A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R

In bacteria, small non-coding RNAs (sRNAs) are critical regulators of cellular adaptation to changes in metabolism, physiology, or the external environment. In the last decade, more than 2000 of sRNA families have been reported in the Rfam database and have been shown to exert various regulatory functions in bacterial transcription and translation. However, little is known about sRNAs and their functions in Mesorhizobium. Here, we predicted putative sRNAs in the intergenic regions (IGRs) of M. huakuii 7653R by genome-wide comparisons with four related Mesorhizobial strains. The expression and transcribed regions of candidate sRNAs were analyzed using a set of high-throughput RNA deep sequencing data. In all, 39 candidate sRNAs were found, with 5 located in the symbiotic megaplasmids and 34 in the chromosome of M. huakuii 7653R. Of these, 24 were annotated as functional sRNAs in the Rfam database and 15 were recognized as putative novel sRNAs. The expression of nine selected sRNAs was confirmed by Northern blotting, and most of the nine selected sRNAs were highly expressed in 28 dpi nodules and under symbiosis-mimicking conditions. For those putative novel sRNAs, functional categorizations of their target genes were performed by analyzing the enriched GO terms. In addition, MH_s15 was shown to be an abundant and conserved sRNA.