diff --git a/content/3.defense-systems/abic.md b/content/3.defense-systems/abic.md
index 6876763def56d214f24799d60ee9f2cd50a52b24..f0ad4e3f794777604045cdaed31f1b66ed8cdd4d 100644
--- a/content/3.defense-systems/abic.md
+++ b/content/3.defense-systems/abic.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF16872
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiC
diff --git a/content/3.defense-systems/abid.md b/content/3.defense-systems/abid.md
index 6cf817e36c00c87aa6f323b9c2eae022e9242a84..6967065860963ad20a3609a84908db5f33dbdb00 100644
--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF07751
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiD
diff --git a/content/3.defense-systems/abie.md b/content/3.defense-systems/abie.md
index 706909d8b55d7d12a1bee81b4a70dde9612aaeee..a7e060536909adf4724bb8642774c75230e986cd 100644
--- a/content/3.defense-systems/abie.md
+++ b/content/3.defense-systems/abie.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF08843, PF09407, PF09952, PF11459, PF13338, PF17194
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1093/nar/gkt1419
---
# AbiE
diff --git a/content/3.defense-systems/abig.md b/content/3.defense-systems/abig.md
index 87b0b1968205c54dd5d4cb32ff22a7515e3c83fd..f41b6ac64e903239cce84c9fe653a540048ca6d1 100644
--- a/content/3.defense-systems/abig.md
+++ b/content/3.defense-systems/abig.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10899, PF16873
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiG
diff --git a/content/3.defense-systems/abii.md b/content/3.defense-systems/abii.md
index 97b709b0c0e0f23f3d0b4e3f32c24f4535c6d59a..e2349fd4c702e07361f8df99ea38712b3a1b6ae7 100644
--- a/content/3.defense-systems/abii.md
+++ b/content/3.defense-systems/abii.md
@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiI
diff --git a/content/3.defense-systems/abij.md b/content/3.defense-systems/abij.md
index 03b87ac96c00ce0a485812367d3c79e45d495648..46b1b9ccc63ef100530352bf154cb16bcced3689 100644
--- a/content/3.defense-systems/abij.md
+++ b/content/3.defense-systems/abij.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14355
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiJ
diff --git a/content/3.defense-systems/abik.md b/content/3.defense-systems/abik.md
index 607fec7f16eeb11021d1d5eb72831eb1283a2903..5be8a8ce03f7680082f6fc4e830d0e4c9d065b50 100644
--- a/content/3.defense-systems/abik.md
+++ b/content/3.defense-systems/abik.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1093/nar/gkac467
---
# AbiK
diff --git a/content/3.defense-systems/abin.md b/content/3.defense-systems/abin.md
index b803307965f8875850b7d764acc05082934da692..3eb41769266fbe4ac42b290280df58439ca2ef61 100644
--- a/content/3.defense-systems/abin.md
+++ b/content/3.defense-systems/abin.md
@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiN
diff --git a/content/3.defense-systems/abio.md b/content/3.defense-systems/abio.md
index 483e179b8bb53fd36aafed2de493aec25beb7027..5392e139fd68c1990e3af97e1dd55db42b6a6e35 100644
--- a/content/3.defense-systems/abio.md
+++ b/content/3.defense-systems/abio.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01443, PF09848
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiO
diff --git a/content/3.defense-systems/abip2.md b/content/3.defense-systems/abip2.md
index 83840172caca6f29540f49d1d79b65a4a8937bc0..e031cc4073cc47922581c4d64e536aa95a66c7a3 100644
--- a/content/3.defense-systems/abip2.md
+++ b/content/3.defense-systems/abip2.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1093/nar/gkac467
---
# AbiP2
diff --git a/content/3.defense-systems/abiq.md b/content/3.defense-systems/abiq.md
index 2c65ede1732f5049eac58eceab15fd447ce8a64e..361f32e14d4ed448da397f623e1d283825cf2bcf 100644
--- a/content/3.defense-systems/abiq.md
+++ b/content/3.defense-systems/abiq.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13958
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1128/AEM.64.12.4748-4756.1998
---
# AbiQ
diff --git a/content/3.defense-systems/abir.md b/content/3.defense-systems/abir.md
index 7edcc5adfbb0e0880dccff38badd820b6f04abe3..277c7ef93c564d76ae147fa34b541a23e74c72b1 100644
--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00176, PF00271, PF04545, PF04851, PF13091
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiR
diff --git a/content/3.defense-systems/abit.md b/content/3.defense-systems/abit.md
index 6e79b4a15afb9f39555134f7d06504a9672b54a2..4e4e2d8d8c9d6698cc8f6b6f1e5185cbc94668eb 100644
--- a/content/3.defense-systems/abit.md
+++ b/content/3.defense-systems/abit.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF18864
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiT
