Merge branch 'bechon27-main-patch-50431' into 'main'

Update gabija.md

See merge request !117

content/3.defense-systems/gabija.md

@@ -10,18 +10,28 @@ tableColumns:
     Activator: Direct
     Effector: Degrading nucleic acids
     PFAM: PF00580, PF11398, PF13175, PF13245, PF13304, PF13361, PF13476
+contributors:
+    - Nathalie Bechon
+relevantAbstracts:
+    - doi: 10.1093/nar/gkab277
+    - doi: 10.1126/science.aar4120
+    - doi: 10.1016/j.chom.2023.06.014
+    - doi: 10.1101/2023.05.01.538945
+    - doi: 10.1101/2023.05.01.538930
 ---
 
 # Gabija
-## Description
 
-According to recent studies, GajA is a sequence-specific DNA nicking endonuclease, whose activity is inhibited by nucleotide concentration. Accordingly, GajA would be fully inhibited at cellular nucleotides concentrations. It was hypothesized that upon nucleotide depletion during phage infection, GajA would become activated (2). 
+## Description
 
-Another study suggests that the *gajB* gene could encode for an NTPase, which would form a complex with GajA to achieve anti-phage defense (3).
+Gabija is named after the Lithuanian spirit of fire, protector of home and family. It is a two gene defense system found in 8.5% of the 4360 bacterial and archeal genomes that were initially analyzed :ref{doi=10.1126/science.aar4120}. Both proteins are necessary for defense and are forming a heteromeric octamer complex: GajA forms a central tetramer surrounded by two GajB dimers ref:{doi=10.1101/2023.05.01.538945,10.1093/nar/gkad951}. A phage protein inhibiting Gabija function was described, Gabidja anti defense 1 (Gad1) :ref{doi=10.1101/2023.05.01.538945,10.1101/2023.05.01.538930}.
 
 ## Molecular mechanism
 
-The precise mechanism of the Gabija system remains to be fully described, yet studies suggest that it could act either as a nucleic acid degrading system or as an abortive infection system.
+The precise mechanism of the Gabija system remains to be fully described, yet studies suggest that it could act through a dual phage inhibition mechanism.
+GajA was shown to be a sequence-specific DNA nicking endonuclease, whose activity is inhibited by nucleotide concentration. This nucleotide sensing is mediated by GajA ATPase-like domain. Accordingly, GajA would be fully inhibited at cellular nucleotides concentrations. It was hypothesized that upon nucleotide depletion during phage infection, GajA would become activated :ref{doi=10.1093/nar/gkab277}. 
+Moreover, a later study suggests that the *gajB* gene encode an NTPase, which would form a complex with GajA to achieve anti-phage defense. GajB is activated by DNA termini produced by GajA activity and then hydrolyzes (d)A/(d)GTP, depleting essential nucleotides and increasing GajA activity :ref{doi=10.1016/j.chom.2023.06.014}.
+Therefore, both proteins would be cooperating to achieve both nucleotide depletion and DNA cleavage, causing abortive infection.
 
 ## Example of genomic structure
 
@@ -105,14 +115,3 @@ 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: 10.1093/nar/gkab277
-    - doi: 10.1126/science.aar4120
-
----
-::
-