| Summary: | <p>Abstract</p> <p>Background</p> <p>The symbiotic soil bacterium <it>Sinorhizobium meliloti </it>often has to face low pH in its natural habitats. To identify genes responding to pH stress a global transcriptional analysis of <it>S. meliloti </it>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.</p> <p>Results</p> <p>The results display a versatile response of <it>S. meliloti </it>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 <it>lpiA</it>, <it>degP1</it>, <it>cah</it>, <it>exoV </it>and <it>exoH </it>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 (<it>exoY</it>, <it>exoQ</it>, <it>exoW</it>, <it>exoV</it>, <it>exoT</it>, <it>exoH</it>, <it>exoK exoL</it>, <it>exoO</it>, <it>exoN</it>, <it>exoP</it>) were up-regulated, the expression level of the flagellar and chemotaxis genes (<it>visR</it>, <it>motA, flgF, flgB, flgC, fliE, flgG, flgE, flgL, flbT</it>, <it>mcpU</it>) simultaneously decreased in response to acidic pH. Other responding functional groups of genes mainly belonged to nitrogen uptake and metabolism (<it>amtB</it>, <it>nrtB</it>, <it>nirB</it>, <it>nirD</it>), methionine metabolism (<it>metA</it>, <it>metF</it>, <it>metH</it>, <it>metK</it>, <it>bmt </it>and <it>ahcY</it>) as well as ion transport systems (<it>sitABCD</it>, <it>phoCD</it>). 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.</p> <p>Conclusion</p> <p>It 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.</p>
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