diff --git a/content/3.defense-systems/abiv.md b/content/3.defense-systems/abiv.md
index db4169184408357fd1e0bc22c6a5b4106b936ca5..89e356c4d5e664b68276060dcb0f34e9824146e2 100644
--- a/content/3.defense-systems/abiv.md
+++ b/content/3.defense-systems/abiv.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF18728
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1128/AEM.00780-08
---
# AbiV
diff --git a/content/3.defense-systems/abiz.md b/content/3.defense-systems/abiz.md
index aa18e65a9d86b328c0e57127972f5ac33bc6482a..68931ced9abfc86ad8e9963d9b0a4dad80a9ea40 100644
--- a/content/3.defense-systems/abiz.md
+++ b/content/3.defense-systems/abiz.md
@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Membrane disrupting
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1128/JB.00904-06
---
# AbiZ
diff --git a/content/3.defense-systems/aditi.md b/content/3.defense-systems/aditi.md
index 452259dceaad96b73967aaef9cbbe683613a5c6a..5e539a1f01b50ac123641427e60a3530d0207782 100644
--- a/content/3.defense-systems/aditi.md
+++ b/content/3.defense-systems/aditi.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF18928
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Aditi
diff --git a/content/3.defense-systems/azaca.md b/content/3.defense-systems/azaca.md
index 15ae31cbf5f5ba9c1edb66605c6434f02fb5fae8..50ea7855ae38e57f6974c9b980a608c583209fba 100644
--- a/content/3.defense-systems/azaca.md
+++ b/content/3.defense-systems/azaca.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00271
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Azaca
diff --git a/content/3.defense-systems/bsta.md b/content/3.defense-systems/bsta.md
index 58ea6fcc54c645f42d19b1c8ca7c33c9a76bf014..882b9ead0b5a7267440e068244fe0afa0301299a 100644
--- a/content/3.defense-systems/bsta.md
+++ b/content/3.defense-systems/bsta.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2021.09.002
---
# BstA
diff --git a/content/3.defense-systems/butters_gp57r.md b/content/3.defense-systems/butters_gp57r.md
index 7279df464b42dbcb86acb3b09d9f7034698140b6..4efd9095390b089de045110e2cdddbb1f5e53e39 100644
--- a/content/3.defense-systems/butters_gp57r.md
+++ b/content/3.defense-systems/butters_gp57r.md
@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1101/2023.01.03.522681
abstract: |
During lysogeny temperate phages establish a truce with the bacterial host. In this state, the phage genome (prophage) is maintained within the host environment. Consequently, many prophages have evolved systems to protect the host from heterotypic viral attack. This phenomenon of prophages mediating defense of their host against competitor phages is widespread among temperate mycobacteriophages. We previously showed that the Mycobacterium phage Butters prophage encodes a two-component system (gp30/31) that inhibits infection from a subset of mycobacteriophages that include PurpleHaze, but not Island3. Here we show that Butters gp57r is both necessary and sufficient to inhibit infection by Island3 and other phages. Gp57r acts post-DNA injection and its antagonism results in the impairment of Island3 DNA amplification. Gp57r inhibition of Island3 is absolute with no defense escape mutants. However, mutations mapping to minor tail proteins allow PurpleHaze to overcome gp57r defense. Gp57r has a HEPN domain which is present in many proteins involved in inter-genomic conflicts, suggesting that gp57r may inhibit heterotypic phage infections via its HEPN domain. We also show that Butters gp57r has orthologues in clinical isolates of Mycobacterium abscessus sp. including the phage therapy candidate strain GD91 which was found to be resistant to the panel of phages tested. It is conceivable that this GD91 orthologue of gp57r may mediate resistance to the subset of phages tested. Challenges of this nature underscore the importance of elucidating mechanisms of antiphage systems and mutations that allow for escape from inhibition. IMPORTANCE The evolutionary arms race between phages and their bacteria host is ancient. During lysogeny, temperate phages establish a ceasefire with the host where they do not kill the host but derive shelter from it. Within the phenomenon of prophage-mediated defense, some temperate phages contribute genes that make their host more fit and resistant to infections by other phages. This arrangement has significance for both phage and bacterial evolutionary dynamics. Further, the prevalence of such antiphage systems poses a challenge to phage therapy. Thus, studies aimed at elucidating antiphage systems will further our understanding of phage-bacteria evolution as well as help with efforts to engineer therapeutic phages that circumvent antiphage systems.
