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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 |
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Springer Science and Business Media LLC
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| Schlagwörter: |
| author_facet |
Hellweg, Christoph Pühler, Alfred Weidner, Stefan Hellweg, Christoph Pühler, Alfred Weidner, Stefan |
|---|---|
| author |
Hellweg, Christoph Pühler, Alfred Weidner, Stefan |
| spellingShingle |
Hellweg, Christoph Pühler, Alfred Weidner, Stefan BMC Microbiology The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH Microbiology (medical) Microbiology |
| author_sort |
hellweg, christoph |
| spelling |
Hellweg, Christoph Pühler, Alfred Weidner, Stefan 1471-2180 Springer Science and Business Media LLC Microbiology (medical) Microbiology http://dx.doi.org/10.1186/1471-2180-9-37 <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> The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH BMC Microbiology |
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10.1186/1471-2180-9-37 |
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Springer Science and Business Media LLC, 2009 |
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Springer Science and Business Media LLC, 2009 |
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hellweg2009thetimecourseofthetranscriptomicresponseofsinorhizobiummeliloti1021followingashifttoacidicph |
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2009 |
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Springer Science and Business Media LLC |
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BMC Microbiology |
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49 |
| title |
The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_unstemmed |
The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_full |
The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_fullStr |
The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_full_unstemmed |
The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_short |
The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_sort |
the time course of the transcriptomic response of sinorhizobium meliloti1021 following a shift to acidic ph |
| topic |
Microbiology (medical) Microbiology |
| url |
http://dx.doi.org/10.1186/1471-2180-9-37 |
| publishDate |
2009 |
| physical |
|
| description |
<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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| description | <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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| imprint | Springer Science and Business Media LLC, 2009 |
| imprint_str_mv | Springer Science and Business Media LLC, 2009 |
| institution | DE-Gla1, DE-Zi4, DE-15, DE-Rs1, DE-Pl11, DE-105, DE-14, DE-Ch1, DE-L229, DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161 |
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| spelling | Hellweg, Christoph Pühler, Alfred Weidner, Stefan 1471-2180 Springer Science and Business Media LLC Microbiology (medical) Microbiology http://dx.doi.org/10.1186/1471-2180-9-37 <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> The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH BMC Microbiology |
| spellingShingle | Hellweg, Christoph, Pühler, Alfred, Weidner, Stefan, BMC Microbiology, The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH, Microbiology (medical), Microbiology |
| title | The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_full | The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_fullStr | The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_full_unstemmed | The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_short | The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| title_sort | the time course of the transcriptomic response of sinorhizobium meliloti1021 following a shift to acidic ph |
| title_unstemmed | The time course of the transcriptomic response of Sinorhizobium meliloti1021 following a shift to acidic pH |
| topic | Microbiology (medical), Microbiology |
| url | http://dx.doi.org/10.1186/1471-2180-9-37 |