Merge branch 'main' into dev

content/3.defense-systems/bunzi.md

@@ -9,9 +9,21 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors: 
+  - Aude Bernheim
+relevantAbstracts:
+  - doi:10.1016/j.chom.2022.09.017
 ---
 
 # Bunzi
+
+## Description
+The Bunzi system is composed of 2 proteins: BnzB and, BnzA. Bunzi is a serpent water spirit and goddess of rain in traditional Kongo religion. 
+There was some homology noted with PFAMS Pfam08000, Pfam05099, Pfam07889 and a TerB domain :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 Bunzi system is composed of 2 proteins: BnzB and, BnzA.
@@ -75,12 +87,4 @@ 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
-
----
-::

content/3.defense-systems/dazbog.md

@@ -9,9 +9,21 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.09.017
+contributors : 
+    - Aude Bernheim
 ---
 
 # Dazbog
+
+## Description
+
+The Dazbog system is composed of 2 proteins: DzbB and, DzbA. Dazbog was name after a slavic god, likely a solar deity.DzbA has homology to Pfam14072 :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 Dazbog system is composed of 2 proteins: DzbB and, DzbA.
@@ -102,12 +114,5 @@ 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
 
----
-::

content/3.defense-systems/dctpdeaminase.md

@@ -3,25 +3,31 @@ title: dCTPdeaminase
 layout: article
 tableColumns:
     article:
-      doi: 10.1016/j.cell.2021.09.031
+      doi: 10.1038/s41564-022-01158-0
       abstract: |
-        The cyclic pyrimidines 3',5'-cyclic cytidine monophosphate (cCMP) and 3',5'-cyclic uridine monophosphate (cUMP) have been reported in multiple organisms and cell types. As opposed to the cyclic nucleotides 3',5'-cyclic adenosine monophosphate (cAMP) and 3',5'-cyclic guanosine monophosphate (cGMP), which are second messenger molecules with well-established regulatory roles across all domains of life, the biological role of cyclic pyrimidines has remained unclear. Here we report that cCMP and cUMP are second messengers functioning in bacterial immunity against viruses. We discovered a family of bacterial pyrimidine cyclase enzymes that specifically synthesize cCMP and cUMP following phage infection and demonstrate that these molecules activate immune effectors that execute an antiviral response. A crystal structure of a uridylate cyclase enzyme from this family explains the molecular mechanism of selectivity for pyrimidines as cyclization substrates. Defense systems encoding pyrimidine cyclases, denoted here Pycsar (pyrimidine cyclase system for antiphage resistance), are widespread in prokaryotes. Our results assign clear biological function to cCMP and cUMP as immunity signaling molecules in bacteria.
-    Sensor: Monitoring of the host cell machinery integrity
-    Activator: Direct
+        DNA viruses and retroviruses consume large quantities of deoxynucleotides (dNTPs) when replicating. The human antiviral factor SAMHD1 takes advantage of this vulnerability in the viral lifecycle, and inhibits viral replication by degrading dNTPs into their constituent deoxynucleosides and inorganic phosphate. Here, we report that bacteria use a similar strategy to defend against bacteriophage infection. We identify a family of defensive bacterial deoxycytidine triphosphate (dCTP) deaminase proteins that convert dCTP into deoxyuracil nucleotides in response to phage infection. We also identify a family of phage resistance genes that encode deoxyguanosine triphosphatase (dGTPase) enzymes, which degrade dGTP into phosphate-free deoxyguanosine and are distant homologues of human SAMHD1. Our results suggest that bacterial defensive proteins deplete specific deoxynucleotides (either dCTP or dGTP) from the nucleotide pool during phage infection, thus starving the phage of an essential DNA building block and halting its replication. Our study shows that manipulation of the dNTP pool is a potent antiviral strategy shared by both prokaryotes and eukaryotes..
+    Sensor: Host integrity monitoring
+    Activator: Unknown
     Effector: Nucleotide modifying
     PFAM: PF00383, PF14437
----
+contributors:
+    - Nathalie Bechon
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01162-4
+    - doi: 10.1038/s41564-022-01158-0
+
+
 
 # dCTPdeaminase
 ## Description
-dCTPdeaminase is a family of systems. dCTPdeaminase from Escherichia coli has been shown to provide resistance against various lytic phages when express heterologously in another Escherichia coli.
+dCTPdeaminase is a family of systems. dCTPdeaminase from Escherichia coli has been shown to provide resistance against various lytic phages when expressed heterologously in another Escherichia coli by degrading the pool of dCTP available for phage DNA replication.
 This system is mostly found in Proteobacteria but a few examples also exist in Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Planctomyces, and Verrucomicrobia.
 Those systems can be found in plasmids (around 8%).
 