+relevantAbstracts:
+ - doi: 10.1101/2023.01.03.522681
---
# Butters_gp57r
diff --git a/content/3.defense-systems/caprel.md b/content/3.defense-systems/caprel.md
index 63938fddc0006c6cff53de6df9e05ec78149f3f7..2abb480ed9b312d57b58d0e946a6064c79437ad6 100644
--- a/content/3.defense-systems/caprel.md
+++ b/content/3.defense-systems/caprel.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
PFAM: PF04607
+relevantAbstracts:
+ - doi: 10.1038/s41586-022-05444-z
---
# CapRel
diff --git a/content/3.defense-systems/cbass.md b/content/3.defense-systems/cbass.md
index 3981e2578f8972f18cd65dd92f02410628eb608d..029e52c7b9d7f8331b7f99984a91f5743ccef252 100644
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -10,6 +10,13 @@ tableColumns:
Activator: Signaling molecules
Effector: Divers (Nucleic acid degrading, Nucleotide modifying, Membrane disrupting)
PFAM: PF00004, PF00027, PF00899, PF01048, PF01734, PF06508, PF10137, PF14461, PF14464, PF18134, PF18138, PF18144, PF18145, PF18153, PF18159, PF18167, PF18173, PF18178, PF18179, PF18186, PF18303, PF18967
+relevantAbstracts:
+ - doi: 10.1016/j.molcel.2019.12.009
+ - doi: 10.1016/j.molcel.2021.10.020
+ - doi: 10.1038/s41564-020-0777-y
+ - doi: 10.1038/s41586-019-1605-5
+ - doi: 10.1038/s41586-020-2719-5
+
---
# CBASS
diff --git a/content/3.defense-systems/charlie_gp32.md b/content/3.defense-systems/charlie_gp32.md
index 397b2562cc09a84ceca033b50f08e5f0f02fdd22..9c39da4053e97e1814ae6a9f971e70cf5e6e9e37 100644
--- a/content/3.defense-systems/charlie_gp32.md
+++ b/content/3.defense-systems/charlie_gp32.md
@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1038/nmicrobiol.2016.251
abstract: |
Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+relevantAbstracts:
+ - doi: 10.1038/nmicrobiol.2016.251
---
# Charlie_gp32
diff --git a/content/3.defense-systems/ddmde.md b/content/3.defense-systems/ddmde.md
index 9f9fe28f4b904838152513001ce9ef52fc1afd54..2e3c30ecc1219219f98ed4b198c7e9eeb194dd6c 100644
--- a/content/3.defense-systems/ddmde.md
+++ b/content/3.defense-systems/ddmde.md
@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1038/s41586-022-04546-y
abstract: |
Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2-4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
+relevantAbstracts:
+ - doi: 10.1038/s41586-022-04546-y
---
# DdmDE
diff --git a/content/3.defense-systems/disarm.md b/content/3.defense-systems/disarm.md
index a1d2d80212ad0e186cb9deb473ee74a44b445fc7..100fac7a5421d1a43d89f9a6dcca76ab0aaa2807 100644
--- a/content/3.defense-systems/disarm.md
+++ b/content/3.defense-systems/disarm.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00145, PF00176, PF00271, PF04851, PF09369, PF13091
+relevantAbstracts:
+ - doi: 10.1038/s41467-022-30673-1
+ - doi: 10.1038/s41564-017-0051-0
---
# DISARM
diff --git a/content/3.defense-systems/dnd.md b/content/3.defense-systems/dnd.md
index 2e06e4faea2e151c5f7f2aaf67ada2b136a02973..7319afe14797f4b26d06b2152e454260e31608e5 100644
--- a/content/3.defense-systems/dnd.md
+++ b/content/3.defense-systems/dnd.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading
PFAM: PF00266, PF01507, PF01935, PF08870, PF13476, PF14072
+relevantAbstracts:
+ - doi: 10.1038/nchembio.2007.39
+ - doi: 10.1038/s41467-019-09390-9
---
# Dnd
diff --git a/content/3.defense-systems/dpd.md b/content/3.defense-systems/dpd.md
index 2301fb984a643fe9b817078786373b055ed63fe4..599a877b0885c60b84e541241e69c36293f6a326 100644
--- a/content/3.defense-systems/dpd.md
+++ b/content/3.defense-systems/dpd.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
PFAM: PF00176, PF00270, PF00271, PF01227, PF01242, PF04055, PF04851, PF06508, PF13091, PF13353, PF13394, PF14072
+relevantAbstracts:
+ - doi: 10.1073/pnas.1518570113
---
# Dpd
diff --git a/content/3.defense-systems/druantia.md b/content/3.defense-systems/druantia.md
index 835f6555141898e3ba9915a5b0724d616743c1a1..3f394efe06c07c44239d23b60c94d4bf421cbf8f 100644
--- a/content/3.defense-systems/druantia.md
+++ b/content/3.defense-systems/druantia.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00145, PF00270, PF00271, PF04851, PF09369, PF14236
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
---
# Druantia
diff --git a/content/3.defense-systems/dsr.md b/content/3.defense-systems/dsr.md
index 03e3cf2348473bebc0764183dea1e5ab1da55b71..12d240d965100aa35078a8192688fb3ee9b33be6 100644
--- a/content/3.defense-systems/dsr.md
+++ b/content/3.defense-systems/dsr.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Direct
Effector: Nucleotide modifying
PFAM: PF13289
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01207-8
+ - doi: 10.1126/science.aba0372
---
# Dsr
diff --git a/content/3.defense-systems/eleos.md b/content/3.defense-systems/eleos.md
index 8220a15c63a07b32db6a3197320ac7b98737237d..5370ae15f338c69362e2fbc30ce29bf654bce96e 100644
--- a/content/3.defense-systems/eleos.md
+++ b/content/3.defense-systems/eleos.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00350, PF01926, PF18709
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Eleos
diff --git a/content/3.defense-systems/fs_giy_yig.md b/content/3.defense-systems/fs_giy_yig.md
index 210603c67b063638b59b35126e6e9d74f0dea9ca..ff41e10102fb903bac68426006d83fd6d0623234 100644
--- a/content/3.defense-systems/fs_giy_yig.md
