Natural Selection Shapes Maintenance of Orthologous sRNAs in Divergent Host-Restricted Bacterial Genomes

Margaret W Thairu,Patrick H Degnan,Venkata Rama Sravani Meduri,Allison K Hansen,Heather Hendrickson

doi:10.1093/molbev/msab202

Margaret W Thairu, Patrick H Degnan + Show 3 more

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https://doi.org/10.1093/molbev/msab202

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Abstract

Historically it has been difficult to study the evolution of bacterial small RNAs (sRNAs) across distantly related species. For example, identifying homologs of sRNAs is often difficult in genomes that have undergone multiple structural rearrangements. Also, some types of regulatory sRNAs evolve at rapid rates. The high degree of genomic synteny among divergent host-restricted bacterial lineages, including intracellular symbionts, is conducive to sRNA maintenance and homolog identification. In turn, symbiont genomes can provide us with novel insights into sRNA evolution. Here, we examine the sRNA expression profile of the obligate symbiont of psyllids, Carsonella ruddii, which has one of the smallest cellular genomes described. Using RNA-seq, we identified 36 and 32 antisense sRNAs (asRNAs) expressed by Carsonella from the psyllids Bactericera cockerelli (Carsonella-BC) and Diaphorina citri (Carsonella-DC), respectively. The majority of these asRNAs were associated with genes that are involved in essential amino acid biosynthetic pathways. Eleven of the asRNAs were conserved in both Carsonella lineages and the majority were maintained by selection. Notably, five of the corresponding coding sequences are also the targets of conserved asRNAs in a distantly related insect symbiont, Buchnera. We detected differential expression of two asRNAs for genes involved in arginine and leucine biosynthesis occurring between two distinct Carsonella-BC life stages. Using asRNAs identified in Carsonella, Buchnera, and Profftella which are all endosymbionts, and Escherichia coli, we determined that regions upstream of these asRNAs encode unique conserved patterns of AT/GC richness, GC skew, and sequence motifs which may be involved in asRNA regulation.

Highlights

Small RNAs have emerged as key players in bacterial gene regulation of virtually all aspects of cellular physiology (Nitzan et al 2017)
Examination of bacterial lineages that possess genomic characteristics that are conducive to small RNAs (sRNAs) maintenance and homolog identification across distantly related species (Ruwe and SchmitzLinneweber 2012; Ro et al 2013; Hansen and Degnan 2014; Thairu et al 2018; Thairu and Hansen 2019a) can provide us with novel insights into bacterial sRNA evolution (Thairu and Hansen 2019b)
To capture a wide range of endosymbiont sRNAs, we sampled across various life stages for both Bactericera cockerelli and Diaphorina citri

Summary

Introduction

Small RNAs (sRNAs) have emerged as key players in bacterial gene regulation of virtually all aspects of cellular physiology (Nitzan et al 2017). The origins of sRNAs in bacteria are facilitated by processes similar to those observed for protein coding genes, such as de novo emergence, gene duplication, and horizontal gene transfer (Dutcher and Raghavan 2018). There is still an incomplete understanding of sRNA evolution and function relative to protein coding genes, and many of the evolutionary studies to date are biased toward sRNAs found in model, free-living bacterial species, which include Escherichia coli, Salmonella enterica, Citrobacter freundii, Klebsiella pneumoniae, Serratia marcescens, and Yersinia enterocolitica (e.g., Skippington and Ragan 2012; Cerutti et al 2017; Chen et al 2017; Kacharia et al 2017). Examination of bacterial lineages that possess genomic characteristics that are conducive to sRNA maintenance and homolog identification across distantly related species (Ruwe and SchmitzLinneweber 2012; Ro et al 2013; Hansen and Degnan 2014; Thairu et al 2018; Thairu and Hansen 2019a) can provide us with novel insights into bacterial sRNA evolution (Thairu and Hansen 2019b)

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