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Genome-wide transcriptome analysis reveals that a pleiotropic antibiotic regulator, AfsS, modulates nutritional stress response in Streptomyces coelicolor A3(2).

Lian W, Jayapal KP, Charaniya S, Mehra S, Glod F, Kyung YS, Sherman DH, Hu WS - BMC Genomics (2008)

Bottom Line: Overexpression of afsS in S. coelicolor and certain related species causes antibiotic stimulatory effects in the host organism.In almost every case, the effect of afsS disruption was not observed until the onset of stationary phase.Our data suggests a comprehensive role for S. coelicolor AfsS as a master regulator of both antibiotic synthesis and nutritional stress response, reminiscent of alternative sigma factors found in several bacteria.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE., Minneapolis, MN 55455, USA. wei.lian@abbott.com

ABSTRACT

Background: A small "sigma-like" protein, AfsS, pleiotropically regulates antibiotic biosynthesis in Streptomyces coelicolor. Overexpression of afsS in S. coelicolor and certain related species causes antibiotic stimulatory effects in the host organism. Although recent studies have uncovered some of the upstream events activating this gene, the mechanisms through which this signal is relayed downstream leading to the eventual induction of antibiotic pathways remain unclear.

Results: In this study, we employed whole-genome DNA microarrays and quantitative PCRs to examine the transcriptome of an afsS disruption mutant that is completely deficient in the production of actinorhodin, a major S. coelicolor antibiotic. The production of undecylprodigiosin, another prominent antibiotic, was, however, perturbed only marginally in the mutant. Principal component analysis of temporal gene expression profiles identified two major gene classes each exhibiting a distinct coordinate differential expression pattern. Surprisingly, nearly 70% of the >117 differentially expressed genes were conspicuously associated with nutrient starvation response, particularly those of phosphate, nitrogen and sulfate. Furthermore, expression profiles of some transcriptional regulators including at least two sigma factors were perturbed in the mutant. In almost every case, the effect of afsS disruption was not observed until the onset of stationary phase.

Conclusion: Our data suggests a comprehensive role for S. coelicolor AfsS as a master regulator of both antibiotic synthesis and nutritional stress response, reminiscent of alternative sigma factors found in several bacteria.

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Related in: MedlinePlus

Validation of microarray results using qRT-PCRs. A plot of log2 expression ratios for 11 different genes (see text) relative to that from the 18 h sample of M145 culture. Samples from 18 h (○), 19 h (□), 21 h (△) and 38 h (◇) for M145 are shown in blue while 17 h (○), 19 h (□), 21 h (△) and 37 h (◇) for YSK4425 are shown in red. A least square straight line fit is also shown.
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Figure 3: Validation of microarray results using qRT-PCRs. A plot of log2 expression ratios for 11 different genes (see text) relative to that from the 18 h sample of M145 culture. Samples from 18 h (○), 19 h (□), 21 h (△) and 38 h (◇) for M145 are shown in blue while 17 h (○), 19 h (□), 21 h (△) and 37 h (◇) for YSK4425 are shown in red. A least square straight line fit is also shown.

Mentions: Quantitative real-time PCRs were performed on reverse transcribed RNA samples to independently validate the microarray results. A total of 11 genes (actIII, redD, redP, phoR, glnII, glnK, cysD, absA1/A2, scbA and scbR) were chosen for analysis. Relative expression levels from qRT-PCR for samples 18 h, 19 h, 21 h and 38 h in M145 and 17 h, 19 h, 21 h and 37 h in YSK4425 with respect to the 18 h of M145 were plotted against those obtained from microarray experiments (Figure 3). The comparison indicates a good concordance between qRT-PCR and microarray results. We note that the range of dynamics for relative log2 ratios obtained from qRT-PCR (-4 to +6) was significantly higher than that from microarray (-2 to +5), indicating that qRT-PCRs are more sensitive particularly in low expression ranges. This probably reflects on the Pearson's correlation coefficient for the plot, resulting in lower value than what could be expected.


