content/2.general-concepts/2.defense-islands.md

 ---
 title: Defense Islands
+layout: article
 ---
 
 

content/2.general-concepts/3.phage_trigger.md → content/2.general-concepts/3.defense-systems_trigger.md

@@ -2,28 +2,19 @@
 title: Defense system triggers
 contributors: 
     - Avigail Stokar-Avihail
+    - Alba Herrero del Valle
+layout: article
 ---
 
 # How anti-phage systems sense invading phages
 Upon phage infection, the bacterial immune system senses a specific phage component or modification that the phage exerts on the cell to elicit the bacterial immune response. Understanding how bacteria sense phage infection is a fundamental question, which remains unanswered for the majority of recently discovered immune systems. There are dozens of cases in which the mechanism of immunity has been elucidated, but the phage trigger remains elusive. Understanding how antiphage systems are activated is key for a full understanding of bacterial immunity and for repurposing them as molecular tools as has been done for restriction enzymes and CRISPR-Cas. 
 
 ## Diversity
-Various determinants of the phage can elicit bacterial immunity either in a direct or indirect manner. The most common and well known prokaryotic anti-phage systems, restriction enzymes and CRISPR-Cas, recognize and cleave phage DNA or RNA. More recently, a CBASS system has been found to directly bind to a structured phage RNA that triggers immune activation1. In other cases, defense systems are activated by protein coding phage genes. In some cases, the phage protein is directly sensed by the defense systems, as has been beautifully demonstrated for the Avs systems that directly bind either the phage terminase or portal protein2. In other cases, the phage protein can be sensed indirectly by the defense system, for example by detecting its activity in the cell. Such an indirect mechanism has been found for example in the case of some retron defense systems that are triggered by phage tampering with the RecBCD protein complex3,4. For a comprehensive coverage of all recent phage detection mechanisms the recent review by Huiting and Bondy-Denomy5 is highly recommended. 
+Various determinants of the phage can elicit bacterial immunity either in a direct or indirect manner. The most common and well known prokaryotic anti-phage systems, restriction enzymes and CRISPR-Cas, recognize and cleave phage DNA or RNA. More recently, a CBASS system has been found to directly bind to a structured phage RNA that triggers immune activation :ref{doi=10.1101/2023.03.07.531596}. In other cases, defense systems are activated by protein coding phage genes. In some cases, the phage protein is directly sensed by the defense systems, as has been beautifully demonstrated for the Avs systems that directly bind either the phage terminase or portal protein :ref{doi=10.1126/science.abm4096}. In other cases, the phage protein can be sensed indirectly by the defense system, for example by detecting its activity in the cell. Such an indirect mechanism has been found for example in the case of some retron defense systems that are triggered by phage tampering with the RecBCD protein complex :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.cell.2023.02.029}. For a comprehensive coverage of all recent phage detection mechanisms the recent review by Huiting and Bondy-Denomy :ref{doi=10.1016/j.mib.2023.102325} is highly recommended. 
 