+++ b/content/3.defense-systems/fs_giy_yig.md
@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1016/j.cell.2022.07.014
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_GIY_YIG
diff --git a/content/3.defense-systems/fs_hepn_tm.md b/content/3.defense-systems/fs_hepn_tm.md
index c53fc9ffd300d52ef86cf507f2dec4dbcc66b71e..0ccac65e2daedc46574ab45be5c292ead6a5d97c 100644
--- a/content/3.defense-systems/fs_hepn_tm.md
+++ b/content/3.defense-systems/fs_hepn_tm.md
@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1016/j.cell.2022.07.014
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_HEPN_TM
diff --git a/content/3.defense-systems/fs_hp_sdh_sah.md b/content/3.defense-systems/fs_hp_sdh_sah.md
index 0334531ae5b8655fddd2b865d97ffff7a409daba..5c0d6e5f105e785d94480c20e5264b6edbde0920 100644
--- a/content/3.defense-systems/fs_hp_sdh_sah.md
+++ b/content/3.defense-systems/fs_hp_sdh_sah.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
PFAM: PF01972
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_HP_SDH_sah
diff --git a/content/3.defense-systems/fs_hsdr_like.md b/content/3.defense-systems/fs_hsdr_like.md
index 90d07a4a27393c65038599a9201a1fb46adede9c..adaff9db295de729298b6c67ff9573b572bab133 100644
--- a/content/3.defense-systems/fs_hsdr_like.md
+++ b/content/3.defense-systems/fs_hsdr_like.md
@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1016/j.cell.2022.07.014
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_HsdR_like
diff --git a/content/3.defense-systems/fs_sma.md b/content/3.defense-systems/fs_sma.md
index 9931ce08c9a82384bd6087d061fb143d0c9f0757..31120a93fb65a4f03f9402d2a484c625aec81c28 100644
--- a/content/3.defense-systems/fs_sma.md
+++ b/content/3.defense-systems/fs_sma.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
PFAM: PF02452
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_Sma
diff --git a/content/3.defense-systems/gao_her.md b/content/3.defense-systems/gao_her.md
index c942058db40bcb5f9b2bad14e4c80bd871670536..1f5cf399a88d7b8b50e4cd301df30314c990b9a3 100644
--- a/content/3.defense-systems/gao_her.md
+++ b/content/3.defense-systems/gao_her.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01935, PF10412, PF13289
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Her
diff --git a/content/3.defense-systems/gao_iet.md b/content/3.defense-systems/gao_iet.md
index 5c0f1dd38492774a05b3d3db2dc6f216cc2fbb61..a2485e4d8aa2004087f7445109f881a9d29b471d 100644
--- a/content/3.defense-systems/gao_iet.md
+++ b/content/3.defense-systems/gao_iet.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00004, PF00082
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Iet
diff --git a/content/3.defense-systems/gao_ppl.md b/content/3.defense-systems/gao_ppl.md
index a5aa0cc2e4cb907e7f0f92933c45b54f74212fb9..f88fe77ccc3fedadeca82a66c8827371ca77f580 100644
--- a/content/3.defense-systems/gao_ppl.md
+++ b/content/3.defense-systems/gao_ppl.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Ppl
diff --git a/content/3.defense-systems/gao_qat.md b/content/3.defense-systems/gao_qat.md
index c0129613a55f0e273e3afcb7c6ba7a21d59bfec9..ecdaaaf44836487fa8b5921678f2863a6225882c 100644
--- a/content/3.defense-systems/gao_qat.md
+++ b/content/3.defense-systems/gao_qat.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01026, PF07693
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Qat
diff --git a/content/3.defense-systems/gao_tery.md b/content/3.defense-systems/gao_tery.md
index 21910352ef09258b1fdc817a41f404d705982b62..d6278bb7e0a13ed0ed869fa1d0f620bd27a75109 100644
--- a/content/3.defense-systems/gao_tery.md
+++ b/content/3.defense-systems/gao_tery.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_TerY
diff --git a/content/3.defense-systems/gaps2.md b/content/3.defense-systems/gaps2.md
index 46a20217bf3ab2516143bf2daa92ab9939bd5415..528a69aff98cac3aed978987e060fad502ee90e4 100644
--- a/content/3.defense-systems/gaps2.md
+++ b/content/3.defense-systems/gaps2.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
PFAM: PF00533, PF01653, PF03119, PF03120, PF12826, PF14520
+relevantAbstracts:
+ - doi: 10.1101/2023.03.28.534373
---
# GAPS2
diff --git a/content/3.defense-systems/gaps4.md b/content/3.defense-systems/gaps4.md
index 4fe4db652d5136337a87b0f74828f84525eef384..f1d8c8063cfb63da2adde21b3608f23da08957f5 100644
--- a/content/3.defense-systems/gaps4.md
+++ b/content/3.defense-systems/gaps4.md
@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1101/2023.03.28.534373
abstract: |
Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+relevantAbstracts:
+ - doi: 10.1101/2023.03.28.534373
---
# GAPS4
diff --git a/content/3.defense-systems/gaps6.md b/content/3.defense-systems/gaps6.md
index 3b218b601ae0e4eee18c3490a24af308afb8fcfe..f22584600ede46531df38f1c8c44c2b94ce8bed8 100644
--- a/content/3.defense-systems/gaps6.md
+++ b/content/3.defense-systems/gaps6.md
@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1101/2023.03.28.534373
abstract: |
Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of defense islands may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+relevantAbstracts:
+ - doi: 10.1101/2023.03.28.534373
---
# GAPS6
diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md
