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Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress.

ABSTRACT: Acid environments are worldwide distributed due to their natural conditions or by the inappropriate use of the intensive agriculture. The moderately low pHs from the soils are an important barrier in the plant-rhizobia interaction. These low pHs affect the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect in the rhizobia-legume is mainly due the low acid-tolerance of the bacteria. Here, we described and identified relevant factors in the acid tolerance of Rhizobium. favelukesii, using RNA-Seq. A total of 1924 genes were differentially expressed under acidic condition, with ca. 60% underexpressed. Remarkably, 60% of the CDS of the symbiotic plasmid were also underexpressed. The in silico functional analysis showed that R. favelukesii acid response involves both general and specific response. Regarding the general response, it includes mainly changes in energetic metabolism and protein turnover, while the specific response is a combination of mechanisms that would contribute to the general phenotype of acid-tolerant in R. favelukesii. GABA and Histidine metabolism, cell envelope changes and reverse proton efflux were significant. Moreover, we confirmed a phenotype acid sensible of a mutant in braD, this gene showed a higher expression under acid stress. Remarkably, we evidenced that a strain without pSym presented an improved performance in acidic condition. Hence, this work supply relevant information in the characterization of genes associated with tolerance or adaptation to abiotic stresses of R. favelukesii LPU83 using transcriptomic tools.

ORGANISM(S): Rhizobium favelukesii

PROVIDER: GSE141742 | GEO | 2020/11/12

REPOSITORIES: GEO

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Project description:Abiotic stresses disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. In particular, the effect of extracellular acidity on rhizobia has been taken as a model example for analysis because of the economic impact and worldwide distribution of these symbionts in agricultural countries. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0â??6.1. Under such a limiting acid stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a remarkably higher aerobic-respiration rate in acid-stressed rhizobia. Changes in the transcripts encoding enzymes for lipid biosynthesis were also observed, consistent with previous data on rhizobial pH-dependent membrane remodelling. Together with increased energy demands under acidity, proteomic and transcriptomic data revealed that while at pH 7.0 the transport and biosynthesis of cellular compounds were quite active processes, under acid stress most overexpressed markers were associated with protein biosynthesis, macromolecular degradation and/or recycling, and energy metabolism. Within this context, the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Moreover, multivariate analysis of global metabolome data (more than 60 compounds) served to unequivocally correlate the specific-metabolite profiles with the extracellular pH for growth, with strikingly sensitive variations being observed in the rhizobial metabolomes upon extracellular-pH changes of less than 0.5 units. Except for a ca. 120-kb DNA stretch within the pSymA no specific genomic regions were associated with the observed acid-stress responses. Further practical analyses should be focussed on the phenotypic impact and time course of the observed changes during the acid-stress perception and on the search for common responses during the previously described sublethal acid-adaptive processes in rhizobia pH 6.1 vs pH 7

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Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress.

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