content/3.defense-systems/abig.md

@@ -10,13 +10,29 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF10899, PF16873
+contributors:
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1128/aem.62.9.3075-3082.1996
 ---
 
 # AbiG
 
+## Description
+
+AbiG was discovered in 1996 on the plasmid pCI750 of *Lactococcus lactis* :ref{doi=10.1128/aem.62.9.3075-3082.1996}.
+
+AbiG is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. AbiG is classified as abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+AbiG is composed of two genes AbiGi and AbiGii. 
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
+
 ## Example of genomic structure
 
 The AbiG is composed of 2 proteins: AbiGi and AbiGii.

content/3.defense-systems/abih.md

@@ -10,20 +10,26 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF14253
+contributors:
+    - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
     - doi: 10.1111/j.1574-6968.1996.tb08446.x
-
 ---
 
 # AbiH
 
 ## Description
-AbiH is a single-gene abortive infection system described in Lactococcus.
+AbiH a system discovered in 1996 :ref{doi=10.1111/j.1574-6968.1996.tb08446.x}.
+
+AbiH is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. Even though, their name corresponds to an abortive infection, their mechanism of action does not necessarily correspond to an abortive infection. For the abortive infection, phenotype AbiH is classified as unknown in :ref{doi=10.1016/j.mib.2023.102312}.
+
+This system is a single gene system with no known domain (except its own PFAM).
+
+## Molecular mechanism
 
-## Molecular mechanism 
-To the best of our knowledge, no molecular mechanism has been described so far for AbiH.
+As far as we are aware, the molecular mechanism is unknown. 
 
 ## Example of genomic structure
 
@@ -64,12 +70,12 @@ dataUrls:
 
 <mermaid>
 graph LR;
-    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+    Prevost_1996[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
     Origin_0[lactococci 
 <a href='https://ncbi.nlm.nih.gov/protein/CAA66252.1'>CAA66252.1</a>] --> Expressed_0[lactococci]
     Expressed_0[lactococci] ----> 936 & c2
     subgraph Title1[Reference]
-        Chopin_2005
+        Prevost_1996
 end
     subgraph Title2[System origin]
         Origin_0

content/3.defense-systems/abii.md

@@ -9,12 +9,24 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1016/S0168-1656(97)01692-1
 ---
 
 # AbiI
+
+## Description
+AbiI is a single gene defense system discovered in *Lactococcus lactis* in 1997 :ref{doi=10.1016/S0168-1656(97)01692-1}.
+
+AbiI is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. Even though, their name corresponds to an abortive infection, their mechanism of action does not necessarily correspond to an abortive infection. AbiI is classified as an abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+## Molecular mechanism
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The AbiI is composed of 1 protein: AbiI.

content/3.defense-systems/abij.md

@@ -10,12 +10,28 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF14355
+contributors:
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1111/j.1574-6968.1997.tb10185.x
 ---
 
 # AbiJ
+
+## Description
+
+AbiJ was discovered in 1997 on a *Lactococcus lactis* biovar. diacetylactis  :ref{doi=10.1111/j.1574-6968.1997.tb10185.x}.
+
+AbiJ is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. AbiJ is classified as abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+AbiJ is composed of one protein AbiJ. AbiJ has some homology with [AbiC](/defense-systems/abic) (PF14355).
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The AbiJ is composed of 1 protein: AbiJ.

content/3.defense-systems/abik.md

@@ -10,13 +10,32 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00078
+contributors:
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-    - doi: 10.1093/nar/gkac467
+  - doi: 10.1023/A:1002027321171
+  - doi: 10.1016/j.mib.2005.06.006
+  - doi: 10.1093/nar/gkac467
+  - doi: 10.1128/aem.63.4.1274-1283.1997
 ---
 
 # AbiK
+
+## Description
+
+
+The AbiK defense system was discovered in 1997 in *Lactococcus lactis* :ref{doi=10.1128/aem.63.4.1274-1283.1997}. AbiK is a single gene system with a size of around 650 amino acids.
+
+AbiK is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. AbiK is classified as abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+Since it was discovered a similarity in amino acids was found with [AbiA](/defense-systems/abia). 
+However, with the discovery of dozens of new systems, it was categorized as one of the UG/Abi defense systems :ref{doi=10.1093/nar/gkac467} along with [DRT](/defense-systems/drt) different subsystems, [AbiA](/defense-systems/abia), [AbiP2](/defense-systems/abip2) and [Rst_RT_Nitralase_TM](/defense-systems/rst_rt-nitrilase-tm).
+
+Those systems are characterized by the presence of a reverse transcriptase domain of the "Unknown Group RT".
+
+## Molecular mechanism
+To our knowledge, the molecular mechanism is unknown. Similarly, for the other systems of this family, the molecular mechanism remains unknown.
+
 ## Example of genomic structure
 
