Nuclease genes occupy boundaries of genetic exchange between bacteriophages

Abstract

Homing endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4s. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.

Sporadic phage defense in epidemicVibrio choleraemediated by the toxin-antitoxin system DarTG is countered by a phage-encoded antitoxin mimic

“…To date, we have witnessed epidemic V. cholerae gain and lose genetic elements that confer defense against the prevalent vibriophage ICP1, and ICP1 gain and lose counter-defenses 15,20,25,29,50 . In this work, we characterize a new addition to this story—clinical V. cholerae isolates from 2008 to 2009 harbored a previously uncharacterized phage defense element that inhibits ICP1.…”