Genome-wide transcriptome analysis reveals that a pleiotropic antibiotic regulator, AfsS, modulates nutritional stress response in Streptomyces coelicolor A3(2).

Lian W, Jayapal KP, Charaniya S, Mehra S, Glod F, Kyung YS, Sherman DH, Hu WS - BMC Genomics (2008)

Validation of microarray results using qRT-PCRs. A plot of log2 expression ratios for 11 different genes (see text) relative to that from the 18 h sample of M145 culture. Samples from 18 h (○), 19 h (□), 21 h (△) and 38 h (◇) for M145 are shown in blue while 17 h (○), 19 h (□), 21 h (△) and 37 h (◇) for YSK4425 are shown in red. A least square straight line fit is also shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2267785&req=5

Figure 3: Validation of microarray results using qRT-PCRs. A plot of log2 expression ratios for 11 different genes (see text) relative to that from the 18 h sample of M145 culture. Samples from 18 h (○), 19 h (□), 21 h (△) and 38 h (◇) for M145 are shown in blue while 17 h (○), 19 h (□), 21 h (△) and 37 h (◇) for YSK4425 are shown in red. A least square straight line fit is also shown.
Mentions: Quantitative real-time PCRs were performed on reverse transcribed RNA samples to independently validate the microarray results. A total of 11 genes (actIII, redD, redP, phoR, glnII, glnK, cysD, absA1/A2, scbA and scbR) were chosen for analysis. Relative expression levels from qRT-PCR for samples 18 h, 19 h, 21 h and 38 h in M145 and 17 h, 19 h, 21 h and 37 h in YSK4425 with respect to the 18 h of M145 were plotted against those obtained from microarray experiments (Figure 3). The comparison indicates a good concordance between qRT-PCR and microarray results. We note that the range of dynamics for relative log2 ratios obtained from qRT-PCR (-4 to +6) was significantly higher than that from microarray (-2 to +5), indicating that qRT-PCRs are more sensitive particularly in low expression ranges. This probably reflects on the Pearson's correlation coefficient for the plot, resulting in lower value than what could be expected.

Bottom Line: Overexpression of afsS in S. coelicolor and certain related species causes antibiotic stimulatory effects in the host organism.In almost every case, the effect of afsS disruption was not observed until the onset of stationary phase.Our data suggests a comprehensive role for S. coelicolor AfsS as a master regulator of both antibiotic synthesis and nutritional stress response, reminiscent of alternative sigma factors found in several bacteria.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE., Minneapolis, MN 55455, USA. wei.lian@abbott.com

ABSTRACT

Background: A small "sigma-like" protein, AfsS, pleiotropically regulates antibiotic biosynthesis in Streptomyces coelicolor. Overexpression of afsS in S. coelicolor and certain related species causes antibiotic stimulatory effects in the host organism. Although recent studies have uncovered some of the upstream events activating this gene, the mechanisms through which this signal is relayed downstream leading to the eventual induction of antibiotic pathways remain unclear.

Results: In this study, we employed whole-genome DNA microarrays and quantitative PCRs to examine the transcriptome of an afsS disruption mutant that is completely deficient in the production of actinorhodin, a major S. coelicolor antibiotic. The production of undecylprodigiosin, another prominent antibiotic, was, however, perturbed only marginally in the mutant. Principal component analysis of temporal gene expression profiles identified two major gene classes each exhibiting a distinct coordinate differential expression pattern. Surprisingly, nearly 70% of the >117 differentially expressed genes were conspicuously associated with nutrient starvation response, particularly those of phosphate, nitrogen and sulfate. Furthermore, expression profiles of some transcriptional regulators including at least two sigma factors were perturbed in the mutant. In almost every case, the effect of afsS disruption was not observed until the onset of stationary phase.

Conclusion: Our data suggests a comprehensive role for S. coelicolor AfsS as a master regulator of both antibiotic synthesis and nutritional stress response, reminiscent of alternative sigma factors found in several bacteria.

Show MeSH
Related in: MedlinePlus