 The AbiK is composed of 1 protein: AbiK.

content/3.defense-systems/abin.md

@@ -9,12 +9,27 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
+  - doi: 10.1023/A:1002027321171
+  - doi: 10.1016/j.mib.2005.06.006
+  - doi: 10.1016/S0378-1097(98)00002-0
 ---
 
 # AbiN
+
+## Description
+AbiN was discovered in *Lactococcus lactis* subsp. cremoris S114 in 1998 :ref{doi=10.1016/S0378-1097(98)00002-0}.
+
+AbiN is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. AbiN is classified as unknown for abortive infection phenotype in :ref{doi=10.1016/j.mib.2023.102312}.
+
+AbiN is a single gene system composed of the protein AbiN.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The AbiN is composed of 1 protein: AbiN.
@@ -76,4 +91,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/abio.md

@@ -10,12 +10,29 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF01443, PF09848
+contributors:
+    - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
+  - doi: 10.1023/A:1002027321171
+  - doi: 10.1016/j.mib.2005.06.006
+  - doi: 10.3168/jds.S0022-0302(98)75713-3
 ---
 
 # AbiO
+
+## Description
+
+AbiO is a single gene defense system discovered in 1998 :ref{doi=10.3168/jds.S0022-0302(98)75713-3}.
+
+AbiO is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. Even though, their name corresponds to an abortive infection, their mechanism of action does not necessarily correspond to an abortive infection. AbiO is classified as a possible Abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+
+This system is only composed of one single gene containing a helicase domain.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The AbiO is composed of 1 protein: AbiO.
@@ -55,12 +72,12 @@ dataUrls:
 
 <mermaid>
 graph LR;
-    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+    Prevots_1998[<a href='https://doi.org/10.3168/jds.S0022-0302(98)75713-3'>Prevots et al., 1998</a>] --> Origin_0
     Origin_0[lactococcal plasmid  
-<a href='https://ncbi.nlm.nih.gov/protein/insideplasmid:I61427.1'>insideplasmid:I61427.1</a>] --> Expressed_0[lactococci]
+<a href='https://ncbi.nlm.nih.gov/protein/I61427.1'>In the plasmid : I61427.1</a>] --> Expressed_0[lactococci]
     Expressed_0[lactococci] ----> 936 & c2
     subgraph Title1[Reference]
-        Chopin_2005
+        Prevots_1998
 end
     subgraph Title2[System origin]
         Origin_0
@@ -78,3 +95,5 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+
+

content/3.defense-systems/abiq.md

@@ -10,13 +10,33 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF13958
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
     - doi: 10.1128/AEM.64.12.4748-4756.1998
+    - doi: 10.1111/mmi.12129
 ---
 
 # AbiQ
+
+## Description
+
+AbiQ was discovered in 1998 on *Lactococcus lactis* plasmid :ref{doi=10.1128/AEM.64.12.4748-4756.1998}.
+
+AbiQ is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. AbiQ is classified as abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+AbiQ is composed of a single protein AbiQ and an RNA antitoxin (antiQ) :ref{doi=10.1111/mmi.12129}.
+
+## Molecular mechanism
+
+AbiQ act as an anti-toxin type III. AbiQ is an RNAase that will bind its antitoxin antiQ :ref{doi=10.1111/mmi.12129}.
+
+The AbiQ is constitutively expressed and bind to its antiQ RNA resulting in an inactivated AbiQ.
+To get activated, AbiQ needs the concentration of antiQ to decrease.
+However, during phage infection, the expression of the antiQ is constant and the authors do not know how the AbiQ is activated :ref{doi=10.1111/mmi.12129}.
+
 ## Example of genomic structure
 
 The AbiQ is composed of 1 protein: AbiQ.
@@ -38,6 +58,18 @@ The system was detected in 111 different species.
 Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
+## Structure
+### Experimentally determined structure
+
+From :ref{doi=10.1111/mmi.12129} in *Lactococcus lactis*:
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abiq/4glk_LlAbiQ_1mer.cif
+---
+::
+
 
