GAPS6

Contributors: Jean Cury

Description

GAPS (GMT-encoded Anti-Phage System) antiphage systems were discovered on newly described Gamma-Mobile-Trio elements.

GAPS6 is composed of two proteins, GAPS6a and GAPS6b. These two proteins are encoded together in diverse Gram-negative bacteria.

Molecular mechanism

GAPS6b is essential for the defense phenotype, however it is not known whether GAPS6b could be sufficient. GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules () . The PINc domain is required for the anti-phage defense activity of GAPS6.

Example of genomic structure

The GAPS6 is composed of 2 proteins: GAPS6a and GAPS6b.

Here is an example found in the RefSeq database:

The GAPS6 system in Escherichia coli (GCF_013372365.1, NZ_CP054227) is composed of 2 proteins GAPS6b (WP_096985931.1) GAPS6a (WP_000346990.1)

Distribution of the system among prokaryotes

Among the 22,803 complete genomes of RefSeq, the GAPS6 is detected in 50 genomes (0.22 %).

The system was detected in 33 different species.

Proportion of genome encoding the GAPS6 system for the 14 phyla with more than 50 genomes in the RefSeq database.

Structure

GAPS6

Example 1

Experimental validation

      
graph LR;
    Mahata_2023[Mahata et al., 2023] --> Origin_0
    Origin_0[Vibrio parahaemolyticus 
WP_248387294.1, WP_248387295.1] --> Expressed_0[Escherichia coli]
    Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir
    subgraph Title1[Reference]
        Mahata_2023
end
    subgraph Title2[System origin]
        Origin_0
end
    subgraph Title3[Expression species]
        Expressed_0
end
    subgraph Title4[Protects against]
        T4
        Lambda-vir
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

    

References

10.1093/protein/gzq081
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