Unraveling the universe of small RNA regulators in the legume symbiont Sinorhizobium meliloti

High-throughput transcriptome profiling (RNAseq) has uncovered large and heterogeneous populations of small noncoding RNA species (sRNAs) with potential regulatory roles in bacteria. These sRNAs act mostly by protein-assisted base-pairing with target mRNAs to fine-tune post-transcriptional reprogramming of gene expression underlying bacterial responses to changing environments. Riboregulation impacts virtually any physiological process, and has been shown to largely influence virulence of pathogenic bacteria. Here, we review our current knowledge on the structure, conservation and function of the noncoding transcriptome of the alpha-rhizobia Sinorhizobium meliloti, the nitrogen-fixing symbiotic partner of alfalfa and related medics. Several RNAseq-based surveys in S. meliloti have shown abundant transcription from hitherto regarded as noncoding intergenic regions (IGRs), strikingly high numbers of mRNA-derived RNAs and pervasive antisense transcription of protein-coding genes. sRNAs encoded within IGRs constitute the most extensively studied group of bacterial riboregulators. They are differentially expressed and modulate translation and/or stability of trans-encoded target mRNAs by short antisense interactions that, in enteric model bacteria, are facilitated by the RNA chaperone Hfq. Among symbiotic rhizobia, regulatory sRNAs have been functionally characterized only in S. meliloti to date. The trans-sRNAs AbcR1 and AbcR2 are examples of Hfq-dependent sRNAs whereas EcpR1 does not bind Hfq. We will provide insights into the transcriptional regulation and activity mechanisms of these sRNAs for the targeting and control of multiple mRNAs involved in nutrient uptake (AbcR1/2) and cell cycle progression (EcpR1).