# Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria
## 4 Assigning Functions to Rhizbial _Trans_-sRNAs
### Nutrient Uptake and Metabolism  
Rhizobia must cope with a broad range of limiting nutrients in soil and specific nutritional needs in the rhizosphere of their host plants. Therefore, nodulation competitiveness first depends on the adequate regulation and coordination of efficient nutrient uptake and metabolism. Thus, it is not surprising the large number of ABC (ATP-binding cassette) transporters encoded by rhizbial genomes [9; 53; 54]. Acquisition of amino acids (aa), peptides, metal ions, or sugars through ABC transporters impacts important cellular processes such as differentiation, virulence or conjugation [55]. Figure 2: Key features of bacterial _trans_-sRNA biology. Differential regulation, target recognition and association with RNA chaperones and ribonucleases. Remarkably, a selective suite of ABC systems is expressed in Rm1021-induced alfalfa nodules, thus supporting a specialized nutrient exchange between symbiont and host [56]. Nutrient uptake through ABC transporters primarily relies on periplasmic solute binding proteins (SBP) that determine substrate-specificity and are induced by its own ligand, typically two or more molecules [53; 55]. This pervasive transcription of transporter genes suggests that rhizobia use post-transcriptional silencing mechanisms to quickly and accurately optimize metabolism with minimal energy costs. As proof of principle, the sRNA rnTrpL, which is produced from transcription attenuation of one of the three tryptophan (trp) biosynthesis operons, \(trpE(G)\), directly interacts with the polycistronic \(trpDC\) mRNA resulting in negative post-transcriptional regulation in \(S\). _meliloti_. Considering that trp is the most costly-to-synthesize aa and the conservation of this mechanism in _Agrobacteriumium_ and _Bradyrhizobium_ but not in \(E\). _coli_, this precedent provides an example of how soil bacteria have evolved post-transcriptional strategies to coordinate transport and metabolism in complex ecological systems as soils [57]. Riboregulation of nutrient uptake was first described in \(E\). _coli_ and _Salmonella_ by characterization of the GcvB sRNAs, which regulon potentially includes \(\sim\)1% of all mRNAs in these bacteria, with prevalence of mRNAs from ABC transporters of aa and short peptides, but also containing mRNAs coding for aa biosynthesis-related proteins and transcription factors [58]. Functionally analogous riboregulators were later discovered in the \(\alpha\)-proteobacterial species \(A\). _tumefaciens_, \(B\). _abortus_ and \(S\). _meliloti_, and were termed AbcR sRNAs (ABC transporter RNA) [59; 60; 61; 62; 63]. _S. _meliloti_ Rm1021 encodes three AbcR homologs that belong to the \(\alpha\)r15 sRNA family, whose members have partial homology to the SuhB sRNA (Rfam model RF00519) [46]. AbcR1 and AbcR2 are Hfq-binding 120 and 114 nt-long transcripts, respectively, that are encoded in tandem in the IGR flanked by the protein-coding genes SMc01226-_lsrB_ (Table 1). Their predicted secondary structures consist of three stem loops (SLs) with two CU-rich anti-Shire Delgarno (aSD) motifs in unpaired regions of the molecules. These motifs are well conserved in AbcR homologs and are putatively responsible for the interaction with the ribosome binding site (RBS) and flanking nucleotides in mRNA targets, which commonly interferes with translation and promotes mRNA decay. The predicted lists of targets for both _trans_-sRNAs are enriched in ABC transporter mRNAs (35-45% of the top scored). Proteomics and further genetic verification identified \(prbA\), SMa0495 and _livK_, all coding for the SBP of aa transporters, as common targets of these sRNAs- except _livK_ that is specifically repressed by AbcR1 [62; 32]. AbcR1 and AbcR2 expression patterns are divergent, suggesting differential transcriptional regulation from independent promoters. Indeed, both 5'-end RACE mapping and dRNA-Seq consistently identified a TSS for each transcript [20; 27].