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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.

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Related in: MedlinePlus

Representation of M. xanthuscore energy metabolism pathways significantly influenced at the transcriptional level during glycerol-induced sporulation. M. xanthus metabolic pathways identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database [47-49] were amended as described in the text and were examined for significantly regulated genes. Genes are designated as the four digit Mxan_ number. Significantly downregulated, upregulated class I, upregulated class II, and not significantly regulated genes are identified by blue, yellow, orange, and white outlined boxes, respectively. Entry sites of amino acids or fatty acids into the metabolic pathways are indicated in red. Consumption of activated sugars as precursors for spore coat components is indicated in green.
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Figure 2: Representation of M. xanthuscore energy metabolism pathways significantly influenced at the transcriptional level during glycerol-induced sporulation. M. xanthus metabolic pathways identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database [47-49] were amended as described in the text and were examined for significantly regulated genes. Genes are designated as the four digit Mxan_ number. Significantly downregulated, upregulated class I, upregulated class II, and not significantly regulated genes are identified by blue, yellow, orange, and white outlined boxes, respectively. Entry sites of amino acids or fatty acids into the metabolic pathways are indicated in red. Consumption of activated sugars as precursors for spore coat components is indicated in green.

Mentions: Further examination of "energy metabolism" subrole categories revealed that 35% (7/20; p = 1.1 × 10-3) and 30% (6/20; p = 3.0 × 10-2) of the genes assigned to the TCA cycle subcategory were down- and up-regulated, respectively. In addition, 39% (6/18; p = 1.8 × 10-2) of the genes assigned to the glycolysis/gluconeogenesis pathways were upregulated. Interestingly, 41% (13/39; p = 1.4 × 10-4) of the genes assigned to the "biosynthesis and degradation of polysaccharides" subrole category were upregulated. To integrate these observations, we examined which genes were significantly up- or down-regulated in the context of M. xanthus metabolic pathways. For these analyses, we started with the pathways assigned by the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways database [47-49] and amended the pathways based on previous literature and data from our analyses (Figure 2). These observations strongly suggest that during glycerol-induced sporulation, M. xanthus cells downregulate large portions of the TCA cycle, upregulate the glyoxylate shunt, and upregulate gluconeogenesis. Most of the upregulated genes in this pathway fall into the class I category of upregulated genes (yellow bars, Figure 2) suggesting these metabolic arrangements occur early in the glycerol-induced sporulation program. These data are consistent with previous studies of specific enzyme activities [50,51]. The net effect of these metabolic actions would likely be production of precursors to carbohydrate synthesis which is important for two reasons: 1) M. xanthus cells do not grow on carbohydrates [31] and obtain both carbon and energy from amino acids and fatty acids [52,53], and 2) carbohydrate production increases by 200% during glycerol-induced sporulation in both soluble and insoluble fractions [51] likely corresponding to protective or storage compounds (e.g. trehalose [30] and glycogen [54]) and spore coat polysaccharides [16], respectively).


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)

Representation of M. xanthuscore energy metabolism pathways significantly influenced at the transcriptional level during glycerol-induced sporulation. M. xanthus metabolic pathways identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database [47-49] were amended as described in the text and were examined for significantly regulated genes. Genes are designated as the four digit Mxan_ number. Significantly downregulated, upregulated class I, upregulated class II, and not significantly regulated genes are identified by blue, yellow, orange, and white outlined boxes, respectively. Entry sites of amino acids or fatty acids into the metabolic pathways are indicated in red. Consumption of activated sugars as precursors for spore coat components is indicated in green.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Representation of M. xanthuscore energy metabolism pathways significantly influenced at the transcriptional level during glycerol-induced sporulation. M. xanthus metabolic pathways identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database [47-49] were amended as described in the text and were examined for significantly regulated genes. Genes are designated as the four digit Mxan_ number. Significantly downregulated, upregulated class I, upregulated class II, and not significantly regulated genes are identified by blue, yellow, orange, and white outlined boxes, respectively. Entry sites of amino acids or fatty acids into the metabolic pathways are indicated in red. Consumption of activated sugars as precursors for spore coat components is indicated in green.
Mentions: Further examination of "energy metabolism" subrole categories revealed that 35% (7/20; p = 1.1 × 10-3) and 30% (6/20; p = 3.0 × 10-2) of the genes assigned to the TCA cycle subcategory were down- and up-regulated, respectively. In addition, 39% (6/18; p = 1.8 × 10-2) of the genes assigned to the glycolysis/gluconeogenesis pathways were upregulated. Interestingly, 41% (13/39; p = 1.4 × 10-4) of the genes assigned to the "biosynthesis and degradation of polysaccharides" subrole category were upregulated. To integrate these observations, we examined which genes were significantly up- or down-regulated in the context of M. xanthus metabolic pathways. For these analyses, we started with the pathways assigned by the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways database [47-49] and amended the pathways based on previous literature and data from our analyses (Figure 2). These observations strongly suggest that during glycerol-induced sporulation, M. xanthus cells downregulate large portions of the TCA cycle, upregulate the glyoxylate shunt, and upregulate gluconeogenesis. Most of the upregulated genes in this pathway fall into the class I category of upregulated genes (yellow bars, Figure 2) suggesting these metabolic arrangements occur early in the glycerol-induced sporulation program. These data are consistent with previous studies of specific enzyme activities [50,51]. The net effect of these metabolic actions would likely be production of precursors to carbohydrate synthesis which is important for two reasons: 1) M. xanthus cells do not grow on carbohydrates [31] and obtain both carbon and energy from amino acids and fatty acids [52,53], and 2) carbohydrate production increases by 200% during glycerol-induced sporulation in both soluble and insoluble fractions [51] likely corresponding to protective or storage compounds (e.g. trehalose [30] and glycogen [54]) and spore coat polysaccharides [16], respectively).

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