 ## Method of discovery:
-The main method used to pinpoint phage components that trigger a specific defense system of interest has been through a simple classic genetics approach, whereby mutant phages that overcome the defense system are examined. Such mutants often occur spontaneously and can thus be selected for by simply picking phage plaques that are able to form on a lawn of bacteria expressing the defense system4,5. The hypothesis is that the phage mutant escapes bacterial immunity due to a mutation in the component sensed by the system. Thus, sequencing these phage mutants and identification of the mutated locus is the first required step. To validate that the mutated phage component is indeed the actual trigger of the defense system, follow up experiments are required. For example, in some cases expression of this phage component without any other phage genes is sufficient to elicit the activity of bacterial immune system. This approach was used to identify Borvo activation by expression of the phage DNA polymerase4, Dazbog activation by expression of a phage DNA methylase4, retron activation by either phage SSB proteins4 or by proteins that inhibit the host RecBCD3, CapRel triggering by the phage Capsid protein6 and many more5. Additional biochemical pulldown assays can be used to assess binding of the defense system to the suspected phage trigger. 
-One major caveat in the above approach is that in some cases mutant phages that escape the immune system cannot be isolated. This can occur for example if the defense system senses a general fold of a highly conserved and essential phage protein. In this case a simple mutation in the protein will not suffice for the phage to escape detection. In such cases, an alternative approach can be used that does not rely on isolation of escape mutants. An overexpression library of all phage genes can be co-expressed with the defense system of interest, and then assayed for immune activation. This approach was successfully applied for identification phage components that trigger diverse Avs systems2. 
+The main method used to pinpoint phage components that trigger a specific defense system of interest has been through a simple classic genetics approach, whereby mutant phages that overcome the defense system are examined. Such mutants often occur spontaneously and can thus be selected for by simply picking phage plaques that are able to form on a lawn of bacteria expressing the defense system :ref{doi=10.1016/j.cell.2023.02.029,10.1016/j.mib.2023.102325}. The hypothesis is that the phage mutant escapes bacterial immunity due to a mutation in the component sensed by the system. Thus, sequencing these phage mutants and identification of the mutated locus is the first required step. To validate that the mutated phage component is indeed the actual trigger of the defense system, follow up experiments are required. For example, in some cases expression of this phage component without any other phage genes is sufficient to elicit the activity of bacterial immune system. This approach was used to identify Borvo activation by expression of the phage DNA polymerase, Dazbog activation by expression of a phage DNA methylase, retron activation by either phage SSB proteins :ref{doi=10.1016/j.cell.2023.02.029} or by proteins that inhibit the host RecBCD3, CapRel triggering by the phage Capsid protein :ref{doi=10.1038/s41586-022-05444-z} and many more :ref{doi=10.1016/j.mib.2023.102325}. Additional biochemical pulldown assays can be used to assess binding of the defense system to the suspected phage trigger. 
+One major caveat in the above approach is that in some cases mutant phages that escape the immune system cannot be isolated. This can occur for example if the defense system senses a general fold of a highly conserved and essential phage protein. In this case a simple mutation in the protein will not suffice for the phage to escape detection. In such cases, an alternative approach can be used that does not rely on isolation of escape mutants. An overexpression library of all phage genes can be co-expressed with the defense system of interest, and then assayed for immune activation. This approach was successfully applied for identification phage components that trigger diverse Avs systems :ref{doi=10.1126/science.abm4096}. 
 
 ## General concepts: 
-Although much is still unknown regarding how bacterial immune systems sense phage infection, by combining the data observed so far, several general concepts in immune sensing are beginning to come to light. First, mechanistically diverse immune systems appear to have converged to sense common conserved phage components4.  These include the phage core replication machinery, host takeover machinery and structural components. Second, several studies have found cases in which defense occurs in a multi-layered fashion, whereby a second system is activated when the first one fails3,7,8. Research in upcoming years is expected to reveal additional guiding principles in the ways bacteria detect phages. 
-
-## References:
-1.	Banh D V, Roberts C G, Amador A M, Brady S F, & Marraffini L A. (2023) Bacterial cGAS senses a viral RNA to initiate immunity. bioRxiv 2023.03.07.531596 doi:10.1101/2023.03.07.531596.
-2.	Gao L A, Wilkinson M E, Strecker J, Makarova K S, Macrae R K, Koonin E V, & Zhang F. (2022) Prokaryotic innate immunity through pattern recognition of conserved viral  proteins. Science 377: eabm4096.
-3.	Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, Oppenheimer-Shaanan Y, & Sorek R. (2020) Bacterial Retrons Function In Anti-Phage Defense. Cell 183: 1551–1561.
-4.	Stokar-Avihail A, Fedorenko T, Hör J, Garb J, Leavitt A, Millman A, Shulman G, Wojtania N, Melamed S, Amitai G, & Sorek R. (2023) Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell 186: 1863-1876.e16.
-5.	Huiting E & Bondy-Denomy J. (2023) Defining the expanding mechanisms of phage-mediated activation of bacterial immunity. Curr. Opin. Microbiol. 74: 102325.
-6.	Zhang T, Tamman H, Coppieters ’t Wallant K, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson G C, Hauryliuk V, Garcia-Pino A, & Laub M T. (2022) Direct activation of a bacterial innate immune system by a viral capsid protein. Nature 612: 132–140.
-7.	Rousset F, Depardieu F, Miele S, Dowding J, Laval A-L, Lieberman E, Garry D, Rocha E P C, Bernheim A, & Bikard D. (2022) Phages and their satellites encode hotspots of antiviral systems. Cell Host Microbe 30: 740–753.
-8.	Penner M, Morad I, Snyder L, & Kaufmann G. (1995) Phage T4-coded Stp: Double-edged effector of coupled DNA and tRNA-restriction systems. J. Mol. Biol. 249: 857–68.
-
+Although much is still unknown regarding how bacterial immune systems sense phage infection, by combining the data observed so far, several general concepts in immune sensing are beginning to come to light. First, mechanistically diverse immune systems appear to have converged to sense common conserved phage components4.  These include the phage core replication machinery, host takeover machinery and structural components. Second, several studies have found cases in which defense occurs in a multi-layered fashion, whereby a second system is activated when the first one fails  :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.chom.2022.02.018,10.1006/jmbi.1995.0343}. Research in upcoming years is expected to reveal additional guiding principles in the ways bacteria detect phages. 