 ## Mechanism
 When activated by a phage infection, dCTPdeaminase, will convert deoxycytidine (dCTP/dCDP/dCMP) into deoxyuridine.
 This action will deplete the pool of CTP nucleotide necessary for the phage replication and will stop the infection.
-The trigger for dCTPdeaminase may be linked to the shutoff of RNAP (σS-dependent host RNA polymerase) that occur during phage infections.
+The trigger for dCTPdeaminase may be linked to the shutoff of RNAP ($\sigma$ S-dependent host RNA polymerase) that occur during phage infections.
 
 ## Example of genomic structure
 
@@ -125,12 +131,5 @@ 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: 10.1038/s41564-022-01162-4
----
-::
 

content/3.defense-systems/gao_rl.md

@@ -10,9 +10,22 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00176, PF00271, PF04465, PF04851, PF06634, PF12635, PF13091, PF13287, PF13290
+
+contributors: 
+  - Aude Bernheim
+relevantAbstracts:
+  - doi: 10.1126/science.aba0372
 ---
 
 # Gao_RL
+
+## Description
+
+The Gao_RL system is composed of 4 proteins: RL_D, RL_C, RL_B and, RL_A. It bears similarity with restriction systems :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_RL system is composed of 4 proteins: RL_D, RL_C, RL_B and, RL_A.
@@ -92,13 +105,3 @@ 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: 10.1126/science.aba0372
-
----
-::
-

content/3.defense-systems/gao_upx.md

@@ -9,9 +9,17 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors:
+    - Marian Dominguez-Mirazo
+relevantAbstracts:
+    - doi: 10.1126/science.aba0372
 ---
 
-# Gao_Upx
+# Gao_upx
+## Description
+The Gao_upx system is composed by a single protein. It was predicted through a guilty by association approach independent of domain annotations and validated in a heterologous system :ref{doi=10.1126/science.aba0372}. It's been identified as part of a highly conserved core defense hotspot in *Pseudomonas aeruginosa* strains :ref{doi=10.1093/nar/gkad317}. 
+## Molecular mechanisms
+As far as we are aware, the molecular mechanism is unknown. 
 ## Example of genomic structure
 
 The Gao_Upx system is composed of one protein: UpxA.
@@ -68,12 +76,3 @@ 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: 10.1126/science.aba0372
-
----
-::

content/3.defense-systems/mqsrac.md

@@ -8,6 +8,8 @@ tableColumns:
         Myriad bacterial anti-phage systems have been described and often the mechanism of programmed cell death is invoked for phage inhibition. However, there is little evidence of ‘suicide’ under physiological conditions for these systems. Instead of death to stop phage propagation, we show here that persister cells, i.e., transiently-tolerant, dormant, antibiotic-insensitive cells, are formed and survive using the Escherichia coli C496_10 tripartite toxin/antitoxin system MqsR/MqsA/MqsC to inhibit T2 phage. Specifically, MqsR/MqsA/MqsC inhibited T2 phage by one million-fold and reduced T2 titers by 500-fold. During T2 phage attack, in the presence of MqsR/MqsA/MqsC, evidence of persistence include the single-cell physiological change of reduced metabolism (via flow cytometry), increased spherical morphology (via transmission electron microscopy), and heterogeneous resuscitation. Critically, we found restriction-modification systems (primarily EcoK McrBC) work in concert with the toxin/antitoxin system to inactivate phage, likely while the cells are in the persister state. Phage attack also induces persistence in Klebsiella and Pseudomonas spp. Hence, phage attack invokes a stress response similar to antibiotics, starvation, and oxidation, which leads to persistence, and this dormant state likely allows restriction/modification systems to clear phage DNA.
          
 contributors:
+    - Héloïse Georjon
+    
 relevantAbstracts:
     - doi: 10.1038/s41564-022-01219-4
     - doi: 10.1101/2023.02.25.529695 
@@ -16,7 +18,11 @@ relevantAbstracts:
 
 # MqsRAC
 ## Description
+MqsRAC is a toxin-antitoxin-chaperone (TAC) system shown to have anti-phage activity.
+
 ## Molecular mechanisms
+As far as we are aware, the molecular mechanism of MqsRAC is unknown.
+
 ## Example of genomic structure
 
 The MqsRAC system is composed of 2 proteins: mqsR and, mqsC.

content/3.defense-systems/shango.md

@@ -4,24 +4,28 @@ layout: article
 tableColumns:
     article:
       doi: 10.1016/j.chom.2022.09.017
-      abstract: |
-        Bacterial anti-phage systems are frequently clustered in microbial genomes, forming defense islands. This property enabled the recent discovery of multiple defense systems based on their genomic co-localization with known systems, but the full arsenal of anti-phage mechanisms remains unknown. We report the discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments. We identified multiple systems with domains involved in eukaryotic antiviral immunity, including those homologous to the ubiquitin-like ISG15 protein, dynamin-like domains, and SEFIR domains, and show their participation in bacterial defenses. Additional systems include domains predicted to manipulate DNA and RNA molecules, alongside toxin-antitoxin systems shown here to function in anti-phage defense. These systems are widely distributed in microbial genomes, and in some bacteria, they form a considerable fraction of the immune arsenal. Our data substantially expand the inventory of defense systems utilized by bacteria to counteract phage infection.
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00270, PF00271, PF05099, PF10923, PF13208, PF15615
+contributors: 
+  - Hugo Vaysset
+  - Aude Bernheim
+relevantAbstracts:
+  - doi: 10.1016/j.chom.2022.09.017
+  - doi: 10.1093/nar/gkad317
 ---
 
