Limits...
The time course of the transcriptomic response of Sinorhizobium meliloti 1021 following a shift to acidic pH.

Hellweg C, Pühler A, Weidner S - BMC Microbiol. (2009)

Bottom Line: Among the strongest up-regulated genes lpiA, degP1, cah, exoV and exoH were found.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, Germany. Christoph.Hellweg@Genetik.Uni-Bielefeld.DE

ABSTRACT

Background: The 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.

Results: The 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.

Conclusion: 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.

Show MeSH

Related in: MedlinePlus

Map of genes in the EPS I biosynthesis region on pSymB and their expression in response to acidic pH. The EPS I biosynthesis gene region on pSymB is schematically displayed with its genes given by open arrows coloured according to the K-means cluster distribution. Gene names are given below. Black arrows indicate known operon structures in this region. The graph above shows on the Y-axis the time after pH-shift and on the Z-axis for each time point the expression of the corresponding genes by the M value.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2651895&req=5

Figure 4: Map of genes in the EPS I biosynthesis region on pSymB and their expression in response to acidic pH. The EPS I biosynthesis gene region on pSymB is schematically displayed with its genes given by open arrows coloured according to the K-means cluster distribution. Gene names are given below. Black arrows indicate known operon structures in this region. The graph above shows on the Y-axis the time after pH-shift and on the Z-axis for each time point the expression of the corresponding genes by the M value.

Mentions: The regulator coding gene chvI was with most of the exo genes distributed to cluster B. Like in A. tumefaciens the gene chvI was up-regulated together with several genes responsible for the succinoglycan biosynthesis [50], although it is believed that chvI is a negative regulator of the exo genes [51]. A closer view on the individual expression levels of the genes of the EPS I biosynthesis gene cluster on pSymB during the time course (Fig. 4) reveals the high induction levels for the majority of the exo genes. The maximum induction in the observation period was always reached at 63 minutes after pH shift. Besides the eight exo genes found in cluster B, three exo genes grouped in cluster A and C. The exo genes in cluster A (exoV and exoH) were among the strongest up-regulated genes in this experiment. The products of these genes are responsible for the final steps of the EPS I biosynthesis. They are involved in the succinylation and pyruvilation of EPS I. It could already be shown for S. meliloti that a mutant strain of exoH is sensitive to low pH [52], indicating a particular impact of exoH on the pH tolerance and of the EPS I biosynthesis genes on the pH tolerance in general. The higher expression value of exoH compared to other exo genes might also be caused by its position as the first gene in a large operon (exoHKLAMONP) [53]. The central genes of this operon (exoA and exoM) did not show a significant change in their expression level during the time course in contrast to the bordering genes. This might be caused by mRNA instability and degradation effects. Three predicted open reading frames of unknown function within the exo gene region (smb21673, smb20952 and smb20953) did not show a differential expression during the time course indicating that they are not protein coding or that they are not connected to the EPS I biosynthesis. Overall the observed induction of exo genes is in agreement with the mucoid phenotype observed for S. meliloti after growing on low pH plates (data not shown). In low pH soils this response could be a strategy of the cell to establish a more favourable microenvironment by secreting succinoglycan. It was shown that an EPS I overproduction results in a reduced nodulation efficiency [54], therefore the induction of EPS I biosynthesis genes could also be one of the reasons for the observed limited nodulation efficiency of rhizobia in low pH soils [2].


The time course of the transcriptomic response of Sinorhizobium meliloti 1021 following a shift to acidic pH.

Hellweg C, Pühler A, Weidner S - BMC Microbiol. (2009)

Map of genes in the EPS I biosynthesis region on pSymB and their expression in response to acidic pH. The EPS I biosynthesis gene region on pSymB is schematically displayed with its genes given by open arrows coloured according to the K-means cluster distribution. Gene names are given below. Black arrows indicate known operon structures in this region. The graph above shows on the Y-axis the time after pH-shift and on the Z-axis for each time point the expression of the corresponding genes by the M value.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651895&req=5

Figure 4: Map of genes in the EPS I biosynthesis region on pSymB and their expression in response to acidic pH. The EPS I biosynthesis gene region on pSymB is schematically displayed with its genes given by open arrows coloured according to the K-means cluster distribution. Gene names are given below. Black arrows indicate known operon structures in this region. The graph above shows on the Y-axis the time after pH-shift and on the Z-axis for each time point the expression of the corresponding genes by the M value.
Mentions: The regulator coding gene chvI was with most of the exo genes distributed to cluster B. Like in A. tumefaciens the gene chvI was up-regulated together with several genes responsible for the succinoglycan biosynthesis [50], although it is believed that chvI is a negative regulator of the exo genes [51]. A closer view on the individual expression levels of the genes of the EPS I biosynthesis gene cluster on pSymB during the time course (Fig. 4) reveals the high induction levels for the majority of the exo genes. The maximum induction in the observation period was always reached at 63 minutes after pH shift. Besides the eight exo genes found in cluster B, three exo genes grouped in cluster A and C. The exo genes in cluster A (exoV and exoH) were among the strongest up-regulated genes in this experiment. The products of these genes are responsible for the final steps of the EPS I biosynthesis. They are involved in the succinylation and pyruvilation of EPS I. It could already be shown for S. meliloti that a mutant strain of exoH is sensitive to low pH [52], indicating a particular impact of exoH on the pH tolerance and of the EPS I biosynthesis genes on the pH tolerance in general. The higher expression value of exoH compared to other exo genes might also be caused by its position as the first gene in a large operon (exoHKLAMONP) [53]. The central genes of this operon (exoA and exoM) did not show a significant change in their expression level during the time course in contrast to the bordering genes. This might be caused by mRNA instability and degradation effects. Three predicted open reading frames of unknown function within the exo gene region (smb21673, smb20952 and smb20953) did not show a differential expression during the time course indicating that they are not protein coding or that they are not connected to the EPS I biosynthesis. Overall the observed induction of exo genes is in agreement with the mucoid phenotype observed for S. meliloti after growing on low pH plates (data not shown). In low pH soils this response could be a strategy of the cell to establish a more favourable microenvironment by secreting succinoglycan. It was shown that an EPS I overproduction results in a reduced nodulation efficiency [54], therefore the induction of EPS I biosynthesis genes could also be one of the reasons for the observed limited nodulation efficiency of rhizobia in low pH soils [2].

Bottom Line: Among the strongest up-regulated genes lpiA, degP1, cah, exoV and exoH were found.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, Germany. Christoph.Hellweg@Genetik.Uni-Bielefeld.DE

ABSTRACT

Background: The 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.

Results: The 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.

Conclusion: 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.

Show MeSH
Related in: MedlinePlus