SJ46* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, RB69, SECphi27 (Zhang et al., 2022) -A system from \*Enterobacter chengduensis\* in \*Escherichia coli\* has an anti-phage effect against T7 (Zhang et al., 2022) +A system from *Enterobacter chengduensis* in *Escherichia coli* has an anti-phage effect against T7 (Zhang et al., 2022) -A system from \*Klebsiella pneumoniae\* in \*Escherichia coli\* has an anti-phage effect against SECphi18 (Zhang et al., 2022) +A system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against SECphi18 (Zhang et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/cbass.md b/content/2.defense-systems/cbass.md index 09a20ef8..39b41d35 100644 --- a/content/2.defense-systems/cbass.md +++ b/content/2.defense-systems/cbass.md @@ -10,19 +10,19 @@ Here is some example found in the RefSeq database:  -CBASS\\_I subsystem in the genome of \*Rhizobium leguminosarum\* (GCF\\_002243365.1) is composed of 2 proteins: 4TM\\_new (WP\\_094230678.1)and, Cyclase\\_SMODS (WP\\_094230679.1). +CBASS_I subsystem in the genome of *Rhizobium leguminosarum* (GCF_002243365.1) is composed of 2 proteins: 4TM_new (WP_094230678.1)and, Cyclase_SMODS (WP_094230679.1).  -CBASS\\_II subsystem in the genome of \*Parvularcula bermudensis\* (GCF\\_000152825.2) is composed of 3 proteins: 4TM\\_new (WP\\_013299178.1), Cyclase\\_II (WP\\_148235131.1)and, AG\\_E2\\_Prok-E2\\_B (WP\\_013299180.1). +CBASS_II subsystem in the genome of *Parvularcula bermudensis* (GCF_000152825.2) is composed of 3 proteins: 4TM_new (WP_013299178.1), Cyclase_II (WP_148235131.1)and, AG_E2_Prok-E2_B (WP_013299180.1).  -CBASS\\_III subsystem in the genome of \*Methylocella tundrae\* (GCF\\_900749825.1) is composed of 5 proteins: Endonuc\\_small (WP\\_134490779.1), Cyclase\\_SMODS (WP\\_134490781.1), bacHORMA\\_2 (WP\\_134490783.1), HORMA (WP\\_134490785.1)and, TRIP13 (WP\\_134490787.1). +CBASS_III subsystem in the genome of *Methylocella tundrae* (GCF_900749825.1) is composed of 5 proteins: Endonuc_small (WP_134490779.1), Cyclase_SMODS (WP_134490781.1), bacHORMA_2 (WP_134490783.1), HORMA (WP_134490785.1)and, TRIP13 (WP_134490787.1).  -CBASS\\_IV subsystem in the genome of \*Bacillus sp.\* (GCF\\_022809835.1) is composed of 4 proteins: 2TM\\_type\\_IV (WP\\_243501124.1), QueC (WP\\_206906219.1), TGT (WP\\_243501126.1)and, Cyclase\\_SMODS (WP\\_243501127.1). +CBASS_IV subsystem in the genome of *Bacillus sp.* (GCF_022809835.1) is composed of 4 proteins: 2TM_type_IV (WP_243501124.1), QueC (WP_206906219.1), TGT (WP_243501126.1)and, Cyclase_SMODS (WP_243501127.1). ## Distribution of the system among prokaryotes @@ -32,19 +32,19 @@ Among the 22k complete genomes of RefSeq, this system is present in 2938 genomes  -\*Proportion of genome encoding the CBASS system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the CBASS system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation CBASS systems were experimentally validated using: -A system from \*Vibrio cholerae\* in \*Escherichia coli\* has an anti-phage effect against P1, T2 (Cohen et al., 2019) +A system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against P1, T2 (Cohen et al., 2019) -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against P1, T2, T4, T5, T6, LambdaVir (Cohen et al., 2019) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, T2, T4, T5, T6, LambdaVir (Cohen et al., 2019) -A system from \*Enterobacter cloacae\* in \*Escherichia coli\* has an anti-phage effect against T2, T7 (Lowey et al., 2020) +A system from *Enterobacter cloacae* in *Escherichia coli* has an anti-phage effect against T2, T7 (Lowey et al., 2020) -A system from \*Pseudomonas aeruginosa\* in \*Pseudomonas aeruginosa\* has an anti-phage effect against PaMx41, PaMx33, PaMx35, PaMx43 (Huiting et al., 2022) +A system from *Pseudomonas aeruginosa* in *Pseudomonas aeruginosa* has an anti-phage effect against PaMx41, PaMx33, PaMx35, PaMx43 (Huiting et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/dartg.md b/content/2.defense-systems/dartg.md index 2f934137..231b3c45 100644 --- a/content/2.defense-systems/dartg.md +++ b/content/2.defense-systems/dartg.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -DarTG system in the genome of \*Mycobacterium tuberculosis\* (GCF\\_904810345.1) is composed of 2 proteins: DarT (WP\\_003400548.1)and, DarG (WP\\_003400551.1). +DarTG system in the genome of *Mycobacterium tuberculosis* (GCF_904810345.1) is composed of 2 proteins: DarT (WP_003400548.1)and, DarG (WP_003400551.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 955 genomes  -\*Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation DarTG systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against RB69, T5, SECphi18, Lust (Leroux et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against RB69, T5, SECphi18, Lust (Leroux et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/dazbog.md b/content/2.defense-systems/dazbog.md index ed1da650..10ba7a13 100644 --- a/content/2.defense-systems/dazbog.md +++ b/content/2.defense-systems/dazbog.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Dazbog system in the genome of \*Bacillus cereus\* (GCF\\_001518875.1) is composed of 2 proteins: DzbA (WP\\_082188833.1)and, DzbB (WP\\_059303380.1). +Dazbog system in the genome of *Bacillus cereus* (GCF_001518875.1) is composed of 2 proteins: DzbA (WP_082188833.1)and, DzbB (WP_059303380.1). ## Distribution of the system among prokaryotes @@ -20,15 +20,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 73 genomes (  -\*Proportion of genome encoding the Dazbog system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Dazbog system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Dazbog systems were experimentally validated using: -A system from \*Bacillus cereus\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, T5, T7 (Millman et al., 2022) +A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, T7 (Millman et al., 2022) -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against Fado, SPR (Millman et al., 2022) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against Fado, SPR (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/dctpdeaminase.md b/content/2.defense-systems/dctpdeaminase.md index 49403373..c01c65bf 100644 --- a/content/2.defense-systems/dctpdeaminase.md +++ b/content/2.defense-systems/dctpdeaminase.md @@ -20,7 +20,7 @@ Here is an example found in the RefSeq database:  -dCTPdeaminase system in the genome of \*Vibrio parahaemolyticus\* (GCF\\_009883855.1) is composed of 1 protein: dCTPdeaminase (WP\\_029845369.1). +dCTPdeaminase system in the genome of *Vibrio parahaemolyticus* (GCF_009883855.1) is composed of 1 protein: dCTPdeaminase (WP_029845369.1). ## Distribution of the system among prokaryotes @@ -30,21 +30,21 @@ Among the 22k complete genomes of RefSeq, this system is present in 501 genomes  -\*Proportion of genome encoding the dCTPdeaminase system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the dCTPdeaminase system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation dCTPdeaminase systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, T2, T4, T6, T7 (Tal et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, T2, T4, T6, T7 (Tal et al., 2022) -Subsystem AvcID with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T3, SECphi17, SECphi18, SECphi27 (Hsueh et al., 2022) +Subsystem AvcID with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, SECphi17, SECphi18, SECphi27 (Hsueh et al., 2022) -Subsystem AvcID with a system from \*Proteus mirabilis\* in \*Escherichia coli\* has an anti-phage effect against T4 (Hsueh et al., 2022) +Subsystem AvcID with a system from *Proteus mirabilis* in *Escherichia coli* has an anti-phage effect against T4 (Hsueh et al., 2022) -Subsystem AvcID with a system from \*Vibrio parahaemolyticus\* in \*Escherichia coli\* has an anti-phage effect against T3, T5, T6, SECphi18 (Hsueh et al., 2022) +Subsystem AvcID with a system from *Vibrio parahaemolyticus* in *Escherichia coli* has an anti-phage effect against T3, T5, T6, SECphi18 (Hsueh et al., 2022) -Subsystem AvcID with a system from \*Vibrio cholerae\* in \*Escherichia coli\* has an anti-phage effect against T2, T3 (Hsueh et al., 2022) +Subsystem AvcID with a system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against T2, T3 (Hsueh et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/dgtpase.md b/content/2.defense-systems/dgtpase.md index b881eac7..3374b717 100644 --- a/content/2.defense-systems/dgtpase.md +++ b/content/2.defense-systems/dgtpase.md @@ -6,13 +6,13 @@ title: dGTPase ## Example of genomic structure -The dGTPase system is composed of one protein: Sp\_dGTPase. +The dGTPase system is composed of one protein: Sp_dGTPase. Here is an example found in the RefSeq database:  -dGTPase system in the genome of \*Acinetobacter pittii\* (GCF\\_002012285.1) is composed of 1 protein: Sp\\_dGTPase (WP\\_213033921.1). +dGTPase system in the genome of *Acinetobacter pittii* (GCF_002012285.1) is composed of 1 protein: Sp_dGTPase (WP_213033921.1). ## Distribution of the system among prokaryotes @@ -20,21 +20,21 @@ The dGTPase system is present in a total of 353 different species. Among the 22k complete genomes of RefSeq, this system is present in 1532 genomes (6.7 %). - + -\*Proportion of genome encoding the dGTPase system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the dGTPase system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation dGTPase systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T7 (Tal et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T7 (Tal et al., 2022) -A system from \*Mesorhizobium ssp.\* in \*Escherichia coli\* has an anti-phage effect against SECphi4, SECphi6, SECphi18, SECphi27, T7 (Tal et al., 2022) +A system from *Mesorhizobium ssp.* in *Escherichia coli* has an anti-phage effect against SECphi4, SECphi6, SECphi18, SECphi27, T7 (Tal et al., 2022) -A system from \*Pseudoalteromonas luteoviolacea\* in \*Escherichia coli\* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T2 (Tal et al., 2022) +A system from *Pseudoalteromonas luteoviolacea* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T2 (Tal et al., 2022) -A system from \*Shewanella putrefaciens\* in \*Escherichia coli\* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T2, T6, T7, SECphi17 (Tal et al., 2022) +A system from *Shewanella putrefaciens* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T2, T6, T7, SECphi17 (Tal et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/disarm.md b/content/2.defense-systems/disarm.md index b5a7aeb8..0fe72771 100644 --- a/content/2.defense-systems/disarm.md +++ b/content/2.defense-systems/disarm.md @@ -6,33 +6,33 @@ title: DISARM DISARM (Defense Island System Associated with Restriction-Modification) is a defense system widespread in prokaryotes, encoded by a 5-gene cassette. DISARM provides broad protection against double-stranded DNA phages, including siphophages, myophages, and podophages (1,3). - It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/list\_defense\_systems/RM)\-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2). + It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/list_defense_systems/RM)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2). ## Molecular mechanism DISARM allows phage adsorption but prevents phage replication. DISARM is thought to cause intracellular phage DNA decay (1), but the molecular of this potential DNA degradation remains unknown. -The \*drmMII\* gene of DISARM system from \*Bacillus paralicheniformis\* was shown to methylate bacterial DNA at CCWGG motifs when expressed in Bacillus subtilis, and in the absence of \*drmMII,\* this DISARM system appears toxic to the cells (1). These observations are consistent with an RM-like mechanism, where nucleic acid degradation targets specific DNA motifs, that are methylated in the bacterial chromosome to prevent auto-immunity. +The *drmMII* gene of DISARM system from *Bacillus paralicheniformis* was shown to methylate bacterial DNA at CCWGG motifs when expressed in Bacillus subtilis, and in the absence of *drmMII,* this DISARM system appears toxic to the cells (1). These observations are consistent with an RM-like mechanism, where nucleic acid degradation targets specific DNA motifs, that are methylated in the bacterial chromosome to prevent auto-immunity. -Yet this system was also shown to protect against phages whose genomes are exempt of CCWGG motifs (1). Moreover, a recent study reports that the absence of methylases (DrmMI or DrmMII) of the DISARM system from a \*Serratia sp.\* does not result in autoimmunity (3). Both these results suggest additional phage DNA recognition mechanisms. +Yet this system was also shown to protect against phages whose genomes are exempt of CCWGG motifs (1). Moreover, a recent study reports that the absence of methylases (DrmMI or DrmMII) of the DISARM system from a *Serratia sp.* does not result in autoimmunity (3). Both these results suggest additional phage DNA recognition mechanisms. Hints of these additional mechanisms can be found in recent structural studies, which show that DrmA and DrmB form a complex that can bind single-stranded DNA (2). Moreover, the DrmAB complex seems to exhibit strong ATPase activity in presence of unmethylated DNA, and  reduced ATPase activity in the presence of a methylated DNA substrate (2). Finally, binding of unmethylated single-stranded DNA appears to mediate major conformational change of the complex, which was hypothesized to be responsible for downstream DISARM activation (2). ## Example of genomic structure -DISARM is encoded by three core genes: \*drmA\* (encoding for a protein containing a putative helicase domain)\*,\* \*drmB\* (encoding for a protein containing a putative helicase-associated domain), and \*drmC\* (encoding for a protein containing a phospholipase D/nuclease domain) (1) +DISARM is encoded by three core genes: *drmA* (encoding for a protein containing a putative helicase domain)*,* *drmB* (encoding for a protein containing a putative helicase-associated domain), and *drmC* (encoding for a protein containing a phospholipase D/nuclease domain) (1) -These three core genes are accompanied by a methyltransferase, which can be either an adenine methylase (\*drmMI\*) for class 1 DISARM systems or a cytosine methylase (\*drmMII\*) for DISARM class 2. Both classes also encode an additional gene (\*drmD\* for class 1, and \*drmE\* for class 2). +These three core genes are accompanied by a methyltransferase, which can be either an adenine methylase (*drmMI*) for class 1 DISARM systems or a cytosine methylase (*drmMII*) for DISARM class 2. Both classes also encode an additional gene (*drmD* for class 1, and *drmE* for class 2). Here is some example found in the RefSeq database:  -DISARM\\_1 subsystem in the genome of \*Pseudomonas aeruginosa\* (GCF\\_009676885.1) is composed of 6 proteins: drmD (WP\\_023093122.1), drmMI (WP\\_023115027.1), drmD (WP\\_023093126.1), drmA (WP\\_033993408.1), drmB (WP\\_023093129.1)and, drmC (WP\\_031637507.1). +DISARM_1 subsystem in the genome of *Pseudomonas aeruginosa* (GCF_009676885.1) is composed of 6 proteins: drmD (WP_023093122.1), drmMI (WP_023115027.1), drmD (WP_023093126.1), drmA (WP_033993408.1), drmB (WP_023093129.1)and, drmC (WP_031637507.1).  -DISARM\\_2 subsystem in the genome of \*Bacillus paralicheniformis\* (GCF\\_009497935.1) is composed of 5 proteins: drmMII (WP\\_020450482.1), drmC (WP\\_020450481.1), drmB (WP\\_025810358.1), drmA (WP\\_020450479.1)and, drmE (WP\\_020450478.1). +DISARM_2 subsystem in the genome of *Bacillus paralicheniformis* (GCF_009497935.1) is composed of 5 proteins: drmMII (WP_020450482.1), drmC (WP_020450481.1), drmB (WP_025810358.1), drmA (WP_020450479.1)and, drmE (WP_020450478.1). ## Distribution of the system among prokaryotes @@ -42,15 +42,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 341 genomes  -\*Proportion of genome encoding the DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation DISARM systems were experimentally validated using: -A system from \*Bacillus paralicheniformis\* in \*Bacillus subtilis\* has an anti-phage effect against SPO1, phi3T, SpBeta, SPR, phi105, rho14, SPP1, phi29 , Nf (Doron et al., 2018; Ofir et al., 2017) +A system from *Bacillus paralicheniformis* in *Bacillus subtilis* has an anti-phage effect against SPO1, phi3T, SpBeta, SPR, phi105, rho14, SPP1, phi29 , Nf (Doron et al., 2018; Ofir et al., 2017) -A system from \*Serratia sp. SCBI\* in \*Escherichia coli\* has an anti-phage effect against T1, Nami, T7, M13 (Aparicio-Maldonado et al., 2021) +A system from *Serratia sp. SCBI* in *Escherichia coli* has an anti-phage effect against T1, Nami, T7, M13 (Aparicio-Maldonado et al., 2021) ## Relevant abstracts diff --git a/content/2.defense-systems/dmdde.md b/content/2.defense-systems/dmdde.md index 3c077fd8..a06f404e 100644 --- a/content/2.defense-systems/dmdde.md +++ b/content/2.defense-systems/dmdde.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -DdmDE subsystem in the genome of \*Vibrio vulnificus\* (GCF\\_002850455.1) is composed of 2 proteins: DdmE (WP\\_101957190.1)and, DdmD (WP\\_101957191.1). +DdmDE subsystem in the genome of *Vibrio vulnificus* (GCF_002850455.1) is composed of 2 proteins: DdmE (WP_101957190.1)and, DdmD (WP_101957191.1). ## Distribution of the system among prokaryotes @@ -20,7 +20,7 @@ Among the 22k complete genomes of RefSeq, this system is present in 145 genomes  -\*Proportion of genome encoding the DmdDE system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the DmdDE system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/dnd.md b/content/2.defense-systems/dnd.md index b886a21c..57c5187b 100644 --- a/content/2.defense-systems/dnd.md +++ b/content/2.defense-systems/dnd.md @@ -10,11 +10,11 @@ Here is some example found in the RefSeq database:  -Dnd\\_ABCDE subsystem in the genome of \*Vibrio tritonius\* (GCF\\_001547935.1) is composed of 6 proteins: DndA (WP\\_068714508.1), DndB (WP\\_068714510.1), DndC (WP\\_068714512.1), DndD (WP\\_068714514.1), DndE (WP\\_068714516.1)and, DndD (WP\\_068714526.1). +Dnd_ABCDE subsystem in the genome of *Vibrio tritonius* (GCF_001547935.1) is composed of 6 proteins: DndA (WP_068714508.1), DndB (WP_068714510.1), DndC (WP_068714512.1), DndD (WP_068714514.1), DndE (WP_068714516.1)and, DndD (WP_068714526.1).  -Dnd\\_ABCDEFGH subsystem in the genome of \*Vibrio sp.\* (GCF\\_023716625.1) is composed of 8 proteins: DptF (WP\\_252041715.1), DptG (WP\\_252041716.1), DptH (WP\\_252041717.1), DndE (WP\\_252041720.1), DndD (WP\\_252041722.1), DndC (WP\\_252041723.1), DndB (WP\\_252041724.1)and, DndA (WP\\_252041725.1). +Dnd_ABCDEFGH subsystem in the genome of *Vibrio sp.* (GCF_023716625.1) is composed of 8 proteins: DptF (WP_252041715.1), DptG (WP_252041716.1), DptH (WP_252041717.1), DndE (WP_252041720.1), DndD (WP_252041722.1), DndC (WP_252041723.1), DndB (WP_252041724.1)and, DndA (WP_252041725.1). ## Distribution of the system among prokaryotes @@ -24,13 +24,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 388 genomes  -\*Proportion of genome encoding the Dnd system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Dnd system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation Dnd systems were experimentally validated using: -Subsystem DndCDEA-PbeABCD with a system from \*Halalkalicoccus jeotgali\* in \*Natrinema sp. CJ7-F\* has an anti-phage effect against SNJ1 (Xiong et al., 2019) +Subsystem DndCDEA-PbeABCD with a system from *Halalkalicoccus jeotgali* in *Natrinema sp. CJ7-F* has an anti-phage effect against SNJ1 (Xiong et al., 2019) ## Relevant abstracts diff --git a/content/2.defense-systems/dodola.md b/content/2.defense-systems/dodola.md index c3604004..f60bcfa8 100644 --- a/content/2.defense-systems/dodola.md +++ b/content/2.defense-systems/dodola.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Dodola system in the genome of \*Streptococcus thermophilus\* (GCF\\_015190465.1) is composed of 2 proteins: DolA (WP\\_084825722.1)and, DolB (WP\\_084825723.1). +Dodola system in the genome of *Streptococcus thermophilus* (GCF_015190465.1) is composed of 2 proteins: DolA (WP_084825722.1)and, DolB (WP_084825723.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 313 genomes  -\*Proportion of genome encoding the Dodola system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Dodola system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Dodola systems were experimentally validated using: -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against SPP1 (Millman et al., 2022) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SPP1 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/dpd.md b/content/2.defense-systems/dpd.md index 0d58f9dd..c1f25b5c 100644 --- a/content/2.defense-systems/dpd.md +++ b/content/2.defense-systems/dpd.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Dpd system in the genome of \*Thalassotalea crassostreae\* (GCF\\_001831495.1) is composed of 15 proteins: QueE (WP\\_068546614.1), DpdE (WP\\_068546526.1), DpdF (WP\\_068546528.1), DpdG (WP\\_068546530.1), DpdH (WP\\_070795901.1), DpdI (WP\\_068546533.1), DpdJ (WP\\_068546534.1), DpdK (WP\\_082897170.1), DpdD (WP\\_068546535.1), QueC (WP\\_068546536.1), DpdB (WP\\_068546537.1), DpdA (WP\\_068546538.1), DpdC (WP\\_157726628.1), QueD (WP\\_068546540.1)and, FolE (WP\\_068546542.1). +Dpd system in the genome of *Thalassotalea crassostreae* (GCF_001831495.1) is composed of 15 proteins: QueE (WP_068546614.1), DpdE (WP_068546526.1), DpdF (WP_068546528.1), DpdG (WP_068546530.1), DpdH (WP_070795901.1), DpdI (WP_068546533.1), DpdJ (WP_068546534.1), DpdK (WP_082897170.1), DpdD (WP_068546535.1), QueC (WP_068546536.1), DpdB (WP_068546537.1), DpdA (WP_068546538.1), DpdC (WP_157726628.1), QueD (WP_068546540.1)and, FolE (WP_068546542.1). ## Distribution of the system among prokaryotes @@ -20,7 +20,7 @@ Among the 22k complete genomes of RefSeq, this system is present in 226 genomes  -\*Proportion of genome encoding the Dpd system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Dpd system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/drt.md b/content/2.defense-systems/drt.md index 4b93d5cb..eb5b5194 100644 --- a/content/2.defense-systems/drt.md +++ b/content/2.defense-systems/drt.md @@ -10,35 +10,35 @@ Here is some example found in the RefSeq database:  -DRT6 subsystem in the genome of \*Methylobacterium sp.\* (GCF\\_003254375.1) is composed of 1 protein: DRT6 (WP\\_111474389.1). +DRT6 subsystem in the genome of *Methylobacterium sp.* (GCF_003254375.1) is composed of 1 protein: DRT6 (WP_111474389.1).  -DRT8 subsystem in the genome of \*Undibacterium sp.\* (GCF\\_009937955.1) is composed of 2 proteins: DRT8b (WP\\_162060770.1)and, DRT8 (WP\\_162060771.1). +DRT8 subsystem in the genome of *Undibacterium sp.* (GCF_009937955.1) is composed of 2 proteins: DRT8b (WP_162060770.1)and, DRT8 (WP_162060771.1).  -DRT9 subsystem in the genome of \*Pseudomonas aeruginosa\* (GCF\\_016864415.1) is composed of 1 protein: DRT9 (WP\\_071567741.1). +DRT9 subsystem in the genome of *Pseudomonas aeruginosa* (GCF_016864415.1) is composed of 1 protein: DRT9 (WP_071567741.1).  -DRT\\_1 subsystem in the genome of \*Vibrio parahaemolyticus\* (GCF\\_000430405.1) is composed of 2 proteins: drt1a (WP\\_020841728.1)and, drt1b (WP\\_020841729.1). +DRT_1 subsystem in the genome of *Vibrio parahaemolyticus* (GCF_000430405.1) is composed of 2 proteins: drt1a (WP_020841728.1)and, drt1b (WP_020841729.1).  -DRT\\_2 subsystem in the genome of \*Klebsiella variicola\* (GCF\\_018324045.1) is composed of 1 protein: drt2 (WP\\_020244644.1). +DRT_2 subsystem in the genome of *Klebsiella variicola* (GCF_018324045.1) is composed of 1 protein: drt2 (WP_020244644.1).  -DRT\\_3 subsystem in the genome of \*Vibrio mimicus\* (GCF\\_019048845.1) is composed of 2 proteins: drt3a (WP\\_217011272.1)and, drt3b (WP\\_217011273.1). +DRT_3 subsystem in the genome of *Vibrio mimicus* (GCF_019048845.1) is composed of 2 proteins: drt3a (WP_217011272.1)and, drt3b (WP_217011273.1).  -DRT\\_4 subsystem in the genome of \*Escherichia albertii\* (GCF\\_003316815.1) is composed of 1 protein: drt4 (WP\\_103054060.1). +DRT_4 subsystem in the genome of *Escherichia albertii* (GCF_003316815.1) is composed of 1 protein: drt4 (WP_103054060.1).  -DRT\\_5 subsystem in the genome of \*Escherichia coli\* (GCF\\_016904115.1) is composed of 1 protein: drt5 (WP\\_001524904.1). +DRT_5 subsystem in the genome of *Escherichia coli* (GCF_016904115.1) is composed of 1 protein: drt5 (WP_001524904.1). ## Distribution of the system among prokaryotes @@ -48,27 +48,27 @@ Among the 22k complete genomes of RefSeq, this system is present in 1365 genomes  -\*Proportion of genome encoding the DRT system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the DRT system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation DRT systems were experimentally validated using: -Subsystem RT-nitrilase (UG1) (Type 1) with a system from \*Klebsiella pneumoniae\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T5 (Gao et al., 2020) +Subsystem RT-nitrilase (UG1) (Type 1) with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against T2, T4, T5 (Gao et al., 2020) -Subsystem RT (UG2) (Type 2) with a system from \*Salmonella enterica\* in \*Escherichia coli\* has an anti-phage effect against T5, T2 (Gao et al., 2020; Mestre et al., 2022) +Subsystem RT (UG2) (Type 2) with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T5, T2 (Gao et al., 2020; Mestre et al., 2022) -Subsystem RT (UG3) + RT (UG8) (Type 3) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T5, Lambda (Gao et al., 2020) +Subsystem RT (UG3) + RT (UG8) (Type 3) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5, Lambda (Gao et al., 2020) -Subsystem RT (UG15) (Type 4) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5, T3, T7, Phi-V1, ZL19 (Gao et al., 2020; Mestre et al., 2022) +Subsystem RT (UG15) (Type 4) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, T3, T7, Phi-V1, ZL19 (Gao et al., 2020; Mestre et al., 2022) -Subsystem RT (UG16) (Type 5) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2 (Gao et al., 2020) +Subsystem RT (UG16) (Type 5) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2 (Gao et al., 2020) -Subsystem RT (UG10) (Type 7) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T5, ZL-19 (Mestre et al., 2022) +Subsystem RT (UG10) (Type 7) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5, ZL-19 (Mestre et al., 2022) -Subsystem RT(UG7) (Type 8) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T5 (Mestre et al., 2022) +Subsystem RT(UG7) (Type 8) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5 (Mestre et al., 2022) -Subsystem RT (UG28) (Type 9) with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T5, ZL-19 (Mestre et al., 2022) +Subsystem RT (UG28) (Type 9) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5, ZL-19 (Mestre et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/druantia.md b/content/2.defense-systems/druantia.md index 59d0afa2..b3e55d57 100644 --- a/content/2.defense-systems/druantia.md +++ b/content/2.defense-systems/druantia.md @@ -10,15 +10,15 @@ Here is some example found in the RefSeq database:  -Druantia\\_I subsystem in the genome of \*Escherichia coli\* (GCF\\_002220215.1) is composed of 5 proteins: DruA (WP\\_000549798.1), DruB (WP\\_001315973.1), DruC (WP\\_021520530.1), DruD (WP\\_000455180.1)and, DruE\\_1 (WP\\_089180326.1). +Druantia_I subsystem in the genome of *Escherichia coli* (GCF_002220215.1) is composed of 5 proteins: DruA (WP_000549798.1), DruB (WP_001315973.1), DruC (WP_021520530.1), DruD (WP_000455180.1)and, DruE_1 (WP_089180326.1).  -Druantia\\_II subsystem in the genome of \*Collimonas pratensis\* (GCF\\_001584185.1) is composed of 4 proteins: DruM (WP\\_082793204.1), DruE\\_2 (WP\\_061945149.1), DruG (WP\\_061945151.1)and, DruF (WP\\_150119800.1). +Druantia_II subsystem in the genome of *Collimonas pratensis* (GCF_001584185.1) is composed of 4 proteins: DruM (WP_082793204.1), DruE_2 (WP_061945149.1), DruG (WP_061945151.1)and, DruF (WP_150119800.1).  -Druantia\\_III subsystem in the genome of \*Acinetobacter baumannii\* (GCF\\_012935125.1) is composed of 2 proteins: DruH (WP\\_005120035.1)and, DruE\\_3 (WP\\_002036795.1). +Druantia_III subsystem in the genome of *Acinetobacter baumannii* (GCF_012935125.1) is composed of 2 proteins: DruH (WP_005120035.1)and, DruE_3 (WP_002036795.1). ## Distribution of the system among prokaryotes @@ -28,13 +28,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 827 genomes  -\*Proportion of genome encoding the Druantia system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Druantia system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation Druantia systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T5, P1, Lambda, T3, T7, PhiV-1, Lambdavir, SECphi18, SECphi27 (Gao et al., 2020; Doron et al., 2018) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, P1, Lambda, T3, T7, PhiV-1, Lambdavir, SECphi18, SECphi27 (Gao et al., 2020; Doron et al., 2018) ## Relevant abstracts diff --git a/content/2.defense-systems/dsr.md b/content/2.defense-systems/dsr.md index 7b35c9cb..c2faac1a 100644 --- a/content/2.defense-systems/dsr.md +++ b/content/2.defense-systems/dsr.md @@ -10,11 +10,11 @@ Here is some example found in the RefSeq database:  -Dsr\\_I subsystem in the genome of \*Escherichia coli\* (GCF\\_016904235.1) is composed of 1 protein: Dsr1 (WP\\_204608492.1). +Dsr_I subsystem in the genome of *Escherichia coli* (GCF_016904235.1) is composed of 1 protein: Dsr1 (WP_204608492.1).  -Dsr\\_II subsystem in the genome of \*Escherichia coli\* (GCF\\_009950125.1) is composed of 1 protein: Dsr2 (WP\\_178103017.1). +Dsr_II subsystem in the genome of *Escherichia coli* (GCF_009950125.1) is composed of 1 protein: Dsr2 (WP_178103017.1). ## Distribution of the system among prokaryotes @@ -24,19 +24,19 @@ Among the 22k complete genomes of RefSeq, this system is present in 641 genomes  -\*Proportion of genome encoding the Dsr system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Dsr system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation Dsr systems were experimentally validated using: -Subsystem DSR1 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020) +Subsystem DSR1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020) -Subsystem DSR2 with a system from \*Cronobacter sakazakii\* in \*Escherichia coli\* has an anti-phage effect against Lambda (Gao et al., 2020) +Subsystem DSR2 with a system from *Cronobacter sakazakii* in *Escherichia coli* has an anti-phage effect against Lambda (Gao et al., 2020) -Subsystem DSR2 with a system from \*Bacillus subtilis\* in \*Bacillus subtilis \* has an anti-phage effect against SPR (Garb et al., 2022) +Subsystem DSR2 with a system from *Bacillus subtilis* in *Bacillus subtilis * has an anti-phage effect against SPR (Garb et al., 2022) -Subsystem DSR1 with a system from \*Bacillus subtilis\* in \*Bacillus subtilis \* has an anti-phage effect against phi29 (Garb et al., 2022) +Subsystem DSR1 with a system from *Bacillus subtilis* in *Bacillus subtilis * has an anti-phage effect against phi29 (Garb et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/eleos.md b/content/2.defense-systems/eleos.md index 37674c2f..9ef0aab7 100644 --- a/content/2.defense-systems/eleos.md +++ b/content/2.defense-systems/eleos.md @@ -11,7 +11,7 @@ Here is an example found in the RefSeq database:  -Dynamins system in the genome of \*Pseudomonas aeruginosa\* (GCF\\_002223805.1) is composed of 2 proteins: LeoBC (WP\\_024947442.1)and, LeoA (WP\\_024947443.1). +Dynamins system in the genome of *Pseudomonas aeruginosa* (GCF_002223805.1) is composed of 2 proteins: LeoBC (WP_024947442.1)and, LeoA (WP_024947443.1). ## Distribution of the system among prokaryotes @@ -21,13 +21,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 2652 genomes  -\*Proportion of genome encoding the Eleos system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Eleos system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Eleos systems were experimentally validated using: -A system from \*Bacillus vietnamensis\* in \*Bacillus subtilis\* has an anti-phage effect against AR9 (Jumbo), PBS1(Jumbo) (Millman et al., 2022) +A system from *Bacillus vietnamensis* in *Bacillus subtilis* has an anti-phage effect against AR9 (Jumbo), PBS1(Jumbo) (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/gabija.md b/content/2.defense-systems/gabija.md index dab338df..7f13e784 100644 --- a/content/2.defense-systems/gabija.md +++ b/content/2.defense-systems/gabija.md @@ -6,7 +6,7 @@ title: Gabija According to recent studies, GajA is a sequence-specific DNA nicking endonuclease, whose activity is inhibited by nucleotide concentration. Accordingly, GajA would be fully inhibited at cellular nucleotides concentrations. It was hypothesized that upon nucleotide depletion during phage infection, GajA would become activated (2). -Another study suggests that the \*gajB\* gene could encode for an NTPase, which would form a complex with GajA to achieve anti-phage defense (3). +Another study suggests that the *gajB* gene could encode for an NTPase, which would form a complex with GajA to achieve anti-phage defense (3). ## Molecular mechanism @@ -14,13 +14,13 @@ The precise mechanism of the Gabija system remains to be fully described, yet st ## Example of genomic structure -The Gabija system is composed of 2 proteins: GajA and, GajB\_2. +The Gabija system is composed of 2 proteins: GajA and, GajB_2. Here is an example found in the RefSeq database:  -Gabija system in the genome of \*Vibrio parahaemolyticus\* (GCF\\_009883895.1) is composed of 2 proteins: GajA (WP\\_085576823.1)and, GajB\\_1 (WP\\_031856308.1). +Gabija system in the genome of *Vibrio parahaemolyticus* (GCF_009883895.1) is composed of 2 proteins: GajA (WP_085576823.1)and, GajB_1 (WP_031856308.1). ## Distribution of the system among prokaryotes @@ -30,17 +30,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 3762 genomes  -\*Proportion of genome encoding the Gabija system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gabija system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Gabija systems were experimentally validated using: -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against SBSphiC, SpBeta, phi105, rho14, phi29 (Doron et al., 2018) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SBSphiC, SpBeta, phi105, rho14, phi29 (Doron et al., 2018) -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against SpBeta, phi105 (Doron et al., 2018) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SpBeta, phi105 (Doron et al., 2018) -A system from \*Bacillus cereus\* in \*Escherichia coli\* has an anti-phage effect against T7 (Cheng et al., 2021) +A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T7 (Cheng et al., 2021) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_ape.md b/content/2.defense-systems/gao_ape.md index dae5c35b..cf14a96d 100644 --- a/content/2.defense-systems/gao_ape.md +++ b/content/2.defense-systems/gao_ape.md @@ -4,29 +4,29 @@ title: Gao_Ape ## Example of genomic structure -The Gao\_Ape system is composed of one protein: ApeA. +The Gao_Ape system is composed of one protein: ApeA. Here is an example found in the RefSeq database:  -Gao\\_Ape system in the genome of \*Klebsiella sp.\* (GCF\\_018388785.1) is composed of 1 protein: ApeA (WP\\_213292831.1). +Gao_Ape system in the genome of *Klebsiella sp.* (GCF_018388785.1) is composed of 1 protein: ApeA (WP_213292831.1). ## Distribution of the system among prokaryotes -The Gao\_Ape system is present in a total of 76 different species. +The Gao_Ape system is present in a total of 76 different species. Among the 22k complete genomes of RefSeq, this system is present in 199 genomes (0.9 %).  -\*Proportion of genome encoding the Gao\_Ape system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_Ape system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_Ape systems were experimentally validated using: +Gao_Ape systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T5, T3, T7, PhiV-1 (Gao et al., 2020) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, T3, T7, PhiV-1 (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_her.md b/content/2.defense-systems/gao_her.md index 3ac030b0..204aa024 100644 --- a/content/2.defense-systems/gao_her.md +++ b/content/2.defense-systems/gao_her.md @@ -4,35 +4,35 @@ title: Gao_Her ## Example of genomic structure -The Gao\_Her system have been describe in a total of 2 subsystems. +The Gao_Her system have been describe in a total of 2 subsystems. Here is some example found in the RefSeq database:  -Gao\\_Her\\_DUF subsystem in the genome of \*Enterobacter roggenkampii\* (GCF\\_014524505.1) is composed of 2 proteins: DUF4297 (WP\\_188074283.1)and, HerA\\_DUF (WP\\_063614829.1). +Gao_Her_DUF subsystem in the genome of *Enterobacter roggenkampii* (GCF_014524505.1) is composed of 2 proteins: DUF4297 (WP_188074283.1)and, HerA_DUF (WP_063614829.1).  -Gao\\_Her\\_SIR subsystem in the genome of \*Escherichia coli\* (GCF\\_012221565.1) is composed of 2 proteins: SIR2 (WP\\_167839366.1)and, HerA\\_SIR2 (WP\\_021577682.1). +Gao_Her_SIR subsystem in the genome of *Escherichia coli* (GCF_012221565.1) is composed of 2 proteins: SIR2 (WP_167839366.1)and, HerA_SIR2 (WP_021577682.1). ## Distribution of the system among prokaryotes -The Gao\_Her system is present in a total of 127 different species. +The Gao_Her system is present in a total of 127 different species. Among the 22k complete genomes of RefSeq, this system is present in 233 genomes (1.0 %).  -\*Proportion of genome encoding the Gao\_Her system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Gao_Her system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation -Gao\_Her systems were experimentally validated using: +Gao_Her systems were experimentally validated using: -Subsystem SIR2 + HerA with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020) +Subsystem SIR2 + HerA with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020) -Subsystem DUF4297 + HerA with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4, P1, Lambda, T3, T7 (Gao et al., 2020) +Subsystem DUF4297 + HerA with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, P1, Lambda, T3, T7 (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_hhe.md b/content/2.defense-systems/gao_hhe.md index ddef56f4..fde14e0c 100644 --- a/content/2.defense-systems/gao_hhe.md +++ b/content/2.defense-systems/gao_hhe.md @@ -4,29 +4,29 @@ title: Gao_Hhe ## Example of genomic structure -The Gao\_Hhe system is composed of one protein: HheA. +The Gao_Hhe system is composed of one protein: HheA. Here is an example found in the RefSeq database:  -Gao\\_Hhe system in the genome of \*Klebsiella pneumoniae\* (GCF\\_011742415.2) is composed of 1 protein: HheA (WP\\_021314612.1). +Gao_Hhe system in the genome of *Klebsiella pneumoniae* (GCF_011742415.2) is composed of 1 protein: HheA (WP_021314612.1). ## Distribution of the system among prokaryotes -The Gao\_Hhe system is present in a total of 49 different species. +The Gao_Hhe system is present in a total of 49 different species. Among the 22k complete genomes of RefSeq, this system is present in 279 genomes (1.2 %).  -\*Proportion of genome encoding the Gao\_Hhe system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_Hhe system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_Hhe systems were experimentally validated using: +Gao_Hhe systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_iet.md b/content/2.defense-systems/gao_iet.md index 6e0fe35c..0e675572 100644 --- a/content/2.defense-systems/gao_iet.md +++ b/content/2.defense-systems/gao_iet.md @@ -4,29 +4,29 @@ title: Gao_Iet ## Example of genomic structure -The Gao\_Iet system is composed of 2 proteins: IetS and, IetA. +The Gao_Iet system is composed of 2 proteins: IetS and, IetA. Here is an example found in the RefSeq database:  -Gao\\_Iet system in the genome of \*Escherichia coli\* (GCF\\_014169855.1) is composed of 2 proteins: IetS (WP\\_001551050.1)and, IetA (WP\\_000385105.1). +Gao_Iet system in the genome of *Escherichia coli* (GCF_014169855.1) is composed of 2 proteins: IetS (WP_001551050.1)and, IetA (WP_000385105.1). ## Distribution of the system among prokaryotes -The Gao\_Iet system is present in a total of 189 different species. +The Gao_Iet system is present in a total of 189 different species. Among the 22k complete genomes of RefSeq, this system is present in 436 genomes (1.9 %).  -\*Proportion of genome encoding the Gao\_Iet system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_Iet system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_Iet systems were experimentally validated using: +Gao_Iet systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_mza.md b/content/2.defense-systems/gao_mza.md index 8da2536c..a08eff93 100644 --- a/content/2.defense-systems/gao_mza.md +++ b/content/2.defense-systems/gao_mza.md @@ -4,29 +4,29 @@ title: Gao_Mza ## Example of genomic structure -The Gao\_Mza system is composed of 5 proteins: MzaB, MzaC, MzaA, MzaD and, MzaE. +The Gao_Mza system is composed of 5 proteins: MzaB, MzaC, MzaA, MzaD and, MzaE. Here is an example found in the RefSeq database:  -Gao\\_Mza system in the genome of \*Enterobacter roggenkampii\* (GCF\\_023023065.1) is composed of 5 proteins: MzaE (WP\\_045418899.1), MzaD (WP\\_045418897.1), MzaC (WP\\_025912266.1), MzaB (WP\\_045418895.1)and, MzaA (WP\\_045418893.1). +Gao_Mza system in the genome of *Enterobacter roggenkampii* (GCF_023023065.1) is composed of 5 proteins: MzaE (WP_045418899.1), MzaD (WP_045418897.1), MzaC (WP_025912266.1), MzaB (WP_045418895.1)and, MzaA (WP_045418893.1). ## Distribution of the system among prokaryotes -The Gao\_Mza system is present in a total of 57 different species. +The Gao_Mza system is present in a total of 57 different species. Among the 22k complete genomes of RefSeq, this system is present in 99 genomes (0.4 %).  -\*Proportion of genome encoding the Gao\_Mza system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_Mza system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_Mza systems were experimentally validated using: +Gao_Mza systems were experimentally validated using: -A system from \*Salmonella enterica\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T5, Lambda, M13 (Gao et al., 2020) +A system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, Lambda, M13 (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_ppl.md b/content/2.defense-systems/gao_ppl.md index 17be4cc5..dbd7a0f6 100644 --- a/content/2.defense-systems/gao_ppl.md +++ b/content/2.defense-systems/gao_ppl.md @@ -4,29 +4,29 @@ title: Gao_Ppl ## Example of genomic structure -The Gao\_Ppl system is composed of one protein: PplA. +The Gao_Ppl system is composed of one protein: PplA. Here is an example found in the RefSeq database:  -Gao\\_Ppl system in the genome of \*Klebsiella pneumoniae\* (GCF\\_002787755.1) is composed of 1 protein: PplA (WP\\_015059139.1). +Gao_Ppl system in the genome of *Klebsiella pneumoniae* (GCF_002787755.1) is composed of 1 protein: PplA (WP_015059139.1). ## Distribution of the system among prokaryotes -The Gao\_Ppl system is present in a total of 106 different species. +The Gao_Ppl system is present in a total of 106 different species. Among the 22k complete genomes of RefSeq, this system is present in 364 genomes (1.6 %).  -\*Proportion of genome encoding the Gao\_Ppl system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_Ppl system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_Ppl systems were experimentally validated using: +Gao_Ppl systems were experimentally validated using: -A system from \*Salmonella enterica\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020) +A system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_qat.md b/content/2.defense-systems/gao_qat.md index 59868acc..001aa452 100644 --- a/content/2.defense-systems/gao_qat.md +++ b/content/2.defense-systems/gao_qat.md @@ -4,29 +4,29 @@ title: Gao_Qat ## Example of genomic structure -The Gao\_Qat system is composed of 4 proteins: QatA, QatB, QatC and, QatD. +The Gao_Qat system is composed of 4 proteins: QatA, QatB, QatC and, QatD. Here is an example found in the RefSeq database:  -Gao\\_Qat system in the genome of \*Raoultella ornithinolytica\* (GCF\\_002214825.1) is composed of 4 proteins: QatA (WP\\_088883811.1), QatB (WP\\_127146083.1), QatC (WP\\_088883813.1)and, QatD (WP\\_088883814.1). +Gao_Qat system in the genome of *Raoultella ornithinolytica* (GCF_002214825.1) is composed of 4 proteins: QatA (WP_088883811.1), QatB (WP_127146083.1), QatC (WP_088883813.1)and, QatD (WP_088883814.1). ## Distribution of the system among prokaryotes -The Gao\_Qat system is present in a total of 246 different species. +The Gao_Qat system is present in a total of 246 different species. Among the 22k complete genomes of RefSeq, this system is present in 645 genomes (2.8 %).  -\*Proportion of genome encoding the Gao\_Qat system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_Qat system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_Qat systems were experimentally validated using: +Gao_Qat systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against P1, Lambda (Gao et al., 2020) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, Lambda (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_rl.md b/content/2.defense-systems/gao_rl.md index dac746a4..859c2735 100644 --- a/content/2.defense-systems/gao_rl.md +++ b/content/2.defense-systems/gao_rl.md @@ -4,29 +4,29 @@ title: Gao_RL ## Example of genomic structure -The Gao\_RL system is composed of 4 proteins: RL\_D, RL\_C, RL\_B and, RL\_A. +The Gao_RL system is composed of 4 proteins: RL_D, RL_C, RL_B and, RL_A. Here is an example found in the RefSeq database:  -Gao\\_RL system in the genome of \*Morganella morganii\* (GCF\\_020790175.1) is composed of 4 proteins: RL\\_D (WP\\_064483389.1), RL\\_C (WP\\_064483388.1), RL\\_B (WP\\_064483387.1)and, RL\\_A (WP\\_064483386.1). +Gao_RL system in the genome of *Morganella morganii* (GCF_020790175.1) is composed of 4 proteins: RL_D (WP_064483389.1), RL_C (WP_064483388.1), RL_B (WP_064483387.1)and, RL_A (WP_064483386.1). ## Distribution of the system among prokaryotes -The Gao\_RL system is present in a total of 77 different species. +The Gao_RL system is present in a total of 77 different species. Among the 22k complete genomes of RefSeq, this system is present in 133 genomes (0.6 %).  -\*Proportion of genome encoding the Gao\_RL system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_RL system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_RL systems were experimentally validated using: +Gao_RL systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against P1, Lambda, M13 (Gao et al., 2020) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, Lambda, M13 (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_tery.md b/content/2.defense-systems/gao_tery.md index 53311528..6727a7fa 100644 --- a/content/2.defense-systems/gao_tery.md +++ b/content/2.defense-systems/gao_tery.md @@ -4,29 +4,29 @@ title: Gao_TerY ## Example of genomic structure -The Gao\_TerY system is composed of 3 proteins: TerYC, TerYB and, TerYA. +The Gao_TerY system is composed of 3 proteins: TerYC, TerYB and, TerYA. Here is an example found in the RefSeq database:  -Gao\\_TerY system in the genome of \*Burkholderia contaminans\* (GCF\\_018223785.1) is composed of 3 proteins: TerYA (WP\\_039364687.1), TerYB (WP\\_039364686.1)and, TerYC (WP\\_039364684.1). +Gao_TerY system in the genome of *Burkholderia contaminans* (GCF_018223785.1) is composed of 3 proteins: TerYA (WP_039364687.1), TerYB (WP_039364686.1)and, TerYC (WP_039364684.1). ## Distribution of the system among prokaryotes -The Gao\_TerY system is present in a total of 69 different species. +The Gao_TerY system is present in a total of 69 different species. Among the 22k complete genomes of RefSeq, this system is present in 126 genomes (0.6 %).  -\*Proportion of genome encoding the Gao\_TerY system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_TerY system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_TerY systems were experimentally validated using: +Gao_TerY systems were experimentally validated using: -A system from \*Citrobacter gillenii\* in \*Escherichia coli\* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020) +A system from *Citrobacter gillenii* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_tmn.md b/content/2.defense-systems/gao_tmn.md index ad91d33d..f1fbc796 100644 --- a/content/2.defense-systems/gao_tmn.md +++ b/content/2.defense-systems/gao_tmn.md @@ -4,29 +4,29 @@ title: Gao_Tmn ## Example of genomic structure -The Gao\_Tmn system is composed of one protein: TmnA. +The Gao_Tmn system is composed of one protein: TmnA. Here is an example found in the RefSeq database:  -Gao\\_Tmn system in the genome of \*Salmonella enterica\* (GCF\\_006384195.1) is composed of 1 protein: TmnA (WP\\_130525902.1). +Gao_Tmn system in the genome of *Salmonella enterica* (GCF_006384195.1) is composed of 1 protein: TmnA (WP_130525902.1). ## Distribution of the system among prokaryotes -The Gao\_Tmn system is present in a total of 82 different species. +The Gao_Tmn system is present in a total of 82 different species. Among the 22k complete genomes of RefSeq, this system is present in 414 genomes (1.8 %).  -\*Proportion of genome encoding the Gao\_Tmn system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_Tmn system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_Tmn systems were experimentally validated using: +Gao_Tmn systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, P1, PhiV-1, PhiX (Gao et al., 2020) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, P1, PhiV-1, PhiX (Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gao_upx.md b/content/2.defense-systems/gao_upx.md index f6ff2758..fe1312a9 100644 --- a/content/2.defense-systems/gao_upx.md +++ b/content/2.defense-systems/gao_upx.md @@ -4,29 +4,29 @@ title: Gao_Upx ## Example of genomic structure -The Gao\_Upx system is composed of one protein: UpxA. +The Gao_Upx system is composed of one protein: UpxA. Here is an example found in the RefSeq database:  -Gao\\_Upx system in the genome of \*Salmonella sp.\* (GCF\\_020268625.1) is composed of 1 protein: UpxA (WP\\_060647174.1). +Gao_Upx system in the genome of *Salmonella sp.* (GCF_020268625.1) is composed of 1 protein: UpxA (WP_060647174.1). ## Distribution of the system among prokaryotes -The Gao\_Upx system is present in a total of 31 different species. +The Gao_Upx system is present in a total of 31 different species. Among the 22k complete genomes of RefSeq, this system is present in 39 genomes (0.2 %).  -\*Proportion of genome encoding the Gao\_Upx system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Gao_Upx system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Gao\_Upx systems were experimentally validated using: +Gao_Upx systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against P1, PhiV-1(Gao et al., 2020) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, PhiV-1(Gao et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/gasdermin.md b/content/2.defense-systems/gasdermin.md index d97a5221..7fedb376 100644 --- a/content/2.defense-systems/gasdermin.md +++ b/content/2.defense-systems/gasdermin.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -GasderMIN system in the genome of \*Rhodoplanes sp.\* (GCF\\_001579845.1) is composed of 1 protein: bGSDM (WP\\_068019379.1). +GasderMIN system in the genome of *Rhodoplanes sp.* (GCF_001579845.1) is composed of 1 protein: bGSDM (WP_068019379.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 29 genomes (  -\*Proportion of genome encoding the GasderMIN system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the GasderMIN system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation GasderMIN systems were experimentally validated using: -A system from \*Lysobacter enzymogenes\* in \*Escherichia coli\* has an anti-phage effect against T5, T4, T6 (Johnson et al., 2022) +A system from *Lysobacter enzymogenes* in *Escherichia coli* has an anti-phage effect against T5, T4, T6 (Johnson et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/gp29_gp30.md b/content/2.defense-systems/gp29_gp30.md index 9f7e24fa..1771ab35 100644 --- a/content/2.defense-systems/gp29_gp30.md +++ b/content/2.defense-systems/gp29_gp30.md @@ -4,23 +4,23 @@ title: gp29_gp30 ## Example of genomic structure -The gp29\_gp30 system is composed of 2 proteins: gp30 and, gp29. +The gp29_gp30 system is composed of 2 proteins: gp30 and, gp29. Here is an example found in the RefSeq database:  -gp29\\_gp30 system in the genome of \*Mycobacterium tuberculosis\* (GCF\\_002448055.1) is composed of 2 proteins: gp29 (WP\\_003407164.1)and, gp30 (WP\\_003407167.1). +gp29_gp30 system in the genome of *Mycobacterium tuberculosis* (GCF_002448055.1) is composed of 2 proteins: gp29 (WP_003407164.1)and, gp30 (WP_003407167.1). ## Distribution of the system among prokaryotes -The gp29\_gp30 system is present in a total of 35 different species. +The gp29_gp30 system is present in a total of 35 different species. Among the 22k complete genomes of RefSeq, this system is present in 314 genomes (1.4 %).  -\*Proportion of genome encoding the gp29\_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/hachiman.md b/content/2.defense-systems/hachiman.md index 72fce25c..e9a9b8ef 100644 --- a/content/2.defense-systems/hachiman.md +++ b/content/2.defense-systems/hachiman.md @@ -4,7 +4,7 @@ title: Hachiman ## Description -Hachiman Type 1 systems were the first discovered and can be found in 3.4% of microbial genomes (1). Hachiman Type 1 systems are encoded by two genes, \*hamA\* (annotated as a Domain of Unknown Function, DUF) and \*hamB\* (annotated as a helicase) (1). +Hachiman Type 1 systems were the first discovered and can be found in 3.4% of microbial genomes (1). Hachiman Type 1 systems are encoded by two genes, *hamA* (annotated as a Domain of Unknown Function, DUF) and *hamB* (annotated as a helicase) (1). More recently, Hachiman Type 2 systems were discovered and appeared to include a third gene, encoded for a DUF protein (HamC) (2). @@ -16,7 +16,7 @@ Here is an example found in the RefSeq database:  -Hachiman system in the genome of \*Mesorhizobium terrae\* (GCF\\_008727715.1) is composed of 2 proteins: HamA\\_1 (WP\\_245317480.1)and, HamB (WP\\_065997554.1). +Hachiman system in the genome of *Mesorhizobium terrae* (GCF_008727715.1) is composed of 2 proteins: HamA_1 (WP_245317480.1)and, HamB (WP_065997554.1). ## Distribution of the system among prokaryotes @@ -26,15 +26,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 1361 genomes  -\*Proportion of genome encoding the Hachiman system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Hachiman system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Hachiman systems were experimentally validated using: -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against SBSphiJ, phi3T, SPbeta, SPR, phi105, rho14, phi29 (Doron et al., 2018) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SBSphiJ, phi3T, SPbeta, SPR, phi105, rho14, phi29 (Doron et al., 2018) -Subsystem Hachiman Type II with a system from \*Sphingopyxis witflariensis\* in \*Escherichia coli\* has an anti-phage effect against T3, PVP-SE1 (Payne et al., 2021) +Subsystem Hachiman Type II with a system from *Sphingopyxis witflariensis* in *Escherichia coli* has an anti-phage effect against T3, PVP-SE1 (Payne et al., 2021) ## Relevant abstracts @@ -49,6 +49,6 @@ items: ## References -1\. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. \*Science\*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120 +1. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. *Science*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120 -2\. Payne LJ, Todeschini TC, Wu Y, Perry BJ, Ronson CW, Fineran PC, Nobrega FL, Jackson SA. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res. 2021 Nov 8;49(19):10868-10878. doi: 10.1093/nar/gkab883. PMID: 34606606; PMCID: PMC8565338. +2. Payne LJ, Todeschini TC, Wu Y, Perry BJ, Ronson CW, Fineran PC, Nobrega FL, Jackson SA. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res. 2021 Nov 8;49(19):10868-10878. doi: 10.1093/nar/gkab883. PMID: 34606606; PMCID: PMC8565338. diff --git a/content/2.defense-systems/isg15-like.md b/content/2.defense-systems/isg15-like.md index d00ef02a..45c0f37d 100644 --- a/content/2.defense-systems/isg15-like.md +++ b/content/2.defense-systems/isg15-like.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -ISG15-like system in the genome of \*Rhizobium phaseoli\* (GCF\\_001664285.1) is composed of 4 proteins: BilA (WP\\_064823699.1), BilB (WP\\_150124924.1), BilC (WP\\_150124925.1)and, BilD (WP\\_190304495.1). +ISG15-like system in the genome of *Rhizobium phaseoli* (GCF_001664285.1) is composed of 4 proteins: BilA (WP_064823699.1), BilB (WP_150124924.1), BilC (WP_150124925.1)and, BilD (WP_190304495.1). ## Distribution of the system among prokaryotes @@ -20,21 +20,21 @@ Among the 22k complete genomes of RefSeq, this system is present in 43 genomes (  -\*Proportion of genome encoding the ISG15-like system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the ISG15-like system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation ISG15-like systems were experimentally validated using: -A system from \*Collimonas sp. OK412\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27, T7, SECphi17 (Millman et al., 2022) +A system from *Collimonas sp. OK412* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27, T7, SECphi17 (Millman et al., 2022) -A system from \*Caulobacter sp. Root343\* in \*Escherichia coli\* has an anti-phage effect against T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27, T7, SECphi17 (Millman et al., 2022) +A system from *Caulobacter sp. Root343* in *Escherichia coli* has an anti-phage effect against T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27, T7, SECphi17 (Millman et al., 2022) -A system from \*Cupriavidus sp. SHE\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27 (Millman et al., 2022) +A system from *Cupriavidus sp. SHE* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27 (Millman et al., 2022) -A system from \*Paraburkholderia caffeinilytica\* in \*Escherichia coli\* has an anti-phage effect against T6, SECphi27 (Millman et al., 2022) +A system from *Paraburkholderia caffeinilytica* in *Escherichia coli* has an anti-phage effect against T6, SECphi27 (Millman et al., 2022) -A system from \*Thiomonas sp. FB-6\* in \*Escherichia coli\* has an anti-phage effect against SECphi27 (Millman et al., 2022) +A system from *Thiomonas sp. FB-6* in *Escherichia coli* has an anti-phage effect against SECphi27 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/kiwa.md b/content/2.defense-systems/kiwa.md index e6059e93..7b896826 100644 --- a/content/2.defense-systems/kiwa.md +++ b/content/2.defense-systems/kiwa.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Kiwa system in the genome of \*Aggregatibacter actinomycetemcomitans\* (GCF\\_001690155.1) is composed of 2 proteins: KwaB (WP\\_005553122.1)and, KwaA (WP\\_005540311.1). +Kiwa system in the genome of *Aggregatibacter actinomycetemcomitans* (GCF_001690155.1) is composed of 2 proteins: KwaB (WP_005553122.1)and, KwaA (WP_005540311.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1104 genomes  -\*Proportion of genome encoding the Kiwa system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Kiwa system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Kiwa systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi18 (Doron et al., 2018) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi18 (Doron et al., 2018) ## Relevant abstracts diff --git a/content/2.defense-systems/lamassu-fam.md b/content/2.defense-systems/lamassu-fam.md index 72b362dc..c59d61b0 100644 --- a/content/2.defense-systems/lamassu-fam.md +++ b/content/2.defense-systems/lamassu-fam.md @@ -4,11 +4,11 @@ title: Lamassu-Fam ## Description -The original types of Lamassu systems are Lamassu Type 1 and 2. They both necessarily comprise two genes \*lmuA\* and \*lmuB\*, to which a third gene (\*lmuC\*) is added in the case of Lamassu Type 2.  +The original types of Lamassu systems are Lamassu Type 1 and 2. They both necessarily comprise two genes *lmuA* and *lmuB*, to which a third gene (*lmuC*) is added in the case of Lamassu Type 2.  More recently, Lamassu has been suggested to be a large family of defense systems, that can be classified into multiple subtypes. -These systems all encode the \*lmuB\* gene, and in most cases also comprise \*lmuC.\* In addition to these two core genes, Lamassu systems of various subtypes encode a third protein, hypothesized to be the Abi effector protein (3). This effector  can not only be LmuA (Lamassu Type1 and 2) but also proteins encoding endonuclease domains, SIR2-domains, or even hydrolase domains (3). Systems of the extended Lamassu-family can be found in 10% of prokaryotic genomes (3). +These systems all encode the *lmuB* gene, and in most cases also comprise *lmuC.* In addition to these two core genes, Lamassu systems of various subtypes encode a third protein, hypothesized to be the Abi effector protein (3). This effector  can not only be LmuA (Lamassu Type1 and 2) but also proteins encoding endonuclease domains, SIR2-domains, or even hydrolase domains (3). Systems of the extended Lamassu-family can be found in 10% of prokaryotic genomes (3). ## Molecular mechanism @@ -18,52 +18,52 @@ Lamassu systems function through abortive infection (Abi), but their molecular m The majority of the Lamassu-Fam systems are composed of 3 proteins: LmuA, LmuB and, an accessory LmuC proteins. -Here is an example of a Lamassu-Fam\\_Cap4\\_nuclease found in the RefSeq database: +Here is an example of a Lamassu-Fam_Cap4_nuclease found in the RefSeq database:  -Lamassu-Fam\\_Cap4\\_nuclease subsystem in the genome of \*Pseudomonas sp.\* (GCF\\_016925675.1) is composed of 3 proteins: LmuB\\_SMC\\_Hydrolase\\_protease (WP\\_205519025.1), LmuC\\_acc\\_Cap4\\_nuclease (WP\\_205478326.1)and, LmuA\\_effector\\_Cap4\\_nuclease\\_II (WP\\_205478325.1). +Lamassu-Fam_Cap4_nuclease subsystem in the genome of *Pseudomonas sp.* (GCF_016925675.1) is composed of 3 proteins: LmuB_SMC_Hydrolase_protease (WP_205519025.1), LmuC_acc_Cap4_nuclease (WP_205478326.1)and, LmuA_effector_Cap4_nuclease_II (WP_205478325.1).  -Lamassu-Fam\\_Mrr subsystem in the genome of \*Escherichia coli\* (GCF\\_011404895.1) is composed of 2 proteins: LmuA\\_effector\\_Mrr (WP\\_044864610.1)and, LmuB\\_SMC\\_Cap4\\_nuclease\\_II (WP\\_226199836.1). +Lamassu-Fam_Mrr subsystem in the genome of *Escherichia coli* (GCF_011404895.1) is composed of 2 proteins: LmuA_effector_Mrr (WP_044864610.1)and, LmuB_SMC_Cap4_nuclease_II (WP_226199836.1).  -Lamassu-Fam\\_Hydrolase subsystem in the genome of \*Caldisphaera lagunensis\* (GCF\\_000317795.1) is composed of 2 proteins: LmuA\\_effector\\_Hydrolase (WP\\_015232255.1)and, LmuB\\_SMC\\_Hydrolase\\_protease (WP\\_015232260.1). +Lamassu-Fam_Hydrolase subsystem in the genome of *Caldisphaera lagunensis* (GCF_000317795.1) is composed of 2 proteins: LmuA_effector_Hydrolase (WP_015232255.1)and, LmuB_SMC_Hydrolase_protease (WP_015232260.1).  -Lamassu-Fam\\_Lipase subsystem in the genome of \*Bradyrhizobium elkanii\* (GCF\\_012871055.1) is composed of 2 proteins: LmuA\\_effector\\_Lipase (WP\\_172647146.1)and, LmuB\\_SMC\\_Lipase (WP\\_172647148.1). +Lamassu-Fam_Lipase subsystem in the genome of *Bradyrhizobium elkanii* (GCF_012871055.1) is composed of 2 proteins: LmuA_effector_Lipase (WP_172647146.1)and, LmuB_SMC_Lipase (WP_172647148.1).  -Lamassu-Fam\\_Hydrolase\\_protease subsystem in the genome of \*Klebsiella pneumoniae\* (GCF\\_022453565.1) is composed of 3 proteins: LmuB\\_SMC\\_Cap4\\_nuclease\\_II (WP\\_023301569.1), LmuA\\_effector\\_Protease (WP\\_023301563.1)and, LmuA\\_effector\\_Hydrolase (WP\\_023301562.1). +Lamassu-Fam_Hydrolase_protease subsystem in the genome of *Klebsiella pneumoniae* (GCF_022453565.1) is composed of 3 proteins: LmuB_SMC_Cap4_nuclease_II (WP_023301569.1), LmuA_effector_Protease (WP_023301563.1)and, LmuA_effector_Hydrolase (WP_023301562.1).  -Lamassu-Fam\\_Hypothetical subsystem in the genome of \*Streptococcus constellatus\* (GCF\\_016127875.1) is composed of 2 proteins: LmuB\\_SMC\\_Cap4\\_nuclease\\_II (WP\\_198458038.1)and, LmuA\\_effector\\_hypothetical (WP\\_198458040.1). +Lamassu-Fam_Hypothetical subsystem in the genome of *Streptococcus constellatus* (GCF_016127875.1) is composed of 2 proteins: LmuB_SMC_Cap4_nuclease_II (WP_198458038.1)and, LmuA_effector_hypothetical (WP_198458040.1).  -Lamassu-Fam\\_Protease subsystem in the genome of \*Azospirillum brasilense\* (GCF\\_022023855.1) is composed of 2 proteins: LmuA\\_effector\\_Protease (WP\\_237905456.1)and, LmuB\\_SMC\\_Cap4\\_nuclease\\_II (WP\\_237905457.1). +Lamassu-Fam_Protease subsystem in the genome of *Azospirillum brasilense* (GCF_022023855.1) is composed of 2 proteins: LmuA_effector_Protease (WP_237905456.1)and, LmuB_SMC_Cap4_nuclease_II (WP_237905457.1).  -Lamassu-Fam\\_PDDEXK subsystem in the genome of \*Janthinobacterium sp.\* (GCF\\_000013625.1) is composed of 2 proteins: LmuA\\_effector\\_PDDEXK (WP\\_012078862.1)and, LmuB\\_SMC\\_Cap4\\_nuclease\\_II (WP\\_012078864.1). +Lamassu-Fam_PDDEXK subsystem in the genome of *Janthinobacterium sp.* (GCF_000013625.1) is composed of 2 proteins: LmuA_effector_PDDEXK (WP_012078862.1)and, LmuB_SMC_Cap4_nuclease_II (WP_012078864.1).  -Lamassu-Fam\\_Sir2 subsystem in the genome of \*Paenibacillus polymyxa\* (GCF\\_022492955.1) is composed of 4 proteins: LmuB\\_SMC\\_Cap4\\_nuclease\\_II (WP\\_240753063.1), LmuB\\_SMC\\_Sir2 (WP\\_240753064.1), LmuC\\_acc\\_Sir2 (WP\\_240753066.1)and, LmuA\\_effector\\_Sir2 (WP\\_240753072.1). +Lamassu-Fam_Sir2 subsystem in the genome of *Paenibacillus polymyxa* (GCF_022492955.1) is composed of 4 proteins: LmuB_SMC_Cap4_nuclease_II (WP_240753063.1), LmuB_SMC_Sir2 (WP_240753064.1), LmuC_acc_Sir2 (WP_240753066.1)and, LmuA_effector_Sir2 (WP_240753072.1).  -Lamassu-Fam\\_FMO subsystem in the genome of \*Acinetobacter johnsonii\* (GCF\\_021496365.1) is composed of 2 proteins: LmuA\\_effector\\_FMO (WP\\_234965678.1)and, LmuB\\_SMC\\_FMO (WP\\_234965680.1). +Lamassu-Fam_FMO subsystem in the genome of *Acinetobacter johnsonii* (GCF_021496365.1) is composed of 2 proteins: LmuA_effector_FMO (WP_234965678.1)and, LmuB_SMC_FMO (WP_234965680.1).  -Lamassu-Fam\\_Amidase subsystem in the genome of \*Bradyrhizobium arachidis\* (GCF\\_015291705.1) is composed of 2 proteins: LmuA\\_effector\\_Amidase (WP\\_143130692.1)and, LmuB\\_SMC\\_Amidase (WP\\_092217687.1). +Lamassu-Fam_Amidase subsystem in the genome of *Bradyrhizobium arachidis* (GCF_015291705.1) is composed of 2 proteins: LmuA_effector_Amidase (WP_143130692.1)and, LmuB_SMC_Amidase (WP_092217687.1). ## Distribution of the system among prokaryotes @@ -73,29 +73,29 @@ Among the 22k complete genomes of RefSeq, this system is present in 3939 genomes  -\*Proportion of genome encoding the Lamassu-Fam system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Lamassu-Fam system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Lamassu-Fam systems were experimentally validated using: -A system from \*Bacillus sp. NIO-1130\* in \*Bacillus subtilis\* has an anti-phage effect against phi3T, SpBeta, SPR (Doron et al., 2018) +A system from *Bacillus sp. NIO-1130* in *Bacillus subtilis* has an anti-phage effect against phi3T, SpBeta, SPR (Doron et al., 2018) -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against SpBeta (Doron et al., 2018) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SpBeta (Doron et al., 2018) -Subsystem LmuB+LmuC+Hydrolase+ Protease with a system from \*Bacillus cereus\* in \*Escherichia coli\* has an anti-phage effect against T4 (Millman et al., 2022) +Subsystem LmuB+LmuC+Hydrolase+ Protease with a system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T4 (Millman et al., 2022) -Subsystem LmuB+LmuC+Hydrolase+ Protease with a system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against SpBeta, phi105, Rho14, SPP1, phi29 (Millman et al., 2022) +Subsystem LmuB+LmuC+Hydrolase+ Protease with a system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SpBeta, phi105, Rho14, SPP1, phi29 (Millman et al., 2022) -Subsystem LmuB+LmuC+Mrr endonuclease with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi27 (Millman et al., 2022) +Subsystem LmuB+LmuC+Mrr endonuclease with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Millman et al., 2022) -Subsystem LmuB+LmuC+PDDEXK nuclease with a system from \*Bacillus cereus\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir (Millman et al., 2022) +Subsystem LmuB+LmuC+PDDEXK nuclease with a system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against LambdaVir (Millman et al., 2022) -Subsystem LmuB+LmuC+PDDEXK nuclease with a system from \*Bacillus sp. UNCCL81\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir (Millman et al., 2022) +Subsystem LmuB+LmuC+PDDEXK nuclease with a system from *Bacillus sp. UNCCL81* in *Escherichia coli* has an anti-phage effect against LambdaVir (Millman et al., 2022) -Subsystem LmuA+LmuC+LmuB with a system from \*Janthinobacterium agaricidamnosum\* in \*Escherichia coli\* has an anti-phage effect against T1, T3, T7, LambdaVir, PVP-SE1 (Payne et al., 2021) +Subsystem LmuA+LmuC+LmuB with a system from *Janthinobacterium agaricidamnosum* in *Escherichia coli* has an anti-phage effect against T1, T3, T7, LambdaVir, PVP-SE1 (Payne et al., 2021) -Subsystem DdmABC with a system from \*Vibrio cholerae\* in \*Escherichia coli\* has an anti-phage effect against P1, Lambda (Jaskólska et al., 2022) +Subsystem DdmABC with a system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against P1, Lambda (Jaskólska et al., 2022) ## Relevant abstracts @@ -112,8 +112,8 @@ items: ## References -1\. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. \*Science\*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120 +1. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. *Science*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120 -2\. Payne LJ, Todeschini TC, Wu Y, et al. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. \*Nucleic Acids Res\*. 2021;49(19):10868-10878. doi:10.1093/nar/gkab883 +2. Payne LJ, Todeschini TC, Wu Y, et al. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. *Nucleic Acids Res*. 2021;49(19):10868-10878. doi:10.1093/nar/gkab883 -3\. Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J.L.M., Dar, D., Kacen, A., Amitai, G., Sorek, R., 2022. An expanding arsenal of immune systems that protect bacteria from phages. bioRxiv. https://doi.org/10.1101/2022.05.11.491447 +3. Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J.L.M., Dar, D., Kacen, A., Amitai, G., Sorek, R., 2022. An expanding arsenal of immune systems that protect bacteria from phages. bioRxiv. https://doi.org/10.1101/2022.05.11.491447 diff --git a/content/2.defense-systems/lit.md b/content/2.defense-systems/lit.md index d5b1dffe..8adf289e 100644 --- a/content/2.defense-systems/lit.md +++ b/content/2.defense-systems/lit.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Lit system in the genome of \*Stenotrophomonas maltophilia\* (GCF\\_012647025.1) is composed of 1 protein: Lit (WP\\_061201506.1). +Lit system in the genome of *Stenotrophomonas maltophilia* (GCF_012647025.1) is composed of 1 protein: Lit (WP_061201506.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 455 genomes  -\*Proportion of genome encoding the Lit system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Lit system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Lit systems were experimentally validated using: -A system from \*Escherichia coli defective prophage e14\* in \*Escherichia coli\* has an anti-phage effect against T4 (Yu and Snyder, 1994) +A system from *Escherichia coli defective prophage e14* in *Escherichia coli* has an anti-phage effect against T4 (Yu and Snyder, 1994) ## Relevant abstracts diff --git a/content/2.defense-systems/menshen.md b/content/2.defense-systems/menshen.md index 6c8d680c..fe9536b9 100644 --- a/content/2.defense-systems/menshen.md +++ b/content/2.defense-systems/menshen.md @@ -4,13 +4,13 @@ title: Menshen ## Example of genomic structure -The Menshen system is composed of 3 proteins: NsnA, NsnB and, NsnC\_2623244837. +The Menshen system is composed of 3 proteins: NsnA, NsnB and, NsnC_2623244837. Here is an example found in the RefSeq database:  -Menshen system in the genome of \*Citrobacter freundii\* (GCF\\_003937345.2) is composed of 3 proteins: NsnA (WP\\_125363058.1), NsnB (WP\\_197964486.1)and, NsnC\\_2617187710 (WP\\_125363056.1). +Menshen system in the genome of *Citrobacter freundii* (GCF_003937345.2) is composed of 3 proteins: NsnA (WP_125363058.1), NsnB (WP_197964486.1)and, NsnC_2617187710 (WP_125363056.1). ## Distribution of the system among prokaryotes @@ -20,15 +20,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 446 genomes  -\*Proportion of genome encoding the Menshen system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Menshen system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Menshen systems were experimentally validated using: -A system from \*Solibacillus silvestris\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022) +A system from *Solibacillus silvestris* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022) -A system from \*Solibacillus silvestris\* in \*Bacillus subtilis\* has an anti-phage effect against Fado (Millman et al., 2022) +A system from *Solibacillus silvestris* in *Bacillus subtilis* has an anti-phage effect against Fado (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/mok_hok_sok.md b/content/2.defense-systems/mok_hok_sok.md index 89d44115..8a714b24 100644 --- a/content/2.defense-systems/mok_hok_sok.md +++ b/content/2.defense-systems/mok_hok_sok.md @@ -4,29 +4,29 @@ title: Mok_Hok_Sok ## Example of genomic structure -The Mok\_Hok\_Sok system is composed of 2 proteins: Mok and, Hok. +The Mok_Hok_Sok system is composed of 2 proteins: Mok and, Hok. Here is an example found in the RefSeq database:  -Mok\\_Hok\\_Sok system in the genome of \*Raoultella terrigena\* (GCF\\_015571975.1) is composed of 2 proteins: Hok (WP\\_227629320.1)and, Mok (WP\\_227699927.1). +Mok_Hok_Sok system in the genome of *Raoultella terrigena* (GCF_015571975.1) is composed of 2 proteins: Hok (WP_227629320.1)and, Mok (WP_227699927.1). ## Distribution of the system among prokaryotes -The Mok\_Hok\_Sok system is present in a total of 57 different species. +The Mok_Hok_Sok system is present in a total of 57 different species. Among the 22k complete genomes of RefSeq, this system is present in 1687 genomes (7.4 %).  -\*Proportion of genome encoding the Mok\_Hok\_Sok system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Mok_Hok_Sok system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Mok\_Hok\_Sok systems were experimentally validated using: +Mok_Hok_Sok systems were experimentally validated using: -A system from \*R1 plasmid of Salmonella paratyphi\* in \*Escherichia coli\* has an anti-phage effect against T4, LambdaVir (Pecota and Wood, 1996) +A system from *R1 plasmid of Salmonella paratyphi* in *Escherichia coli* has an anti-phage effect against T4, LambdaVir (Pecota and Wood, 1996) ## Relevant abstracts diff --git a/content/2.defense-systems/mokosh.md b/content/2.defense-systems/mokosh.md index f562ef04..062420f3 100644 --- a/content/2.defense-systems/mokosh.md +++ b/content/2.defense-systems/mokosh.md @@ -10,11 +10,11 @@ Here is some example found in the RefSeq database:  -Mokosh\\_TypeI subsystem in the genome of \*Vibrio alginolyticus\* (GCF\\_022343125.1) is composed of 2 proteins: MkoB2 (WP\\_238970063.1)and, MkoA2 (WP\\_238970065.1). +Mokosh_TypeI subsystem in the genome of *Vibrio alginolyticus* (GCF_022343125.1) is composed of 2 proteins: MkoB2 (WP_238970063.1)and, MkoA2 (WP_238970065.1).  -Mokosh\\_TypeII subsystem in the genome of \*Shigella flexneri\* (GCF\\_022354205.1) is composed of 1 protein: MkoC (WP\\_000344091.1). +Mokosh_TypeII subsystem in the genome of *Shigella flexneri* (GCF_022354205.1) is composed of 1 protein: MkoC (WP_000344091.1). ## Distribution of the system among prokaryotes @@ -24,15 +24,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 2540 genomes  -\*Proportion of genome encoding the Mokosh system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Mokosh system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation Mokosh systems were experimentally validated using: -Subsystem Type I with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, LambdaVir, T5, SECphi27 (Millman et al., 2022) +Subsystem Type I with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, T5, SECphi27 (Millman et al., 2022) -Subsystem Type II with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against SECphi17 (Millman et al., 2022) +Subsystem Type II with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi17 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/mqsrac.md b/content/2.defense-systems/mqsrac.md index 8fd109e3..bba701db 100644 --- a/content/2.defense-systems/mqsrac.md +++ b/content/2.defense-systems/mqsrac.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -MqsRAC system in the genome of \*Escherichia coli\* (GCF\\_900636115.1) is composed of 2 proteins: mqsR (WP\\_024222007.1)and, mqsC (WP\\_021568458.1). +MqsRAC system in the genome of *Escherichia coli* (GCF_900636115.1) is composed of 2 proteins: mqsR (WP_024222007.1)and, mqsC (WP_021568458.1). ## Distribution of the system among prokaryotes @@ -20,7 +20,7 @@ Among the 22k complete genomes of RefSeq, this system is present in 26 genomes (  -\*Proportion of genome encoding the MqsRAC system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the MqsRAC system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/nhi.md b/content/2.defense-systems/nhi.md index 1652fa61..70efc5bd 100644 --- a/content/2.defense-systems/nhi.md +++ b/content/2.defense-systems/nhi.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Nhi system in the genome of \*Enterococcus avium\* (GCF\\_003711125.1) is composed of 1 protein: Nhi (WP\\_148712513.1). +Nhi system in the genome of *Enterococcus avium* (GCF_003711125.1) is composed of 1 protein: Nhi (WP_148712513.1). ## Distribution of the system among prokaryotes @@ -20,21 +20,21 @@ Among the 22k complete genomes of RefSeq, this system is present in 202 genomes  -\*Proportion of genome encoding the Nhi system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Nhi system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Nhi systems were experimentally validated using: -Subsystem Nhi-like with a system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against phi3T, SpBeta, SPR (Millman et al., 2022) +Subsystem Nhi-like with a system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against phi3T, SpBeta, SPR (Millman et al., 2022) -A system from \*Staphylococcus epidermidis\* in \*Staphylococcus epidermidis\* has an anti-phage effect against JBug18, Pike, CNPx (Bari et al., 2022) +A system from *Staphylococcus epidermidis* in *Staphylococcus epidermidis* has an anti-phage effect against JBug18, Pike, CNPx (Bari et al., 2022) -A system from \*Staphylococcus epidermidis\* in \*Staphylococcus aureus\* has an anti-phage effect against Lorac (Bari et al., 2022) +A system from *Staphylococcus epidermidis* in *Staphylococcus aureus* has an anti-phage effect against Lorac (Bari et al., 2022) -A system from \*Staphylococcus aureus\* in \*Staphylococcus aureus\* has an anti-phage effect against Lorac (Bari et al., 2022) +A system from *Staphylococcus aureus* in *Staphylococcus aureus* has an anti-phage effect against Lorac (Bari et al., 2022) -A system from \*Vibrio vulnificus\* in \*Staphylococcus aureus\* has an anti-phage effect against Lorac (Bari et al., 2022) +A system from *Vibrio vulnificus* in *Staphylococcus aureus* has an anti-phage effect against Lorac (Bari et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/nixi.md b/content/2.defense-systems/nixi.md index a40033ee..9c182e3e 100644 --- a/content/2.defense-systems/nixi.md +++ b/content/2.defense-systems/nixi.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -NixI system in the genome of \*Vibrio cholerae\* (GCF\\_009646135.1) is composed of 2 proteins: NixI (WP\\_001147214.1)and, Stix (WP\\_000628297.1). +NixI system in the genome of *Vibrio cholerae* (GCF_009646135.1) is composed of 2 proteins: NixI (WP_001147214.1)and, Stix (WP_000628297.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 19 genomes (  -\*Proportion of genome encoding the NixI system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the NixI system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation NixI systems were experimentally validated using: -A system from \*Vibrio cholerae\* in \*Vibrio cholerae\* has an anti-phage effect against ICP1 (Legault et al., 2022) +A system from *Vibrio cholerae* in *Vibrio cholerae* has an anti-phage effect against ICP1 (Legault et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/nlr.md b/content/2.defense-systems/nlr.md index 8a2596d3..05e7f48d 100644 --- a/content/2.defense-systems/nlr.md +++ b/content/2.defense-systems/nlr.md @@ -10,11 +10,11 @@ Here is some example found in the RefSeq database:  -NLR\\_like\\_bNACHT01 subsystem in the genome of \*Pseudomonas psychrotolerans\* (GCF\\_001913135.1) is composed of 1 protein: NLR\\_like\\_bNACHT01 (WP\\_074528296.1). +NLR_like_bNACHT01 subsystem in the genome of *Pseudomonas psychrotolerans* (GCF_001913135.1) is composed of 1 protein: NLR_like_bNACHT01 (WP_074528296.1).  -NLR\\_like\\_bNACHT09 subsystem in the genome of \*Escherichia coli\* (GCF\\_900636105.1) is composed of 1 protein: NLR\\_like\\_bNACHT09 (WP\\_089572057.1). +NLR_like_bNACHT09 subsystem in the genome of *Escherichia coli* (GCF_900636105.1) is composed of 1 protein: NLR_like_bNACHT09 (WP_089572057.1). ## Distribution of the system among prokaryotes @@ -24,29 +24,29 @@ Among the 22k complete genomes of RefSeq, this system is present in 453 genomes  -\*Proportion of genome encoding the NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation NLR systems were experimentally validated using: -Subsystem bNACHT01 with a system from \*Klebsiella pneumoniae\* in \*Escherichia coli\* has an anti-phage effect against T4, T5, T6 (Kibby et al., 2022) +Subsystem bNACHT01 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against T4, T5, T6 (Kibby et al., 2022) -Subsystem bNACHT02 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T7, MS2 (Kibby et al., 2022) +Subsystem bNACHT02 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, MS2 (Kibby et al., 2022) -Subsystem bNACHT11 with a system from \*Klebsiella pneumoniae\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Kibby et al., 2022) +Subsystem bNACHT11 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Kibby et al., 2022) -Subsystem bNACHT12 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4, T6, MS2 (Kibby et al., 2022) +Subsystem bNACHT12 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, T6, MS2 (Kibby et al., 2022) -Subsystem bNACHT23 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T6, T5 (Kibby et al., 2022) +Subsystem bNACHT23 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T6, T5 (Kibby et al., 2022) -Subsystem bNACHT25 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, LambdaVir, MS2 (Kibby et al., 2022) +Subsystem bNACHT25 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, MS2 (Kibby et al., 2022) -Subsystem bNACHT32 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, LambdaVir, MS2 (Kibby et al., 2022) +Subsystem bNACHT32 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, MS2 (Kibby et al., 2022) -Subsystem bNACHT67 with a system from \*Klebsiella michiganensis\* in \*Escherichia coli\* has an anti-phage effect against T2, T4 (Kibby et al., 2022) +Subsystem bNACHT67 with a system from *Klebsiella michiganensis* in *Escherichia coli* has an anti-phage effect against T2, T4 (Kibby et al., 2022) -Subsystem bNACHT09 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T5, LambdaVir, T3, T7 (Kibby et al., 2022) +Subsystem bNACHT09 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, LambdaVir, T3, T7 (Kibby et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/old_exonuclease.md b/content/2.defense-systems/old_exonuclease.md index d76b1eb7..e079a3ef 100644 --- a/content/2.defense-systems/old_exonuclease.md +++ b/content/2.defense-systems/old_exonuclease.md @@ -4,32 +4,32 @@ title: Old_exonuclease ## Example of genomic structure -The Old\_exonuclease system is composed of one protein: Old\_exonuclease. +The Old_exonuclease system is composed of one protein: Old_exonuclease. Here is an example found in the RefSeq database:  -Old\\_exonuclease system in the genome of \*Escherichia coli\* (GCF\\_016904335.1) is composed of 1 protein: Old\\_exonuclease (WP\\_015979595.1). +Old_exonuclease system in the genome of *Escherichia coli* (GCF_016904335.1) is composed of 1 protein: Old_exonuclease (WP_015979595.1). ## Distribution of the system among prokaryotes -The Old\_exonuclease system is present in a total of 53 different species. +The Old_exonuclease system is present in a total of 53 different species. Among the 22k complete genomes of RefSeq, this system is present in 102 genomes (0.4 %).  -\*Proportion of genome encoding the Old\_exonuclease system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Old_exonuclease system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Old\_exonuclease systems were experimentally validated using: +Old_exonuclease systems were experimentally validated using: -A system from \*Enterobacteria phage P2\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T4, LF82\_P8, Al505\_P2 (Rousset et al., 2022) +A system from *Enterobacteria phage P2* in *Escherichia coli* has an anti-phage effect against Lambda, T4, LF82_P8, Al505_P2 (Rousset et al., 2022) ## Relevant abstracts -\*\*Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host & Microbe 30, 740-753.e5 (2022).\*\* +**Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host & Microbe 30, 740-753.e5 (2022).** Bacteria carry diverse genetic systems to defend against viral infection, some of which are found within prophages where they inhibit competing viruses. Phage satellites pose additional pressures on phages by hijacking key viral elements to their own benefit. Here, we show that E. coli P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems. We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Antiviral hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Notably, the anti-phage activity of satellites can benefit the helper phage during competition with virulent phages, turning a parasitic relationship into a mutualistic one. Anti-phage hotspots are present across distant species and constitute a substantial source of systems that participate in the competition between mobile genetic elements. diff --git a/content/2.defense-systems/olokun.md b/content/2.defense-systems/olokun.md index 7ef26b38..d57d1225 100644 --- a/content/2.defense-systems/olokun.md +++ b/content/2.defense-systems/olokun.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Olokun system in the genome of \*Vibrio cyclitrophicus\* (GCF\\_023206035.1) is composed of 2 proteins: OloA (WP\\_016800143.1)and, OloB (WP\\_029203700.1). +Olokun system in the genome of *Vibrio cyclitrophicus* (GCF_023206035.1) is composed of 2 proteins: OloA (WP_016800143.1)and, OloB (WP_029203700.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 252 genomes  -\*Proportion of genome encoding the Olokun system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Olokun system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Olokun systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi27 (Millman et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pago.md b/content/2.defense-systems/pago.md index c9dffa18..6b69e61f 100644 --- a/content/2.defense-systems/pago.md +++ b/content/2.defense-systems/pago.md @@ -4,13 +4,13 @@ title: pAgo ## Example of genomic structure -The pAgo system is composed of one protein: pAgo\_Short. +The pAgo system is composed of one protein: pAgo_Short. Here is an example found in the RefSeq database:  -pAgo system in the genome of \*Ensifer adhaerens\* (GCF\\_020405145.1) is composed of 1 protein: pAgo\\_LongB (WP\\_218685258.1). +pAgo system in the genome of *Ensifer adhaerens* (GCF_020405145.1) is composed of 1 protein: pAgo_LongB (WP_218685258.1). ## Distribution of the system among prokaryotes @@ -20,29 +20,29 @@ Among the 22k complete genomes of RefSeq, this system is present in 598 genomes  -\*Proportion of genome encoding the pAgo system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the pAgo system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation pAgo systems were experimentally validated using: -Subsystem Ago with a system from \*Clostridium butyricum\* in \*Escherichia coli\* has an anti-phage effect against M13, P1vir (Kuzmenko et al., 2020) +Subsystem Ago with a system from *Clostridium butyricum* in *Escherichia coli* has an anti-phage effect against M13, P1vir (Kuzmenko et al., 2020) -A system from \*Natronobacterium gregoryi\* in \*Escherichia coli\* has an anti-phage effect against T7 (Xing et al., 2022) +A system from *Natronobacterium gregoryi* in *Escherichia coli* has an anti-phage effect against T7 (Xing et al., 2022) -Subsystem GsSir2/Ago with a system from \*Geobacter sulfurreducens\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022) +Subsystem GsSir2/Ago with a system from *Geobacter sulfurreducens* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022) -Subsystem GsSir2/Ago with a system from \*Geobacter sulfurreducens\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022) +Subsystem GsSir2/Ago with a system from *Geobacter sulfurreducens* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022) -Subsystem CcSir2/Ago with a system from \*Caballeronia cordobensis\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir (Zaremba et al., 2022) +Subsystem CcSir2/Ago with a system from *Caballeronia cordobensis* in *Escherichia coli* has an anti-phage effect against LambdaVir (Zaremba et al., 2022) -Subsystem PgSir2/Ago with a system from \*araburkholderia graminis\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022) +Subsystem PgSir2/Ago with a system from *araburkholderia graminis* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022) -Subsystem Ago with a system from \*Exiguobacterium marinum\* in \*Escherichia coli\* has an anti-phage effect against P1vir (Lisitskaya et al., 2022) +Subsystem Ago with a system from *Exiguobacterium marinum* in *Escherichia coli* has an anti-phage effect against P1vir (Lisitskaya et al., 2022) -Subsystem Sir2/Ago with a system from \*Geobacter sulfurreducens\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir (Garb et al., 2022) +Subsystem Sir2/Ago with a system from *Geobacter sulfurreducens* in *Escherichia coli* has an anti-phage effect against LambdaVir (Garb et al., 2022) -Subsystem SiAgo/Aga1/Aga2 with a system from \*Sulfolobus islandicus\* in \*Sulfolobus islandicus\* has an anti-phage effect against SMV1 (Zeng et al., 2021) +Subsystem SiAgo/Aga1/Aga2 with a system from *Sulfolobus islandicus* in *Sulfolobus islandicus* has an anti-phage effect against SMV1 (Zeng et al., 2021) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-lambda-1.md b/content/2.defense-systems/pd-lambda-1.md index 823c9d05..0552f8e3 100644 --- a/content/2.defense-systems/pd-lambda-1.md +++ b/content/2.defense-systems/pd-lambda-1.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-Lambda-1 system in the genome of \*Olleya sp.\* (GCF\\_002831645.1) is composed of 1 protein: PD-Lambda-1 (WP\\_101017806.1). +PD-Lambda-1 system in the genome of *Olleya sp.* (GCF_002831645.1) is composed of 1 protein: PD-Lambda-1 (WP_101017806.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1323 genomes  -\*Proportion of genome encoding the PD-Lambda-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-Lambda-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-Lambda-1 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-lambda-2.md b/content/2.defense-systems/pd-lambda-2.md index 514e03ba..832810be 100644 --- a/content/2.defense-systems/pd-lambda-2.md +++ b/content/2.defense-systems/pd-lambda-2.md @@ -4,13 +4,13 @@ title: PD-Lambda-2 ## Example of genomic structure -The PD-Lambda-2 system is composed of 3 proteins: PD-Lambda-2\_C, PD-Lambda-2\_B and, PD-Lambda-2\_A. +The PD-Lambda-2 system is composed of 3 proteins: PD-Lambda-2_C, PD-Lambda-2_B and, PD-Lambda-2_A. Here is an example found in the RefSeq database:  -PD-Lambda-2 system in the genome of \*Pseudomonas aeruginosa\* (GCF\\_013341295.1) is composed of 3 proteins: PD-Lambda-2\\_C (WP\\_023115149.1), PD-Lambda-2\\_B (WP\\_014833925.1)and, PD-Lambda-2\\_A (WP\\_003116393.1). +PD-Lambda-2 system in the genome of *Pseudomonas aeruginosa* (GCF_013341295.1) is composed of 3 proteins: PD-Lambda-2_C (WP_023115149.1), PD-Lambda-2_B (WP_014833925.1)and, PD-Lambda-2_A (WP_003116393.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 122 genomes  -\*Proportion of genome encoding the PD-Lambda-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-Lambda-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-Lambda-2 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi17, SECphi18, SECphi27, T3 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi17, SECphi18, SECphi27, T3 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-lambda-3.md b/content/2.defense-systems/pd-lambda-3.md index 23c5735e..54981889 100644 --- a/content/2.defense-systems/pd-lambda-3.md +++ b/content/2.defense-systems/pd-lambda-3.md @@ -4,13 +4,13 @@ title: PD-Lambda-3 ## Example of genomic structure -The PD-Lambda-3 system is composed of 2 proteins: PD-Lambda-3\_B and, PD-Lambda-3\_A. +The PD-Lambda-3 system is composed of 2 proteins: PD-Lambda-3_B and, PD-Lambda-3_A. Here is an example found in the RefSeq database:  -PD-Lambda-3 system in the genome of \*Serratia rubidaea\* (GCF\\_900478395.1) is composed of 2 proteins: PD-Lambda-3\\_A (WP\\_227673955.1)and, PD-Lambda-3\\_B (WP\\_047063039.1). +PD-Lambda-3 system in the genome of *Serratia rubidaea* (GCF_900478395.1) is composed of 2 proteins: PD-Lambda-3_A (WP_227673955.1)and, PD-Lambda-3_B (WP_047063039.