.gitlab-ci.yml

@@ -279,14 +279,14 @@ get-zotero:
   rules:
     - if: $CI_COMMIT_BRANCH == "main"
 
-get-pfam:
-  extends: .df-wiki-cli-run
-  stage: get-data
-  script:
-    - df-wiki-cli pfam --output public/pfam-a-hmm.csv
-  artifacts:
-    paths:
-      - public/pfam-a-hmm.csv
+# get-pfam:
+#   extends: .df-wiki-cli-run
+#   stage: get-data
+#   script:
+#     - df-wiki-cli pfam --output public/pfam-a-hmm.csv
+#   artifacts:
+#     paths:
+#       - public/pfam-a-hmm.csv
   # rules:
   #   - if: $CI_COMMIT_BRANCH == "main"
 
@@ -319,7 +319,7 @@ build:dev:wiki:
   extends: .build
   needs:
     - set-meili-env:dev
-    - get-pfam
+    # - get-pfam
   variables:
     BASE_URL: /wiki/
   rules:
@@ -331,7 +331,7 @@ build:prod:wiki:
   needs:
     - set-meili-env:prod
     - get-zotero
-    - get-pfam
+    # - get-pfam
   variables:
     BASE_URL: /wiki/
   rules:

content/3.defense-systems/nixi.md

@@ -3,15 +3,25 @@ title: NixI
 layout: article
 tableColumns:
     article:
-      doi: 10.1101/2021.07.12.452122
+      doi: 10.1093/nar/gkac002
       abstract: |
-        PLEs are phage parasites integrated into the chromosome of epidemic Vibrio cholerae. In response to infection by its viral host ICP1, PLE excises, replicates and hijacks ICP1 structural components for transduction. Through an unknown mechanism PLE prevents ICP1 from transitioning to rolling circle replication (RCR), a prerequisite for efficient packaging of the viral genome. Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1’s genome as it transitions to RCR. NixI-dependent cleavage sites appear in ICP1’s genome during infection of PLE(+) V. cholerae. Purified NixI demonstrates in vitro specificity for sites in ICP1’s genome and NixI activity is enhanced by a putative specificity determinant co-expressed with NixI during phage infection. Importantly, NixI is sufficient to limit ICP1 genome replication and eliminate progeny production. We identify distant NixI homologs in an expanded family of putative phage satellites in Vibrios that lack nucleotide homology to PLEs but nonetheless share genomic synteny with PLEs. More generally, our results reveal a previously unknown mechanism deployed by phage parasites to limit packaging of their viral hosts’ genome and highlight the prominent role of nuclease effectors as weapons in the arms race between antagonizing genomes.
+        PLEs (phage-inducible chromosomal island-like elements) are phage parasites integrated into the chromosome of epidemic Vibrio cholerae. In response to infection by its viral host ICP1, PLE excises, replicates and hijacks ICP1 structural components for transduction. Through an unknown mechanism, PLE prevents ICP1 from transitioning to rolling circle replication (RCR), a prerequisite for efficient packaging of the viral genome. Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1’s genome as it transitions to RCR. NixI-dependent cleavage sites appear in ICP1’s genome during infection of PLE(+) V. cholerae. Purified NixI demonstrates in vitro nuclease activity specifically for sites in ICP1’s genome and we identify a motif that is necessary for NixI-mediated cleavage. Importantly, NixI is sufficient to limit ICP1 genome replication and eliminate progeny production, representing the most inhibitory PLE-encoded mechanism revealed to date. We identify distant NixI homologs in an expanded family of putative phage parasites in vibrios that lack nucleotide homology to PLEs but nonetheless share genomic synteny with PLEs. More generally, our results reveal a previously unknown mechanism deployed by phage parasites to limit packaging of their viral hosts’ genome and highlight the prominent role of nuclease effectors as weapons in the arms race between antagonizing genomes.
     Sensor: Unknown
     Activator: Unknown
     Effector: Nucleic acid degrading
+contributors:
+    - Marian Dominguez Mirazo 
+relevantAbstracts:
+    - doi: 10.1093/nar/gkac002
 ---
 
 # NixI
+## Description
+Phage-inducible chromosomal island-like elements (PLEs) are chromosomally-integrated phage parasites described in *Vibrio cholerae* :ref{doi=10.7554/eLife.53200}. PLEs excise in response to infection by phage ICP1 and halt its progeny production. PLE halts ICP1 infection by means of redirecting virion packaging and interfiring with ICP1 genome replication :ref{doi=10.1093/nar/gkz1005}. NixI is a PLE-encoded nuclease that nicks the ICP1 genome at specific sites preventing transition to the rolling circle replication (RCR) :ref{doi=10.1093/nar/gkac002}. 
+
+## Molecular mechanisms
+The NixI endonuclease cleaves the ICP1 genome at the GNAANCTT motif :ref{doi=10.1093/nar/gkac002}. It creates nicks and does not cause double stranded breaks ref:{doi=10.1093/nar/gkac002}. 
+
 ## Example of genomic structure
 
