Old_exonuclease

Contributors: Marian Dominguez-Mirazo

Description

The OLD proteins are a family of nucleases present in bacteria, archaea, and viruses () . The OLD protein found in the P2 E.coli prophage is the best characterized one. The protein is an exonuclease that digests dsDNA in the 5' to 3' direction () . It also has nuclease activity against single-stranded DNA and RNA () . It's been shown to protect against phage lambda () , and when cloned with the P2 Tin accessory gene, it was shown to protect against other E. coli phages () . The protein also contains an ATPase domain that affects nuclease activity () . Inhibition of the RecBCD complex activates the OLD nuclease () . OLD proteins are divided into two classes based on amino acid sequence conservation and gene neighborhood () . The P2-associated protein belongs to class 2 () .

Molecular Mechanisms

The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction () . To our knowledge, other aspects of the molecular mechanisms remain unknown.

Example of genomic structure

The Old_exonuclease is composed of 1 protein: Old_exonuclease.

Here is an example found in the RefSeq database:

The Old_exonuclease system in Shewanella xiamenensis (GCF_022453805.1, NZ_CP092630) is composed of 1 protein: Old_exonuclease (WP_240293412.1)

Distribution of the system among prokaryotes

Among the 22,803 complete genomes of RefSeq, the Old_exonuclease is detected in 102 genomes (0.45 %).

The system was detected in 56 different species.

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

Structure

Old_exonuclease

Example 1

Experimental validation

      
graph LR;
    Rousset_2022[Rousset et al., 2022] --> Origin_0
    Origin_0[Enterobacteria phage P2 
NP_046798.1] --> Expressed_0[Escherichia coli]
    Expressed_0[Escherichia coli] ----> Lambda & T4 & LF82_P8 & Al505_P2
    subgraph Title1[Reference]
        Rousset_2022
end
    subgraph Title2[System origin]
        Origin_0
end
    subgraph Title3[Expression species]
        Expressed_0
end
    subgraph Title4[Protects against]
        Lambda
        T4
        LF82_P8
        Al505_P2
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

10.1128/jb.177.3.497-501.1995
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10.1128/jb.177.3.497-501.1995
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10.1093/nar/gkz703
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10.1016/j.chom.2022.02.018
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10.1016/j.mib.2023.102325
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