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/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/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>
-

content/3.defense-systems/fs_sma.md

@@ -7,27 +7,34 @@ tableColumns:
       abstract: |
         Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
     PFAM: PF02452
+contributors:
+    - Héloïse Georjon
 relevantAbstracts:
-    - doi: 10.1016/j.cell.2022.07.014
+  - doi: 10.1016/j.cell.2022.07.014
 ---
 
 # FS_Sma
 
-## To do 
+## Description
+SMA (single-protein MazF-like antiphage system) was identified in a phage-inducible chromosomal island (PICI) found in *Staphylococcus aureus* :ref{doi=10.1016/j.cell.2022.07.014}. SMA was shown to inhibit phage infection and to inhibit the formation of new virions after prophage induction.
+
+## Molecular mechanisms
+The SMA protein comprises a domain analogous to MazF. MazF a protein that is normally part of the MazEF toxin-antitoxin systems, in which MazF is a toxic endoribonuclease that targets mRNA :ref{doi=10.1016/s1097-2765(03)00402-7}.
+As far as we are aware, the precise molecular mechanism of SMA is unknown.
 
 ## Example of genomic structure
 
-The FS_Sma is composed of 1 protein: Sma.
+The Sma is composed of 1 protein: Sma.
 
 Here is an example found in the RefSeq database:
 
 ![fs_sma](/fs_sma/FS_Sma.svg){max-width=750px}
 
-The FS_Sma system in *Staphylococcus aureus* (GCF_022869625.1, NZ_CP064365) is composed of 1 protein: Sma (WP_000041883.1) 
+The Sma system in *Staphylococcus aureus* (GCF_022869625.1, NZ_CP064365) is composed of 1 protein: Sma (WP_000041883.1) 
 
 ## Distribution of the system among prokaryotes
 
-Among the 22,803 complete genomes of RefSeq, the FS_Sma is detected in 578 genomes (2.53 %).
+Among the 22,803 complete genomes of RefSeq, the Sma is detected in 578 genomes (2.53 %).
 
 The system was detected in 20 different species.
 

content/3.defense-systems/gaps6.md

@@ -6,14 +6,37 @@ tableColumns:
       doi: 10.1101/2023.03.28.534373
       abstract: |
         Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of defense islands may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
-relevantAbstracts:
+contributors:
+    - Jean Cury
+relevantAbstract:
     - doi: 10.1101/2023.03.28.534373
 ---
 
 # GAPS6
 
-## To do 
+## Description
 
+<<<<<<< content/3.defense-systems/gaps6.md
+GAPS (GMT-encoded Anti-Phage System) antiphage systems were discovered on newly described Gamma-Mobile-Trio elements. 
+
+GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.
+
+## Molecular mechanism
+
+GAPS6b is essential for the defense phenotype, however it is not known whether GAPS6b could be sufficient.
+GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.
+
+## Example of genomic structure
+
+TODO
+
+## Distribution
+
+TODO
+
+## Predicted structure
+
+=======
 ## Example of genomic structure
 
 The GAPS6 is composed of 2 proteins: GAPS6a and GAPS6b.
@@ -37,6 +60,7 @@ Proportion of genome encoding the GAPS6 system for the 14 phyla with more than 5
 
 
 ## Structure
+>>>>>>> content/3.defense-systems/gaps6.md
 ### GAPS6
 ##### Example 1
 
@@ -68,9 +92,7 @@ end
         Expressed_0
 end
     subgraph Title4[Phage infected]
-        T7
         T4
-        P1-vir
         Lambda-vir
 end
     style Title1 fill:none,stroke:none,stroke-width:none
@@ -78,4 +100,7 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+<<<<<<< content/3.defense-systems/gaps6.md
+=======
 
+>>>>>>> content/3.defense-systems/gaps6.md

content/3.defense-systems/lamassu-fam.md

@@ -30,7 +30,7 @@ Lamassu has been suggested to be a large family of defense systems, that can be
 
 These systems all encode the *lmuB* gene, and in most cases also comprise *lmuC*. In addition to these two core genes, Lamassu systems of various subtypes encode a third protein, hypothesized to be the Abi effector protein :ref{doi=10.1101/2022.05.11.491447}. This effector  can be proteins encoding endonuclease domains, SIR2-domains, or even hydrolase domains :ref{doi=10.1016/j.chom.2022.09.017}. Systems of the extended Lamassu-family can be found in 10% of prokaryotic genomes :ref{doi=10.1016/j.chom.2022.09.017}.
 
