Merge branch 'ftesson_septu' into 'main'

Update septu.md

See merge request !173

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