Limits...
Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation.

Müller FD, Treuner-Lange A, Heider J, Huntley SM, Higgs PI - BMC Genomics (2010)

Bottom Line: Most of the previously identified sporulation marker genes were significantly upregulated.Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate.These results suggest that microarray analysis of chemical-induced spore formation is an excellent system to specifically identify genes necessary for the core sporulation process of a Gram negative model organism for differentiation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.

ABSTRACT

Background: Myxococcus xanthus is a Gram negative bacterium that can differentiate into metabolically quiescent, environmentally resistant spores. Little is known about the mechanisms involved in differentiation in part because sporulation is normally initiated at the culmination of a complex starvation-induced developmental program and only inside multicellular fruiting bodies. To obtain a broad overview of the sporulation process and to identify novel genes necessary for differentiation, we instead performed global transcriptome analysis of an artificial chemically-induced sporulation process in which addition of glycerol to vegetatively growing liquid cultures of M. xanthus leads to rapid and synchronized differentiation of nearly all cells into myxospore-like entities.

Results: Our analyses identified 1 486 genes whose expression was significantly regulated at least two-fold within four hours of chemical-induced differentiation. Most of the previously identified sporulation marker genes were significantly upregulated. In contrast, most genes that are required to build starvation-induced multicellular fruiting bodies, but which are not required for sporulation per se, were not significantly regulated in our analysis. Analysis of functional gene categories significantly over-represented in the regulated genes, suggested large rearrangements in core metabolic pathways, and in genes involved in protein synthesis and fate. We used the microarray data to identify a novel operon of eight genes that, when mutated, rendered cells unable to produce viable chemical- or starvation-induced spores. Importantly, these mutants displayed no defects in building fruiting bodies, suggesting these genes are necessary for the core sporulation process. Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate.

Conclusions: These results suggest that microarray analysis of chemical-induced spore formation is an excellent system to specifically identify genes necessary for the core sporulation process of a Gram negative model organism for differentiation.

Show MeSH

Related in: MedlinePlus

Twenty percent of the protein coding genes are significantly regulated during glycerol-induced sporulation. A. A heat map displaying average fold-changes of 1 485 genes whose expression is significantly regulated in at least one time point ≥ two-fold above (yellow) or below (blue) vegetative cells at the indicated hours after induction with glycerol. Upregulated genes were first organized into two self-organizing maps of genes whose expression peaks early (class I) and late (class II) and sorted by descending fold induction at 0.5 and 2 hours, respectively. Downregulated genes were sorted by descending fold induction at 0.5 hours. The number of class I and class II upregulated and downregulated genes is indicated to the right according to the colour scheme in B. B. Functional characterization of gene expression patterns. The percent of significantly down- (blue), class I up- (yellow), and class II up- (orange) genes in the listed JCVI main role categories. Role assignments were modified as described in Materials and Methods. *: main role abbreviations: Fa & Pl metabolism: Fatty acid and phospholipid metabolism; Biosynthesis of cofactors etc.: Biosynthesis of cofactors, prosthetic groups, and carriers; Purines and pyrimidines: Purines, pyrimidines, nucleosides, and nucleotides.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2875238&req=5

Figure 1: Twenty percent of the protein coding genes are significantly regulated during glycerol-induced sporulation. A. A heat map displaying average fold-changes of 1 485 genes whose expression is significantly regulated in at least one time point ≥ two-fold above (yellow) or below (blue) vegetative cells at the indicated hours after induction with glycerol. Upregulated genes were first organized into two self-organizing maps of genes whose expression peaks early (class I) and late (class II) and sorted by descending fold induction at 0.5 and 2 hours, respectively. Downregulated genes were sorted by descending fold induction at 0.5 hours. The number of class I and class II upregulated and downregulated genes is indicated to the right according to the colour scheme in B. B. Functional characterization of gene expression patterns. The percent of significantly down- (blue), class I up- (yellow), and class II up- (orange) genes in the listed JCVI main role categories. Role assignments were modified as described in Materials and Methods. *: main role abbreviations: Fa & Pl metabolism: Fatty acid and phospholipid metabolism; Biosynthesis of cofactors etc.: Biosynthesis of cofactors, prosthetic groups, and carriers; Purines and pyrimidines: Purines, pyrimidines, nucleosides, and nucleotides.

Mentions: Analysis of the resulting microarray data revealed a total of 1 486 significantly regulated genes, corresponding to 22% of the analyzable orfs included on the chip. Of these regulated genes, 843 (13%) were upregulated and 643 (10%) downregulated. To validate the microarray data, the expression patterns of certain up- (sigB, sigC, mspC, prU), down- (Mxan_5543, atpE) and un-regulated (devR) genes were confirmed by real-time PCR (Additional file 1). The 843 significantly upregulated genes were next grouped into self organizing maps in which genes were clustered based on similar transcriptional expression patterns. Our analysis revealed two patterns of expression: genes whose expression peaked either at 0.5 - 1 hour (class I; 366 genes) or at 2-4 hours (class II; 477 genes) after induction with glycerol. These results are summarized in heat maps (Figure 1A) and in Additional file 2.


Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation.

Müller FD, Treuner-Lange A, Heider J, Huntley SM, Higgs PI - BMC Genomics (2010)

Twenty percent of the protein coding genes are significantly regulated during glycerol-induced sporulation. A. A heat map displaying average fold-changes of 1 485 genes whose expression is significantly regulated in at least one time point ≥ two-fold above (yellow) or below (blue) vegetative cells at the indicated hours after induction with glycerol. Upregulated genes were first organized into two self-organizing maps of genes whose expression peaks early (class I) and late (class II) and sorted by descending fold induction at 0.5 and 2 hours, respectively. Downregulated genes were sorted by descending fold induction at 0.5 hours. The number of class I and class II upregulated and downregulated genes is indicated to the right according to the colour scheme in B. B. Functional characterization of gene expression patterns. The percent of significantly down- (blue), class I up- (yellow), and class II up- (orange) genes in the listed JCVI main role categories. Role assignments were modified as described in Materials and Methods. *: main role abbreviations: Fa & Pl metabolism: Fatty acid and phospholipid metabolism; Biosynthesis of cofactors etc.: Biosynthesis of cofactors, prosthetic groups, and carriers; Purines and pyrimidines: Purines, pyrimidines, nucleosides, and nucleotides.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875238&req=5

Figure 1: Twenty percent of the protein coding genes are significantly regulated during glycerol-induced sporulation. A. A heat map displaying average fold-changes of 1 485 genes whose expression is significantly regulated in at least one time point ≥ two-fold above (yellow) or below (blue) vegetative cells at the indicated hours after induction with glycerol. Upregulated genes were first organized into two self-organizing maps of genes whose expression peaks early (class I) and late (class II) and sorted by descending fold induction at 0.5 and 2 hours, respectively. Downregulated genes were sorted by descending fold induction at 0.5 hours. The number of class I and class II upregulated and downregulated genes is indicated to the right according to the colour scheme in B. B. Functional characterization of gene expression patterns. The percent of significantly down- (blue), class I up- (yellow), and class II up- (orange) genes in the listed JCVI main role categories. Role assignments were modified as described in Materials and Methods. *: main role abbreviations: Fa & Pl metabolism: Fatty acid and phospholipid metabolism; Biosynthesis of cofactors etc.: Biosynthesis of cofactors, prosthetic groups, and carriers; Purines and pyrimidines: Purines, pyrimidines, nucleosides, and nucleotides.
Mentions: Analysis of the resulting microarray data revealed a total of 1 486 significantly regulated genes, corresponding to 22% of the analyzable orfs included on the chip. Of these regulated genes, 843 (13%) were upregulated and 643 (10%) downregulated. To validate the microarray data, the expression patterns of certain up- (sigB, sigC, mspC, prU), down- (Mxan_5543, atpE) and un-regulated (devR) genes were confirmed by real-time PCR (Additional file 1). The 843 significantly upregulated genes were next grouped into self organizing maps in which genes were clustered based on similar transcriptional expression patterns. Our analysis revealed two patterns of expression: genes whose expression peaked either at 0.5 - 1 hour (class I; 366 genes) or at 2-4 hours (class II; 477 genes) after induction with glycerol. These results are summarized in heat maps (Figure 1A) and in Additional file 2.

Bottom Line: Most of the previously identified sporulation marker genes were significantly upregulated.Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate.These results suggest that microarray analysis of chemical-induced spore formation is an excellent system to specifically identify genes necessary for the core sporulation process of a Gram negative model organism for differentiation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.

ABSTRACT

Background: Myxococcus xanthus is a Gram negative bacterium that can differentiate into metabolically quiescent, environmentally resistant spores. Little is known about the mechanisms involved in differentiation in part because sporulation is normally initiated at the culmination of a complex starvation-induced developmental program and only inside multicellular fruiting bodies. To obtain a broad overview of the sporulation process and to identify novel genes necessary for differentiation, we instead performed global transcriptome analysis of an artificial chemically-induced sporulation process in which addition of glycerol to vegetatively growing liquid cultures of M. xanthus leads to rapid and synchronized differentiation of nearly all cells into myxospore-like entities.

Results: Our analyses identified 1 486 genes whose expression was significantly regulated at least two-fold within four hours of chemical-induced differentiation. Most of the previously identified sporulation marker genes were significantly upregulated. In contrast, most genes that are required to build starvation-induced multicellular fruiting bodies, but which are not required for sporulation per se, were not significantly regulated in our analysis. Analysis of functional gene categories significantly over-represented in the regulated genes, suggested large rearrangements in core metabolic pathways, and in genes involved in protein synthesis and fate. We used the microarray data to identify a novel operon of eight genes that, when mutated, rendered cells unable to produce viable chemical- or starvation-induced spores. Importantly, these mutants displayed no defects in building fruiting bodies, suggesting these genes are necessary for the core sporulation process. Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate.

Conclusions: These results suggest that microarray analysis of chemical-induced spore formation is an excellent system to specifically identify genes necessary for the core sporulation process of a Gram negative model organism for differentiation.

Show MeSH
Related in: MedlinePlus