# Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria
## 1 Introduction
Many of these newly discovered transcripts are not translated into proteins, but fulfil important regulatory roles, especially in the adaptation of bacteria to fluctuating environments [13]. Bacterial non-coding transcriptomes typically consist of heterogeneous populations of 50 to 250 nt-long RNA species (sRNAs) with diverse biogenesis pathways and regulatory activity mechanisms. Some untranslated regions at 5'-ends (5'-UTRs) of mRNAs sense shifts in temperature (RNA thermometers) or intracellular levels of certain metabolites (riboswitches) to modulate transcription and/or translation of the downstream coding sequence in a structure-dependent manner. Few other sRNAs mimic sequence or structural DNA or RNA motifs recognized by specific proteins to outcompete them at their cognate cellular targets. Nonetheless, the activity of most sRNAs thus far characterized relies on base pairing interactions to fine-tune translation and/or turnover rates of mRNA targets that can be either antisense-transcribed (asRNAs) or encoded in _trans_ (_trans_-sRNAs). Complementarity between the asRNA and its mRNA target is perfect and may extend over regions even longer than 200-nt. Conversely, regulation by _trans_-sRNAs typically involves short and discontinuous series of complementary nucleotides in both molecules, requiring the assistance of proteins (e.g., Hfq) as RNA matchmakers [14]. Regardless of the type of sRNA involved in regulation and the possible effect on translation, formation of RNA duplexes through base pairing usually promote degradation of the mRNA targets by cellular ribonucleases (e.g., RNase E or RNase III). RNA-mediated post-transcriptional regulation of gene expression is ubiquitous in bacteria, influencing virtually any cellular process, e.g., stress responses, biofilm formation, quorum sensing, and other virulence traits [13]. Figure 1: The prokaryotic non-coding transcriptome as revealed by dRNA-Seq. Identified Transcription Start Sites (TSSs; shown by arrows) can be assigned to mRNA and the different sRNA types (_trans_-sRNAs, asRNAs and mRNA-derived sense-sRNAs). See text for further details. Research on prokaryotic riboregulation has been pioneered in the early post-genomic era by work on the model bacterium _Escherichia coli_. Soon afterwards, studies in related enterobacteria (i.e., _Salmonella_ spp.) and other clinically relevant microbes revealed the unprecedented prominent roles of sRNAs in the establishment of host-pathogen interactions [13]. In the last decade, functional rNomics is continuously providing new paradigms to the contribution of sRNAs to the ecological specializations of phylogenetically distant bacteria with complex lifestyles, bringing RNA to the forefront of microbial research. In legume symbionts, the knowledge about riboregulation is still scarce and rather limited to _Sinorhizobium melioti_, the symbiotic partner of the forage legume alfalfa (_Medicago sativa_ L.) and other related _Medicago_ species [15; 16; 17]. Here, we summarize and discuss known insights into the structure, function and mechanistic principles of the rhizbial non-coding transcriptome.