 The NixI system is composed of 2 proteins: NixI and, Stix.
@@ -67,12 +77,3 @@ 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: 10.1101/2021.07.12.452122
-
----
-::

content/3.defense-systems/pd-t4-7.md

@@ -9,9 +9,23 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors:
+    - Ernest Mordret  
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T4-7
+
+## Description
+
+PD-T4-7 is a single gene system. Its protein contains a RelE domain and a phage Sheath. 
+protect against T2,T4,T6
+
+## Molecular mechanism
+
+Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism
+
 ## Example of genomic structure
 
 The PD-T4-7 system is composed of one protein: PD-T4-7.
@@ -69,12 +83,3 @@ 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: 10.1038/s41564-022-01219-4
-
----
-::

content/3.defense-systems/psyrta.md

@@ -10,9 +10,41 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00270, PF00271, PF02481, PF04851, PF18306
+contributors:
+    - Ernest Mordret
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.09.017
+    - doi: 10.1016/j.molcel.2013.02.002
+    - doi: 10.1371/journal.ppat.1005317
 ---
 
 # PsyrTA
+
+## Description
+
+Originally found in a high throughput shotgun cloning of bacterial fragments in E. coli looking for Toxin-Antitoxin pairs. PsyrTA is composed of two proteins, PsyrT, the toxin, is a RecQ family DNA helicase, and PsyrA, the antitoxin, was shown to be a Nucleotide-binding protein. Note that that system is sometimes called RqlHI :ref{doi=10.1371/journal.ppat.1005317}, where RqlH refers to PsyrT and RqlI to PsyrA
+
+## Molecular mechanisms
+
+from :ref{doi=10.1016/j.molcel.2013.02.002} :
+
+> The psyrT shares homology with domains of the RecQ helicase,
+> a family of proteins implicated in DNA repair (Bernstein et al.,
+> 2010); and the antitoxin of the same system, psyrA, has a nucle-
+> otide binding domain (COG0758) that was previously described
+> in proteins involved in DNA uptake
+
+
+from :ref{doi=10.1016/j.chom.2022.09.017} :
+
+> Both systems encode an antitoxin
+> with homology to DprA, a single-stranded DNA (ssDNA)-binding
+> protein known to be involved in DNA transformation (Mortier-
+> Barrière et al., 2007). The toxin contains a phosphoribosyl trans-
+> ferase (PRTase) domain, which was previously found in effectors
+> of retron abortive infection systems "
+
+
 ## Example of genomic structure
 
 The PsyrTA system is composed of 2 proteins: PsyrT and, PsyrA.
@@ -77,14 +109,5 @@ 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: 10.1016/j.chom.2022.09.017
-    - doi: 10.1016/j.molcel.2013.02.002
-
----
 ::
 

content/3.defense-systems/sefir.md

@@ -10,16 +10,26 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF08357, PF13676
+contributors: 
+  - Helena Shomar
+  - Marie Guillaume
+relevantAbstracts:
+  - doi: 10.1016/j.chom.2022.09.017
+  - doi: 10.1016/S0968-0004(03)00067-7
+
 ---
 
 # SEFIR
 ## Description
-The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes, were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in *Bacillus sp.* NIO-1130 against phage phi29 [1]. 
+The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes, were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in *Bacillus sp.* NIO-1130 against phage Phi29 :ref{doi=10.1016/j.chom.2022.09.017}. 
+
+Bacterial SEFIR domains were named after their eukaryotic homologs which were already known to be part of several eukayrotic immune proteins (e.g. SEFs and Interleukin-17 Receptors):ref{doi=10.1016/S0968-0004(03)00067-7}.
+
+Homologs of SEFIR domain proteins were also found in archaeal species : _Methanosarcina barkeri_ and _Methanosarcina mazei_ :ref{doi=10.1016/j.chom.2022.09.017}.  
 
-Bacterial SEFIR domains were named after their eukaryotic homologs which were already known to be part of several eukayrotic immune proteins (e.g. SEFs and Interleukin-17 Receptors) [2].
 
 ## Molecular mechanism
-SEFIR was shown to protect against phage infection through an abortive infection mechanism *via* NAD+ depletion. This is similar to what can be observed in other defense systems containing a TIR domain which shares homology with the SEFIR domain (in eukaryotes, both domains are part of the STIR super family) [1].
+SEFIR was shown to protect against phage infection through an abortive infection mechanism *via* NAD+ depletion. This is similar to what can be observed in other defense systems containing a TIR domain which shares homology with the SEFIR domain (in eukaryotes, both domains are part of the STIR super family) :ref{doi=10.1016/j.chom.2022.09.017}.
 
 ## Example of genomic structure
 
@@ -76,18 +86,5 @@ 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: 10.1016/j.chom.2022.09.017
-
----
-::
-
 
-## References
-[1] Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556-1569.e5 (2022).
-[2] Novatchkova, M., Leibbrandt, A., Werzowa, J., Neubüser, A., & Eisenhaber, F. (2003). The STIR-domain superfamily in signal transduction, development and immunity. _Trends in biochemical sciences_, _28_(5), 226-229.