 ## Structure
 ### AbiQ

content/3.defense-systems/abir.md

@@ -10,12 +10,29 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00176, PF00271, PF04545, PF04851, PF13091
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
+  - doi: 10.1023/A:1002027321171
+  - doi: 10.1016/j.mib.2005.06.006
+  - doi: 10.1128/aem.66.6.2647-2651.2000
 ---
 
 # AbiR
+
+## Description
+AbiR is a defense system discovered in 2000 :ref{doi=10.1128/aem.66.6.2647-2651.2000}.
+
+AbiR is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. AbiR is classified as abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+AbiR is composed of 3 genes: AbiRa, AbiRb, AbiRc.
+AbiRa encodes a sigma70 RNA polymerase subunit. AbiRb as homology with ParB nuclease domain according to HHpred.
+AbiRc has two different domains: a N_terminal PLD domain (PF13091) and at the C term an SNF2 DNA dependant ATPase.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The AbiR is composed of 3 proteins: AbiRa, AbiRb and AbiRc.

content/3.defense-systems/abit.md

@@ -10,12 +10,28 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF18864
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1128/jb.184.22.6325-6332.2002
 ---
 
 # AbiT
+
+## Description
+AbiT was discovered in *Lactococcus lactis* in 2022 :ref{doi=10.1128/jb.184.22.6325-6332.2002}.
+
+AbiT is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. Even though, their name corresponds to abortive infection, their mechanism of action does not necessarily correspond to an abortive infection phenotype. AbiT is classified as an abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+AbiT is composed of two proteins: AbiTi with a transmembrane helix domain and AbiTii.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
+
 ## Example of genomic structure
 
 The AbiT is composed of 2 proteins: AbiTi and AbiTii.

content/3.defense-systems/abiv.md

@@ -10,12 +10,25 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF18728
+contributors:
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1023/A:1002027321171
-    - doi: 10.1128/AEM.00780-08
+  - doi: 10.1023/A:1002027321171
+  - doi: 10.1128/AEM.00780-08
 ---
 
 # AbiV
+
+## Description
+AbiV was discovered was discovered in 2008 in *Lactococcus lactis* ref:{doi=10.1023/A:1002027321171}.
+
+AbiO is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. Even though their name corresponds to an abortive infection, their mechanism of action does not necessarily correspond to an abortive infection. AbiV system is classified as an abortive infection in :ref{doi=10.1016/j.mib.2023.102312}
+
+This system is composed of one single protein containing a HEPN domain (HEPN_AbiV PF18728).
+
+## Molecular mechanism
+As far as we are aware, the molecular mechanism is unknown. 
+
 ## Example of genomic structure
 
 The AbiV is composed of 1 protein: AbiV.
@@ -47,7 +60,6 @@ Proportion of genome encoding the AbiV system for the 14 phyla with more than 50
 height: 700
 dataUrls:
    - /abiv/AbiV__AbiV.cif
-
 ---
 ::
 

content/3.defense-systems/abiz.md

@@ -9,12 +9,26 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Membrane disrupting
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1128/JB.00904-06
 ---
 
 # AbiZ
+
+## Description
+
+AbiZ was discovered in 2006 on a *Lactococcus lactis* conjugative plasmid pTR2030 :ref{doi=10.1128/JB.00904-06}.
+
+AbiZ is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. AbiZ is classified as abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+AbiZ is composed of a single protein AbiZ.
+
+## Molecular mechanism
+AbiZ acts as an abortive infection system. AbiZ proteins sense holins and lysins from the infecting bacteriophage and use them to induce premature cell lysis :ref{doi=10.1128/JB.00904-06,10.1146/annurev-virology-011620-040628}.  
+
 ## Example of genomic structure
 
 The AbiZ is composed of 1 protein: AbiZ.

content/3.defense-systems/aditi.md

@@ -10,11 +10,22 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF18928
+contributors:
+    - Rachel Lavenir
 relevantAbstracts:
     - doi: 10.1016/j.chom.2022.09.017
 ---
 
 # Aditi
+## Description
+Aditi was discovered among other systems in 2022 :ref{doi=10.1016/j.chom.2022.09.017}.
+
+Aditi is composed of two genes: DitA, DitB. Both are of unknown function, and have no homology to any known domain.
+Aditi is named after the Hindu guardian goddess of all life.
+
+## Molecular mechanisms
+As far as we are aware, the molecular mechanism is unknown. 
+
 ## Example of genomic structure
 
