Insights into the function and activity mechanism of stress-induced small non-coding RNAs and the endoribonuclease YbeY in the legume symbiont Sinorhizobium meliloti

Abstract

In the rhizobia-legume symbiosis, the transition from a free-living state in soil to an intracellular residence within the plant host demands a flexible adaption of invading bacteria to external changes, which involves the coordinated expression of complex gene networks. Therefore, sRNAs expressed by the microsymbiont are expected to be essential regulatory elements for the integration of diverse soil and plant signals and the coordination of the appropriate physiological bacterial response. Despite this evidence, the role of riboregulation in this mutualistic endosymbiosis has remained largely unexplored. Recently, the non-coding RNome of the model rhizobia, Sinorhizobium meliloti, has been extensively characterized by diverse post-genomic high-throughput approaches. The challenge now is deciphering the function of the thousands of sRNA molecules of different type expressed by this bacterium. In this work, we deepened into the knowledge of two sRNAs, previously identified in our group in the S. meliloti genome (del Val et al., 2007), and we explored the involvement in riboregulation of the conserved bacterial YbeY protein. The stress-induced AbcR2 sRNA (Torres-Quesada et al., 2013) integrates the regulon of RpoH1 (σH1factor) acting downstream in the post-transcriptional regulation of multiple transporter mRNAs coding for proteins involved in the uptake of amino acids and other nitrogen sources. The salt- induced NfeR1 is widespread in phylogenetically related α-proteobacteria interacting with eukaryotic hosts (del Val et al., 2012; Reinkensmeier and Giegerich, 2015). Its expression profile and associated phenotypes place this sRNA as a novel regulator of a salt stress response influencing both osmoadaptation and the overall symbiotic performance of S. meliloti on alfalfa roots. The S. meliloti endoribonuclease YbeY influence core RNA metabolism, energy-producing pathways and plasmid-encoded symbiotic functions. Profiling of the SmYbeY-dependent genes and RNA ligands envisages a number of Hfq-independent and -dependent substrates for this RNase, e.g. the nitrogen fixation genes. Although the data presented here reveal that Hfq and SmYbeY participate in largely independent RNA networks, we provide evidence that the Hfq-dependent silencing of genes related to nitrogen fixation and amino acid uptake requires SmYbeY.