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.

content/3.defense-systems/thoeris.md

@@ -7,15 +7,34 @@ tableColumns:
       abstract: |
         The arms race between bacteria and phages led to the development of sophisticated antiphage defense systems, including CRISPR-Cas and restriction-modification systems. Evidence suggests that known and unknown defense systems are located in "defense islands" in microbial genomes. Here, we comprehensively characterized the bacterial defensive arsenal by examining gene families that are clustered next to known defense genes in prokaryotic genomes. Candidate defense systems were systematically engineered and validated in model bacteria for their antiphage activities. We report nine previously unknown antiphage systems and one antiplasmid system that are widespread in microbes and strongly protect against foreign invaders. These include systems that adopted components of the bacterial flagella and condensin complexes. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria.
     Sensor: Unknown
-    Activator: Signaling
+    Activator: Signaling system
     Effector: Nucleotide modifying
     PFAM: PF08937, PF13289, PF18185
+contributors: 
+  - Marie Guillaume
+  - Helena Shomar
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1038/s41586-021-04098-7
-    - doi: 10.1126/science.aar4120
+  - doi: 10.1038/s41586-021-04098-7
+  - doi: 10.1126/science.aar4120
+  - doi: 10.1038/s41467-020-16703-w
 ---
 
 # Thoeris
+
+## Description
+Thoeris is a two-gene defense system identified in more than 2000 bacterial genomes. It consists of the genes ThsA and thsB. Its anti-phage function was experimentally validated in *Bacillus subtilis* :ref{doi=10.1126/science.aar4120}. In response to phage infection, it produces an isomer of cyclic ADP-ribose, which leads to  depletion of NAD+ and results in abortive infection.
+
+ThsA contains the sirtuin-like domain which binds to nicotinamide adenine dinucleotide (NAD) metabolites. The N112A point mutation neutralizes the Thoeris defense system and abolishes the NAD+ hydrolase activity of thsA :ref{doi=10.1126/science.aar4120}. It lacks a N-terminal transmembrane domain, and is predicted to be cytoplasmic. 
+
+ThsB contains a TIR domain :ref{doi=10.1126/science.aar4120} is proposed to participate in the recognition of phage infection, as various thsB proteins sense different phage components.ThsB is found in more than 50% of Thoeris systems in multiple diverse copies :ref{doi=10.1126/science.aar4120}.
+
+## Molecular mechanism
+
+The Thoeris system functions by degrading NAD+ (a cofactor of central metabolism) to stop the growth of phage-infected cells and prevent the transmission of the phage to neighboring bacteria :ref{doi=10.1038/s41467-020-16703-w}.
+
+The protein ThsB, featuring the TIR domain, plays a cruial role in identifying phage invasion. Upon detecting the infection, the TIR domain becomes enzymatically active, initiating the synthesis of a cADPR isomer molecule :ref{doi=10.1038/s41586-021-04098-7}. This molecule acts as a signal, binding to the ThsA effector, likely through its C-terminal SLOG domain, thereby activating its NADase activity :ref{doi=10.1038/s41586-021-04098-7}. Consequently, the NADase effector reduces NAD+ cellular levels, creating an environment unsuitable for phage replication :ref{doi=10.1038/s41586-021-04098-7,10.1038/s41467-020-16703-w}.
+
 ## Example of genomic structure
 
 The Thoeris is composed of 2 proteins: ThsA and ThsB.
@@ -39,6 +58,21 @@ Proportion of genome encoding the Thoeris system for the 14 phyla with more than
 
 
 ## Structure
+
+### Experimentaly determined structure
+
+From :ref{doi=10.1038/s41467-020-16703-w} in *Bacillus cereus* MSX-D12:
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls: 
+    - /thoeris/6lhx_BcThsA_4mer.pdb
+    - /thoeris/6lhy_BcThsB_1mer.pdb
+    - /thoeris/7uxs_BcThsA_2mer_cdpr.pdb
+---
+::
+
 ### Thoeris_I
 ##### Example 1