content/1.help/2.Contributing-Wiki.md

@@ -98,6 +98,16 @@ dataUrls:
 ::
 ```
 
+
+**3. To edit the Experimental validation section**
+
+This part is a bit tricky to edit. Your first option is to create an issue or send us an email and we'll do it on our side. You need to provide the reference, in which bug it was discovered, in which bug it was expressed and against which phages it was effective.
+
+The second option is that you can try within this live editor : https://mermaid.live/
+
+You can copy paste everything that is within `<mermaid></mermaid>` tags in the editor field of the [live editor](https://mermaid.live/), it should reproduce what you site on the website. From there you can try to modify it until you get what you want.
+Here is the documentation about mermaid (the software behind this syntax) : https://mermaid.js.org/intro/
+
 **Custom containers:**
 
 Custom containers can be defined by their types, titles, and contents.

content/3.defense-systems/abic.md

@@ -10,13 +10,29 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF16872
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1128/jb.174.22.7463-7469.1992
 ---
 
 # AbiC
 
+## Description
+
+AbiC was discovered in *Lactococcus lactis* plasmid in 1992 :ref{doi=10.1128/jb.174.22.7463-7469.1992}
+
+AbiC 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}. AbiC is classified as abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+AbiC is a single gene system composed of the protein AbiC.  
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
+
 ## Example of genomic structure
 
 The AbiC is composed of 1 protein: AbiC.

content/3.defense-systems/abid.md

@@ -10,13 +10,29 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF07751
+contributors:
+  - Marian Dominguez-Mirazo
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1023/A:1002027321171
     - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1128/aem.61.5.2023-2026.1995
 ---
 
 # AbiD
 
+## Description
+
+AbiD is a single gene system system discovered in May 1995 in the plasmid pBF61 of *Lactococcus lactis* :ref{doi=10.1128/aem.61.5.2023-2026.1995}. An homolog of AbiD, named AbiD1 was discovered in July 1995 :ref{doi=10.1128/jb.177.13.3818-3823.1995}.
+
+AbiD 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 a possible abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
+
+This antiphage defense system is very close to AbiD1 and AbiF :ref{doi=10.1128/aem.61.12.4321-4328.1995} and is categorized as the same system. Furthermore, AbiD is also detected as the [Abi2](/defense-systems/abi2) system.
+
+### Molecular mechanism
+
+For AbiD1 :ref{doi=10.1128/jb.177.13.3824-3829.1995} ([AAA79209](https://www.ncbi.nlm.nih.gov/protein/AAA79209)), the expression of the protein is toxic to the bacteria and is therefore highly regulated. Expression of the protein is triggered by the orf1 of phage bIL66 which results in inhibition of the phage RuvC-like endonuclease activity and stops phage multiplication.
+
 ## Example of genomic structure
 
 The AbiD is composed of 1 protein: AbiD.
@@ -79,4 +95,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/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/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/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/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/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/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/gao_her.md

@@ -10,8 +10,12 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF01935, PF10412, PF13289
+contributors: 
+  - To do
 relevantAbstracts:
-    - doi: 10.1126/science.aba0372
+  - doi: 10.1126/science.aba0372
+  - doi: 10.1016/j.molcel.2023.11.007
+  - doi: 10.1016/j.molcel.2023.11.010
 ---
 
 # Gao_Her
@@ -42,6 +46,31 @@ Proportion of genome encoding the Gao_Her system for the 14 phyla with more than
 
 
 ## Structure
+
+### Experimentaly determined structure
+
+From :ref{doi=10.1016/j.molcel.2023.11.010} in *Escherichia coli*:
+
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /gao_her/8j4u_EcHerA_SIR2_6_12mer.cif
+---
+::
+
+From :ref{doi=10.1016/j.molcel.2023.11.007} in *Escherichia coli*:
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls: 
+    - /gao_her/8sxx_EcSIR2_12mer.pdb
+    - /gao_her/8sxx_EcHerA_SIR2_5_12mer.cif
+    - /gao_her/8uae_EcHerA_SIR2_6_12mer_atpgamas.cif
+    - /gao_her/8uaf_EcHerA_SIR2_6_12mer_nad.cif
+---
+::
+
 ### Gao_Her_DUF
 ##### Example 1
 

content/3.defense-systems/gao_iet.md

@@ -15,6 +15,17 @@ relevantAbstracts:
 ---
 
 # Gao_Iet
+
+## Description
+
+Gao_Iet or Iet or IetAS was discovered in 2020 among other defense systems by :ref{doi=10.1126/science.aba0372}.
+
+The Iet system is composed of two proteins: IetA (an ATPase) and IetS (a protease) :ref{doi=10.1126/science.aba0372}.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The Gao_Iet is composed of 2 proteins: IetA and IetS.

