Nhi

Contributors: Alba Herrero del Valle

Description

The Nhi (nuclease-helicase immunity) system targets and degrades specific phage DNA replication intermediates () . Nayeemul Bari et al. showed that Nhi from Staphylococcus epidermidis protects against a diverse panel of staphylococcal phages and Millman et al. showed that a protein Nhi-like (that shares the domain organization with Nhi but not the sequence) from Bacillus cereus protects against some Bacillus phages (, ) .

Molecular mechanisms

Nhi contains two domains, a nuclease and a helicase domain that are both needed for the anti-phage activity. The nuclease domain has 3′–5′ exonuclease and plasmid nicking activities while the helicase unwinds dsDNA biderctionally. Nhi specifically recognizes phage single-stranded DNA binding proteins (SSB) that cover the phage genome to target this DNA for degradation thanks to its helicase and nuclease domains () .

Example of genomic structure

The Nhi is composed of 1 protein: Nhi.

Here is an example found in the RefSeq database:

The Nhi system in Staphylococcus sp. MZ9 (GCF_018622975.1, NZ_CP076029) is composed of 1 protein: Nhi (WP_045177897.1)

Distribution of the system among prokaryotes

Among the 22,803 complete genomes of RefSeq, the Nhi is detected in 199 genomes (0.87 %).

The system was detected in 61 different species.

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

Structure

Nhi

Example 1

Experimental validation

      
graph LR;
    Millman_2022[Millman et al., 2022] --> Origin_0
    Origin_0[ Nhi-like
Bacillus cereus] --> Expressed_0[Bacillus subtilis]
    Expressed_0[Bacillus subtilis] ----> phi3T & SpBeta & SPR
    Bari_2022[Bari et al., 2022] --> Origin_1
    Origin_1[Staphylococcus epidermidis 
AAW53361.1] --> Expressed_1[Staphylococcus epidermidis]
    Expressed_1[Staphylococcus epidermidis] ----> JBug18 & Pike & CNPx
    Bari_2022[Bari et al., 2022] --> Origin_1
    Origin_1[Staphylococcus epidermidis 
AAW53361.1] --> Expressed_2[Staphylococcus aureus]
    Expressed_2[Staphylococcus aureus] ----> Lorac
    Bari_2022[Bari et al., 2022] --> Origin_2
    Origin_2[Staphylococcus aureus 
WP_000632676.1] --> Expressed_3[Staphylococcus aureus]
    Expressed_3[Staphylococcus aureus] ----> Lorac
    Bari_2022[Bari et al., 2022] --> Origin_3
    Origin_3[Staphylococcus aureus 
WP_045177897.1] --> Expressed_4[Staphylococcus aureus]
    Expressed_4[Staphylococcus aureus] ----> Lorac
    Bari_2022[Bari et al., 2022] --> Origin_4
    Origin_4[Vibrio vulnificus 
WP_101958732.1] --> Expressed_5[Staphylococcus aureus]
    Expressed_5[Staphylococcus aureus] ----> Lorac
    subgraph Title1[Reference]
        Millman_2022
        Bari_2022
end
    subgraph Title2[System origin]
        Origin_0
        Origin_1
        Origin_1
        Origin_2
        Origin_3
        Origin_4
end
    subgraph Title3[Expression species]
        Expressed_0
        Expressed_1
        Expressed_2
        Expressed_3
        Expressed_4
        Expressed_5
end
    subgraph Title4[Protects against]
        phi3T
        SpBeta
        SPR
        JBug18
        Pike
        CNPx
        Lorac
        Lorac
        Lorac
        Lorac
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

10.1016/j.chom.2022.03.001
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10.1016/j.chom.2022.09.017
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