Theses Doctoral
PhD student:
Supervisors:
José Ignacio Jiménez Zurdo, Marta Robledo Garrido
Date of presentation:
31-05-2022
Faculty and University:
Universidad de Granada
Qualification grade:
Sobresaliente cum laude
Title:
RNA regulation of metabolism in the legume symbiont Sinorhizobium meliloti
Summary:
Post‑transcriptional regulation of gene expression by small RNAs (sRNAs) is a major and ubiquitous adaptive trait, contributing greatly to bacterial fitness in fluctuating environments. The so-called trans-sRNAs are differentially expressed from intergenic regions and most commonly modulate translation and/or stability of multiple mRNA targets by short and discontinuous antisense interactions. Primary characterization of the homologous ABC Regulators AbcR1 and AbcR2 and the Nodule Formation Efficiency Regulator NfeR1 trans-sRNAs anticipated a major impact of riboregulation in the metabolism of the alfalfa symbiont Sinorhizobium meliloti.
In this Thesis, we have deciphered the architecture of the AbcR1/2 and NfeR1 regulatory network and its function in the S. meliloti adaptive metabolism. AbcR1 expression occurs during bacterial exponential growth and depends on the LysR-type transcriptional regulator LsrB, whereas AbcR2 is a stress-induced sRNA transcribed by the alternative RNA polymerase σ factor RpoH1. On the other hand, NfeR1 is under the control of a dual-mode promoter activated by LsrB and repressed by the master regulator of the nitrogen stress response, NtrC. Deciphering of the respective interactomes at a genome-wide scale revealed that AbcR1, AbcR2 and NfeR1 govern an exceptionally large dense overlapping post-transcriptional regulon, mostly consisting of mRNAs encoding uptake and catabolic proteins. This pervasive RNA regulation of metabolism contribute to the S. meliloti metabolic reprogramming during the symbiotic transition. Remarkably, AbcR1 enhances the ability of S. meliloti to colonize the root rhizoplane, whereas NfeR1 strengthens the S. meliloti nitrogen stress response. MetK, the synthetase of the major methyl donor S-adanosylmethionine, as well as the endoribonucleases YbeY and RNase III, are also proteins that contribute to regulation by AbcR1/2 and NfeR1 by yet unknown mechanisms. Because riboregulation mostly relies on modifiable base pairing interactions, this network could be rewired at different levels, thereby opening yet unexplored avenues for the engineering of highly competitive biofertilizers and symbiotic nitrogen-fixation in the sustainable agricultural practices.
