Expression profiles of sRNA genes in Caldimonas thermodepolymerans

Abstract

Regulation of gene expression represents a complex process that monitors the requirements of cells for specific gene products and adjusts their production accordingly. Each stage of gene expression employs different regulatory mechanisms. Here, we pay attention to post-transcriptional regulation by non-coding genomic elements - small RNAs (sRNAs). The aim is to address the problem of missing structural annotations of sRNA genes that play a key role in the rapid response of bacterial cells to stress conditions. For these purposes, we analyse the transcriptomic data of Caldimonas thermodepolymerans DSM 15344T, a promising adept for industrial biotechnology applications, especially for producing polyhydroxyalkanoates (PHA). Analysis of the RNASeq data results in a list of predicted sRNAs. Furthermore, the association of these regulatory elements with specific genes is indicated using loci information and sRNA gene co-expression analysis. Finally, sRNA expression analysis was performed to reveal the relationship of sRNA regulation to genes involved in PHA metabolism.