content/2.general-concepts/4.defense-systems_effector.md

+---
+title: Abortive Infection
+layout: article
+toc: true
+---
+
+
+This section is empty. You can help by adding to it.
+
+
+## test article
+

content/2.general-concepts/5.defense-systems-discovery.md

+---
+title: Discovery of defense systems
+layout: article
+toc: true
+---
+
+Defense systems are known since the birth of molecular biology. Then, more were discovered.

content/2.general-concepts/6.defensive-domains.md

+---
+title: Defensive Domains
+layout: article
+toc: true
+---
+
+Among proteins involved in defense systems, a few domains appear to be frequent. 

content/2.general-concepts/7.mge-defense-systems.md

+---
+title: Defense Systems and MGE
+layout: article-no-toc
+---
+
+Defense systems help bacteria against mobile genetic elements (MGE), such as phage or plasmids.
+Yet, some defense systems favor certain MGE, or some MGE carry defense systems.
\ No newline at end of file

content/2.general-concepts/8.anti-defense-systems.md

+---
+title: Anti Defense Systems
+layout: article
+toc: true
+---
+
+Anti defense systems are systems that act against defense system, and thus help bypass the defense mechanism.
+

content/3.defense-systems/abi2.md

@@ -16,22 +16,24 @@ relevantAbstracts:
 
 # Abi2
 
-The Abi2 system is composed of one protein: Abi_2.
 
-Here is an example found in the RefSeq database:
+## Example of genomic structure
+
+The Abi2 is composed of 1 protein: Abi_2.
 
+Here is an example found in the RefSeq database:
 
-![abi2](/abi2/Abi2.svg)
+![abi2](/abi2/Abi2.svg){max-width=750px}
 
-Abi2 system in the genome of *Clostridium butyricum* (GCF_014131795.1) is composed of 1 protein: Abi_2 (WP_035763709.1).
+The Abi2 system in *Veillonella parvula* (GCF_002005185.1, NZ_CP019721) is composed of 1 protein: Abi_2 (WP_077707938.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Abi2 system is present in a total of 176 different species.
+Among the 22,803 complete genomes of RefSeq, the Abi2 is detected in 1231 genomes (5.4 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes (5.3 %).
+The system was detected in 202 different species.
 
-![abi2](/abi2/Distribution_Abi2.svg)
+![abi2](/abi2/Distribution_Abi2.svg){max-width=750px}
 
-*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.
 

content/3.defense-systems/abia.md

@@ -19,29 +19,30 @@ relevantAbstracts:
 # AbiA 
 
 
-The AbiA system have been describe in a total of 2 subsystems.
+## Example of genomic structure
 
-Here is some example found in the RefSeq database:
+A total of 2 subsystems have been described for the AbiA system.
 
-![abia](/abia/AbiA_large.svg){max-width=750px}
+Here is some examples 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](/abia/AbiA_large.svg){max-width=750px}
 
-![abia](/abia/AbiA_small.svg){max-width=750px}
+The AbiA_large system in *Staphylococcus nepalensis* (GCF_002442935.1, NZ_CP017466) is composed of 1 protein: AbiA_large (WP_096808013.1) 
 
-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](/abia/AbiA_small.svg){max-width=750px}
 
-## Distribution of the system among prokaryotes 
+The AbiA_small system in *Alicyclobacillus sp. SO9* (GCF_016406125.1, NZ_CP066339) is composed of 2 proteins AbiA_small (WP_198850075.1) AbiA_SLATT (WP_198850076.1) 
 
-The AbiA system is present in a total of 35 different species.
+## Distribution of the system among prokaryotes
 
+Among the 22,803 complete genomes of RefSeq, the AbiA is detected in 50 genomes (0.22 %).
 
