Identifying the Effect of Bacterial asRNA Regulation on mRNA Targets

Abstract

The symbiotic relationship between bacteria and humans can be readily observed in the human gastrointestinal (GI) tract, where gut bacteria play a role in immune system functions and metabolism. Healthy individuals have diverse and stable microbiomes, and disruption of this microbiome composition correlates with disease. To understand bacterial involvement in human processes and elucidate microbe-host interactions, it is important to study how bacteria regulate their own behavior. Small regulatory RNAs (sRNAs) are one of the mechanisms by which bacteria control gene expression and respond to environmental stimuli. Cis-encoded antisense sRNAs bind mRNA targets with full complementarity and post-transcriptionally regulate mRNA translation. Since few asRNAs have been experimentally confirmed, this study computationally selected two potential mRNA-asRNA pairs from Bacteroides thetaiotaomicron using sequencing data of bacterial RNA transcripts from human fecal samples. A previously designed computational pipeline annotated noncoding RNAs in this metatranscriptomic dataset by potential gene, identifying the selected sod and cshA genes as encoding superoxide dismutase [Mn/Fe] and ATP-dependent RNA helicase CshA, respectively. This work establishes a model for experimentally identifying biologically relevant asRNAs by co-expressing asRNAs and their mRNA targets in Escherichia coli.