Type II toxin/antitoxin system ParE_SO /CopA_SO stabilizes prophage CP4So in Shewanella oneidensis

Toxin/antitoxin (TA) loci are commonly found in mobile genetic elements such as plasmids and prophages. However, the physiological functions of these TA loci in prophages and cross-regulation among these TA loci remain largely unexplored. Here, we characterized a newly discovered type II TA pair, ParE_SO /CopA_SO , in the CP4So prophage in Shewanella oneidensis. We demonstrated that ParE_SO /CopA_SO plays a critical role in the maintenance of CP4So in host cells after its excision. The toxin ParE_SO inhibited cell growth, resulting in filamentous growth and eventually cell death. The antitoxin CopA_SO neutralized the toxicity of ParE_SO through direct protein-protein interactions and repressed transcription of the TA operon by binding to a DNA motif in the promoter region containing two inverted repeats [5'-GTANTAC (N)₃ GTANTAC-3']. CopA_SO also repressed transcription of another TA system PemK_SO /PemI_SO in megaplasmid pMR-1 of S. oneidensis through binding to a highly similar DNA motif in its promoter region. CopA_SO homologs are widely spread in Shewanella and other Proteobacteria, either as a component of a TA pair or as orphan antitoxins. Our study thus illustrated the cross-regulation of the TA systems in different mobile genetic elements and expanded our understanding of the physiological function of TA systems.