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 74 genomes (  -\*Proportion of genome encoding the PD-Lambda-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-Lambda-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-Lambda-3 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-lambda-4.md b/content/2.defense-systems/pd-lambda-4.md index caea84c1..b4db24c4 100644 --- a/content/2.defense-systems/pd-lambda-4.md +++ b/content/2.defense-systems/pd-lambda-4.md @@ -4,13 +4,13 @@ title: PD-Lambda-4 ## Example of genomic structure -The PD-Lambda-4 system is composed of 2 proteins: PD-Lambda-4\_A and, PD-Lambda-4\_B. +The PD-Lambda-4 system is composed of 2 proteins: PD-Lambda-4_A and, PD-Lambda-4_B. Here is an example found in the RefSeq database:  -PD-Lambda-4 system in the genome of \*Enterobacter asburiae\* (GCF\\_023023265.1) is composed of 2 proteins: PD-Lambda-4\\_A (WP\\_246916891.1)and, PD-Lambda-4\\_B (WP\\_241182936.1). +PD-Lambda-4 system in the genome of *Enterobacter asburiae* (GCF_023023265.1) is composed of 2 proteins: PD-Lambda-4_A (WP_246916891.1)and, PD-Lambda-4_B (WP_241182936.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 75 genomes (  -\*Proportion of genome encoding the PD-Lambda-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-Lambda-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-Lambda-4 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4, LambdaVir, SECphi27, T7 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, LambdaVir, SECphi27, T7 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-lambda-5.md b/content/2.defense-systems/pd-lambda-5.md index 1ff6bd29..cbcbd308 100644 --- a/content/2.defense-systems/pd-lambda-5.md +++ b/content/2.defense-systems/pd-lambda-5.md @@ -4,13 +4,13 @@ title: PD-Lambda-5 ## Example of genomic structure -The PD-Lambda-5 system is composed of 2 proteins: PD-Lambda-5\_A and, PD-Lambda-5\_B. +The PD-Lambda-5 system is composed of 2 proteins: PD-Lambda-5_A and, PD-Lambda-5_B. Here is an example found in the RefSeq database:  -PD-Lambda-5 system in the genome of \*Chromobacterium rhizoryzae\* (GCF\\_020544465.1) is composed of 2 proteins: PD-Lambda-5\\_B (WP\\_227108065.1)and, PD-Lambda-5\\_A (WP\\_227108067.1). +PD-Lambda-5 system in the genome of *Chromobacterium rhizoryzae* (GCF_020544465.1) is composed of 2 proteins: PD-Lambda-5_B (WP_227108065.1)and, PD-Lambda-5_A (WP_227108067.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 361 genomes  -\*Proportion of genome encoding the PD-Lambda-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-Lambda-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-Lambda-5 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-lambda-6.md b/content/2.defense-systems/pd-lambda-6.md index 797d8817..7905b3c6 100644 --- a/content/2.defense-systems/pd-lambda-6.md +++ b/content/2.defense-systems/pd-lambda-6.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-Lambda-6 system in the genome of \*Escherichia albertii\* (GCF\\_003864095.1) is composed of 1 protein: PD-Lambda-6 (WP\\_125059614.1). +PD-Lambda-6 system in the genome of *Escherichia albertii* (GCF_003864095.1) is composed of 1 protein: PD-Lambda-6 (WP_125059614.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 21 genomes (  -\*Proportion of genome encoding the PD-Lambda-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-Lambda-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-Lambda-6 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, T5 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, T5 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-1.md b/content/2.defense-systems/pd-t4-1.md index 1e25c4d2..a6194dee 100644 --- a/content/2.defense-systems/pd-t4-1.md +++ b/content/2.defense-systems/pd-t4-1.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T4-1 system in the genome of \*Bradyrhizobium diazoefficiens\* (GCF\\_016616885.1) is composed of 1 protein: PD-T4-1 (WP\\_200471933.1). +PD-T4-1 system in the genome of *Bradyrhizobium diazoefficiens* (GCF_016616885.1) is composed of 1 protein: PD-T4-1 (WP_200471933.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 209 genomes  -\*Proportion of genome encoding the PD-T4-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-1 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-10.md b/content/2.defense-systems/pd-t4-10.md index 97107779..8b5a2c6c 100644 --- a/content/2.defense-systems/pd-t4-10.md +++ b/content/2.defense-systems/pd-t4-10.md @@ -4,13 +4,13 @@ title: PD-T4-10 ## Example of genomic structure -The PD-T4-10 system is composed of 2 proteins: PD-T4-10\_B and, PD-T4-10\_A. +The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. Here is an example found in the RefSeq database:  -PD-T4-10 system in the genome of \*Salmonella enterica\* (GCF\\_022559465.1) is composed of 2 proteins: PD-T4-10\\_A (WP\\_109288182.1)and, PD-T4-10\\_B (WP\\_001585426.1). +PD-T4-10 system in the genome of *Salmonella enterica* (GCF_022559465.1) is composed of 2 proteins: PD-T4-10_A (WP_109288182.1)and, PD-T4-10_B (WP_001585426.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 68 genomes (  -\*Proportion of genome encoding the PD-T4-10 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-10 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-10 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, T5, SECphi27 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi27 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-2.md b/content/2.defense-systems/pd-t4-2.md index 51ff20ad..ea7510b5 100644 --- a/content/2.defense-systems/pd-t4-2.md +++ b/content/2.defense-systems/pd-t4-2.md @@ -4,13 +4,13 @@ title: PD-T4-2 ## Example of genomic structure -The PD-T4-2 system is composed of 2 proteins: PD-T4-2\_B and, PD-T4-2\_A. +The PD-T4-2 system is composed of 2 proteins: PD-T4-2_B and, PD-T4-2_A. Here is an example found in the RefSeq database:  -PD-T4-2 system in the genome of \*Microcystis viridis\* (GCF\\_003945305.1) is composed of 2 proteins: PD-T4-2\\_B (WP\\_164517006.1)and, PD-T4-2\\_A (WP\\_125731928.1). +PD-T4-2 system in the genome of *Microcystis viridis* (GCF_003945305.1) is composed of 2 proteins: PD-T4-2_B (WP_164517006.1)and, PD-T4-2_A (WP_125731928.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 33 genomes (  -\*Proportion of genome encoding the PD-T4-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-2 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, T5, SECphi27 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi27 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-3.md b/content/2.defense-systems/pd-t4-3.md index d374dd09..7891ae06 100644 --- a/content/2.defense-systems/pd-t4-3.md +++ b/content/2.defense-systems/pd-t4-3.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T4-3 system in the genome of \*Salmonella enterica\* (GCF\\_009664795.1) is composed of 1 protein: PD-T4-3 (WP\\_000353908.1). +PD-T4-3 system in the genome of *Salmonella enterica* (GCF_009664795.1) is composed of 1 protein: PD-T4-3 (WP_000353908.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1313 genomes  -\*Proportion of genome encoding the PD-T4-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-3 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-4.md b/content/2.defense-systems/pd-t4-4.md index 68a83f0a..101d7af9 100644 --- a/content/2.defense-systems/pd-t4-4.md +++ b/content/2.defense-systems/pd-t4-4.md @@ -4,13 +4,13 @@ title: PD-T4-4 ## Example of genomic structure -The PD-T4-4 system is composed of 2 proteins: PD-T4-4\_A and, PD-T4-4\_B. +The PD-T4-4 system is composed of 2 proteins: PD-T4-4_A and, PD-T4-4_B. Here is an example found in the RefSeq database:  -PD-T4-4 system in the genome of \*Escherichia coli\* (GCF\\_013376895.1) is composed of 2 proteins: PD-T4-4\\_B (WP\\_176670803.1)and, PD-T4-4\\_A (WP\\_027920142.1). +PD-T4-4 system in the genome of *Escherichia coli* (GCF_013376895.1) is composed of 2 proteins: PD-T4-4_B (WP_176670803.1)and, PD-T4-4_A (WP_027920142.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 53 genomes (  -\*Proportion of genome encoding the PD-T4-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-4 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, SECphi17 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, SECphi17 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-5.md b/content/2.defense-systems/pd-t4-5.md index d3b03c61..4af680d5 100644 --- a/content/2.defense-systems/pd-t4-5.md +++ b/content/2.defense-systems/pd-t4-5.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T4-5 system in the genome of \*Achromobacter sp.\* (GCF\\_020541125.1) is composed of 1 protein: PD-T4-5 (WP\\_180098530.1). +PD-T4-5 system in the genome of *Achromobacter sp.* (GCF_020541125.1) is composed of 1 protein: PD-T4-5 (WP_180098530.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 587 genomes  -\*Proportion of genome encoding the PD-T4-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-5 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4, T6, LambdaVir, T5 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, T6, LambdaVir, T5 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-6.md b/content/2.defense-systems/pd-t4-6.md index 59d05aa1..a385ab35 100644 --- a/content/2.defense-systems/pd-t4-6.md +++ b/content/2.defense-systems/pd-t4-6.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T4-6 system in the genome of \*Pseudomonas aeruginosa\* (GCF\\_016584725.1) is composed of 1 protein: PD-T4-6 (WP\\_023875836.1). +PD-T4-6 system in the genome of *Pseudomonas aeruginosa* (GCF_016584725.1) is composed of 1 protein: PD-T4-6 (WP_023875836.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 88 genomes (  -\*Proportion of genome encoding the PD-T4-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-6 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-7.md b/content/2.defense-systems/pd-t4-7.md index 39e5cb8f..aa90a1ba 100644 --- a/content/2.defense-systems/pd-t4-7.md +++ b/content/2.defense-systems/pd-t4-7.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T4-7 system in the genome of \*Providencia alcalifaciens\* (GCF\\_915401745.1) is composed of 1 protein: PD-T4-7 (WP\\_036975088.1). +PD-T4-7 system in the genome of *Providencia alcalifaciens* (GCF_915401745.1) is composed of 1 protein: PD-T4-7 (WP_036975088.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 156 genomes  -\*Proportion of genome encoding the PD-T4-7 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-7 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-7 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-8.md b/content/2.defense-systems/pd-t4-8.md index eff24099..f25ba6a4 100644 --- a/content/2.defense-systems/pd-t4-8.md +++ b/content/2.defense-systems/pd-t4-8.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T4-8 system in the genome of \*Pectobacterium brasiliense\* (GCF\\_001932635.1) is composed of 1 protein: PD-T4-8 (WP\\_075277998.1). +PD-T4-8 system in the genome of *Pectobacterium brasiliense* (GCF_001932635.1) is composed of 1 protein: PD-T4-8 (WP_075277998.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 91 genomes (  -\*Proportion of genome encoding the PD-T4-8 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-8 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-8 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, SECphi18, SECphi27 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, SECphi18, SECphi27 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t4-9.md b/content/2.defense-systems/pd-t4-9.md index 475c805d..70e9b201 100644 --- a/content/2.defense-systems/pd-t4-9.md +++ b/content/2.defense-systems/pd-t4-9.md @@ -4,13 +4,13 @@ title: PD-T4-9 ## Example of genomic structure -The PD-T4-9 system is composed of 3 proteins: PD-T4-9\_C, PD-T4-9\_B and, PD-T4-9\_A. +The PD-T4-9 system is composed of 3 proteins: PD-T4-9_C, PD-T4-9_B and, PD-T4-9_A. Here is an example found in the RefSeq database:  -PD-T4-9 system in the genome of \*Escherichia coli\* (GCF\\_018223665.1) is composed of 3 proteins: PD-T4-9\\_A (WP\\_061089969.1), PD-T4-9\\_B (WP\\_061089970.1)and, PD-T4-9\\_C (WP\\_061089971.1). +PD-T4-9 system in the genome of *Escherichia coli* (GCF_018223665.1) is composed of 3 proteins: PD-T4-9_A (WP_061089969.1), PD-T4-9_B (WP_061089970.1)and, PD-T4-9_C (WP_061089971.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 148 genomes  -\*Proportion of genome encoding the PD-T4-9 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T4-9 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T4-9 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t7-1.md b/content/2.defense-systems/pd-t7-1.md index 5acbdaac..87d8bab5 100644 --- a/content/2.defense-systems/pd-t7-1.md +++ b/content/2.defense-systems/pd-t7-1.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T7-1 system in the genome of \*Escherichia coli\* (GCF\\_007833255.1) is composed of 1 protein: PD-T7-1 (WP\\_000008839.1). +PD-T7-1 system in the genome of *Escherichia coli* (GCF_007833255.1) is composed of 1 protein: PD-T7-1 (WP_000008839.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 755 genomes  -\*Proportion of genome encoding the PD-T7-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T7-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T7-1 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T7(Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7(Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t7-2.md b/content/2.defense-systems/pd-t7-2.md index c41d865f..fe98a596 100644 --- a/content/2.defense-systems/pd-t7-2.md +++ b/content/2.defense-systems/pd-t7-2.md @@ -4,13 +4,13 @@ title: PD-T7-2 ## Example of genomic structure -The PD-T7-2 system is composed of 2 proteins: PD-T7-2\_A and, PD-T7-2\_B. +The PD-T7-2 system is composed of 2 proteins: PD-T7-2_A and, PD-T7-2_B. Here is an example found in the RefSeq database:  -PD-T7-2 system in the genome of \*Sphingobium amiense\* (GCF\\_003967075.1) is composed of 2 proteins: PD-T7-2\\_B (WP\\_066704003.1)and, PD-T7-2\\_A (WP\\_066704000.1). +PD-T7-2 system in the genome of *Sphingobium amiense* (GCF_003967075.1) is composed of 2 proteins: PD-T7-2_B (WP_066704003.1)and, PD-T7-2_A (WP_066704000.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1535 genomes  -\*Proportion of genome encoding the PD-T7-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T7-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T7-2 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t7-3.md b/content/2.defense-systems/pd-t7-3.md index 254a02f4..9037abee 100644 --- a/content/2.defense-systems/pd-t7-3.md +++ b/content/2.defense-systems/pd-t7-3.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T7-3 system in the genome of \*Alistipes sp.\* (GCF\\_009557455.1) is composed of 1 protein: PD-T7-3 (WP\\_153498146.1). +PD-T7-3 system in the genome of *Alistipes sp.* (GCF_009557455.1) is composed of 1 protein: PD-T7-3 (WP_153498146.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 215 genomes  -\*Proportion of genome encoding the PD-T7-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T7-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T7-3 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6, T5, SECphi17, T3, T7 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi17, T3, T7 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t7-4.md b/content/2.defense-systems/pd-t7-4.md index 2e5e95bf..6f76ac01 100644 --- a/content/2.defense-systems/pd-t7-4.md +++ b/content/2.defense-systems/pd-t7-4.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T7-4 system in the genome of \*Parashewanella tropica\* (GCF\\_004358445.1) is composed of 1 protein: PD-T7-4 (WP\\_133406898.1). +PD-T7-4 system in the genome of *Parashewanella tropica* (GCF_004358445.1) is composed of 1 protein: PD-T7-4 (WP_133406898.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 501 genomes  -\*Proportion of genome encoding the PD-T7-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T7-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T7-4 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pd-t7-5.md b/content/2.defense-systems/pd-t7-5.md index ba062723..aafcaccb 100644 --- a/content/2.defense-systems/pd-t7-5.md +++ b/content/2.defense-systems/pd-t7-5.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PD-T7-5 system in the genome of \*Bacillus cereus\* (GCF\\_001941885.1) is composed of 1 protein: PD-T7-5 (WP\\_075395673.1). +PD-T7-5 system in the genome of *Bacillus cereus* (GCF_001941885.1) is composed of 1 protein: PD-T7-5 (WP_075395673.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 363 genomes  -\*Proportion of genome encoding the PD-T7-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PD-T7-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PD-T7-5 systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against SECphi17, T3, T7 (Vassallo et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi17, T3, T7 (Vassallo et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pfiat.md b/content/2.defense-systems/pfiat.md index 5f8155e9..3bdf29b2 100644 --- a/content/2.defense-systems/pfiat.md +++ b/content/2.defense-systems/pfiat.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PfiAT system in the genome of \*Pseudomonas amygdali\* (GCF\\_023207855.1) is composed of 2 proteins: PfiT (WP\\_096134620.1)and, PfiA (WP\\_057431469.1). +PfiAT system in the genome of *Pseudomonas amygdali* (GCF_023207855.1) is composed of 2 proteins: PfiT (WP_096134620.1)and, PfiA (WP_057431469.1). ## Distribution of the system among prokaryotes @@ -20,7 +20,7 @@ Among the 22k complete genomes of RefSeq, this system is present in 819 genomes  -\*Proportion of genome encoding the PfiAT system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PfiAT system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/pif.md b/content/2.defense-systems/pif.md index ebbec7c7..8669ca65 100644 --- a/content/2.defense-systems/pif.md +++ b/content/2.defense-systems/pif.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Pif system in the genome of \*Escherichia coli\* (GCF\\_018628815.1) is composed of 2 proteins: PifA (WP\\_000698737.1)and, PifC (WP\\_000952217.1). +Pif system in the genome of *Escherichia coli* (GCF_018628815.1) is composed of 2 proteins: PifA (WP_000698737.1)and, PifC (WP_000952217.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 143 genomes  -\*Proportion of genome encoding the Pif system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Pif system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Pif systems were experimentally validated using: -A system from \*Escherichia coli F-plasmid\* in \*Escherichia coli\* has an anti-phage effect against T7 (Cheng et al., 2004) +A system from *Escherichia coli F-plasmid* in *Escherichia coli* has an anti-phage effect against T7 (Cheng et al., 2004) ## Relevant abstracts diff --git a/content/2.defense-systems/prrc.md b/content/2.defense-systems/prrc.md index 1ce9dea5..ee6d3b78 100644 --- a/content/2.defense-systems/prrc.md +++ b/content/2.defense-systems/prrc.md @@ -4,13 +4,13 @@ title: PrrC ## Example of genomic structure -The PrrC system is composed of 4 proteins: EcoprrI, Type\_I\_S, PrrC and, Type\_I\_REases. +The PrrC system is composed of 4 proteins: EcoprrI, Type_I_S, PrrC and, Type_I_REases. Here is an example found in the RefSeq database:  -PrrC system in the genome of \*Streptococcus canis\* (GCF\\_900636575.1) is composed of 4 proteins: Type\\_I\\_REases (WP\\_003046543.1), PrrC (WP\\_003046540.1), Type\\_I\\_S (WP\\_129544911.1)and, Type\\_I\\_MTases (WP\\_003046534.1). +PrrC system in the genome of *Streptococcus canis* (GCF_900636575.1) is composed of 4 proteins: Type_I_REases (WP_003046543.1), PrrC (WP_003046540.1), Type_I_S (WP_129544911.1)and, Type_I_MTases (WP_003046534.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 705 genomes  -\*Proportion of genome encoding the PrrC system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PrrC system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PrrC systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T4 Dec8 (Jabbar and Snyder, 1984) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T4 Dec8 (Jabbar and Snyder, 1984) ## Relevant abstracts diff --git a/content/2.defense-systems/psyrta.md b/content/2.defense-systems/psyrta.md index 3bc102d2..4460b4c4 100644 --- a/content/2.defense-systems/psyrta.md +++ b/content/2.defense-systems/psyrta.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -PsyrTA system in the genome of \*Photorhabdus laumondii\* (GCF\\_003343225.1) is composed of 2 proteins: PsyrT (WP\\_109791883.1)and, PsyrA (WP\\_113049635.1). +PsyrTA system in the genome of *Photorhabdus laumondii* (GCF_003343225.1) is composed of 2 proteins: PsyrT (WP_109791883.1)and, PsyrA (WP_113049635.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1435 genomes  -\*Proportion of genome encoding the PsyrTA system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the PsyrTA system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation PsyrTA systems were experimentally validated using: -A system from \*Bacillus sp. FJAT-29814\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022) +A system from *Bacillus sp. FJAT-29814* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/pycsar.md b/content/2.defense-systems/pycsar.md index 196eb31d..b730c49b 100644 --- a/content/2.defense-systems/pycsar.md +++ b/content/2.defense-systems/pycsar.md @@ -4,13 +4,13 @@ title: Pycsar ## Example of genomic structure -The Pycsar system is composed of 2 proteins: AG\_cyclase and, Effector\_TIR. +The Pycsar system is composed of 2 proteins: AG_cyclase and, Effector_TIR. Here is an example found in the RefSeq database:  -Pycsar system in the genome of \*Staphylococcus aureus\* (GCF\\_003186105.1) is composed of 2 proteins: AG\\_cyclase (WP\\_065316016.1)and, 2TM\\_5 (WP\\_000073144.1). +Pycsar system in the genome of *Staphylococcus aureus* (GCF_003186105.1) is composed of 2 proteins: AG_cyclase (WP_065316016.1)and, 2TM_5 (WP_000073144.1). ## Distribution of the system among prokaryotes @@ -20,15 +20,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 559 genomes  -\*Proportion of genome encoding the Pycsar system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Pycsar system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Pycsar systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5, P1, LambdaVir, SECphi27 (Tal et al., 2021) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, P1, LambdaVir, SECphi27 (Tal et al., 2021) -A system from \*Xanthomonas perforans\* in \*Escherichia coli\* has an anti-phage effect against T7 (Tal et al., 2021) +A system from *Xanthomonas perforans* in *Escherichia coli* has an anti-phage effect against T7 (Tal et al., 2021) ## Relevant abstracts diff --git a/content/2.defense-systems/radar.md b/content/2.defense-systems/radar.md index e5658e4f..65a8b766 100644 --- a/content/2.defense-systems/radar.md +++ b/content/2.defense-systems/radar.md @@ -19,11 +19,11 @@ Here is some example found in the RefSeq database:  -radar\\_I subsystem in the genome of \*Dickeya dianthicola\* (GCF\\_014893095.1) is composed of 2 proteins: rdrB\\_I (WP\\_192988590.1)and, rdrA\\_I (WP\\_192988591.1). +radar_I subsystem in the genome of *Dickeya dianthicola* (GCF_014893095.1) is composed of 2 proteins: rdrB_I (WP_192988590.1)and, rdrA_I (WP_192988591.1).  -radar\\_II subsystem in the genome of \*Klebsiella aerogenes\* (GCF\\_008693885.1) is composed of 3 proteins: rdrD\\_II (WP\\_015705078.1), rdrB\\_II (WP\\_015705077.1)and, rdrA\\_II (WP\\_015705076.1). +radar_II subsystem in the genome of *Klebsiella aerogenes* (GCF_008693885.1) is composed of 3 proteins: rdrD_II (WP_015705078.1), rdrB_II (WP_015705077.1)and, rdrA_II (WP_015705076.1). ## Distribution of the system among prokaryotes @@ -33,17 +33,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 135 genomes  -\*Proportion of genome encoding the RADAR system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the RADAR system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation RADAR systems were experimentally validated using: -A system from \*Citrobacter rodentium\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T5, T3, T6 (Gao et al., 2020; Duncan-Lowey et al., 2022) +A system from *Citrobacter rodentium* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, T3, T6 (Gao et al., 2020; Duncan-Lowey et al., 2022) -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Duncan-Lowey et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Duncan-Lowey et al., 2022) -A system from \*Streptococcus suis\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T5, T6 (Duncan-Lowey et al., 2022) +A system from *Streptococcus suis* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, T6 (Duncan-Lowey et al., 2022) ## Relevant abstracts @@ -58,4 +58,4 @@ items: ## References -1. Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. \*Science\*. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372 +1. Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. *Science*. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372 diff --git a/content/2.defense-systems/retron.md b/content/2.defense-systems/retron.md index 65a83b95..8e0a8d3b 100644 --- a/content/2.defense-systems/retron.md +++ b/content/2.defense-systems/retron.md @@ -8,14 +8,14 @@ Retrons are genetic elements constituted of a non-coding RNA (ncRNA) associated  -\_Fig 1. (Mestre et al., 2020) Structure and organisation of a retron\_ . The two non-coding contiguous inverted sequences (named msr and msd) are transcribed as a single RNA. The RT recognizes its specific structure and reverse-transcribes it, generating an RNA-DNA hybrid +_Fig 1. (Mestre et al., 2020) Structure and organisation of a retron_ . The two non-coding contiguous inverted sequences (named msr and msd) are transcribed as a single RNA. The RT recognizes its specific structure and reverse-transcribes it, generating an RNA-DNA hybrid The majority of retrons are encoded on a gene cassette that encodes the retron and one or two additional proteins, which act as the retrons effectors. Bioinformatic prediction reveals that these effectors are very diverse and include transmembrane proteins, proteases, Cold-shock proteins, TIR domains proteins, ATPase, endonucleases, etc. Interestingly, several of these effector domains have already been described in other defense systems, including CBASS and Septu. Most retrons appear to act through an Abortive infection strategy (1). ## Molecular mechanisms -The \*E.coli\* retron system Ec48 mediates growth arrest upon sensing the inactivation of the bacterial RecBCD complex, a key element of the bacterial DNA repair system and immunity (1). Another study demonstrates that several retrons are part of Toxin-Antitoxin systems, where the RT-msDNA complex acts as an antitoxin that binds to and inhibits its cognate toxin. The tempering of the RT-msDNA, possibly by phage-encoded anti-RM systems, abolishes the antitoxin properties of the retron element, resulting in cell death mediated by the toxin activity (2). +The *E.coli* retron system Ec48 mediates growth arrest upon sensing the inactivation of the bacterial RecBCD complex, a key element of the bacterial DNA repair system and immunity (1). Another study demonstrates that several retrons are part of Toxin-Antitoxin systems, where the RT-msDNA complex acts as an antitoxin that binds to and inhibits its cognate toxin. The tempering of the RT-msDNA, possibly by phage-encoded anti-RM systems, abolishes the antitoxin properties of the retron element, resulting in cell death mediated by the toxin activity (2). ## Example of genomic structure @@ -26,51 +26,51 @@ Here is some example found in the RefSeq database:  -Retron\\_II subsystem in the genome of \*Klebsiella pneumoniae\* (GCF\\_904866255.1) is composed of 2 proteins: NDT2 (WP\\_057222224.1)and, RT\\_Tot (WP\\_048289034.1). +Retron_II subsystem in the genome of *Klebsiella pneumoniae* (GCF_904866255.1) is composed of 2 proteins: NDT2 (WP_057222224.1)and, RT_Tot (WP_048289034.1).  -Retron\\_IV subsystem in the genome of \*Aliivibrio fischeri\* (GCF\\_000011805.1) is composed of 2 proteins: RT\\_Tot (WP\\_011261677.1)and, 2TM (WP\\_236727775.1). +Retron_IV subsystem in the genome of *Aliivibrio fischeri* (GCF_000011805.1) is composed of 2 proteins: RT_Tot (WP_011261677.1)and, 2TM (WP_236727775.1).  -Retron\\_I\\_A subsystem in the genome of \*Vibrio harveyi\* (GCF\\_009184745.1) is composed of 3 proteins: RT\\_Tot (WP\\_152163686.1), ATPase\\_TypeIA (WP\\_152163687.1)and, HNH\\_TIGR02646 (WP\\_152163688.1). +Retron_I_A subsystem in the genome of *Vibrio harveyi* (GCF_009184745.1) is composed of 3 proteins: RT_Tot (WP_152163686.1), ATPase_TypeIA (WP_152163687.1)and, HNH_TIGR02646 (WP_152163688.1).  -Retron\\_I\\_B subsystem in the genome of \*Vibrio vulnificus\* (GCF\\_009665475.1) is composed of 2 proteins: ATPase\\_TOPRIM\\_COG3593 (WP\\_103277404.1)and, RT\\_Tot (WP\\_043877188.1). +Retron_I_B subsystem in the genome of *Vibrio vulnificus* (GCF_009665475.1) is composed of 2 proteins: ATPase_TOPRIM_COG3593 (WP_103277404.1)and, RT_Tot (WP_043877188.1).  -Retron\\_I\\_C subsystem in the genome of \*Listeria monocytogenes\* (GCF\\_905219385.1) is composed of 1 protein: RT\\_1\\_C2 (WP\\_003726410.1). +Retron_I_C subsystem in the genome of *Listeria monocytogenes* (GCF_905219385.1) is composed of 1 protein: RT_1_C2 (WP_003726410.1).  -Retron\\_V subsystem in the genome of \*Proteus terrae\* (GCF\\_013171285.1) is composed of 2 proteins: CSD (WP\\_004244726.1)and, RT\\_Tot (WP\\_109418979.1). +Retron_V subsystem in the genome of *Proteus terrae* (GCF_013171285.1) is composed of 2 proteins: CSD (WP_004244726.1)and, RT_Tot (WP_109418979.1).  -Retron\\_VI subsystem in the genome of \*Pseudomonas eucalypticola\* (GCF\\_013374995.1) is composed of 2 proteins: HTH (WP\\_245217789.1)and, RT\\_Tot (WP\\_176571652.1). +Retron_VI subsystem in the genome of *Pseudomonas eucalypticola* (GCF_013374995.1) is composed of 2 proteins: HTH (WP_245217789.1)and, RT_Tot (WP_176571652.1).  -Retron\\_VII\\_1 subsystem in the genome of \*Pseudoxanthomonas mexicana\* (GCF\\_014397415.1) is composed of 1 protein: RT\\_7\\_A1 (WP\\_187572543.1). +Retron_VII_1 subsystem in the genome of *Pseudoxanthomonas mexicana* (GCF_014397415.1) is composed of 1 protein: RT_7_A1 (WP_187572543.1).  -Retron\\_VII\\_2 subsystem in the genome of \*Bacillus mycoides\* (GCF\\_018742105.1) is composed of 2 proteins: DUF3800 (WP\\_215564565.1)and, RT\\_Tot (WP\\_215564572.1). +Retron_VII_2 subsystem in the genome of *Bacillus mycoides* (GCF_018742105.1) is composed of 2 proteins: DUF3800 (WP_215564565.1)and, RT_Tot (WP_215564572.1).  -Retron\\_XI subsystem in the genome of \*Planococcus kocurii\* (GCF\\_001465835.2) is composed of 1 protein: RT\\_11 (WP\\_058386256.1). +Retron_XI subsystem in the genome of *Planococcus kocurii* (GCF_001465835.2) is composed of 1 protein: RT_11 (WP_058386256.1).  -Retron\\_XII subsystem in the genome of \*Stenotrophomonas acidaminiphila\* (GCF\\_014109845.1) is composed of 1 protein: RT\\_12 (WP\\_182333825.1). +Retron_XII subsystem in the genome of *Stenotrophomonas acidaminiphila* (GCF_014109845.1) is composed of 1 protein: RT_12 (WP_182333825.1).  -Retron\\_XIII subsystem in the genome of \*Delftia acidovorans\* (GCF\\_016026535.1) is composed of 3 proteins: ARM (WP\\_197944577.1), WHSWIM (WP\\_197944578.1)and, RT\\_Tot (WP\\_065344905.1). +Retron_XIII subsystem in the genome of *Delftia acidovorans* (GCF_016026535.1) is composed of 3 proteins: ARM (WP_197944577.1), WHSWIM (WP_197944578.1)and, RT_Tot (WP_065344905.1). ## Distribution of the system among prokaryotes @@ -80,55 +80,55 @@ Among the 22k complete genomes of RefSeq, this system is present in 2601 genomes  -\*Proportion of genome encoding the Retron system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Retron system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation Retron systems were experimentally validated using: -Subsystem SLATT + RT\_G2\_intron with a system from \*Klebsiella pneumoniae's PICI (KpCIUCICRE 8)\* in \*Escherichia coli\* has an anti-phage effect against T5, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022) +Subsystem SLATT + RT_G2_intron with a system from *Klebsiella pneumoniae's PICI (KpCIUCICRE 8)* in *Escherichia coli* has an anti-phage effect against T5, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022) -Subsystem SLATT + RT\_G2\_intron with a system from \*Klebsiella pneumoniae's PICI (KpCIUCICRE 8)\* in \*Samonella enterica\* has an anti-phage effect against P22, BTP1, ES18 (Fillol-Salom et al., 2022) +Subsystem SLATT + RT_G2_intron with a system from *Klebsiella pneumoniae's PICI (KpCIUCICRE 8)* in *Samonella enterica* has an anti-phage effect against P22, BTP1, ES18 (Fillol-Salom et al., 2022) -Subsystem SLATT + RT\_G2\_intron with a system from \*Klebsiella pneumoniae's PICI (KpCIUCICRE 8)\* in \*Klebsiella pneumoniae\* has an anti-phage effect against Pokey, Raw, Eggy, KaID (Fillol-Salom et al., 2022) +Subsystem SLATT + RT_G2_intron with a system from *Klebsiella pneumoniae's PICI (KpCIUCICRE 8)* in *Klebsiella pneumoniae* has an anti-phage effect against Pokey, Raw, Eggy, KaID (Fillol-Salom et al., 2022) -Subsystem RT Ec67 + TOPRIM with a system from \*Klebsiella pneumoniae's PICI (KpCIB28906)\* in \*Escherichia coli\* has an anti-phage effect against T4, T5, HK578, T7 (Fillol-Salom et al., 2022) +Subsystem RT Ec67 + TOPRIM with a system from *Klebsiella pneumoniae's PICI (KpCIB28906)* in *Escherichia coli* has an anti-phage effect against T4, T5, HK578, T7 (Fillol-Salom et al., 2022) -Subsystem RT Ec67 + TOPRIM with a system from \*Klebsiella pneumoniae's PICI (KpCIB28906)\* in \*Samonella enterica\* has an anti-phage effect against det7 (Fillol-Salom et al., 2022) +Subsystem RT Ec67 + TOPRIM with a system from *Klebsiella pneumoniae's PICI (KpCIB28906)* in *Samonella enterica* has an anti-phage effect against det7 (Fillol-Salom et al., 2022) -Subsystem RT Ec67 + TOPRIM with a system from \*Klebsiella pneumoniae's PICI (KpCIB28906)\* in \*Samonella enterica\* has an anti-phage effect against Pokey, KalD (Fillol-Salom et al., 2022) +Subsystem RT Ec67 + TOPRIM with a system from *Klebsiella pneumoniae's PICI (KpCIB28906)* in *Samonella enterica* has an anti-phage effect against Pokey, KalD (Fillol-Salom et al., 2022) -Subsystem Retron-TIR with a system from \*Shigella dysenteriae\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T3, T7, PhiV-1 (Gao et al., 2020) +Subsystem Retron-TIR with a system from *Shigella dysenteriae* in *Escherichia coli* has an anti-phage effect against T2, T4, T3, T7, PhiV-1 (Gao et al., 2020) -Subsystem Retron Ec67 + TOPRIM with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T5 (Gao et al., 2020) +Subsystem Retron Ec67 + TOPRIM with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5 (Gao et al., 2020) -Subsystem Retron Ec86 + Nuc\_deoxy with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4 (Gao et al., 2020) +Subsystem Retron Ec86 + Nuc_deoxy with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4 (Gao et al., 2020) -Subsystem Retron Ec78 + ATPase + HNH with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5 (Gao et al., 2020) +Subsystem Retron Ec78 + ATPase + HNH with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Gao et al., 2020) -Subsystem Ec73 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against SECphi4, SECphi6, SECphi27, P1, T7 (Millman et al., 2020) +Subsystem Ec73 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi4, SECphi6, SECphi27, P1, T7 (Millman et al., 2020) -Subsystem Ec86 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5 (Millman et al., 2020) +Subsystem Ec86 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2020) -Subsystem Ec48 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against Lambda-Vir, T5, T2, T4, T7 (Millman et al., 2020) +Subsystem Ec48 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda-Vir, T5, T2, T4, T7 (Millman et al., 2020) -Subsystem Ec67 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5 (Millman et al., 2020) +Subsystem Ec67 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2020) -Subsystem Se72 with a system from \*Salmonella enterica\* in \*Escherichia coli\* has an anti-phage effect against Lambda-Vir (Millman et al., 2020) +Subsystem Se72 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against Lambda-Vir (Millman et al., 2020) -Subsystem Ec78 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5 (Millman et al., 2020) +Subsystem Ec78 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2020) -Subsystem Ec83 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Millman et al., 2020) +Subsystem Ec83 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2020) -Subsystem Vc95 with a system from \*Vibrio cholerae\* in \*Escherichia coli\* has an anti-phage effect against T2, T4, T6 (Millman et al., 2020) +Subsystem Vc95 with a system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2020) -Subsystem Retron-Eco8 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against SECphi4, SECphi6, SECphi18, T4, T6, T7 (Millman et al., 2020) +Subsystem Retron-Eco8 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi4, SECphi6, SECphi18, T4, T6, T7 (Millman et al., 2020) -Subsystem Retron-Sen2 with a system from \*Salmonella enterica serovar Typhimurium\* in \*Escherichia coli\* has an anti-phage effect against T5 (Bobonis et al., 2022) +Subsystem Retron-Sen2 with a system from *Salmonella enterica serovar Typhimurium* in *Escherichia coli* has an anti-phage effect against T5 (Bobonis et al., 2022) -Subsystem Retron-Eco9 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against P1vir, T2, T3, T5, T7, Ffm, Br60 (Bobonis et al., 2022) +Subsystem Retron-Eco9 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1vir, T2, T3, T5, T7, Ffm, Br60 (Bobonis et al., 2022) -Subsystem Retron-Eco1 with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5 (Bobonis et al., 2022) +Subsystem Retron-Eco1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Bobonis et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rexab.md b/content/2.defense-systems/rexab.md index 90b98180..fadfb5b2 100644 --- a/content/2.defense-systems/rexab.md +++ b/content/2.defense-systems/rexab.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -RexAB system in the genome of \*Escherichia coli\* (GCF\\_008033315.1) is composed of 2 proteins: RexA (WP\\_000788349.1)and, RexB (WP\\_001245922.1). +RexAB system in the genome of *Escherichia coli* (GCF_008033315.1) is composed of 2 proteins: RexA (WP_000788349.1)and, RexB (WP_001245922.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 73 genomes (  -\*Proportion of genome encoding the RexAB system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the RexAB system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation RexAB systems were experimentally validated using: -A system from \*Escherichia coli lambda prophage\* in \*Escherichia coli\* has an anti-phage effect against T4, Lamboid phages (Parma et al., 1992) +A system from *Escherichia coli lambda prophage* in *Escherichia coli* has an anti-phage effect against T4, Lamboid phages (Parma et al., 1992) ## Relevant abstracts diff --git a/content/2.defense-systems/rloc.md b/content/2.defense-systems/rloc.md index 68367c6d..f67db981 100644 --- a/content/2.defense-systems/rloc.md +++ b/content/2.defense-systems/rloc.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -RloC system in the genome of \*Flavobacterium arcticum\* (GCF\\_003344925.1) is composed of 1 protein: RloC (WP\\_114676820.1). +RloC system in the genome of *Flavobacterium arcticum* (GCF_003344925.1) is composed of 1 protein: RloC (WP_114676820.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1961 genomes  -\*Proportion of genome encoding the RloC system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the RloC system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation RloC systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4 (Penner et al., 1995) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4 (Penner et al., 1995) ## Relevant abstracts diff --git a/content/2.defense-systems/rm.md b/content/2.defense-systems/rm.md index 58ec8aab..6eb57cdb 100644 --- a/content/2.defense-systems/rm.md +++ b/content/2.defense-systems/rm.md @@ -10,23 +10,23 @@ Here is some example found in the RefSeq database:  -RM\\_Type\\_I subsystem in the genome of \*Aeromonas veronii\* (GCF\\_014169835.1) is composed of 4 proteins: Type\\_I\\_MTases (WP\\_182963881.1), Type\\_I\\_MTases (WP\\_182963881.1), Type\\_I\\_S (WP\\_182963883.1)and, Type\\_I\\_REases (WP\\_182963884.1). +RM_Type_I subsystem in the genome of *Aeromonas veronii* (GCF_014169835.1) is composed of 4 proteins: Type_I_MTases (WP_182963881.1), Type_I_MTases (WP_182963881.1), Type_I_S (WP_182963883.1)and, Type_I_REases (WP_182963884.1).  -RM\\_Type\\_II subsystem in the genome of \*Mannheimia haemolytica\* (GCF\\_007965905.1) is composed of 2 proteins: Type\\_II\\_MTases (WP\\_006248352.1)and, Type\\_II\\_REases (WP\\_006253295.1). +RM_Type_II subsystem in the genome of *Mannheimia haemolytica* (GCF_007965905.1) is composed of 2 proteins: Type_II_MTases (WP_006248352.1)and, Type_II_REases (WP_006253295.1).  -RM\\_Type\\_IIG subsystem in the genome of \*Spirochaeta africana\* (GCF\\_000242595.2) is composed of 1 protein: Type\\_IIG (WP\\_014455422.1). +RM_Type_IIG subsystem in the genome of *Spirochaeta africana* (GCF_000242595.2) is composed of 1 protein: Type_IIG (WP_014455422.1).  -RM\\_Type\\_III subsystem in the genome of \*Pannonibacter phragmitetus\* (GCF\\_001484065.1) is composed of 2 proteins: Type\\_III\\_MTases (WP\\_058898889.1)and, Type\\_III\\_REases (WP\\_058898890.1). +RM_Type_III subsystem in the genome of *Pannonibacter phragmitetus* (GCF_001484065.1) is composed of 2 proteins: Type_III_MTases (WP_058898889.1)and, Type_III_REases (WP_058898890.1).  -RM\\_Type\\_IV subsystem in the genome of \*Clostridioides difficile\* (GCF\\_018884605.1) is composed of 1 protein: Type\\_IV\\_REases (WP\\_021364579.1). +RM_Type_IV subsystem in the genome of *Clostridioides difficile* (GCF_018884605.1) is composed of 1 protein: Type_IV_REases (WP_021364579.1). ## Distribution of the system among prokaryotes @@ -36,7 +36,7 @@ Among the 22k complete genomes of RefSeq, this system is present in 19087 genome  -\*Proportion of genome encoding the RM system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the RM system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/rnlab.md b/content/2.defense-systems/rnlab.md index bd38e210..238b3857 100644 --- a/content/2.defense-systems/rnlab.md +++ b/content/2.defense-systems/rnlab.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -RnlAB system in the genome of \*Escherichia coli\* (GCF\\_014338505.1) is composed of 2 proteins: RnlA (WP\\_000155570.1)and, RnlB (WP\\_000461704.1). +RnlAB system in the genome of *Escherichia coli* (GCF_014338505.1) is composed of 2 proteins: RnlA (WP_000155570.1)and, RnlB (WP_000461704.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 284 genomes  -\*Proportion of genome encoding the RnlAB system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the RnlAB system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation RnlAB systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4 (Koga et al., 2011) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4 (Koga et al., 2011) ## Relevant abstracts diff --git a/content/2.defense-systems/rosmerta.md b/content/2.defense-systems/rosmerta.md index d68025da..2134c7cc 100644 --- a/content/2.defense-systems/rosmerta.md +++ b/content/2.defense-systems/rosmerta.md @@ -4,13 +4,13 @@ title: RosmerTA ## Example of genomic structure -The RosmerTA system is composed of 2 proteins: RmrA\_2634932349 and, RmrT\_2634932349. +The RosmerTA system is composed of 2 proteins: RmrA_2634932349 and, RmrT_2634932349. Here is an example found in the RefSeq database:  -RosmerTA system in the genome of \*Acinetobacter indicus\* (GCF\\_002953575.2) is composed of 2 proteins: RmrT\\_2641389401 (WP\\_045796188.1)and, RmrA\\_2641389401 (WP\\_045796189.1). +RosmerTA system in the genome of *Acinetobacter indicus* (GCF_002953575.2) is composed of 2 proteins: RmrT_2641389401 (WP_045796188.1)and, RmrA_2641389401 (WP_045796189.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 2124 genomes  -\*Proportion of genome encoding the RosmerTA system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the RosmerTA system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation RosmerTA systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against P1, LambdaVir (Millman et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, LambdaVir (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rst_2tm_1tm_tir.md b/content/2.defense-systems/rst_2tm_1tm_tir.md index 0d27a2c4..8be9f52b 100644 --- a/content/2.defense-systems/rst_2tm_1tm_tir.md +++ b/content/2.defense-systems/rst_2tm_1tm_tir.md @@ -4,23 +4,23 @@ title: Rst_2TM_1TM_TIR ## Example of genomic structure -The Rst\_2TM\_1TM\_TIR system is composed of 3 proteins: Rst\_TIR\_tm, Rst\_1TM\_TIR and, Rst\_2TM\_TIR. +The Rst_2TM_1TM_TIR system is composed of 3 proteins: Rst_TIR_tm, Rst_1TM_TIR and, Rst_2TM_TIR. Here is an example found in the RefSeq database:  -Rst\\_2TM\\_1TM\\_TIR system in the genome of \*Escherichia coli\* (GCF\\_001900375.1) is composed of 3 proteins: Rst\\_TIR\\_tm (WP\\_023140578.1), Rst\\_1TM\\_TIR (WP\\_001534953.1)and, Rst\\_2TM\\_TIR (WP\\_023140577.1). +Rst_2TM_1TM_TIR system in the genome of *Escherichia coli* (GCF_001900375.1) is composed of 3 proteins: Rst_TIR_tm (WP_023140578.1), Rst_1TM_TIR (WP_001534953.1)and, Rst_2TM_TIR (WP_023140577.1). ## Distribution of the system among prokaryotes -The Rst\_2TM\_1TM\_TIR system is present in a total of 1 different species. +The Rst_2TM_1TM_TIR system is present in a total of 1 different species. Among the 22k complete genomes of RefSeq, this system is present in 2 genomes (0.0 %).  -\*Proportion of genome encoding the Rst\_2TM\_1TM\_TIR system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Rst_2TM_1TM_TIR system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/rst_3hp.md b/content/2.defense-systems/rst_3hp.md index b74e9936..897575c4 100644 --- a/content/2.defense-systems/rst_3hp.md +++ b/content/2.defense-systems/rst_3hp.md @@ -4,29 +4,29 @@ title: Rst_3HP ## Example of genomic structure -The Rst\_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. +The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. Here is an example found in the RefSeq database:  -Rst\\_3HP system in the genome of \*Klebsiella pneumoniae\* (GCF\\_016403065.1) is composed of 3 proteins: Hp3 (WP\\_004151009.1), Hp2 (WP\\_004151008.1)and, Hp1 (WP\\_004151007.1). +Rst_3HP system in the genome of *Klebsiella pneumoniae* (GCF_016403065.1) is composed of 3 proteins: Hp3 (WP_004151009.1), Hp2 (WP_004151008.1)and, Hp1 (WP_004151007.1). ## Distribution of the system among prokaryotes -The Rst\_3HP system is present in a total of 83 different species. +The Rst_3HP system is present in a total of 83 different species. Among the 22k complete genomes of RefSeq, this system is present in 420 genomes (1.8 %).  -\*Proportion of genome encoding the Rst\_3HP system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Rst_3HP system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Rst\_3HP systems were experimentally validated using: +Rst_3HP systems were experimentally validated using: -A system from \*Escherichia coli (P2 loci)\* in \*Escherichia coli\* has an anti-phage effect against P1 (Rousset et al., 2022) +A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against P1 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rst_duf4238.md b/content/2.defense-systems/rst_duf4238.md index 7ca091d6..86b917f3 100644 --- a/content/2.defense-systems/rst_duf4238.md +++ b/content/2.defense-systems/rst_duf4238.md @@ -4,29 +4,29 @@ title: Rst_DUF4238 ## Example of genomic structure -The Rst\_DUF4238 system is composed of one protein: DUF4238\_Pers. +The Rst_DUF4238 system is composed of one protein: DUF4238_Pers. Here is an example found in the RefSeq database:  -Rst\\_DUF4238 system in the genome of \*Enterobacter kobei\* (GCF\\_008365235.1) is composed of 1 protein: DUF4238\\_Pers (WP\\_058689834.1). +Rst_DUF4238 system in the genome of *Enterobacter kobei* (GCF_008365235.1) is composed of 1 protein: DUF4238_Pers (WP_058689834.1). ## Distribution of the system among prokaryotes -The Rst\_DUF4238 system is present in a total of 34 different species. +The Rst_DUF4238 system is present in a total of 34 different species. Among the 22k complete genomes of RefSeq, this system is present in 46 genomes (0.2 %).  -\*Proportion of genome encoding the Rst\_DUF4238 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Rst_DUF4238 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Rst\_DUF4238 systems were experimentally validated using: +Rst_DUF4238 systems were experimentally validated using: -A system from \*Escherichia coli (P2 loci)\* in \*Escherichia coli\* has an anti-phage effect against T7 (Rousset et al., 2022) +A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rst_gop_beta_cll.md b/content/2.defense-systems/rst_gop_beta_cll.md index 20e9852e..e059ea08 100644 --- a/content/2.defense-systems/rst_gop_beta_cll.md +++ b/content/2.defense-systems/rst_gop_beta_cll.md @@ -4,29 +4,29 @@ title: Rst_gop_beta_cll ## Example of genomic structure -The Rst\_gop\_beta\_cll system is composed of 3 proteins: gop, beta and, cll. +The Rst_gop_beta_cll system is composed of 3 proteins: gop, beta and, cll. Here is an example found in the RefSeq database:  -Rst\\_gop\\_beta\\_cll system in the genome of \*Escherichia coli\* (GCF\\_003018615.1) is composed of 3 proteins: cll (WP\\_001357997.1), beta (WP\\_001357996.1)and, gop (WP\\_000931915.1). +Rst_gop_beta_cll system in the genome of *Escherichia coli* (GCF_003018615.1) is composed of 3 proteins: cll (WP_001357997.1), beta (WP_001357996.1)and, gop (WP_000931915.1). ## Distribution of the system among prokaryotes -The Rst\_gop\_beta\_cll system is present in a total of 14 different species. +The Rst_gop_beta_cll system is present in a total of 14 different species. Among the 22k complete genomes of RefSeq, this system is present in 37 genomes (0.2 %).  -\*Proportion of genome encoding the Rst\_gop\_beta\_cll system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Rst_gop_beta_cll system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Rst\_gop\_beta\_cll systems were experimentally validated using: +Rst_gop_beta_cll systems were experimentally validated using: -A system from \*Enterobacteria phage P4\* in \*Escherichia coli\* has an anti-phage effect against Lambda, P1 (Rousset et al., 2022) +A system from *Enterobacteria phage P4* in *Escherichia coli* has an anti-phage effect against Lambda, P1 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rst_helicaseduf2290.md b/content/2.defense-systems/rst_helicaseduf2290.md index 55374a76..94ac8230 100644 --- a/content/2.defense-systems/rst_helicaseduf2290.md +++ b/content/2.defense-systems/rst_helicaseduf2290.md @@ -4,29 +4,29 @@ title: Rst_HelicaseDUF2290 ## Example of genomic structure -The Rst\_HelicaseDUF2290 system is composed of 2 proteins: Helicase and, DUF2290. +The Rst_HelicaseDUF2290 system is composed of 2 proteins: Helicase and, DUF2290. Here is an example found in the RefSeq database:  -Rst\\_HelicaseDUF2290 system in the genome of \*Xylella fastidiosa\* (GCF\\_021459885.1) is composed of 2 proteins: Helicase (WP\\_012338122.1)and, DUF2290 (WP\\_004084731.1). +Rst_HelicaseDUF2290 system in the genome of *Xylella fastidiosa* (GCF_021459885.1) is composed of 2 proteins: Helicase (WP_012338122.1)and, DUF2290 (WP_004084731.1). ## Distribution of the system among prokaryotes -The Rst\_HelicaseDUF2290 system is present in a total of 124 different species. +The Rst_HelicaseDUF2290 system is present in a total of 124 different species. Among the 22k complete genomes of RefSeq, this system is present in 211 genomes (0.9 %).  -\*Proportion of genome encoding the Rst\_HelicaseDUF2290 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Rst_HelicaseDUF2290 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Rst\_HelicaseDUF2290 systems were experimentally validated using: +Rst_HelicaseDUF2290 systems were experimentally validated using: -A system from \*Klebsiella pneumoniae (P4 loci)\* in \*Escherichia coli\* has an anti-phage effect against T7 (Rousset et al., 2022) +A system from *Klebsiella pneumoniae (P4 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rst_hydrolase-3tm.md b/content/2.defense-systems/rst_hydrolase-3tm.md index a03da922..e72fe3fb 100644 --- a/content/2.defense-systems/rst_hydrolase-3tm.md +++ b/content/2.defense-systems/rst_hydrolase-3tm.md @@ -4,29 +4,29 @@ title: Rst_Hydrolase-3Tm ## Example of genomic structure -The Rst\_Hydrolase-3Tm system is composed of 2 proteins: Hydrolase and, Hydrolase-Tm. +The Rst_Hydrolase-3Tm system is composed of 2 proteins: Hydrolase and, Hydrolase-Tm. Here is an example found in the RefSeq database:  -Rst\\_Hydrolase-Tm subsystem in the genome of \*Escherichia coli\* (GCF\\_004792495.1) is composed of 2 proteins: Hydrolase-Tm (WP\\_000998640.1)and, Hydrolase (WP\\_000754434.1). +Rst_Hydrolase-Tm subsystem in the genome of *Escherichia coli* (GCF_004792495.1) is composed of 2 proteins: Hydrolase-Tm (WP_000998640.1)and, Hydrolase (WP_000754434.1). ## Distribution of the system among prokaryotes -The Rst\_Hydrolase-3Tm system is present in a total of 34 different species. +The Rst_Hydrolase-3Tm system is present in a total of 34 different species. Among the 22k complete genomes of RefSeq, this system is present in 42 genomes (0.2 %).  -\*Proportion of genome encoding the Rst\_Hydrolase-3Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Rst_Hydrolase-3Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Rst\_Hydrolase-3Tm systems were experimentally validated using: +Rst_Hydrolase-3Tm systems were experimentally validated using: -A system from \*Escherichia coli (P4 loci)\* in \*Escherichia coli\* has an anti-phage effect against T7 (Rousset et al., 2022) +A system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rst_paris.md b/content/2.defense-systems/rst_paris.md index 52efa098..cd73c384 100644 --- a/content/2.defense-systems/rst_paris.md +++ b/content/2.defense-systems/rst_paris.md @@ -6,47 +6,47 @@ title: Rst_PARIS PARIS (for Phage Anti-Restriction-Induced System) is a novel anti-phage system. PARIS is found in 4% of prokaryotic genomes. It comprises an ATPase associated with a DUF4435 protein, which can be found either as a two-gene cassette or a single-gene fusion (1). -This system relies on an unknown [Abortive infection](/general\_concepts/Abi) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3). +This system relies on an unknown [Abortive infection](/general_concepts/Abi) mechanism to trigger growth arrest upon sensing a phage-encoded protein (Ocr). Interestingly, the Ocr protein has been found to inhibit R-M systems and BREX systems, making PARIS a suitable defense mechanism against RM resistant and/or BREX resistant phages (1, 2, 3). ## Example of genomic structure -The Rst\_PARIS system have been describe in a total of 4 subsystems. +The Rst_PARIS system have been describe in a total of 4 subsystems. Here is some example found in the RefSeq database:  -PARIS\\_I subsystem in the genome of \*Salmonella enterica\* (GCF\\_020715485.1) is composed of 2 proteins: AAA\\_15 (WP\\_001520831.1)and, DUF4435 (WP\\_010989064.1). +PARIS_I subsystem in the genome of *Salmonella enterica* (GCF_020715485.1) is composed of 2 proteins: AAA_15 (WP_001520831.1)and, DUF4435 (WP_010989064.1).  -PARIS\\_II subsystem in the genome of \*Enterobacter cloacae\* (GCF\\_023238665.1) is composed of 2 proteins: DUF4435 (WP\\_071830092.1)and, AAA\\_21 (WP\\_061772587.1). +PARIS_II subsystem in the genome of *Enterobacter cloacae* (GCF_023238665.1) is composed of 2 proteins: DUF4435 (WP_071830092.1)and, AAA_21 (WP_061772587.1).  -PARIS\\_II\\_merge subsystem in the genome of \*Desulfovibrio desulfuricans\* (GCF\\_017815575.1) is composed of 1 protein: AAA\\_21\\_DUF4435 (WP\\_209818471.1). +PARIS_II_merge subsystem in the genome of *Desulfovibrio desulfuricans* (GCF_017815575.1) is composed of 1 protein: AAA_21_DUF4435 (WP_209818471.1).  -PARIS\\_I\\_merge subsystem in the genome of \*Sideroxydans lithotrophicus\* (GCF\\_000025705.1) is composed of 1 protein: AAA\\_15\\_DUF4435 (WP\\_013030315.1). +PARIS_I_merge subsystem in the genome of *Sideroxydans lithotrophicus* (GCF_000025705.1) is composed of 1 protein: AAA_15_DUF4435 (WP_013030315.1). ## Distribution of the system among prokaryotes -The Rst\_PARIS system is present in a total of 463 different species. +The Rst_PARIS system is present in a total of 463 different species. Among the 22k complete genomes of RefSeq, this system is present in 1145 genomes (5.0 %).  -\*Proportion of genome encoding the Rst\_PARIS system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Rst_PARIS system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation -Rst\_PARIS systems were experimentally validated using: +Rst_PARIS systems were experimentally validated using: -Subsystem Paris 1 with a system from \*Escherichia coli (P4 loci)\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T4, CLB\_P2, LF82\_P8, Al505\_P2, T7 (Rousset et al., 2022) +Subsystem Paris 1 with a system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T4, CLB_P2, LF82_P8, Al505_P2, T7 (Rousset et al., 2022) -Subsystem Paris 2 with a system from \*Escherichia coli (P4 loci)\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T4, CLB\_P2, LF82\_P8, T7 (Rousset et al., 2022) +Subsystem Paris 2 with a system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T4, CLB_P2, LF82_P8, T7 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rst_rt-nitrilase-tm.md b/content/2.defense-systems/rst_rt-nitrilase-tm.md index cd3a5a9f..03064e64 100644 --- a/content/2.defense-systems/rst_rt-nitrilase-tm.md +++ b/content/2.defense-systems/rst_rt-nitrilase-tm.md @@ -4,29 +4,29 @@ title: Rst_RT-nitrilase-Tm ## Example of genomic structure -The Rst\_RT-nitrilase-Tm system is composed of 2 proteins: RT-Tm and, RT. +The Rst_RT-nitrilase-Tm system is composed of 2 proteins: RT-Tm and, RT. Here is an example found in the RefSeq database:  -Rst\\_RT-Tm subsystem in the genome of \*Morganella morganii\* (GCF\\_900478755.1) is composed of 2 proteins: RT (WP\\_061057569.1)and, RT-Tm (WP\\_004234654.1). +Rst_RT-Tm subsystem in the genome of *Morganella morganii* (GCF_900478755.1) is composed of 2 proteins: RT (WP_061057569.1)and, RT-Tm (WP_004234654.1). ## Distribution of the system among prokaryotes -The Rst\_RT-nitrilase-Tm system is present in a total of 5 different species. +The Rst_RT-nitrilase-Tm system is present in a total of 5 different species. Among the 22k complete genomes of RefSeq, this system is present in 25 genomes (0.1 %).  -\*Proportion of genome encoding the Rst\_RT-nitrilase-Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Rst_RT-nitrilase-Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Rst\_RT-nitrilase-Tm systems were experimentally validated using: +Rst_RT-nitrilase-Tm systems were experimentally validated using: -A system from \*Escherichia coli (P4 loci)\* in \*Escherichia coli\* has an anti-phage effect against Al505\_P2 (Rousset et al., 2022) +A system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Al505_P2 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/rst_tir-nlr.md b/content/2.defense-systems/rst_tir-nlr.md index 74ebbafc..5b7803b7 100644 --- a/content/2.defense-systems/rst_tir-nlr.md +++ b/content/2.defense-systems/rst_tir-nlr.md @@ -4,29 +4,29 @@ title: Rst_TIR-NLR ## Example of genomic structure -The Rst\_TIR-NLR system is composed of one protein: TIR. +The Rst_TIR-NLR system is composed of one protein: TIR. Here is an example found in the RefSeq database:  -Rst\\_TIR-NLR system in the genome of \*Escherichia coli\* (GCF\\_016903595.1) is composed of 1 protein: TIR (WP\\_059327187.1). +Rst_TIR-NLR system in the genome of *Escherichia coli* (GCF_016903595.1) is composed of 1 protein: TIR (WP_059327187.1). ## Distribution of the system among prokaryotes -The Rst\_TIR-NLR system is present in a total of 43 different species. +The Rst_TIR-NLR system is present in a total of 43 different species. Among the 22k complete genomes of RefSeq, this system is present in 254 genomes (1.1 %).  -\*Proportion of genome encoding the Rst\_TIR-NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Rst_TIR-NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation -Rst\_TIR-NLR systems were experimentally validated using: +Rst_TIR-NLR systems were experimentally validated using: -A system from \*Klebsiella pneumoniae (P4 loci)\* in \*Escherichia coli\* has an anti-phage effect against T4, P1, CLB\_P2, LF82\_P8, AL505\_P2, T7 (Rousset et al., 2022) +A system from *Klebsiella pneumoniae (P4 loci)* in *Escherichia coli* has an anti-phage effect against T4, P1, CLB_P2, LF82_P8, AL505_P2, T7 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/sanata.md b/content/2.defense-systems/sanata.md index 2b676b22..d731813d 100644 --- a/content/2.defense-systems/sanata.md +++ b/content/2.defense-systems/sanata.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -SanaTA system in the genome of \*Methylovorus glucosetrophus\* (GCF\\_000023745.1) is composed of 2 proteins: SanaT (WP\\_015830669.1)and, SanaA (WP\\_015830670.1). +SanaTA system in the genome of *Methylovorus glucosetrophus* (GCF_000023745.1) is composed of 2 proteins: SanaT (WP_015830669.1)and, SanaA (WP_015830670.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1071 genomes  -\*Proportion of genome encoding the SanaTA system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the SanaTA system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation SanaTA systems were experimentally validated using: -A system from \*Shewanella sp. ANA-3\* in \*Escherichia coli\* has an anti-phage effect against T7 (Sberro et al., 2013) +A system from *Shewanella sp. ANA-3* in *Escherichia coli* has an anti-phage effect against T7 (Sberro et al., 2013) ## Relevant abstracts diff --git a/content/2.defense-systems/sefir.md b/content/2.defense-systems/sefir.md index 5a5f7bd1..2fd76b03 100644 --- a/content/2.defense-systems/sefir.md +++ b/content/2.defense-systems/sefir.md @@ -3,12 +3,12 @@ title: SEFIR --- ## Description -The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes, were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in \*Bacillus sp.\* NIO-1130 against phage phi29 [1]. +The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes, were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in *Bacillus sp.* NIO-1130 against phage phi29 [1]. Bacterial SEFIR domains were named after their eukaryotic homologs which were already known to be part of several eukayrotic immune proteins (e.g. SEFs and Interleukin-17 Receptors) [2]. ## Molecular mechanism -SEFIR was shown to protect against phage infection through an abortive infection mechanism \*via\* NAD+ depletion. This is similar to what can be observed in other defense systems containing a TIR domain which shares homology with the SEFIR domain (in eukaryotes, both domains are part of the STIR super family) [1]. +SEFIR was shown to protect against phage infection through an abortive infection mechanism *via* NAD+ depletion. This is similar to what can be observed in other defense systems containing a TIR domain which shares homology with the SEFIR domain (in eukaryotes, both domains are part of the STIR super family) [1]. ## Example of genomic structure @@ -18,7 +18,7 @@ Here is an example found in the RefSeq database:  -SEFIR system in the genome of \*Lactiplantibacillus plantarum\* (GCF\\_003020005.1) is composed of 1 protein: bSEFIR (WP\\_106904862.1). +SEFIR system in the genome of *Lactiplantibacillus plantarum* (GCF_003020005.1) is composed of 1 protein: bSEFIR (WP_106904862.1). ## Distribution of the system among prokaryotes @@ -28,13 +28,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 377 genomes  -\*Proportion of genome encoding the SEFIR system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the SEFIR system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation SEFIR systems were experimentally validated using: -A system from \*Bacillus sp. NIO-1130\* in \*Bacillus subtilis\* has an anti-phage effect against phi29 (Millman et al., 2022) +A system from *Bacillus sp. NIO-1130* in *Bacillus subtilis* has an anti-phage effect against phi29 (Millman et al., 2022) ## Relevant abstracts @@ -49,4 +49,4 @@ items: ## References [1] Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556-1569.e5 (2022). -[2] Novatchkova, M., Leibbrandt, A., Werzowa, J., Neubüser, A., & Eisenhaber, F. (2003). The STIR-domain superfamily in signal transduction, development and immunity. \_Trends in biochemical sciences\_, \_28\_(5), 226-229. +[2] Novatchkova, M., Leibbrandt, A., Werzowa, J., Neubüser, A., & Eisenhaber, F. (2003). The STIR-domain superfamily in signal transduction, development and immunity. _Trends in biochemical sciences_, _28_(5), 226-229. diff --git a/content/2.defense-systems/septu.md b/content/2.defense-systems/septu.md index 2bb5aa9a..8db0fc3f 100644 --- a/content/2.defense-systems/septu.md +++ b/content/2.defense-systems/septu.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Septu system in the genome of \*Arcobacter porcinus\* (GCF\\_004299785.2) is composed of 2 proteins: PtuA (WP\\_066386194.1)and, PtuB\\_2 (WP\\_066386193.1). +Septu system in the genome of *Arcobacter porcinus* (GCF_004299785.2) is composed of 2 proteins: PtuA (WP_066386194.1)and, PtuB_2 (WP_066386193.1). ## Distribution of the system among prokaryotes @@ -20,15 +20,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 2193 genomes  -\*Proportion of genome encoding the Septu system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Septu system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Septu systems were experimentally validated using: -A system from \*Bacillus thuringiensis\* in \*Bacillus subtilis\* has an anti-phage effect against SBSphiJ, SBSphiC (Doron et al., 2018) +A system from *Bacillus thuringiensis* in *Bacillus subtilis* has an anti-phage effect against SBSphiJ, SBSphiC (Doron et al., 2018) -A system from \*Bacillus weihenstephanensis\* in \*Bacillus subtilis\* has an anti-phage effect against SBSphiC, SpBeta (Doron et al., 2018) +A system from *Bacillus weihenstephanensis* in *Bacillus subtilis* has an anti-phage effect against SBSphiC, SpBeta (Doron et al., 2018) ## Relevant abstracts diff --git a/content/2.defense-systems/shango.md b/content/2.defense-systems/shango.md index baee8af5..ee02533b 100644 --- a/content/2.defense-systems/shango.md +++ b/content/2.defense-systems/shango.md @@ -4,7 +4,7 @@ title: Shango ## Description -Shango is a three genes defense system which was discovered in parallel in two works in both \*E.coli\* and \*P.aeruginosa\* and was shown to have antiphage activity against the Lambda-phage in \*E.coli\* [1] and against diverse podo- and siphoviridae in \*P.aeruginosa\* [2]. +Shango is a three genes defense system which was discovered in parallel in two works in both *E.coli* and *P.aeruginosa* and was shown to have antiphage activity against the Lambda-phage in *E.coli* [1] and against diverse podo- and siphoviridae in *P.aeruginosa* [2]. Shango is composed of (i) a TerB-like domain, (ii) an Helicase and (iii) an ATPase. The TerB domain was previously shown to be associated to the perisplasmic membrane of bacteria [3]. @@ -21,7 +21,7 @@ Here is an example found in the RefSeq database:  -Shango system in the genome of \*Paenibacillus sp.\* (GCF\\_022637315.1) is composed of 3 proteins: SngA (WP\\_241931534.1), SngB (WP\\_241931535.1)and, SngC (WP\\_241931536.1). +Shango system in the genome of *Paenibacillus sp.* (GCF_022637315.1) is composed of 3 proteins: SngA (WP_241931534.1), SngB (WP_241931535.1)and, SngC (WP_241931536.1). ## Distribution of the system among prokaryotes @@ -31,13 +31,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 1112 genomes  -\*Proportion of genome encoding the Shango system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Shango system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Shango systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi18 (Millman et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi18 (Millman et al., 2022) ## Relevant abstracts @@ -53,8 +53,8 @@ items: ## References Shango was discovered in parallel by Adi Millman (Sorek group) and the team of J. Bondy-Denomy (UCSF). -[1] Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Garb, J., Bechon, N., Brandis, A., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J. L. M., Dar, D., … Sorek, R. (2022). An expanded arsenal of immune systems that protect bacteria from phages. \_Cell Host & Microbe\_, \_30\_(11), 1556-1569.e5. [https://doi.org/10.1016/j.chom.2022.09.017](https://doi.org/10.1016/j.chom.2022.09.017) +[1] Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Garb, J., Bechon, N., Brandis, A., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J. L. M., Dar, D., … Sorek, R. (2022). An expanded arsenal of immune systems that protect bacteria from phages. _Cell Host & Microbe_, _30_(11), 1556-1569.e5. [https://doi.org/10.1016/j.chom.2022.09.017](https://doi.org/10.1016/j.chom.2022.09.017) -[2] Johnson, Matthew, Laderman, Eric, Huiting, Erin, Zhang, Charles, Davidson, Alan, & Bondy-Denomy, Joseph. (2022). \_Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems\_. [https://doi.org/10.5281/ZENODO.7254690](https://doi.org/10.5281/ZENODO.7254690) +[2] Johnson, Matthew, Laderman, Eric, Huiting, Erin, Zhang, Charles, Davidson, Alan, & Bondy-Denomy, Joseph. (2022). _Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems_. [https://doi.org/10.5281/ZENODO.7254690](https://doi.org/10.5281/ZENODO.7254690) -[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. \_General physiology and biophysics\_, \_30\_(3), 286-292. \ No newline at end of file +[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292. \ No newline at end of file diff --git a/content/2.defense-systems/shedu.md b/content/2.defense-systems/shedu.md index 144dced8..2ca934f6 100644 --- a/content/2.defense-systems/shedu.md +++ b/content/2.defense-systems/shedu.