Abstract
BackgroundThe symbiotic soil bacterium Sinorhizobium meliloti often has to face low pH in its natural habitats. To identify genes responding to pH stress a global transcriptional analysis of S. meliloti strain 1021 following a pH shift from pH 7.0 to pH 5.75 was carried out. In detail, oligo-based whole genome microarrays were used in a time course experiment. The monitoring period covered a time span of about one hour after the pH shift. The obtained microarray data was filtered and grouped by K-means clustering in order to obtain groups of genes behaving similarly concerning their expression levels throughout the time course.ResultsThe results display a versatile response of S. meliloti 1021 represented by distinct expression profiles of subsets of genes with functional relation. The eight generated clusters could be subdivided into a group of four clusters containing genes that were up-regulated and another group of four clusters containing genes that were down-regulated in response to the acidic pH shift. The respective mean expression progression of the four up-regulated clusters could be described as (i) permanently and strong, (ii) permanently and intermediate, (iii) permanently and progressive, and (iv) transiently up-regulated. The expression profile of the four down-regulated clusters could be characterized as (i) permanently, (ii) permanently and progressive, (iii) transiently, and (iv) ultra short down-regulated. Genes coding for proteins with functional relation were mostly cumulated in the same cluster, pointing to a characteristic expression profile for distinct cellular functions. Among the strongest up-regulated genes lpiA, degP1, cah, exoV and exoH were found. The most striking functional groups responding to the shift to acidic pH were genes of the exopolysaccharide I biosynthesis as well as flagellar and chemotaxis genes. While the genes of the exopolysaccharide I biosynthesis (exoY, exoQ, exoW, exoV, exoT, exoH, exoK exoL, exoO, exoN, exoP) were up-regulated, the expression level of the flagellar and chemotaxis genes (visR, motA, flgF, flgB, flgC, fliE, flgG, flgE, flgL, flbT, mcpU) simultaneously decreased in response to acidic pH. Other responding functional groups of genes mainly belonged to nitrogen uptake and metabolism (amtB, nrtB, nirB, nirD), methionine metabolism (metA, metF, metH, metK, bmt and ahcY) as well as ion transport systems (sitABCD, phoCD). It is noteworthy, that several genes coding for hypothetical proteins of unknown function could be identified as up-regulated in response to the pH shift.ConclusionIt was shown that the short term response to acidic pH stress does not result in a simple induction or repression of genes, but in a sequence of responses varying in their intensity over time. Obviously, the response to acidic pH is not based on a few specific genes, but involves whole sets of genes associated with various cellular functions.
Highlights
The symbiotic soil bacterium Sinorhizobium meliloti often has to face low pH in its natural habitats
Another situation where rhizobia are commonly facing a low pH environment is the rhizoplane of their leguminous host plants, where the pH is decreased by protons and organic acids excreted by the plants [5]
Growth analysis of S. meliloti 1021 cultures exposed to neutral and acidic pH The aim of this study was to analyse the transcriptional response of S. meliloti 1021 following a shift from a neutral to an acidic pH
Summary
The symbiotic soil bacterium Sinorhizobium meliloti often has to face low pH in its natural habitats. Rhizobia in turn differentiate into bacteroids and live as endosymbionts inside plant cells They fix atmospheric nitrogen and provide the fixed nitrogen to the host plant. The efficiency of this symbiosis is constrained by several factors relating to the soil and the rate of nodulation and nitrogen fixation is diminished. At acidic pH conditions the bacterial partner is limited in survival and persistence and the nodulation efficiency is reduced [2,3,4] Another situation where rhizobia are commonly facing a low pH environment is the rhizoplane of their leguminous host plants, where the pH is decreased by protons and organic acids excreted by the plants [5]. Several research groups have been trying to identify pH tolerant strains [3,7] and to reveal the genetic mechanisms enabling those strains to outperform other strains in low pH soils, up until now the basis of the rhizobial pH tolerance remains unknown
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