index 64bd8d76d2e3b9e55e0ad75a7950446e626378c2..792766c7b1a806db741b0eb3038cd3d396fbfa82 100644
--- a/content/3.defense-systems/gasdermin.md
+++ b/content/3.defense-systems/gasdermin.md
@@ -12,8 +12,8 @@ tableColumns:
contributors:
- Aude Bernheim
relevantAbstracts:
-- doi: 10.1126/science.abj8432
-- doi: 10.1101/2023.05.28.542683
+ - doi: 10.1126/science.abj8432
+ - doi: 10.1101/2023.05.28.542683
---
# GasderMIN
diff --git a/content/3.defense-systems/hachiman.md b/content/3.defense-systems/hachiman.md
index 5a8515cf333d53b71414d4a4fbcff7e5ce09f034..f2b53acd2828ae4289710511064a3b026cebb8f4 100644
--- a/content/3.defense-systems/hachiman.md
+++ b/content/3.defense-systems/hachiman.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00270, PF00271, PF04851, PF08878, PF14130
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
---
# Hachiman
diff --git a/content/3.defense-systems/hna.md b/content/3.defense-systems/hna.md
index 56a84f17e58ce9fbde520a4cd0d9ca856558a056..5134b8445469287661431a574baddde01de756d9 100644
--- a/content/3.defense-systems/hna.md
+++ b/content/3.defense-systems/hna.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
PFAM: PF00270, PF04851, PF13307
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2023.01.010
---
# Hna
diff --git a/content/3.defense-systems/isg15-like.md b/content/3.defense-systems/isg15-like.md
index 314be5d18fa45b18e939f4baaee844e578035f6b..242a75ede7ff65b75b9521cad4e527ab632b29e7 100644
--- a/content/3.defense-systems/isg15-like.md
+++ b/content/3.defense-systems/isg15-like.md
@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
+
---
# ISG15-like
diff --git a/content/3.defense-systems/jukab.md b/content/3.defense-systems/jukab.md
index b650585efd48ec979a2d95efa78768dec9e2a9c3..c153378bb60740e2c5ec2d679b0c33cc477cb4cf 100644
--- a/content/3.defense-systems/jukab.md
+++ b/content/3.defense-systems/jukab.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
Jumbo bacteriophages of the ?KZ-like family are characterized by large genomes (>200 kb) and the remarkable ability to assemble a proteinaceous nucleus-like structure. The nucleus protects the phage genome from canonical DNA-targeting immune systems, such as CRISPR-Cas and restriction-modification. We hypothesized that the failure of common bacterial defenses creates selective pressure for immune systems that target the unique jumbo phage biology. Here, we identify the "jumbo phage killer"(Juk) immune system that is deployed by a clinical isolate of Pseudomonas aeruginosa to resist PhiKZ. Juk immunity rescues the cell by preventing early phage transcription, DNA replication, and nucleus assembly. Phage infection is first sensed by JukA (formerly YaaW), which localizes rapidly to the site of phage infection at the cell pole, triggered by ejected phage factors. The effector protein JukB is recruited by JukA, which is required to enable immunity and the subsequent degradation of the phage DNA. JukA homologs are found in several bacterial phyla and are associated with numerous other putative effectors, many of which provided specific antiPhiKZ activity when expressed in P. aeruginosa. Together, these data reveal a novel strategy for immunity whereby immune factors are recruited to the site of phage protein and DNA ejection to prevent phage progression and save the cell.
PFAM: PF13099
+relevantAbstracts:
+ - doi: 10.1101/2022.09.17.508391
---
# JukAB
diff --git a/content/3.defense-systems/mads.md b/content/3.defense-systems/mads.md
index e13fcc404f870026c9f1484c67af2e611998b6a4..4c44664de167394912f1eb40b457fdfcdf380d0f 100644
--- a/content/3.defense-systems/mads.md
+++ b/content/3.defense-systems/mads.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
The constant arms race between bacteria and their phages has resulted in a large diversity of bacterial defence systems1,2, with many bacteria carrying several systems3,4. In response, phages often carry counter-defence genes5-9. If and how bacterial defence mechanisms interact to protect against phages with counter-defence genes remains unclear. Here, we report the existence of a novel defence system, coined MADS (Methylation Associated Defence System), which is located in a strongly conserved genomic defence hotspot in Pseudomonas aeruginosa and distributed across Gram-positive and Gram-negative bacteria. We find that the natural co-existence of MADS and a Type IE CRISPR-Cas adaptive immune system in the genome of P. aeruginosa SMC4386 provides synergistic levels of protection against phage DMS3, which carries an anti-CRISPR (acr) gene. Previous work has demonstrated that Acr-phages need to cooperate to overcome CRISPR immunity, with a first sacrificial phage causing host immunosuppression to enable successful secondary phage infections10,11. Modelling and experiments show that the co-existence of MADS and CRISPR-Cas provides strong and durable protection against Acr-phages by disrupting their cooperation and limiting the spread of mutants that overcome MADS. These data reveal that combining bacterial defences can robustly neutralise phage with counter-defence genes, even if each defence on its own can be readily by-passed, which is key to understanding how selection acts on defence combinations and their coevolutionary consequences.