 # Shango
 
 ## Description
-Shango is a three genes defense system which was discovered in parallel in two works in both *E.coli* and *P.aeruginosa* and was shown to have antiphage activity against the Lambda-phage in *E.coli* [1] and against diverse podo- and siphoviridae in *P.aeruginosa* [2].
+Shango is a three genes defense system which was discovered in parallel in two works in both *E.coli* and *P.aeruginosa* and was shown to have antiphage activity against the Lambda-phage in *E.coli* :ref{doi=10.1016/j.chom.2022.09.017} and against diverse podo- and siphoviridae in *P.aeruginosa* :ref{doi=10.1093/nar/gkad317}.
 
-Shango is composed of (i) a TerB-like domain, (ii) an Helicase and (iii) an ATPase. The TerB domain was previously shown to be associated to the perisplasmic membrane of bacteria [3]. 
+Shango is composed of (i) a TerB-like domain, (ii) an Helicase and (iii) an ATPase. The TerB domain was previously shown to be associated to the perisplasmic membrane of bacteria :ref{doi=10.4149/gpb_2011_03_286}. 
 
 ## Molecular mechanism
 
-The exact mechanism of action of the Shango defense has not yet been characterized, but it was shown that the TerB domain and the catalytic activity of the ATPase and the Helicase are required to provide antiviral defense. The fact that TerB domains are known to be associated to the periplasmic membrane could indicate that Shango might be involved in membrane surveillance [1].
+The exact mechanism of action of the Shango defense has not yet been characterized, but it was shown that the TerB domain and the catalytic activity of the ATPase and the Helicase are required to provide antiviral defense. The fact that TerB domains are known to be associated to the periplasmic membrane could indicate that Shango might be involved in membrane surveillance :ref{doi=10.1016/j.chom.2022.09.017}.
 
 
 ## Example of genomic structure
@@ -97,23 +101,4 @@ 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
-Shango was discovered in parallel by Adi Millman (Sorek group) and the team of J. Bondy-Denomy (UCSF). 
-
-[1] Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Garb, J., Bechon, N., Brandis, A., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J. L. M., Dar, D., … Sorek, R. (2022). An expanded arsenal of immune systems that protect bacteria from phages. _Cell Host & Microbe_, _30_(11), 1556-1569.e5. [https://doi.org/10.1016/j.chom.2022.09.017](https://doi.org/10.1016/j.chom.2022.09.017)
-
-[2] Johnson, Matthew, Laderman, Eric, Huiting, Erin, Zhang, Charles, Davidson, Alan, & Bondy-Denomy, Joseph. (2022). _Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems_. [https://doi.org/10.5281/ZENODO.7254690](https://doi.org/10.5281/ZENODO.7254690)
-
-[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292.
 

content/3.defense-systems/tiamat.md

@@ -10,9 +10,23 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00656, PF13020
+contributors: 
+  - Helena Shomar, Marie Guillaume
+relevantAbstracts:
+  - doi: 10.1016/j.chom.2022.09.017
+
 ---
 
 # Tiamat
+
+## Description
+This defense system is composed of one gene refered to as TmtA.
+This systems is widespread across diverse prokaryotic phyla, and was experimentally validated in _Escherichia coli_ (confers protection against phages T6 and T5).
+
+## Molecular mechanism
+
+To our knowledge the molecular mechanism is unknown. Please update.
+
 ## Example of genomic structure
 
 The Tiamat system is composed of one protein: TmtA_2599863134.
@@ -69,13 +83,6 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1016/j.chom.2022.09.017
 
 ---
-::
 

deploy/df-wiki/templates/deployment.yaml

@@ -39,14 +39,14 @@ spec:
             - name: http
               containerPort: {{ .Values.service.port }}
               protocol: TCP
-          livenessProbe:
-            httpGet:
-              path: /
-              port: http
-          readinessProbe:
-            httpGet:
-              path: /
-              port: http
+          # livenessProbe:
+          #   httpGet:
+          #     path: /
+          #     port: http
+          # readinessProbe:
+          #   httpGet:
+          #     path: /
+          #     port: http
           resources:
             {{- toYaml .Values.resources | nindent 12 }}
       {{- with .Values.nodeSelector }}