 The Aditi is composed of 2 proteins: DitA and DitB.
@@ -47,7 +58,6 @@ height: 700
 dataUrls:
    - /aditi/Aditi.Aditi__DitB.0.V.cif
    - /aditi/Aditi.Aditi__DitA.0.V.cif
-
 ---
 ::
 
@@ -79,3 +89,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/bsta.md

@@ -9,20 +9,25 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+    PFAM: 
+contributors: 
+    - Rachel Lavenir
 relevantAbstracts:
-    - doi: 10.1016/j.chom.2021.09.002
+ - doi: 10.1016/j.chom.2021.09.002
 ---
 
 # 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 :ref{doi=10.1016/j.chom.2021.09.002}.
 
-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 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 :ref{doi=10.1016/j.chom.2021.09.002}.
 
-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 :ref{doi=10.1016/j.chom.2021.09.002}. 
 
-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). 
+## Molecular mechanism
+
+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 :ref{doi=10.1016/j.chom.2021.09.002}.
 
 ## Example of genomic structure
 

content/3.defense-systems/butters_gp30_gp31.md

@@ -22,22 +22,14 @@ relevantAbstracts:
 
 ## Description
 The anti-phage defense system Butters_gp30_gp31 is encoded in the genomes of Actinobacteria, including in prophages.
-It was experimentally validated in the host _Mycobacterium smegmatis_, and displayed resistance against phages PurpleHaze and Alma.  
+It was experimentally validated in the host *Mycobacterium smegmatis* and displayed resistance against phages PurpleHaze and Alma.  
 
 ## Molecular mechanism
-To our knowledge the mechanism of action remains unknown.
-However the proteins of this system are predicted as a cytoplasmic protein (gp30) and a 4-pass transmembrane protein (gp31). The proposed mechanism of action is hypothesized to ressemble the RexA/B system of coliphage Lambda, where activation of gp30 by phage infection stimulates the ion channel gp31 which causes membrane depolarization and loss of intracellular ATP, which in turn, causes abortive infection.
+To our knowledge, the mechanism of action remains unknown.
+However, the proteins of this system are predicted as a cytoplasmic protein (gp30) and a 4-pass transmembrane protein (gp31). The proposed mechanism of action is hypothesized to resemble the RexA/B system of coliphage Lambda, where activation of gp30 by phage infection stimulates the ion channel gp31 which causes membrane depolarization and loss of intracellular ATP, which in turn, causes abortive infection.
  
 ## Example of genomic structure
 
-TODO
-
-## Distribution of the system among prokaryotes
-
-TODO
-
-## Example of genomic structure
-
 The Butters_gp30_gp31 is composed of 2 proteins: Butters_gp30 and Butters_gp31.
 
 Here is an example found in the RefSeq database:

content/3.defense-systems/caprel.md

@@ -10,18 +10,21 @@ tableColumns:
     Activator: Direct
     Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
     PFAM: PF04607
+contributors: 
+  - Héloïse Georjon
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1038/s41586-022-05444-z
+  - doi: 10.1038/s41586-022-05444-z
 ---
 
 # 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* :ref{doi=10.1038/s41586-022-05444-z}. 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
 
-The CapRel system of Salmonella temperate phage SJ46 is normally found in a closed conformation, which is thought to maintain CapRel in an auto-inhibited state. However during phage SECPhi27 infection, binding of the major phage capsid protein (Gp57) to CapRel releases it from is inhibited state, allowing pyrophosphorylation of tRNAs by the toxin domain and resulting in translation inhibition. Other phage capsid proteins can be recognized by CapRel, as observed during infection by phage Bas8.
+The CapRel system of Salmonella temperate phage SJ46 is normally found in a closed conformation, which is thought to maintain CapRel in an auto-inhibited state. However during phage SECPhi27 infection, binding of the major phage capsid protein (Gp57) to CapRel releases it from is inhibited state, allowing pyrophosphorylation of tRNAs by the toxin domain and resulting in translation inhibition :ref{doi=10.1038/s41586-022-05444-z}. Other phage capsid proteins can be recognized by CapRel, as observed during infection by phage Bas8.
 
