Update abi2.md

content/3.defense-systems/abi2.md

@@ -6,16 +6,28 @@ tableColumns:
       doi: 10.1016/j.mib.2005.06.006
       abstract: |
         Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
-    Sensor: ''
-    Activator: ''
-    Effector: ''
+    Sensor: Unknown
+    Activator: Direct Binding
+    Effector: Unknown
     PFAM: PF07751
+contributors:
+  - Marian Dominguez-Mirazo
 relevantAbstracts:
   - doi: 10.1016/j.mib.2005.06.006
 ---
 
 # Abi2
 
+## Description
+
+The Abi2 system corresponds to a group of abortive infection systems: [AbiD](/defense-systems/abid), AbiD1 and AbiF.
+
+The Abi2/AbiD1 system of lactococci is composed of a single protein Abi_2 :ref{doi=10.1016/j.mib.2005.06.006}. Expression of the protein is toxic to the bacteria and is therefore highly regulated. Expression of the protein is triggered by the orf1 of phage bIL66 which results in inhibition of the phage RuvC-like endonuclease activity and stops phage multiplication. 
+
+## Molecular mechanism
+
+For AbiD1 :ref{doi=10.1128/jb.177.13.3824-3829.1995} (AAA79209), the expression of the protein is toxic to the bacteria and is therefore highly regulated. Expression of the protein is triggered by the orf1 of phage bIL66 which results in inhibition of the phage RuvC-like endonuclease activity and stops phage multiplication.
+
 
 ## Example of genomic structure
 
@@ -27,6 +39,9 @@ Here is an example found in the RefSeq database:
 
 The Abi2 system in *Veillonella parvula* (GCF_002005185.1, NZ_CP019721) is composed of 1 protein: Abi_2 (WP_077707938.1) 
 
+## Molecular mechanisms
+As far as we are aware, the molecular mechanisms remain unclear.
+
 ## Distribution of the system among prokaryotes
 
 Among the 22,803 complete genomes of RefSeq, the Abi2 is detected in 1231 genomes (5.4 %).
@@ -37,3 +52,48 @@ The system was detected in 202 different species.
 
 Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
+## Structure 
+
+### Abi2/AbiD
+
+##### Example 1
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+   - /abid/AbiD__AbiD.cif
+
+---
+::
+
+
+## Experimental validation 
+
+As Abi2 is a group of different Abortive infection systems, here is the experimental validation of AbiD:
+
+<mermaid>
+graph LR;
+    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+    Origin_0[lactococcal plasmid  
+<a href='https://ncbi.nlm.nih.gov/protein/AAA63619.1'>AAA63619.1</a>] --> Expressed_0[lactococci]
+    Expressed_0[lactococci] ----> 936 & c2 & P335
+    subgraph Title1[Reference]
+        Chopin_2005
+end
+    subgraph Title2[System origin]
+        Origin_0
+end
+    subgraph Title3[Expression species]
+        Expressed_0
+end
+    subgraph Title4[Phage infected]
+        936
+        c2
+        P335
+end
+    style Title1 fill:none,stroke:none,stroke-width:none
+    style Title2 fill:none,stroke:none,stroke-width:none
+    style Title3 fill:none,stroke:none,stroke-width:none
+    style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>