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The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH
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| Zeitschriftentitel: | BMC Microbiology |
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| Personen und Körperschaften: | , , |
| In: | BMC Microbiology, 9, 2009, 1 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Springer Science and Business Media LLC
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| Schlagwörter: |
| Zusammenfassung: | <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>The symbiotic soil bacterium <jats:italic>Sinorhizobium meliloti</jats:italic> often has to face low pH in its natural habitats. To identify genes responding to pH stress a global transcriptional analysis of <jats:italic>S. meliloti</jats:italic> 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.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>The results display a versatile response of <jats:italic>S. meliloti</jats:italic> 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 <jats:italic>lpiA</jats:italic>, <jats:italic>degP1</jats:italic>, <jats:italic>cah</jats:italic>, <jats:italic>exoV</jats:italic> and <jats:italic>exoH</jats:italic> 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 (<jats:italic>exoY</jats:italic>, <jats:italic>exoQ</jats:italic>, <jats:italic>exoW</jats:italic>, <jats:italic>exoV</jats:italic>, <jats:italic>exoT</jats:italic>, <jats:italic>exoH</jats:italic>, <jats:italic>exoK exoL</jats:italic>, <jats:italic>exoO</jats:italic>, <jats:italic>exoN</jats:italic>, <jats:italic>exoP</jats:italic>) were up-regulated, the expression level of the flagellar and chemotaxis genes (<jats:italic>visR</jats:italic>, <jats:italic>motA, flgF, flgB, flgC, fliE, flgG, flgE, flgL, flbT</jats:italic>, <jats:italic>mcpU</jats:italic>) simultaneously decreased in response to acidic pH. Other responding functional groups of genes mainly belonged to nitrogen uptake and metabolism (<jats:italic>amtB</jats:italic>, <jats:italic>nrtB</jats:italic>, <jats:italic>nirB</jats:italic>, <jats:italic>nirD</jats:italic>), methionine metabolism (<jats:italic>metA</jats:italic>, <jats:italic>metF</jats:italic>, <jats:italic>metH</jats:italic>, <jats:italic>metK</jats:italic>, <jats:italic>bmt</jats:italic> and <jats:italic>ahcY</jats:italic>) as well as ion transport systems (<jats:italic>sitABCD</jats:italic>, <jats:italic>phoCD</jats:italic>). 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.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion</jats:title> <jats: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.</jats:p> </jats:sec> |
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| ISSN: |
1471-2180
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| DOI: | 10.1186/1471-2180-9-37 |