-
-Among the 22k complete genomes of RefSeq, this system is present in 50 genomes (0.2 %).
+The system was detected in 35 different species.
 
 ![abia](/abia/Distribution_AbiA.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 

content/3.defense-systems/abib.md

@@ -9,29 +9,43 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors:
+    - Nathalie Bechon
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1128/aem.57.12.3547-3551.1991
+    - doi: 10.1046/j.1365-2958.1996.371896.x
 ---
 
 # AbiB
-The AbiB system is composed of one protein: AbiB.
 
-Here is an example found in the RefSeq database: 
+## Description
+AbiB is a single-protein abortive infection defense system from *Lactococcus* that degrades mRNA.
+
+## Molecular mechanism
+AbiB system is still poorly understood. It is a single-protein system that was described as an abortive infection system. Upon phage infection, AbiB activation leads to a strong degradation of mRNAs :ref{doi=10.1046/j.1365-2958.1996.371896.x} that is expected to be the mechanism of phage inhibition. AbiB expression is constitutive and does increase during phage infection. It is only activated during phage infection, most likely through the recognition of an early phage protein. Which protein, and whether this activation is direct or indirect remains to be elucidated.
+
+## Example of genomic structure
+
+The AbiB is composed of 1 protein: AbiB.
+
+Here is an example found in the RefSeq database:
 
 ![abib](/abib/AbiB.svg){max-width=750px}
 
-AbiB system in the genome of *Lactococcus lactis* (GCF_020221755.1) is composed of 1 protein: AbiB (WP_047687114.1).
+The AbiB system in *Lactococcus cremoris* (GCF_000312685.1, NC_019430) is composed of 1 protein: AbiB (WP_144019851.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiB system is present in a total of 5 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiB is detected in 11 genomes (0.05 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 13 genomes (0.1 %).
+The system was detected in 5 different species.
 
 ![abib](/abib/Distribution_AbiB.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 

content/3.defense-systems/abic.md

@@ -13,23 +13,27 @@ tableColumns:
 ---
 
 # AbiC
-The AbiC system is composed of one protein: AbiC.
 
-Here is an example found in the RefSeq database: 
+## Example of genomic structure
+
+The AbiC is composed of 1 protein: AbiC.
+
+Here is an example found in the RefSeq database:
 
 ![abic](/abic/AbiC.svg){max-width=750px}
 
-AbiC system in the genome of *Enterococcus faecium* (GCF_012933295.2) is composed of 1 protein: AbiC (WP_098388098.1).
+The AbiC system in *Cupriavidus pauculus* (GCF_008693385.1, NZ_CP044066) is composed of 1 protein: AbiC (WP_150373977.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiC system is present in a total of 110 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 91 genomes (0.4 %).
+
+The system was detected in 57 different species.
 
-Among the 22k complete genomes of RefSeq, this system is present in 196 genomes (0.9 %).
+![abic](/abic/Distribution_AbiC.svg){max-width=750px}
 
-![abic](/abic/Distribution_AbiC.svg){max-width="750"}
+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.* 
 
 ## Structure
 

content/3.defense-systems/abid.md

@@ -13,23 +13,27 @@ tableColumns:
 ---
 
 # AbiD
-The AbiD system is composed of one protein: AbiD.
 
-Here is an example found in the RefSeq database: 
+## Example of genomic structure
 
-![abid](/abid/AbiD.svg){max-width="750"}
+The AbiD is composed of 1 protein: AbiD.
 
-AbiD system in the genome of *Lachnospira eligens* (GCF_020735745.1) is composed of 1 protein: AbiD (WP_041688924.1).
+Here is an example found in the RefSeq database:
+
+![abid](/abid/AbiD.svg){max-width=750px}
+
+The AbiD system in *Idiomarina sp. OT37-5b* (GCF_002968395.1, NZ_CP027188) is composed of 1 protein: AbiD (WP_105307479.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiD system is present in a total of 874 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiD is detected in 2713 genomes (11.9 %).
+
+The system was detected in 964 different species.
 
