Project: Mechanisms underlying riboregulation of metabolism and symbiotic nitrogen fixation in rhizobia

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Principal investigators: 

Associated with:

  • Consejo Superior de Investigaciones Científicas (CSIC). Funding body: Ministerio de Economía y Competitividad (Spain)

Project Summary:

Regulation of gene expression by non-coding RNAs (sRNAs) is ubiquitous in bacteria, underlying virtually any physiological adaptation to changing environments. The canonical activity mechanism of sRNAs involves base-pairing interactions with one or multiple trans-encoded mRNA targets, which typically results into blocking of translation and mRNA decay. However, the involvement of a diversity of proteins in the process add new regulatory possibilities, which is becoming evident in bacteria with complex biology and phylogenetically distant of the classical models.

Sinorhizobium meliloti is a α-proteobacterium within the rhizobia group, which are known for their ability to fix nitrogen in symbiosis with legumes. S. meliloti encodes an exceptionally large repertoire of ABC transporters, which endows this bacterium with the metabolic versatility required to cope with the oligotrophy of soil and the intracellular environment within the host. We already know that many of the mRNAs encoding ABC transporters for the uptake of nitrogen compounds integrate a dense overlapping regulon governed by at least three sRNAs, AbcR1, AbcR2 and NfeR1, by a canonical post-transcriptional RNA silencing mechanism. The endoribonuclease SmYbeY and the S-adenosylmethionine synthetase (MetK) are proteins functionally linked to these sRNAs. SmYbeY is unique for its ability to degrade both single- and double-stranded RNA molecules, being some of its substrates AbcR1/2 mRNA targets and some other transcripts related to nitrogen fixation probably regulated by antisense sRNAs (asRNAs). AbcR2 and NfeR1 counteract MetK activity by biding to this protein, which abates the intracellular levels of the major methyl donor, S-adenosyl methionine (SAM), with unknown physiological consequences.

The general objective of this project is to deepen into the mechanisms underlying regulation of metabolism and nitrogen fixation by trans-sRNAs, i.e. AbcR1/2 and NfeR1, and asRNAs in S. meliloti. Specific goals are to (1) dissect the AbcR1/2 and NfeR1 regulon by RNAseq, (2) decipher the molecular bases of the catalytic versatility of SmYbeY and its contribution to sRNA-mediated post-transcriptional gene silencing, and (3) gain insights into riboregulation of SAM homeostasis and its physiological impact.