-Lamassu were also described as DdmABC in *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y,10.1101/2022.11.18.517080}. They were found to be antiplasmids and thus to eliminate plasmids from seventh pandemic *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y}.
+Lamassu were also described as DdmABC in *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y,10.1101/2022.11.18.517080}. They were found to be antiplasmids and thus to eliminate plasmids from seventh pandemic *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y}. The DdmABC system corresponds to a Lamassu-Fam Cap4 nuclease system.
 
 ## Molecular mechanism
 

content/3.defense-systems/panchino_gp28.md

@@ -7,13 +7,21 @@ tableColumns:
       abstract: |
         Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
     PFAM: PF01170, PF02384, PF13588
+contributors: 
+  - Lucas Paoli
 relevantAbstracts:
-    - doi: 10.1038/nmicrobiol.2016.251
+  - doi: 10.1038/nmicrobiol.2016.251
 ---
 
 # Panchino_gp28
 
-## To do 
+## Description
+
+The Panchino gp28 defense system was described in :ref{doi=10.1038/nmicrobiol.2016.251} and is named after the Panchino prophage (on which it is located) and the corresponding gene. It is a single gene system.
+
+## Molecular mechanisms
+
+Panchino gp28 is act as a single gene type I restriction system :ref{doi=10.1038/nmicrobiol.2016.251,10.1016/j.mib.2023.102321}.
 
 ## Example of genomic structure
 
@@ -79,4 +87,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/rnlab.md

@@ -10,11 +10,22 @@ tableColumns:
     Activator: Direct
     Effector: Nucleic acid degrading
     PFAM: PF15933, PF15935, PF18869, PF19034
+contributors: 
+  - Lucas Paoli
 relevantAbstracts:
-    - doi: 10.1534/genetics.110.121798
+  - doi: 10.1534/genetics.110.121798
 ---
 
 # RnlAB
+
+## Description
+
+RnlAB is a type II toxin-antitoxin system, in which RnlA is the toxin and RnlB the antitoxin :ref{doi=10.1534/genetics.110.121798}.
+
+## Molecular mechanisms
+
+The RnlA toxin has a RNase activity. RnlB (formerly yfjO) is the antitoxin and suppresses the RNase LS activity :ref{doi=10.1534/genetics.110.121798}.
+
 ## Example of genomic structure
 
 The RnlAB is composed of 2 proteins: RnlA and RnlB.
@@ -75,4 +86,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/rst_duf4238.md

@@ -10,11 +10,22 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF14022
-relevantAbstracts:
-    - doi: 10.1016/j.chom.2022.02.018
+contributors:
+    - Ernest Mordret
+relevant abstracts:
+    - 10.1016/j.chom.2022.02.018
 ---
 
 # Rst_DUF4238
+
+## Description
+
+Rst_DUF4238 is a single gene system found in a screen of phage and phage-satellites antiviral hotspots :ref{doi=10.1016/j.chom.2022.02.018}. It was shown to provide E.coli with a strong resistance against phage T7.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The Rst_DUF4238 is composed of 1 protein: DUF4238.
@@ -75,4 +86,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/rst_rt-nitrilase-tm.md

@@ -10,11 +10,25 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00078
+contributors:
+    - Hugo Vaysset
 relevantAbstracts:
     - doi: 10.1016/j.chom.2022.02.018
+    - doi: 10.1093/nar/gkac467
 ---
 
-# Rst_RT-nitrilase-Tm
+# RT-nitrilase-Tm
+
+## Description
+RT-nitrilase-Tm (also named UG5-large) is a two genes defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.01} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae). 
+
+The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase) ; the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}.
+
+The presence of a RT protein allows to draw a parallel between this system and the [DRT defense system](/defense-systems/drt).
+
+## Molecular mechanism
+As far as we are aware, the molecular mechanism is unknown. 
+
 ## Example of genomic structure
 
 The Rst_RT-nitrilase-Tm is composed of 2 proteins: RT and RT-Tm.