-Among the 22k complete genomes of RefSeq, this system is present in 2748 genomes (12.1 %).
+![abid](/abid/Distribution_AbiD.svg){max-width=750px}
 
-![abid](/abid/Distribution_AbiD.svg){max-width="750"}
+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.* 
 
 ## Structure
 

content/3.defense-systems/abie.md

@@ -25,23 +25,24 @@ 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 is composed of 2 proteins: AbiEii and AbiEi.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abie](/abie/AbiE.svg){max-width=750px}
 
-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).
+The AbiE system in *Halomonas piezotolerans* (GCF_012427705.1, NZ_CP048602) is composed of 2 proteins AbiEi_3 (WP_231125510.1) AbiEii (WP_231125511.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiE system is present in a total of 962 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiE is detected in 3708 genomes (16.26 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 3742 genomes (16.4 %).
+The system was detected in 1107 different species.
 
 ![abie](/abie/Distribution_AbiE.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 

content/3.defense-systems/abig.md

@@ -13,23 +13,27 @@ tableColumns:
 ---
 
 # AbiG
-The AbiG system is composed of 2 proteins: AbiGi and, AbiGii.
 
-Here is an example found in the RefSeq database: 
+## Example of genomic structure
+
+The AbiG is composed of 2 proteins: AbiGi and AbiGii.
+
+Here is an example found in the RefSeq database:
 
 ![abig](/abig/AbiG.svg){max-width=750px}
 
-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).
+The AbiG system in *Staphylococcus simulans* (GCF_900474685.1, NZ_LS483313) is composed of 2 proteins AbiGi (WP_103364194.1) AbiGii (WP_070462993.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiG system is present in a total of 23 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiG is detected in 32 genomes (0.14 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 33 genomes (0.1 %).
+The system was detected in 22 different species.
 
 ![abig](/abig/Distribution_AbiG.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 

content/3.defense-systems/abih.md

@@ -20,23 +20,24 @@ relevantAbstracts:
 # AbiH
 ## Example of genomic structure
 
-The AbiH system is composed of one protein: AbiH.
+The AbiH is composed of 1 protein: AbiH.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abih](/abih/AbiH.svg){max-width=750px}
 
-AbiH system in the genome of *Agrobacterium tumefaciens* (GCF_005221405.1) is composed of 1 protein: AbiH (WP_045021548.1).
+The AbiH system in *Bacteroides faecium* (GCF_012113595.1, NZ_CP050831) is composed of 1 protein: AbiH (WP_167962074.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiH system is present in a total of 408 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiH is detected in 1225 genomes (5.37 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1277 genomes (5.6 %).
+The system was detected in 439 different species.
 
 ![abih](/abih/Distribution_AbiH.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 

content/3.defense-systems/abii.md

@@ -14,23 +14,24 @@ tableColumns:
 # AbiI
 ## Example of genomic structure
 
-The AbiI system is composed of one protein: AbiI.
+The AbiI is composed of 1 protein: AbiI.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abii](/abii/AbiI.svg){max-width=750px}
 
-AbiI system in the genome of *Enterococcus faecalis* (GCF_002814115.1) is composed of 1 protein: AbiI (WP_002367720.1).
+The AbiI system in *Macrococcus brunensis* (GCF_022343725.1, NZ_CP092179) is composed of 1 protein: AbiI (WP_239034930.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiI system is present in a total of 8 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiI is detected in 6 genomes (0.03 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 8 genomes (0.0 %).
+The system was detected in 6 different species.
 
 ![abii](/abii/Distribution_AbiI.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 

content/3.defense-systems/abij.md

@@ -15,23 +15,24 @@ tableColumns:
 # AbiJ
 ## Example of genomic structure
 
-The AbiJ system is composed of one protein: AbiJ.
+The AbiJ is composed of 1 protein: AbiJ.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abij](/abij/AbiJ.svg){max-width=750px}
 
-AbiJ system in the genome of *Loigolactobacillus backii* (GCF_001663735.1) is composed of 1 protein: AbiJ (WP_068377534.1).
+The AbiJ system in *Marinobacter sp. LQ44* (GCF_001447155.2, NZ_CP014754) is composed of 1 protein: AbiJ (WP_058091398.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiJ system is present in a total of 321 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiJ is detected in 686 genomes (3.01 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 807 genomes (3.5 %).
+The system was detected in 261 different species.
 
