Gabija

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 (N/A) . Both proteins are necessary for defense and are forming a heteromeric octamer complex: GajA forms a central tetramer surrounded by two GajB dimers (N/A, N/A) . A phage protein inhibiting Gabija function was described, Gabidja anti-defense 1 (Gad1) (N/A, N/A) .

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 nucleotide concentrations. It was hypothesized that upon nucleotide depletion during phage infection, GajA would become activated (N/A) .  Moreover, a later study suggests that the gajB gene encodes 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 (N/A) . Therefore, both proteins would cooperate 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

Structure

Experimental validation

      
graph LR;
    Doron_2018[Doron et al., 2018] --> Origin_0
    Origin_0[Bacillus cereus strain VD045 
EJR29742.1, EJR29743.1] --> Expressed_0[Bacillus subtilis]
    Expressed_0[Bacillus subtilis] ----> SBSphiC & SpBeta & phi105 & rho14 & phi29
    Cheng_2021[Cheng et al., 2021] --> Origin_0
    Origin_0[Bacillus cereus strain VD045 
EJR29742.1, EJR29743.1] --> Expressed_2[Escherichia coli]
    Expressed_2[Escherichia coli] ----> T7
    Doron_2018[Doron et al., 2018] --> Origin_1
    Origin_1[Bacillus cereus strain HuB5-5 
EJQ91274.1, EJQ91275.1] --> Expressed_1[Bacillus subtilis]
    Expressed_1[Bacillus subtilis] ----> SpBeta & phi105
    subgraph Title1[Reference]
        Doron_2018
        Cheng_2021
end
    subgraph Title2[System origin]
        Origin_0
        Origin_0
        Origin_1
end
    subgraph Title3[Expression species]
        Expressed_0
        Expressed_2
        Expressed_1
end
    subgraph Title4[Protects against]
        SBSphiC
        SpBeta
        phi105
        rho14
        phi29
        T7
        SpBeta
        phi105
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