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -Shedu system in the genome of \*Mycolicibacterium psychrotolerans\* (GCF\\_010729305.1) is composed of 1 protein: SduA (WP\\_246228780.1). +Shedu system in the genome of *Mycolicibacterium psychrotolerans* (GCF_010729305.1) is composed of 1 protein: SduA (WP_246228780.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 899 genomes  -\*Proportion of genome encoding the Shedu system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Shedu system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Shedu systems were experimentally validated using: -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against phi105, rho14, SPP1, phi29 (Doron et al., 2018) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against phi105, rho14, SPP1, phi29 (Doron et al., 2018) ## Relevant abstracts diff --git a/content/2.defense-systems/shosta.md b/content/2.defense-systems/shosta.md index 8c477503..f181c751 100644 --- a/content/2.defense-systems/shosta.md +++ b/content/2.defense-systems/shosta.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -ShosTA system in the genome of \*Escherichia coli\* (GCF\\_011404895.1) is composed of 2 proteins: ShosA (WP\\_001567470.1)and, ShosT (WP\\_001567471.1). +ShosTA system in the genome of *Escherichia coli* (GCF_011404895.1) is composed of 2 proteins: ShosA (WP_001567470.1)and, ShosT (WP_001567471.1). ## Distribution of the system among prokaryotes @@ -20,15 +20,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 668 genomes  -\*Proportion of genome encoding the ShosTA system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the ShosTA system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation ShosTA systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi4, SECphi6, SECphi18, T7 (Millman et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi4, SECphi6, SECphi18, T7 (Millman et al., 2022) -A system from \*Escherichia coli (P2 loci)\* in \*Escherichia coli\* has an anti-phage effect against Lambda, T7 (Rousset et al., 2022) +A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T7 (Rousset et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/sofic.md b/content/2.defense-systems/sofic.md index 42caab08..c62aa5a9 100644 --- a/content/2.defense-systems/sofic.md +++ b/content/2.defense-systems/sofic.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -SoFic subsystem in the genome of \*Fusobacterium nucleatum\* (GCF\\_019552125.1) is composed of 1 protein: SoFic (WP\\_220308819.1). +SoFic subsystem in the genome of *Fusobacterium nucleatum* (GCF_019552125.1) is composed of 1 protein: SoFic (WP_220308819.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 2265 genomes  -\*Proportion of genome encoding the SoFIC system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the SoFIC system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation SoFIC systems were experimentally validated using: -A system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T5 (Millman et al., 2022) +A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/spbk.md b/content/2.defense-systems/spbk.md index 3c826c9d..de597b7c 100644 --- a/content/2.defense-systems/spbk.md +++ b/content/2.defense-systems/spbk.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -SpbK system in the genome of \*Clostridium beijerinckii\* (GCF\\_900010805.1) is composed of 1 protein: SpbK (WP\\_077841417.1). +SpbK system in the genome of *Clostridium beijerinckii* (GCF_900010805.1) is composed of 1 protein: SpbK (WP_077841417.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 219 genomes  -\*Proportion of genome encoding the SpbK system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the SpbK system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation SpbK systems were experimentally validated using: -A system from \*Bacillus subtilis\* in \*Bacillus subtilis\* has an anti-phage effect against SPbeta (Johnson et al., 2022) +A system from *Bacillus subtilis* in *Bacillus subtilis* has an anti-phage effect against SPbeta (Johnson et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/sspbcde.md b/content/2.defense-systems/sspbcde.md index 00af2d4e..a3501233 100644 --- a/content/2.defense-systems/sspbcde.md +++ b/content/2.defense-systems/sspbcde.md @@ -10,7 +10,7 @@ Here is an example found in the RefSeq database:  -SspBCDE system in the genome of \*Bordetella hinzii\* (GCF\\_006770405.1) is composed of 7 proteins: SspF (WP\\_221886990.1), SspG (WP\\_142096192.1), SspH (WP\\_142096195.1), SspE (WP\\_142096198.1), SspD (WP\\_142096201.1), SspC (WP\\_142096204.1)and, SspB (WP\\_142096207.1). +SspBCDE system in the genome of *Bordetella hinzii* (GCF_006770405.1) is composed of 7 proteins: SspF (WP_221886990.1), SspG (WP_142096192.1), SspH (WP_142096195.1), SspE (WP_142096198.1), SspD (WP_142096201.1), SspC (WP_142096204.1)and, SspB (WP_142096207.1). ## Distribution of the system among prokaryotes @@ -20,19 +20,19 @@ Among the 22k complete genomes of RefSeq, this system is present in 579 genomes  -\*Proportion of genome encoding the SspBCDE system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the SspBCDE system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation SspBCDE systems were experimentally validated using: -Subsystem SspABCD+SspE with a system from \*Vibrio cyclitrophicus\* in \*Escherichia coli\* has an anti-phage effect against T4, T1, JMPW1, JMPW2, EEP, T7 (Xiong et al., 2020) +Subsystem SspABCD+SspE with a system from *Vibrio cyclitrophicus* in *Escherichia coli* has an anti-phage effect against T4, T1, JMPW1, JMPW2, EEP, T7 (Xiong et al., 2020) -Subsystem SspBCD+SspE with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T4, T1, JMPW1, JMPW2, EEP, T7, PhiX174 (Xiong et al., 2020) +Subsystem SspBCD+SspE with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, T1, JMPW1, JMPW2, EEP, T7, PhiX174 (Xiong et al., 2020) -Subsystem SspBCD+SspE with a system from \*Streptomyces yokosukanensis\* in \*Streptomyces lividans\* has an anti-phage effect against JXY1 (Xiong et al., 2020) +Subsystem SspBCD+SspE with a system from *Streptomyces yokosukanensis* in *Streptomyces lividans* has an anti-phage effect against JXY1 (Xiong et al., 2020) -Subsystem SspBCD+SspFGH with a system from \*Vibrio anguillarum\* in \*Escherichia coli\* has an anti-phage effect against T1, JMPW2, T4, EEP (Wang et al., 2021) +Subsystem SspBCD+SspFGH with a system from *Vibrio anguillarum* in *Escherichia coli* has an anti-phage effect against T1, JMPW2, T4, EEP (Wang et al., 2021) ## Relevant abstracts diff --git a/content/2.defense-systems/stk2.md b/content/2.defense-systems/stk2.md index fa6e6e4b..6b3d9095 100644 --- a/content/2.defense-systems/stk2.md +++ b/content/2.defense-systems/stk2.md @@ -19,7 +19,7 @@ Here is an example found in the RefSeq database:  -Stk2 system in the genome of \*Staphylococcus aureus\* (GCF\\_009739755.1) is composed of 1 protein: Stk2 (WP\\_001001347.1). +Stk2 system in the genome of *Staphylococcus aureus* (GCF_009739755.1) is composed of 1 protein: Stk2 (WP_001001347.1). ## Distribution of the system among prokaryotes @@ -29,15 +29,15 @@ Among the 22k complete genomes of RefSeq, this system is present in 141 genomes  -\*Proportion of genome encoding the Stk2 system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Stk2 system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Stk2 systems were experimentally validated using: -A system from \*Staphylococcus epidermidis\* in \*Staphylococcus epidermidis\* has an anti-phage effect against CNPx (Depardieu et al., 2016) +A system from *Staphylococcus epidermidis* in *Staphylococcus epidermidis* has an anti-phage effect against CNPx (Depardieu et al., 2016) -A system from \*Staphylococcus epidermidis\* in \*Staphylococcus aureus\* has an anti-phage effect against phage 80alpha, phage 85, phiNM1, phiNM2, phiNM4 (Depardieu et al., 2016) +A system from *Staphylococcus epidermidis* in *Staphylococcus aureus* has an anti-phage effect against phage 80alpha, phage 85, phiNM1, phiNM2, phiNM4 (Depardieu et al., 2016) ## Relevant abstracts diff --git a/content/2.defense-systems/thoeris.md b/content/2.defense-systems/thoeris.md index 7fbb2559..8c175628 100644 --- a/content/2.defense-systems/thoeris.md +++ b/content/2.defense-systems/thoeris.md @@ -10,11 +10,11 @@ Here is some example found in the RefSeq database:  -Thoeris\\_I subsystem in the genome of \*Bacillus thuringiensis\* (GCF\\_020809205.1) is composed of 2 proteins: ThsA\\_new\\_grand (WP\\_021728720.1)and, ThsB\\_Global (WP\\_021728719.1). +Thoeris_I subsystem in the genome of *Bacillus thuringiensis* (GCF_020809205.1) is composed of 2 proteins: ThsA_new_grand (WP_021728720.1)and, ThsB_Global (WP_021728719.1).  -Thoeris\\_II subsystem in the genome of \*Acinetobacter baumannii\* (GCF\\_014672775.1) is composed of 2 proteins: ThsB\\_Global (WP\\_000120680.1)and, ThsA\\_new\\_petit (WP\\_005134880.1). +Thoeris_II subsystem in the genome of *Acinetobacter baumannii* (GCF_014672775.1) is composed of 2 proteins: ThsB_Global (WP_000120680.1)and, ThsA_new_petit (WP_005134880.1). ## Distribution of the system among prokaryotes @@ -24,17 +24,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 812 genomes  -\*Proportion of genome encoding the Thoeris system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Thoeris system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation Thoeris systems were experimentally validated using: -A system from \*Bacillus amyloliquefaciens\* in \*Bacillus subtilis\* has an anti-phage effect against SPO1, SBSphiJ, SBSphiC (Doron et al., 2018) +A system from *Bacillus amyloliquefaciens* in *Bacillus subtilis* has an anti-phage effect against SPO1, SBSphiJ, SBSphiC (Doron et al., 2018) -A system from \*Bacillus cereus\* in \*Bacillus subtilis\* has an anti-phage effect against phi29, SBSphiC, SPO1, SBSphiJ (Doron et al., 2018; Ofir et al., 2021) +A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against phi29, SBSphiC, SPO1, SBSphiJ (Doron et al., 2018; Ofir et al., 2021) -A system from \*Bacillus dafuensis\* in \*Bacillus subtilis\* has an anti-phage effect against phi3T, SPBeta, SPR, SBSphi11, SBSphi13, phi29, SBSphiJ, SPO1 (Ofir et al., 2021) +A system from *Bacillus dafuensis* in *Bacillus subtilis* has an anti-phage effect against phi3T, SPBeta, SPR, SBSphi11, SBSphi13, phi29, SBSphiJ, SPO1 (Ofir et al., 2021) ## Relevant abstracts diff --git a/content/2.defense-systems/tiamat.md b/content/2.defense-systems/tiamat.md index 5d3829e4..e6ce8b75 100644 --- a/content/2.defense-systems/tiamat.md +++ b/content/2.defense-systems/tiamat.md @@ -4,13 +4,13 @@ title: Tiamat ## Example of genomic structure -The Tiamat system is composed of one protein: TmtA\_2599863134. +The Tiamat system is composed of one protein: TmtA_2599863134. Here is an example found in the RefSeq database:  -Tiamat system in the genome of \*Pseudomonas aeruginosa\* (GCF\\_022638055.1) is composed of 1 protein: TmtA\\_2731770353 (WP\\_023121076.1). +Tiamat system in the genome of *Pseudomonas aeruginosa* (GCF_022638055.1) is composed of 1 protein: TmtA_2731770353 (WP_023121076.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 342 genomes  -\*Proportion of genome encoding the Tiamat system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Tiamat system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Tiamat systems were experimentally validated using: -A system from \*Bacillus cereus\* in \*Escherichia coli\* has an anti-phage effect against T6, T5 (Millman et al., 2022) +A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T6, T5 (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/uzume.md b/content/2.defense-systems/uzume.md index 994e6e65..bb70cb9c 100644 --- a/content/2.defense-systems/uzume.md +++ b/content/2.defense-systems/uzume.md @@ -4,13 +4,13 @@ title: Uzume ## Example of genomic structure -The Uzume system is composed of one protein: UzuA\_2660320622. +The Uzume system is composed of one protein: UzuA_2660320622. Here is an example found in the RefSeq database:  -Uzume system in the genome of \*Nocardioides euryhalodurans\* (GCF\\_004564375.1) is composed of 1 protein: UzuA (WP\\_135074908.1). +Uzume system in the genome of *Nocardioides euryhalodurans* (GCF_004564375.1) is composed of 1 protein: UzuA (WP_135074908.1). ## Distribution of the system among prokaryotes @@ -20,13 +20,13 @@ Among the 22k complete genomes of RefSeq, this system is present in 125 genomes  -\*Proportion of genome encoding the Uzume system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Uzume system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Uzume systems were experimentally validated using: -A system from \*Bacillus sp. FJAT-27231\* in \*Bacillus subtilis\* has an anti-phage effect against SPO1, SP82G, SBSphiC (Millman et al., 2022) +A system from *Bacillus sp. FJAT-27231* in *Bacillus subtilis* has an anti-phage effect against SPO1, SP82G, SBSphiC (Millman et al., 2022) ## Relevant abstracts diff --git a/content/2.defense-systems/viperin.md b/content/2.defense-systems/viperin.md index f803cf5f..3f760a93 100644 --- a/content/2.defense-systems/viperin.md +++ b/content/2.defense-systems/viperin.md @@ -13,7 +13,7 @@ Recently,  Viperin-like enzymes were found in prokaryotes (pVips).  Strikingly Fig.1: Catalytic activity of human Viperin generates ddhCTP (Ebrahimi et al. al., 2020) -Viperins are members of the radical S-adenosylmethionine (rSAM) superfamily. This group of enzymes use a \[4Fe-4S\] cluster to cleave S-adenosylmethionine (SAM) reductively, generating a radical which is generally transferred to a substrate. It was demonstrated that through their \[4Fe-4S\] cluster catalytic activity, eukaryotic viperins convert a ribonucleotide, the cytidine triphosphate (CTP) into a modified ribonucleotide, the 3′-deoxy-3′,4′-didehydro-CTP (ddhCTP) (4,5). +Viperins are members of the radical S-adenosylmethionine (rSAM) superfamily. This group of enzymes use a [4Fe-4S] cluster to cleave S-adenosylmethionine (SAM) reductively, generating a radical which is generally transferred to a substrate. It was demonstrated that through their [4Fe-4S] cluster catalytic activity, eukaryotic viperins convert a ribonucleotide, the cytidine triphosphate (CTP) into a modified ribonucleotide, the 3′-deoxy-3′,4′-didehydro-CTP (ddhCTP) (4,5). Prokaryotic Viperins also convert ribonucleotides triphosphate into modified ribonucleotides, but contrary to their eukaryotic counterparts can use a diversity of substrates to produce  ddhCTP,  or ddh-guanosine triphosphate (ddhGTP), or ddh-uridine triphosphate (ddhUTP), or several of these nucleotides for certain pVips (2). @@ -27,7 +27,7 @@ Here is an example found in the RefSeq database:  -Viperin system in the genome of \*Moritella yayanosii\* is composed of 1 protein: pVip (WP\\_112711942.1). +Viperin system in the genome of *Moritella yayanosii* is composed of 1 protein: pVip (WP_112711942.1). ## Distribution of the system among prokaryotes @@ -37,47 +37,47 @@ Among the 22k complete genomes of RefSeq, this system is present in 118 genomes  -\*Proportion of genome encoding the Viperin system for the 14 phyla with more than 50 genomes in the RefSeq database.\* +*Proportion of genome encoding the Viperin system for the 14 phyla with more than 50 genomes in the RefSeq database.* ## Experimental validation Viperin systems were experimentally validated using: -Subsystem pVip6 with a system from \*Selenomonas ruminatium\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip6 with a system from *Selenomonas ruminatium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip7 with a system from \*Fibrobacter sp. UWT3\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip7 with a system from *Fibrobacter sp. UWT3* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip9 with a system from \*Vibrio porteresiae\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip9 with a system from *Vibrio porteresiae* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip12 with a system from \*Ruegeria intermedia\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip12 with a system from *Ruegeria intermedia* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip15 with a system from \*Coraliomargarita akajimensis\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip15 with a system from *Coraliomargarita akajimensis* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip21 with a system from \*Lewinella persica\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip21 with a system from *Lewinella persica* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip32 with a system from \*Phormidium sp. OSCR GFM\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip32 with a system from *Phormidium sp. OSCR GFM* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip34 with a system from \*Cryomorphaceae bacterium\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip34 with a system from *Cryomorphaceae bacterium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip37 with a system from \*Shewanella sp. cp20\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip37 with a system from *Shewanella sp. cp20* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip39 with a system from \*Burkholderiales-76 (UID4002)\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip39 with a system from *Burkholderiales-76 (UID4002)* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip44 with a system from \*Chondromyces crocatus\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip44 with a system from *Chondromyces crocatus* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip46 with a system from \*Photobacterium swingsii\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip46 with a system from *Photobacterium swingsii* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip57 with a system from \*Flavobacterium lacus\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip57 with a system from *Flavobacterium lacus* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip58 with a system from \*Pseudoalteromonas ulvae\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip58 with a system from *Pseudoalteromonas ulvae* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip60 with a system from \*Lacinutrix sp. JCM 13824\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip60 with a system from *Lacinutrix sp. JCM 13824* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip61 with a system from \*Euryarchaeota archaeon SCGC AG-487\_M08\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip61 with a system from *Euryarchaeota archaeon SCGC AG-487_M08* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip62 with a system from \*Fibrobacteria bacterium\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip62 with a system from *Fibrobacteria bacterium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) -Subsystem pVip63 with a system from \*Pseudoalteromonas sp. XI10\* in \*Escherichia coli\* has an anti-phage effect against T7 (Bernheim et al., 2020) +Subsystem pVip63 with a system from *Pseudoalteromonas sp. XI10* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020) ## Relevant abstracts diff --git a/content/2.defense-systems/wadjet.md b/content/2.defense-systems/wadjet.md index f4f36646..bae527b4 100644 --- a/content/2.defense-systems/wadjet.md +++ b/content/2.defense-systems/wadjet.md @@ -10,15 +10,15 @@ Here is some example found in the RefSeq database:  -Wadjet\\_I subsystem in the genome of \*Bifidobacterium pseudocatenulatum\* (GCF\\_021484885.1) is composed of 4 proteins: JetA\\_I (WP\\_195524168.1), JetB\\_I (WP\\_195523897.1), JetC\\_I (WP\\_195523898.1)and, JetD\\_I (WP\\_229067172.1). +Wadjet_I subsystem in the genome of *Bifidobacterium pseudocatenulatum* (GCF_021484885.1) is composed of 4 proteins: JetA_I (WP_195524168.1), JetB_I (WP_195523897.1), JetC_I (WP_195523898.1)and, JetD_I (WP_229067172.1).  -Wadjet\\_II subsystem in the genome of \*Streptomyces sp.\* (GCF\\_023273835.1) is composed of 4 proteins: JetD\\_II (WP\\_248777007.1), JetC\\_II (WP\\_248777008.1), JetB\\_II (WP\\_248777009.1)and, JetA\\_II (WP\\_248777010.1). +Wadjet_II subsystem in the genome of *Streptomyces sp.* (GCF_023273835.1) is composed of 4 proteins: JetD_II (WP_248777007.1), JetC_II (WP_248777008.1), JetB_II (WP_248777009.1)and, JetA_II (WP_248777010.1).  -Wadjet\\_III subsystem in the genome of \*Caldibacillus thermoamylovorans\* (GCF\\_003096215.1) is composed of 4 proteins: JetD\\_III (WP\\_108897743.1), JetA\\_III (WP\\_108897744.1), JetB\\_III (WP\\_034768879.1)and, JetC\\_III (WP\\_108897745.1). +Wadjet_III subsystem in the genome of *Caldibacillus thermoamylovorans* (GCF_003096215.1) is composed of 4 proteins: JetD_III (WP_108897743.1), JetA_III (WP_108897744.1), JetB_III (WP_034768879.1)and, JetC_III (WP_108897745.1). ## Distribution of the system among prokaryotes @@ -28,7 +28,7 @@ Among the 22k complete genomes of RefSeq, this system is present in 2380 genomes  -\*Proportion of genome encoding the Wadjet system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Wadjet system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Relevant abstracts diff --git a/content/2.defense-systems/zorya.md b/content/2.defense-systems/zorya.md index b1174735..d969dffb 100644 --- a/content/2.defense-systems/zorya.md +++ b/content/2.defense-systems/zorya.md @@ -10,11 +10,11 @@ Here is some example found in the RefSeq database:  -Zorya\\_TypeI subsystem in the genome of \*Pseudomonas aeruginosa\* (GCF\\_002085605.1) is composed of 4 proteins: ZorD (WP\\_015649020.1), ZorC (WP\\_015649021.1), ZorB (WP\\_015649022.1)and, ZorA (WP\\_025297974.1). +Zorya_TypeI subsystem in the genome of *Pseudomonas aeruginosa* (GCF_002085605.1) is composed of 4 proteins: ZorD (WP_015649020.1), ZorC (WP_015649021.1), ZorB (WP_015649022.1)and, ZorA (WP_025297974.1).  -Zorya\\_TypeII subsystem in the genome of \*Legionella longbeachae\* (GCF\\_011465255.1) is composed of 3 proteins: ZorA2 (WP\\_050777601.1), ZorB (WP\\_003632756.1)and, ZorE (WP\\_050777600.1). +Zorya_TypeII subsystem in the genome of *Legionella longbeachae* (GCF_011465255.1) is composed of 3 proteins: ZorA2 (WP_050777601.1), ZorB (WP_003632756.1)and, ZorE (WP_050777600.1). ## Distribution of the system among prokaryotes @@ -24,17 +24,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 840 genomes  -\*Proportion of genome encoding the Zorya system for the 14 phyla with more than 50 genomes in the RefSeq database.\* \*Pie chart of the repartition of all the subsystems found in the RefSeq database.\* +*Proportion of genome encoding the Zorya system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.* ## Experimental validation Zorya systems were experimentally validated using: -Subsystem Type I with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against LambdaVir, SECphi27, T7 (Doron et al., 2018) +Subsystem Type I with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27, T7 (Doron et al., 2018) -Subsystem Type II with a system from \*Escherichia coli\* in \*Escherichia coli\* has an anti-phage effect against T7, SECphi17 (Doron et al., 2018) +Subsystem Type II with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, SECphi17 (Doron et al., 2018) -Subsystem Type III with a system from \*Stenotrophomonas nitritireducens\* in \*Escherichia coli\* has an anti-phage effect against T1, T4, T7, LambdaVir, PVP-SE1 (Payne et al., 2021) +Subsystem Type III with a system from *Stenotrophomonas nitritireducens* in *Escherichia coli* has an anti-phage effect against T1, T4, T7, LambdaVir, PVP-SE1 (Payne et al., 2021) ## Relevant abstracts -- GitLab