 ![abij](/abij/Distribution_AbiJ.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 

content/3.defense-systems/abik.md

@@ -15,23 +15,24 @@ tableColumns:
 # AbiK
 ## Example of genomic structure
 
-The AbiK system is composed of one protein: AbiK.
+The AbiK is composed of 1 protein: AbiK.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abik](/abik/AbiK.svg){max-width=750px}
 
-AbiK system in the genome of *Lactococcus lactis* (GCF_002078995.2) is composed of 1 protein: AbiK (WP_081199340.1).
+The AbiK system in *Lactobacillus ultunensis* (GCF_016647595.1, NZ_CP059829) is composed of 1 protein: AbiK (WP_007126124.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiK system is present in a total of 32 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiK is detected in 107 genomes (0.47 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 107 genomes (0.5 %).
+The system was detected in 32 different species.
 
 ![abik](/abik/Distribution_AbiK.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 

content/3.defense-systems/abil.md

@@ -3,35 +3,51 @@ title: AbiL
 layout: article
 tableColumns:
     article:
-      doi: 10.1016/j.mib.2005.06.006
+      doi: 10.1111/j.1574-6968.1997.tb10185.x
       abstract: |
-        Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
+        A 16-kb plasmid (pND859) was identified from Lactococcus lactis biovar. diacetylactis UK12922 which encodes phage resistance to the small isometric phage 712 when tested in L. lactis LM0230. The gene encoding phage abortive infection, designated abi-859, was localized on a 1.2-kb region which consists of an open reading frame (ORF) of 846 bp preceded by a potential ribosome-binding site and a putative promoter region. A helix-turn-helix region typical of DNA-binding motifs was identified near the N-terminal of the abi-859 product, suggesting a possible interaction with the phage DNA.
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
     PFAM: PF13175, PF13304, PF13707
+contributors: 
+  - Ernest Mordret
+relevantAbstracts:
+  - doi: 10.1111/j.1574-6968.1997.tb10185.x
+  - doi: 10.1016/j.mib.2005.06.006
+
 ---
 
 # AbiL
+
+## Description
+
+AbiL was discovered in Lactococcus lactis. A plasmid containing the defense system was found to prevent infection by phage 712 through an abortive infection system
+
+## Molecular mechanism
+
+Abortive infection. the PF13707 domain includes the RloB protein that is found within a bacterial restriction modification operon. This family includes the AbiLii protein that is found as part of a plasmid encoded phage abortive infection mechanism. Deletion within abiLii abolished the phage resistance. The family includes some proteins annotated as CRISPR Csm2 proteins.
+
 ## Example of genomic structure
 
-The AbiL system is composed of 2 proteins: AbiLii2 and, AbiLi2.
+The AbiL is composed of 2 proteins: AbiLi and AbiLii.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abil](/abil/AbiL.svg){max-width=750px}
 
-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).
+The AbiL system in *Sulfurimonas sp. SWIR-19* (GCF_020410885.1, NZ_CP084578) is composed of 2 proteins AbiLi2 (WP_226066409.1) AbiLii2 (WP_226066410.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiL system is present in a total of 456 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiL is detected in 188 genomes (0.82 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 783 genomes (3.4 %).
+The system was detected in 126 different species.
 
 ![abil](/abil/Distribution_AbiL.svg){max-width=750px}
 
-*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.
+
 
 ## Structure
 
@@ -76,14 +92,6 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
 
-::relevant-abstracts
----
-items:
-    - doi: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
 
----
-::
 

content/3.defense-systems/abin.md

@@ -14,23 +14,24 @@ tableColumns:
 # AbiN
 ## Example of genomic structure
 
-The AbiN system is composed of one protein: AbiN.
+The AbiN is composed of 1 protein: AbiN.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abin](/abin/AbiN.svg){max-width=750px}
 
-AbiN system in the genome of *Enterococcus faecalis* (GCF_016743895.1) is composed of 1 protein: AbiN (WP_002384355.1).
+The AbiN system in *Listeria innocua* (GCF_023078395.1, NZ_CP095723) is composed of 1 protein: AbiN (WP_238929053.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiN system is present in a total of 51 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiN is detected in 165 genomes (0.72 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 167 genomes (0.7 %).
+The system was detected in 52 different species.
 
 ![abin](/abin/Distribution_AbiN.svg){max-width=750px}
 
-*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.
+
 
 ## Structure