PFAM: PF00069, PF01170, PF02384, PF07714, PF08378, PF12728, PF13304, PF13588
+relevantAbstracts:
+ - doi: 10.1101/2023.03.30.534895
---
# MADS
diff --git a/content/3.defense-systems/nlr.md b/content/3.defense-systems/nlr.md
index c463d48387b602d9ead55c76a8446b5cb0163a1f..9fb50ad8136bc22bd9165c263743a07408b4ef59 100644
--- a/content/3.defense-systems/nlr.md
+++ b/content/3.defense-systems/nlr.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF05729
+relevantAbstracts:
+ - doi: 10.1101/2022.07.19.500537
---
# NLR
diff --git a/content/3.defense-systems/panchino_gp28.md b/content/3.defense-systems/panchino_gp28.md
index e197f1d87baefa57d3020bd5b25d6d474d4050a9..b526b5280be0a07c35299f2ff4f210a1048fa301 100644
--- a/content/3.defense-systems/panchino_gp28.md
+++ b/content/3.defense-systems/panchino_gp28.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
PFAM: PF01170, PF02384, PF13588
+relevantAbstracts:
+ - doi: 10.1038/nmicrobiol.2016.251
---
# Panchino_gp28
diff --git a/content/3.defense-systems/paris.md b/content/3.defense-systems/paris.md
index c9b25cc499eb0aab115c307360cd175036aabe83..06b902d58e99044bd52bbf6c441f902838c77bb1 100644
--- a/content/3.defense-systems/paris.md
+++ b/content/3.defense-systems/paris.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Sensing of phage protein
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Paris
diff --git a/content/3.defense-systems/pd-lambda-2.md b/content/3.defense-systems/pd-lambda-2.md
index a6d47cfc8ab135029cf7a37d05a7e9ebadc9d1a3..e39dc537560076a1bc30476a02532006e0f89c24 100644
--- a/content/3.defense-systems/pd-lambda-2.md
+++ b/content/3.defense-systems/pd-lambda-2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF06114, PF09907, PF14350
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-2
diff --git a/content/3.defense-systems/pd-lambda-4.md b/content/3.defense-systems/pd-lambda-4.md
index 2890057bdf19a6939dedc0ef6e4dbe31c105871a..7dc2f86c2e7c0f984897e4be79f427624010e3ff 100644
--- a/content/3.defense-systems/pd-lambda-4.md
+++ b/content/3.defense-systems/pd-lambda-4.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-4
diff --git a/content/3.defense-systems/pd-lambda-6.md b/content/3.defense-systems/pd-lambda-6.md
index 70128d2a8b5dfbfe2e228d06e8162331366de4a3..76136adc5a07b6ad4491e85c807b47b0b499ee17 100644
--- a/content/3.defense-systems/pd-lambda-6.md
+++ b/content/3.defense-systems/pd-lambda-6.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-6
diff --git a/content/3.defense-systems/pd-t4-1.md b/content/3.defense-systems/pd-t4-1.md
index 5f5d9c36abbac78f58a73265553fa81be3433f9a..5b22a9476fdca6aa0152d5b398e5cfedfe29d635 100644
--- a/content/3.defense-systems/pd-t4-1.md
+++ b/content/3.defense-systems/pd-t4-1.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13020
+relevantAbstracts:
+ - doi: 10.1371/journal.pgen.1010065
---
# PD-T4-1
diff --git a/content/3.defense-systems/pd-t4-2.md b/content/3.defense-systems/pd-t4-2.md
index 289fd9cb051b252de5c3a7ffb5f182bd3059c763..1d2a11f3f4ea07a9faaec218c623e1d03b14f329 100644
--- a/content/3.defense-systems/pd-t4-2.md
+++ b/content/3.defense-systems/pd-t4-2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF03235, PF18735
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-2
diff --git a/content/3.defense-systems/pd-t4-5.md b/content/3.defense-systems/pd-t4-5.md
index dd2b311865fc0c68b99a7bdd67e104a2d6df1147..37d1c023580c420a35f70457fc19a30a57562130 100644
--- a/content/3.defense-systems/pd-t4-5.md
+++ b/content/3.defense-systems/pd-t4-5.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF07751
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-5
diff --git a/content/3.defense-systems/pd-t4-9.md b/content/3.defense-systems/pd-t4-9.md
index 8a6b8a36cb7a5e1ea5827c4afeb19a235b82aaae..ee080a2e737825adbc6c747fa6914dd1175ca98d 100644
--- a/content/3.defense-systems/pd-t4-9.md
+++ b/content/3.defense-systems/pd-t4-9.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02556
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-9
diff --git a/content/3.defense-systems/pd-t7-1.md b/content/3.defense-systems/pd-t7-1.md
index c095375395a96419c6de8468bf501925b3b89e6f..2ea58ee02e5744d24963a01264b43e641f81d158 100644
--- a/content/3.defense-systems/pd-t7-1.md
+++ b/content/3.defense-systems/pd-t7-1.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-1
diff --git a/content/3.defense-systems/pd-t7-2.md b/content/3.defense-systems/pd-t7-2.md
index bd62bba08dd1a0016816b8e66a31d4b827f3c262..39a84ff68af800543e83fcf8fa14febcf62937fd 100644
--- a/content/3.defense-systems/pd-t7-2.md
+++ b/content/3.defense-systems/pd-t7-2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01935, PF13289
