Independent Activity of the Homologous Small Regulatory RNAs AbcR1 and AbcR2 in the Legume Symbiont Sinorhizobium meliloti

Abstract

The legume symbiont Sinorhizobium meliloti expresses a plethora of small noncoding RNAs (sRNAs) whose function is mostly unknown. Here, we have functionally characterized two tandemly encoded S. meliloti Rm1021 sRNAs that are similar in sequence and structure. Homologous sRNAs (designated AbcR1 and AbcR2) have been shown to regulate several ABC transporters in the related α-proteobacteria Agrobacterium tumefaciens and Brucella abortus. In Rm1021, AbcR1 and AbcR2 exhibit divergent unlinked regulation and are stabilized by the RNA chaperone Hfq. AbcR1 is transcribed in actively dividing bacteria, either in culture, rhizosphere or within the invasion zone of mature alfalfa nodules. Conversely, AbcR2 expression is induced upon entry into stationary phase and under abiotic stress. Only deletion of AbcR1 resulted into a discrete growth delay in rich medium, but both are dispensable for symbiosis. Periplasmic proteome profiling revealed down-regulation of the branched-chain amino acid binding protein LivK by AbcR1, but not by AbcR2. A double-plasmid reporter assay confirmed the predicted specific targeting of the 5′-untranslated region of the livK mRNA by AbcR1 in vivo. Our findings provide evidences of independent regulatory functions of these sRNAs, probably to fine-tune nutrient uptake in free-living and undifferentiated symbiotic rhizobia.

Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons inSinorhizobium meliloti

“…In S. meliloti targeting of the livK mRNA by the so-called AbcR1 sRNA is the only sRNA-mRNA pair experimentally validated to date. 42 AbcR1 and its homologous AbcR2 sRNA are tandemly encoded in a S. meliloti chromosomal IGR and both have been reported to be Hfq-dependent. 29,41,42 Accordingly, these sRNAs were enriched in our Hfq CoIP-RNA libraries (Fig.…”

“…A number of additional target mRNAs of AbcR1 and/or AbcR2, mostly coding for ABC transport systems, have been computationally predicted. 31,42 We selected three of these mRNAs, namely SMa0495, prbA (SMc01642), and oppA (SMb21196), which as livK code for amino acid binding proteins, are Hfq-bound and upregulated in an hfq mutant (Table S3), to further assess their regulation by AbcR1/2 in vivo using a double-plasmid reporter system. 42 This assay failed to demonstrate targeting of oppA (not shown) but revealed downregulation of SMa0495 and prbA by both AbcR1 and AbcR2 (Fig.…”

“…23,[36][37][38][39][40] The biological functions of the vast majority of the identified sRNAs remain to be elucidated, although a few have been already shown to bind Hfq. 29,41,42 In this work we have used a generic strategy relying on the combination of co-immunoprecipitation (CoIP) of an epitope-tagged Hfq and its associated RNA with RNAseq to generate an atlas of S. meliloti Hfq-bound transcripts. Our data reveal that major S. meliloti stress response and symbiotic gene networks are extensively subjected to Hfq-mediated post-transcriptional regulation.…”

Small Noncoding RNA AbcR1 Addressing Multiple Target mRNAs From Transcriptional Factor and Two-Component Response Regulator of Brucella melitensis

“…Likewise, AbcR sRNA is encoded in the intragenic region of Sinorhizobium meliloti and plays a vital role in regulating the gene expression of branched-chain amino acid binding protein, LivK, by AbcR1, not AbcR2 (12). Transcriptional regulators are important study topics at the molecular level.…”

Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans -Encoded Small RNA MmgR

“…In addition, S. meliloti expresses a functional homolog of the Escherichia coli Hfq protein, a chaperone of RNA-RNA interactions and a modulator of RNA activity (22)(23)(24)(25)(26)(27)(28)(29). Nevertheless, the biological implications of the large S. meliloti RNome remain largely unexplored (20), since only four small RNAs have been functionally characterized so far, i.e., the cell cycle regulator sRNA EcpR1 (30), the quorumsensing regulator sRNA RcsR1 (31), and the tandemly encoded orthologs AbcR1 and AbcR2 (32). We are tempted to speculate that the large regulatory network is yet to be revealed.…”