 
 Different CapRel homologues confer defense against different phages, suggesting variable phage specificity of CapRel system which seems to be mediated by the C-terminal region of CapRel. 
@@ -105,4 +108,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/disarm.md

@@ -5,11 +5,13 @@ tableColumns:
     article:
       doi: 10.1038/s41564-017-0051-0
       abstract: |
-        The evolutionary pressure imposed by phage predation on bacteria and archaea has resulted in the development of effective anti-phage defence mechanisms, including restriction–modification and CRISPR–Cas systems. Here, we report on a new defence system, DISARM (defence island system associated with restriction–modification), which is widespread in bacteria and archaea. DISARM is composed of five genes, including a DNA methylase and four other genes annotated as a helicase domain, a phospholipase D (PLD) domain, a DUF1998 domain and a gene of unknown function. Engineering the Bacillus paralicheniformis 9945a DISARM system into Bacillus subtilis has rendered the engineered bacteria protected against phages from all three major families of tailed double-stranded DNA phages. Using a series of gene deletions, we show that four of the five genes are essential for DISARM-mediated defence, with the fifth (PLD) being redundant for defence against some of the phages. We further show that DISARM restricts incoming phage DNA and that the B. paralicheniformis DISARM methylase modifies host CCWGG motifs as a marker of self DNA akin to restriction–modification systems. Our results suggest that DISARM is a new type of multi-gene restriction–modification module, expanding the arsenal of defence systems known to be at the disposal of prokaryotes against their viruses.
+        The evolutionary pressure imposed by phage predation on bacteria and archaea has resulted in the development of effective anti-phage defence mechanisms, including restriction-modification and CRISPR–Cas systems. Here, we report on a new defence system, DISARM (defence island system associated with restriction-modification), which is widespread in bacteria and archaea. DISARM is composed of five genes, including a DNA methylase and four other genes annotated as a helicase domain, a phospholipase D (PLD) domain, a DUF1998 domain and a gene of unknown function. Engineering the Bacillus paralicheniformis 9945a DISARM system into Bacillus subtilis has rendered the engineered bacteria protected against phages from all three major families of tailed double-stranded DNA phages. Using a series of gene deletions, we show that four of the five genes are essential for DISARM-mediated defence, with the fifth (PLD) being redundant for defence against some of the phages. We further show that DISARM restricts incoming phage DNA and that the B. paralicheniformis DISARM methylase modifies host CCWGG motifs as a marker of self DNA akin to restriction-modification systems. Our results suggest that DISARM is a new type of multi-gene restriction-modification module, expanding the arsenal of defence systems known to be at the disposal of prokaryotes against their viruses.
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00145, PF00176, PF00271, PF04851, PF09369, PF13091
+contributors:
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1038/s41467-022-30673-1
     - doi: 10.1038/s41564-017-0051-0
@@ -18,24 +20,24 @@ relevantAbstracts:
 # DISARM
 ## Description
 
-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).
+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 :ref{doi=10.1038/s41564-017-0051-0,10.1101/2021.12.28.474362}.
 
- 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](/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 :ref{doi=10.1038/s41564-017-0051-0}. This suggests a [Restriction-Modification](/defense-systems/rm)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM acts through a novel and uncharacterized molecular mechanism :ref{doi=10.1038/s41564-017-0051-0,10.1038/s41467-022-30673-1}.
 
 ## 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.
+DISARM allows phage adsorption but prevents phage replication. DISARM is thought to cause intracellular phage DNA decay :ref{doi=10.1038/s41564-017-0051-0}, 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 :ref{doi=10.1038/s41564-017-0051-0}. 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 :ref{doi=10.1038/s41564-017-0051-0}. 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 :ref{doi=10.1101/2021.12.28.474362}. 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).
+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 :ref{doi=10.1038/s41467-022-30673-1}. Moreover, the DrmAB complex seems to exhibit strong ATPase activity in the presence of unmethylated DNA, and reduced ATPase activity in the presence of a methylated DNA substrate :ref{doi=10.1038/s41467-022-30673-1}. 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 :ref{doi=10.1038/s41467-022-30673-1}.
 
 
 ## 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) :ref{doi=10.1038/s41564-017-0051-0}
 
 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). 
 
@@ -61,8 +63,19 @@ The system was detected in 201 different species.
 
