-
6cbf2507
- Gabija
- Description
- Molecular mechanism
- Example of genomic structure
- Distribution of the system among prokaryotes
- Structure
- Gabija
- ::molstar-pdbe-plugin
- height: 700 dataUrl: /gabija/Gabija,Gabija_GajB,0,V-plddts_91.3911.pdb
- ::molstar-pdbe-plugin
- height: 700 dataUrl: /gabija/Gabija,Gabija__GajA,0,V-plddts_86.08162.pdb
- Experimental validation
title: Gabija
layout: article
tableColumns:
article:
doi: 10.1126/science.aar4120
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: 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: 10.1038/s41586-023-06855-2
- doi: 10.1038/s41586-023-06869-wGabija
Description
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 in :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=10.1038/s41586-023-06855-2,10.1093/nar/gkad951}. A phage protein inhibiting Gabija function was described, Gabidja anti defense 1 (Gad1) :ref{doi=10.1038/s41586-023-06855-2,10.1038/s41586-023-06869-w}.
Molecular mechanism
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
The Gabija is composed of 2 proteins: GajA and GajB.
Here is an example found in the RefSeq database:
The Gabija system in Roseomonas fluvialis (GCF_022846615.1, NZ_AP025637) is composed of 2 proteins GajA (WP_244458879.1) GajB_2 (WP_244458880.1)
Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the Gabija is detected in 2999 genomes (13.15 %).
The system was detected in 1375 different species.
Proportion of genome encoding the Gabija system for the 14 phyla with more than 50 genomes in the RefSeq database.
Structure
Gabija
::molstar-pdbe-plugin
height: 700 dataUrl: /gabija/Gabija,Gabija_GajB,0,V-plddts_91.3911.pdb
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::molstar-pdbe-plugin
height: 700 dataUrl: /gabija/Gabija,Gabija__GajA,0,V-plddts_86.08162.pdb
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