A peroxide-responding sRNA evolved from a peroxidase mRNA

Abstract

ABSTRACTSmall RNAs (sRNAs) are critical regulators of gene expression in bacteria, but we lack a clear understanding of how new sRNAs originate and get integrated into regulatory networks. A major obstacle to elucidating their evolution is the difficulty in tracing sRNAs across large phylogenetic distances. To overcome this roadblock, we investigated the prevalence of sRNAs in more than a thousand genomes across Enterobacterales, a bacterial order with a rare confluence of factors that allows robust genome-scale sRNA analyses: several well-studied organisms with fairly conserved genome structures, an established phylogeny, and substantial nucleotide diversity within a narrow evolutionary space. Using a covariance modeling-based approach, we analyzed the presence of hundreds of sRNAs and discovered that a majority of sRNAs arose recently, and uncovered protein-coding genes as a potential source for the generation of new sRNA genes. A detailed investigation of the emergence of OxyS, a peroxide-responding sRNA, demonstrated that it evolved from a 3′ end fragment of a peroxidase mRNA. Collectively, our data show that the erosion of protein-coding genes can result in the formation of new sRNAs that continue to be part of the original protein’s regulon. This novel insight provides a fresh framework for understanding how new sRNAs originate and get incorporated into preexisting regulatory networks.AUTHOR SUMMARYSmall RNAs (sRNAs) are important gene regulators in bacteria, but it is unclear how new sRNAs originate and become part of regulatory networks that coordinate bacterial response to environmental stimuli. Here, we show that new sRNAs could arise from protein-coding genes and potentially be incorporated into the ancestral proteins’ regulatory networks. We illustrate this process by defining the origin of OxyS. This peroxide-responding sRNA evolved from and replaced a peroxidase gene, but continues to be part of the peroxide-response regulon. In sum, we describe the source from which OxyS, one of the most well-studied sRNAs, arose, identify protein-coding genes as a potential raw material from which new sRNAs could emerge, and suggest a novel evolutionary path through which new sRNAs could get incorporated into pre-existing regulatory networks.