content/3.defense-systems/gao_ppl.md

@@ -9,11 +9,22 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors:
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1126/science.aba0372
+  - doi: 10.1126/science.aba0372
 ---
 
 # Gao_Ppl
+
+## Description
+
+Gao_Ppl or Ppl system is a single gene system. This system was discovered among others in :ref{doi=10.1126/science.aba0372}. This single gene system is described with 2 different domains: PHP (Polymerase and Histidinol Phosphatase) which is a putative nuclease and an ATPase domain.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The Gao_Ppl is composed of 1 protein: PplA.
@@ -78,3 +89,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/gaps2.md

@@ -7,13 +7,21 @@ 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
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1101/2023.03.28.534373
+  - doi: 10.1101/2023.03.28.534373
 ---
 
 # GAPS2
+## Description
+The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym.
 
-## To do 
+GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.
+
+## Molecular mechanisms
+
+As far as we are aware, the molecular mechanism is unknown.
 
 ## Example of genomic structure
 

content/3.defense-systems/rosmerta.md

@@ -24,11 +24,11 @@ The RosmerTA system was found to have antiviral activity and named after Gallo-R
 
 ## Molecular mechanisms
 
-The RosmerTA system encodes a Zn-peptidase and a toxin of unknown function :ref{doi=10.1016/j.chom.2022.09.017} and was later found to induce membrane depolarization :ref{doi=10.1073/pnas.2305393120}.
+The RosmerTA system encodes a Zn-peptidase and a toxin of unknown function :ref{doi=10.1016/j.chom.2022.09.017}. One toxin representative has been found to induce membrane depolarization :ref{doi=10.1073/pnas.2305393120}.
 
 ## Example of genomic structure
 
-The RosmerTA is composed of 2 proteins: RmrT and RmrA.
+The RosmerTA is composed of 2 proteins: RmrT and RmrA. The toxin can vary in sequence and structure.
 
 Here is an example found in the RefSeq database:
 
@@ -88,3 +88,27 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+<mermaid>
+graph LR;
+    Ernits_2023[<a href='https://www.pnas.org/doi/10.1073/pnas.2305393120'>Ernits et al., 2023</a>] --> Origin_0
+    Origin_0[Gordonia phage Kita 
+<a href='https://www.ncbi.nlm.nih.gov/protein/YP_009301394.1/'>YP_009301394.1</a>, <a href='https://www.ncbi.nlm.nih.gov/protein/YP_009301394.1'>YP_009301394.1</a>] --> Expressed_0[Escherichia coli]
+    Expressed_0[Escherichia coli] ----> Bas54 and Bas59
+    subgraph Title1[Reference]
+        Ernits_2023
+end
+    subgraph Title2[System origin]
+        Origin_0
+end
+    subgraph Title3[Expression species]
+        Expressed_0
+end
+    subgraph Title4[Phage infected]
+        Bas54 
+        Bas59
+end
+    style Title1 fill:none,stroke:none,stroke-width:none
+    style Title2 fill:none,stroke:none,stroke-width:none
+    style Title3 fill:none,stroke:none,stroke-width:none
+    style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>

content/3.defense-systems/rst_gop_beta_cll.md

@@ -10,11 +10,29 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF14350
+contributors:
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1016/j.chom.2022.02.018
 ---
 
 # Rst_gop_beta_cll
+
+## Description
+
+The gop-beta-cll system was shown to have an antiphage activity in 2022 :ref{doi=10.1016/j.chom.2022.02.018} against Escherichia coli phage lambda and P1.
+
+The gop-beta-cll was first described as a nonessential region of the bacteriophage P4 :ref{doi=10.1128/jvi.64.1.24-36.1990}.
+
+This system is composed of 3 genes: gop, beta and cll.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
+The production of the gop protein without beta is toxic :ref{doi=10.1128/jvi.64.1.24-36.1990} suggesting a toxin antitoxin mechanism :ref{doi=10.1016/j.chom.2022.02.018}.
+
+
 ## Example of genomic structure
 
 The Rst_gop_beta_cll is composed of 3 proteins: beta, cll and gop.

content/3.defense-systems/septu.md

@@ -10,13 +10,36 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF13175, PF13304, PF13476
+contributors: 
+  - Florian Tesson
 relevantAbstracts:
     - doi: 10.1016/j.cell.2020.09.065
     - doi: 10.1093/nar/gkab883
     - doi: 10.1126/science.aar4120
+    - doi: 10.1038/s41594-023-01172-8
 ---
-
 # Septu
+
+## Description
+The Septu defense system was discovered in 2018 in *Bacillus* :ref{doi=10.1126/science.aar4120}. The name of the system is related to Septu (or Sopdu) the ancient Egypt god of the sky and eastern border regions.
