dCTPdeaminase

Contributors: Nathalie Bechon

Description

dCTPdeaminase is a family of systems. dCTPdeaminase from Escherichia coli has been shown to provide resistance against various lytic phages when expressed heterologously in another Escherichia coli by degrading the pool of dCTP available for phage DNA replication. This system is mostly found in Proteobacteria but a few examples also exist in Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Planctomyces, and Verrucomicrobia. Those systems can be found in plasmids (around 8%).

Mechanism

When activated by a phage infection, dCTPdeaminase will convert deoxycytidine (dCTP/dCDP/dCMP) into deoxyuridine. This action will deplete the pool of CTP nucleotide necessary for the phage replication and will stop the infection. The trigger for dCTPdeaminase may be linked to the shutoff of RNAP ($\sigma$ S-dependent host RNA polymerase) that occurs during phage infections.

Example of genomic structure

The dCTPdeaminase is composed of 1 protein: dCTPdeaminase.

Here is an example found in the RefSeq database:

The dCTPdeaminase system in Pseudomonas entomophila (GCF_023277925.1, NZ_CP063832) is composed of 1 protein: dCTPdeaminase (WP_248918739.1)

Distribution of the system among prokaryotes

Among the 22,803 complete genomes of RefSeq, the dCTPdeaminase is detected in 501 genomes (2.2 %).

The system was detected in 294 different species.

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

Structure

dCTPdeaminase

Example 1

Experimental validation

      
graph LR;
    Tal_2022[Tal et al., 2022] --> Origin_0
    Origin_0[Escherichia coli 
WP_045268677.1] --> Expressed_0[Escherichia coli]
    Expressed_0[Escherichia coli] ----> T5 & SECphi4 & SECphi6 & SECphi18 & T2 & T4 & T6 & T7
    Hsueh_2022[Hsueh et al., 2022] --> Origin_1
    Origin_1[ AvcID
Escherichia coli 
WP_096882215.1] --> Expressed_1[Escherichia coli]
    Expressed_1[Escherichia coli] ----> T3 & SECphi17 & SECphi18 & SECphi27
    Hsueh_2022[Hsueh et al., 2022] --> Origin_2
    Origin_2[ AvcID
Proteus mirabilis 
WP_108717204.1] --> Expressed_2[Escherichia coli]
    Expressed_2[Escherichia coli] ----> T4
    Hsueh_2022[Hsueh et al., 2022] --> Origin_3
    Origin_3[ AvcID
Vibrio parahaemolyticus 
WP_020839904.1] --> Expressed_3[Escherichia coli]
    Expressed_3[Escherichia coli] ----> T3 & T5 & T6 & SECphi18
    Hsueh_2022[Hsueh et al., 2022] --> Origin_4
    Origin_4[ AvcID
Vibrio cholerae 
WP_001901328.1] --> Expressed_4[Escherichia coli]
    Expressed_4[Escherichia coli] ----> T2 & T3
    subgraph Title1[Reference]
        Tal_2022
        Hsueh_2022
end
    subgraph Title2[System origin]
        Origin_0
        Origin_1
        Origin_2
        Origin_3
        Origin_4
end
    subgraph Title3[Expression species]
        Expressed_0
        Expressed_1
        Expressed_2
        Expressed_3
        Expressed_4
end
    subgraph Title4[Protects against]
        T5
        SECphi4
        SECphi6
        SECphi18
        T2
        T4
        T6
        T7
        T3
        SECphi17
        SECphi18
        SECphi27
        T4
        T3
        T5
        T6
        SECphi18
        T2
        T3
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

10.1038/s41564-022-01162-4
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10.1038/s41564-022-01158-0
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