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-2
diff --git a/content/3.defense-systems/pd-t7-4.md b/content/3.defense-systems/pd-t7-4.md
index 6658dba56df3154a728f3c8d7b5cf085c4126439..3d1085e1fa3b6b21af83e80cf09393e526483eb4 100644
--- a/content/3.defense-systems/pd-t7-4.md
+++ b/content/3.defense-systems/pd-t7-4.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13643
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-4
diff --git a/content/3.defense-systems/pd-t7-5.md b/content/3.defense-systems/pd-t7-5.md
index 564c4bfebfdf1ed74109857b46cca7e2058f7d39..34db3bbbe946ddea53572045d4eb8d972d681245 100644
--- a/content/3.defense-systems/pd-t7-5.md
+++ b/content/3.defense-systems/pd-t7-5.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-5
diff --git a/content/3.defense-systems/pfiat.md b/content/3.defense-systems/pfiat.md
index c21eec60e2a709f9ce05347f0e50b29c84ec41d2..ebfbe341b25dd6064bb69e24007b4c346205f5b7 100644
--- a/content/3.defense-systems/pfiat.md
+++ b/content/3.defense-systems/pfiat.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02604, PF05016
+relevantAbstracts:
+ - doi: 10.1111/1751-7915.13570
---
# PfiAT
diff --git a/content/3.defense-systems/pycsar.md b/content/3.defense-systems/pycsar.md
index f33d2091cc6e175b093a927815bc25a576573496..6a6469e03f6a87a4bc8c86fd8afbc71e7fcb50e0 100644
--- a/content/3.defense-systems/pycsar.md
+++ b/content/3.defense-systems/pycsar.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Signaling molecules
Effector: Membrane disrupting, Nucleotides modifying
PFAM: PF00004, PF00027, PF00211, PF00899, PF01734, PF10137, PF14461, PF14464, PF18145, PF18153, PF18303, PF18967
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2021.09.031
---
# Pycsar
diff --git a/content/3.defense-systems/radar.md b/content/3.defense-systems/radar.md
index dffd65f80d6aaf5434be926c213cb5cecc680930..0510cece62846a97ce2d8cd51f66d0068b0cb50f 100644
--- a/content/3.defense-systems/radar.md
+++ b/content/3.defense-systems/radar.md
@@ -9,7 +9,6 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading
-
contributors:
- Hugo Vaysset
- Aude Bernheim
diff --git a/content/3.defense-systems/rexab.md b/content/3.defense-systems/rexab.md
index ee6c0c51a5bbd9dca8c47bb82d71650efe17669b..e02d441418ed5bbbd8440ebae7842bf240ad7f12 100644
--- a/content/3.defense-systems/rexab.md
+++ b/content/3.defense-systems/rexab.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Membrane disrupting
PFAM: PF15968, PF15969
+relevantAbstracts:
+ - doi: 10.1101/gad.6.3.497
---
# RexAB
diff --git a/content/3.defense-systems/rloc.md b/content/3.defense-systems/rloc.md
index 3bb3916436b9e52a41283a33aaba629df8903923..273ede0650dd61c323cdd499ae56f542061fb4a8 100644
--- a/content/3.defense-systems/rloc.md
+++ b/content/3.defense-systems/rloc.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading
PFAM: PF13166
+relevantAbstracts:
+ - doi: 10.1111/j.1365-2958.2008.06387.x
+ - doi: 10.1111/mmi.13074
---
# RloC
diff --git a/content/3.defense-systems/rnlab.md b/content/3.defense-systems/rnlab.md
index 7aec609fe786fe8cc90dd07dfa36f4a002d9bfd9..282a78756dedac59ad14895f3a01d3ee792821d9 100644
--- a/content/3.defense-systems/rnlab.md
+++ b/content/3.defense-systems/rnlab.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF15933, PF15935, PF18869, PF19034
+relevantAbstracts:
+ - doi: 10.1534/genetics.110.121798
---
# RnlAB
diff --git a/content/3.defense-systems/rosmerta.md b/content/3.defense-systems/rosmerta.md
index c59f85c1215e335f5bce2abcbd097ca247d210b3..ee968724001afe3f198d6c27a24a7d20a118b93f 100644
--- a/content/3.defense-systems/rosmerta.md
+++ b/content/3.defense-systems/rosmerta.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01381, PF06114, PF12844, PF13443, PF13560
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# RosmerTA
diff --git a/content/3.defense-systems/rst_duf4238.md b/content/3.defense-systems/rst_duf4238.md
index c96e888d4fb0f2622470c06f775f21d403ce61cd..cda9b5f62f47b3a4215a5cdb2876bf751e543548 100644
--- a/content/3.defense-systems/rst_duf4238.md
+++ b/content/3.defense-systems/rst_duf4238.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14022
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_DUF4238
diff --git a/content/3.defense-systems/rst_gop_beta_cll.md b/content/3.defense-systems/rst_gop_beta_cll.md
index 44af6c64667cc43f08e771d6fe3f6fd9e457319f..6a49f423bb46d1c65e5e813f54322060f5163de1 100644
--- a/content/3.defense-systems/rst_gop_beta_cll.md
+++ b/content/3.defense-systems/rst_gop_beta_cll.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14350
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_gop_beta_cll
