GAPS4

Contributors: Hugo Vaysset

Description

GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded Anti-Phage System.

GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in E. coli and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 () .

Molecular mechanism

GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system () .

Example of genomic structure

The GAPS4 is composed of 2 proteins: GAPS4a and GAPS4b.

Here is an example found in the RefSeq database:

The GAPS4 system in Hafnia alvei (GCF_902387815.1, NZ_LR699008) is composed of 2 proteins GAPS4a (WP_111329122.1) GAPS4b (WP_111329123.1)

Distribution of the system among prokaryotes

Among the 22,803 complete genomes of RefSeq, the GAPS4 is detected in 118 genomes (0.52 %).

The system was detected in 74 different species.

Proportion of genome encoding the GAPS4 system for the 14 phyla with more than 50 genomes in the RefSeq database.

Structure

GAPS4

Example 1

Experimental validation

      
graph LR;
    Mahata_2023[Mahata et al., 2023] --> Origin_0
    Origin_0[Vibrio parahaemolyticus 
WP_055466293.1, WP_055466294.1] --> 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]
        T7
        T4
        P1-vir
        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

10.1101/2023.03.28.534373
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