+
+The Septu defense system is composed of two proteins PtuA and PtuB: PtuA encoding for an ATPase (AAA15/AAA21) and PtuB with an HNH endonuclease domain.
+
+After the discovery of Septu, two studies discovered separately another form of Septu :ref{doi=10.1093/nar/gkab883,10.1016/j.cell.2020.09.065}. This new subtype encodes a third protein with a reverse transcriptase domain. This system is either referred as Septu Type II :ref{doi=10.1093/nar/gkab883} or as [Retron](/defense-systems/retron) subtype RT-I-A :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.cell.2020.09.065}.
+
+The Septu defense system is part of a large category of systems that encodes the AAA15/21 ABC ATPase :ref{doi=10.1111/mmi.15074}.
+
+## Molecular mechanism
+The structure of the PtuAB complex shows a stoichiometry of 6:2 (A:B) :ref{doi=10.1038/s41594-023-01172-8}.
+The 6 PtuA proteins form a horseshoe-like trimer of dimers.
+The CTD terminal domains of the external PtuA bind to the PtuB endonuclease.
+
+The PtuB is an HNH endonuclease like  Cas9 :ref{doi=10.1016/j.cell.2014.02.001} that cleaves the phage DNA :ref{doi=10.1038/s41594-023-01172-8}.
+
+Interestingly, the ATPase domain of PtuA has no ATPase activity. However, the experimentally determined structure shows that 4 ATPs bind inside the PtuA hexamer :ref{doi=10.1038/s41594-023-01172-8}. The authors then show that the endonuclease activity of PtuAB is down-regulated by ATP in a concentration-dependent manner.
+
+Authors :ref{doi=10.1038/s41594-023-01172-8} hypothesize that the PtuAB complex is inactive in noninfected cells by the physiological concentration of ATP. During phage infection, the pool of ATP can be depleted leading to the activation of the PtuAB complex and the phage DNA cleavage by PtuB HNH endonuclease.
+
 ## Example of genomic structure
 
 The Septu is composed of 2 proteins: PtuA and PtuB.
@@ -40,6 +63,21 @@ Proportion of genome encoding the Septu system for the 14 phyla with more than 5
 
 
 ## Structure
+
+### Experimentaly determined structure
+
+From :ref{doi=10.1038/s41594-023-01172-8} in *Escherichia coli*:
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls: 
+    - /septu/8ee4_EcPtuA_6mer.pdb
+    - /septu/8ee7_EcPtuAB_2_1mer.pdb
+    - /septu/8eea_EcPtuAB_6_3mer.pdb
+---
+::
+
 ### Septu
 ##### Example 1
 
@@ -52,6 +90,7 @@ dataUrls:
 
 ---
 ::
+
 ##### Example 2
 
 ::molstar-pdbe-plugin
@@ -76,22 +115,32 @@ graph LR;
     Origin_1[Bacillus weihenstephanensis 
 <a href='https://ncbi.nlm.nih.gov/protein/ABY44616.1'>ABY44616.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ABY44615.1'>ABY44615.1</a>] --> Expressed_1[Bacillus subtilis]
     Expressed_1[Bacillus subtilis] ----> SBSphiC & SpBeta
+    Yi_2024[<a href='https://doi.org/10.1038/s41594-023-01172-8'>Yi et al., 2024</a>] --> Origin_2
+    Origin_2[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/AIL15948.1'>AIL15948.1</a>, <a href:'https://ncbi.nlm.nih.gov/protein/AIL15172.1>AIL15172.1</
+a>] --> Expressed_2[Escherichia coli]
+    Expressed_2[Escherichia coli] ----> T5 & T7
     subgraph Title1[Reference]
         Doron_2018
+        Yi_2024
 end
     subgraph Title2[System origin]
         Origin_0
         Origin_1
+        Origin_2
 end
     subgraph Title3[Expression species]
         Expressed_0
         Expressed_1
+        Expressed_2
 end
     subgraph Title4[Phage infected]
         SBSphiJ
         SBSphiC
         SBSphiC
         SpBeta
+        T5
+        T7
 end
     style Title1 fill:none,stroke:none,stroke-width:none
     style Title2 fill:none,stroke:none,stroke-width:none

layouts/db.vue

@@ -4,7 +4,7 @@ const { page } = useContent();
 
 </script>
 <template>
-    <LayoutWrapper :title="page?.title" :fluid="true" :toc="false" :edit="false" :nav-drawer="false">
+    <LayoutWrapper :title="page?.title" :fluid="true" :toc="false" :edit="false" :nav-drawer="true">
         <slot />
     </LayoutWrapper>
 </template>