 Proportion of genome encoding the DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
-
 ## Structure
+### Experimentally determined structure
+From :ref{doi=10.1038/s41586-023-06855-2} in *Serratia sp*:
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls: 
+    - /disarm/7s9v_DrmAB_1_1mer.cif
+    - /disarm/7s9w_DrmAB_1_1mer_dna.cif
+---
+::
+
 ### DISARM_1
 ##### Example 1
 
@@ -157,3 +170,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/dodola.md

@@ -20,11 +20,12 @@ relevantAbstracts:
 
 ## Description
 
-Dodola is named after a figure from Slavic mythology, often associated with rain and fertility. The Dodola defense system was first discovered through its common association with known defense systems, and characterized in B. subtilis, demonstrating its efficacy against the SPP1 phage. It is composed of two proteins, DolA and DolB
+Dodola is named after a figure from Slavic mythology, often associated with rain and fertility. The Dodola defense system was first discovered through its common association with known defense systems, and characterized in B. subtilis, demonstrating its efficacy against the SPP1 phage :ref{doi=10.1016/j.chom.2022.09.017}.
+Dodola is composed of two proteins, DolA and DolB. DolA contains a DUF6414 domain, and DolB contains a ClpB-like domain.
 
 ## Molecular mechanisms
 
-The molecular mechanism is unknown. DolA contains a DUF6414 domain, and DolB contains a ClpB-like domain.
+As far as we are aware, the molecular mechanism is unknown.
 
 ## Example of genomic structure
 

content/3.defense-systems/druantia.md

@@ -10,11 +10,22 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00145, PF00270, PF00271, PF04851, PF09369, PF14236
+contributors: 
+  - Lucas Paoli
 relevantAbstracts:
-    - doi: 10.1126/science.aar4120
+  - doi: 10.1126/science.aar4120
 ---
 
 # Druantia
+
+## Description
+
+The Druantia system was described by Doron et al. 2018 :ref{doi=10.1126/science.aar4120} and includes multiple subtypes, including type I (DruABCDE), type II (DruMFGE), and Type III (DruHE). Druantia is a particularly large system (~12 kb) and was named after the Gallic tree goddess. Type III was further tested by Wang et al. 2023 :ref{doi=10.1128/jvi.00599-23}.
+
+## Molecular mechanisms
+
+As far as we are aware, the molecular mechanism is unknown. 
+
 ## Example of genomic structure
 
 A total of 3 subsystems have been described for the Druantia system.

content/3.defense-systems/eleos.md

@@ -10,16 +10,26 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00350, PF01926, PF18709
+contributors: 
+    - Alba Herrero del Valle
 relevantAbstracts:
     - doi: 10.1016/j.chom.2022.09.017
+    - doi: 10.1101/2022.12.12.520048
 ---
 
 # Eleos
-The Eleos system was previously described as the Dynamins-like system in (Millman et al, 2022).
+
+## Description
+
+\The Eleos (for the greek goddess of mercy) system was previously described as the Dynamins-like system in :ref{doi=10.1016/j.chom.2022.09.017}. It is formed by the LeoA and LeoBC proteins. LeoBC has been found to be analogous to GIMAPs (GTPases immunity-associated proteins), that are interferon inducible :ref{doi=10.1101/2022.12.12.520048}. LeoA in *E. coli* ETEC H10407 localises to the periplasm and has been suggested to potientiate bacterial virulence. Its crystal structure has been solved :ref{doi=10.1371/journal.pone.0107211}. Eleos from *Bacillus vietnamensis* NBRC 101237 has been found to protect against jumbo-phages in *Bacillus subtilis* :ref{doi=10.1016/j.chom.2022.09.017}.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown. 
 
 ## Example of genomic structure
 
-The Eleos is composed of 4 proteins: LeoA, LeoBC, LeoB and LeoC.
+The Eleos system is composed of 2 proteins: LeoA and, LeoBC. Sometimes, the system is in three genes: LeoA, LeoB and LeoC.
 
 Here is an example found in the RefSeq database:
 
@@ -40,6 +50,18 @@ Proportion of genome encoding the Eleos system for the 14 phyla with more than 5
 
 
 ## Structure
+### Experimentaly determined structure
+From :ref{doi=10.1371/journal.pone.0107211} in *Escherichia coli* (ETEC) strain H10407:
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /eleos/4aur_LeoA_1mer.pdb
+---
+::
+
+
+
 ### Eleos
 ##### Example 1
 
@@ -79,4 +101,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-