Frequent nonhomologous replacement of replicative helicase loaders by viruses in <i>Vibrionaceae</i>.

Abstract

Several microbial genomes lack textbook-defined essential genes. If an essential gene is absent from a genome, then an evolutionarily independent gene of unknown function complements its function. Here, we identified frequent nonhomologous replacement of an essential component of DNA replication initiation, a replicative helicase loader gene, in <i>Vibrionaceae</i>. Our analysis of <i>Vibrionaceae</i> genomes revealed two genes with unknown function, named <i>vdhL1</i> and <i>vdhL2</i>, that were substantially enriched in genomes without the known helicase-loader genes. These genes showed no sequence similarities to genes with known function but encoded proteins structurally similar with a viral helicase loader. Analyses of genomic syntenies and coevolution with helicase genes suggested that <i>vdhL1/2</i> encodes a helicase loader. The in vitro assay showed that <i>Vibrio harveyi</i> VdhL1 and <i>Vibrio ezurae</i> VdhL2 promote the helicase activity of DnaB. Furthermore, molecular phylogenetics suggested that <i>vdhL1</i>/<i>2</i> were derived from phages and replaced an intrinsic helicase loader gene of <i>Vibrionaceae</i> over 20 times. This high replacement frequency implies the host's advantage in acquiring a viral helicase loader gene.