diff --git a/content/3.defense-systems/rst_hydrolase-3tm.md b/content/3.defense-systems/rst_hydrolase-3tm.md
index 3f777d180a81802521a91a047ddef7a5ca2728b8..ecf86fe5e727228f431a08f14c16890a7d91e332 100644
--- a/content/3.defense-systems/rst_hydrolase-3tm.md
+++ b/content/3.defense-systems/rst_hydrolase-3tm.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13242, PF13419
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_Hydrolase-3Tm
diff --git a/content/3.defense-systems/rst_rt-nitrilase-tm.md b/content/3.defense-systems/rst_rt-nitrilase-tm.md
index 286a6be9f17cf70accc1664ee1b22b1948f77590..c11121196d227b4cb4dc9a6160ad41ac8bcc2e81 100644
--- a/content/3.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/3.defense-systems/rst_rt-nitrilase-tm.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_RT-nitrilase-Tm
diff --git a/content/3.defense-systems/septu.md b/content/3.defense-systems/septu.md
index 232f9b3ccc2a4baefdcd00f2feaaa0c0fa2045b7..2addac55da261ef8482b974bece8df5346ac2ed8 100644
--- a/content/3.defense-systems/septu.md
+++ b/content/3.defense-systems/septu.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13175, PF13304, PF13476
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2020.09.065
+ - doi: 10.1093/nar/gkab883
+ - doi: 10.1126/science.aar4120
---
# Septu
diff --git a/content/3.defense-systems/sofic.md b/content/3.defense-systems/sofic.md
index 3988f556d94b6e7588b802a54d51d30e3d96ef2f..9b38dbc4bd7072007a975089f637cc32c27a2434 100644
--- a/content/3.defense-systems/sofic.md
+++ b/content/3.defense-systems/sofic.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02661, PF13784
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# SoFIC
diff --git a/content/3.defense-systems/spbk.md b/content/3.defense-systems/spbk.md
index 6377138a815ff08ca4248fb556d501f4d449b70d..8b3f25f7eab596a4fdbc569d54b75f9e75e3f220 100644
--- a/content/3.defense-systems/spbk.md
+++ b/content/3.defense-systems/spbk.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13676
+relevantAbstracts:
+ - doi: 10.1371/journal.pgen.1010065
---
# SpbK
diff --git a/content/3.defense-systems/sspbcde.md b/content/3.defense-systems/sspbcde.md
index fabced18a8dbb1a3f566615919694a3817c47923..acb6b9bb45d7b02c5c01dbc69f4ac8cb962c74d1 100644
--- a/content/3.defense-systems/sspbcde.md
+++ b/content/3.defense-systems/sspbcde.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF01507, PF01580, PF03235, PF07510, PF13182
+relevantAbstracts:
+ - doi: 10.1128/mBio.00613-21
+ - doi: 10.1128/mBio.00613-21
---
# SspBCDE
diff --git a/content/3.defense-systems/stk2.md b/content/3.defense-systems/stk2.md
index ce9a908eee7bbf2a1c247f95d55a1cda0ccca820..b90aff235be13dde6a23eb8895dfb514d08a80c3 100644
--- a/content/3.defense-systems/stk2.md
+++ b/content/3.defense-systems/stk2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Other (protein modifying)
PFAM: PF00069, PF07714
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2016.08.010
---
# Stk2
diff --git a/content/3.defense-systems/thoeris.md b/content/3.defense-systems/thoeris.md
index 3f8baaf0db0be52af94d65a816652fe5291fbcb5..37cc0da5cc541a39768c664c34594358cee7956b 100644
--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Signaling
Effector: Nucleotide modifying
PFAM: PF08937, PF13289, PF18185
+relevantAbstracts:
+ - doi: 10.1038/s41586-021-04098-7
+ - doi: 10.1126/science.aar4120
---
# Thoeris
diff --git a/content/3.defense-systems/uzume.md b/content/3.defense-systems/uzume.md
index 4bdf5245ed9f5c1038c309f21ad01bf1148d802b..eb205809f41373073c44265fc8c144c83630e9c9 100644
--- a/content/3.defense-systems/uzume.md
+++ b/content/3.defense-systems/uzume.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Uzume
diff --git a/content/3.defense-systems/wadjet.md b/content/3.defense-systems/wadjet.md
index 8d55567adb3dcf645579a5b08d3d781509343061..a4c099bad69e6e2f76cdf8a14600ca36dcd48ec5 100644
--- a/content/3.defense-systems/wadjet.md
+++ b/content/3.defense-systems/wadjet.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF09660, PF09661, PF09664, PF09983, PF11795, PF11796, PF11855, PF13555, PF13558, PF13835
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
---
# Wadjet
diff --git a/content/3.defense-systems/zorya.md b/content/3.defense-systems/zorya.md
index ae950966a2bbc371fd96916b614fed8f6b8a5d1c..a83c1d3cf4d215d97c689a819febf53c05e08107 100644
--- a/content/3.defense-systems/zorya.md
+++ b/content/3.defense-systems/zorya.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00176, PF00271, PF00691, PF04851, PF15611
+relevantAbstracts:
+ - doi: 10.1093/nar/gkab883
+ - doi: 10.1126/science.aar4120
---
# Zorya