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Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli.

Vázquez CD, Freyre-González JA, Gosset G, Loza JA, Gutiérrez-Ríos RM - BMC Microbiol. (2009)

Bottom Line: In terms of topological functional units in both these bacteria, we found interconnected modules that cluster together genes relating to heat shock, respiratory functions, carbon and peroxide metabolism.Interestingly, B. subtilis functions not found in E. coli, such as sporulation and competence were shown to be interconnected, forming modules subject to catabolic repression at the level of transcription.Our results demonstrate that the response to glucose is partially conserved in model organisms E. coli and B. subtilis, including genes encoding basic functions such as transcription, translation, replication and genes involved in the central carbon metabolism.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamentos de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, Postal 510-3, Cuernavaca, Morelos 62250, México. cvazquez@ibt.unam.mx

ABSTRACT

Background: Glucose is the preferred carbon and energy source for Bacillus subtilis and Escherichia coli. A complex regulatory network coordinates gene expression, transport and enzymatic activities, in response to the presence of this sugar. We present a comparison of the cellular response to glucose in these two model organisms, using an approach combining global transcriptome and regulatory network analyses.

Results: Transcriptome data from strains grown in Luria-Bertani medium (LB) or LB+glucose (LB+G) were analyzed, in order to identify differentially transcribed genes in B. subtilis. We detected 503 genes in B. subtilis that change their relative transcript levels in the presence of glucose. A similar previous study identified 380 genes in E. coli, which respond to glucose. Catabolic repression was detected in the case of transport and metabolic interconversion activities for both bacteria in LB+G. We detected an increased capacity for de novo synthesis of nucleotides, amino acids and proteins. A comparison between orthologous genes revealed that global regulatory functions such as transcription, translation, replication and genes relating to the central carbon metabolism, presented similar changes in their levels of expression. An analysis of the regulatory network of a subset of genes in both organisms revealed that the set of regulatory proteins responsible for similar physiological responses observed in the transcriptome analysis are not orthologous. An example of this observation is that of transcription factors mediating catabolic repression for most of the genes that displayed reduced transcript levels in the case of both organisms. In terms of topological functional units in both these bacteria, we found interconnected modules that cluster together genes relating to heat shock, respiratory functions, carbon and peroxide metabolism. Interestingly, B. subtilis functions not found in E. coli, such as sporulation and competence were shown to be interconnected, forming modules subject to catabolic repression at the level of transcription.

Conclusion: Our results demonstrate that the response to glucose is partially conserved in model organisms E. coli and B. subtilis, including genes encoding basic functions such as transcription, translation, replication and genes involved in the central carbon metabolism.

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A metabolic view of the transcriptome profile of B. subtilis, comparing growth in LB+G to that in LB. Genes displaying higher and lower transcript levels, due to the presence of glucose are shown in red and green respectively. Abbreviations: AcCoA, acetyl coenzyme-A; Ac~P, acetyl phosphate; AKG, α-ketoglutarate; CIT, citrate; F1,6BP, fructose-1,6-bisphosphate; F6P, fructose-6-phosphate; FUM, fumarate; G3P, glycerol-3-phosphate; G6P, glucose-6-phosphate; ICIT, isocitrate; MAL, malate;OAA, oxaloacetate; PEP, phosphoenolpyruvate; PYR, pyruvate; SUC, succinate; SUCCoA, succinyl-CoA;. G2P 2-phospho-glycerate.
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Figure 1: A metabolic view of the transcriptome profile of B. subtilis, comparing growth in LB+G to that in LB. Genes displaying higher and lower transcript levels, due to the presence of glucose are shown in red and green respectively. Abbreviations: AcCoA, acetyl coenzyme-A; Ac~P, acetyl phosphate; AKG, α-ketoglutarate; CIT, citrate; F1,6BP, fructose-1,6-bisphosphate; F6P, fructose-6-phosphate; FUM, fumarate; G3P, glycerol-3-phosphate; G6P, glucose-6-phosphate; ICIT, isocitrate; MAL, malate;OAA, oxaloacetate; PEP, phosphoenolpyruvate; PYR, pyruvate; SUC, succinate; SUCCoA, succinyl-CoA;. G2P 2-phospho-glycerate.

Mentions: We performed an analysis of transcriptome data obtained from previous reports of experiments, employing B. subtilis [8]. Following the procedure described in the methods section, 504 genes were found to display significant differential expression, when grown in either the absence or presence of glucose and these were compared (see Additional File 1: Table 1SM). In figure 1, we present the genes with known functions, where transcription was found to consist of a response to the presence of glucose in LB medium (LB+G). Among this set of genes, we found those induced in the presence of glucose, to be related to transport and metabolism, for example the general PTS protein enzyme I and the glucose-specific IICBGlc permease, as well as the pgk, pgm, eno and pdhC genes, which encode enzymes from the glycolytic pathway. The transcriptional activation of the aforementioned genes is expected to increase the cellular glucose capacity for transport and catabolism. On the other hand, down-regulation was observed in the case of genes encoding most of the enzymes from the TCA cycle and the glyoxylate bypass [7].


Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli.

Vázquez CD, Freyre-González JA, Gosset G, Loza JA, Gutiérrez-Ríos RM - BMC Microbiol. (2009)

A metabolic view of the transcriptome profile of B. subtilis, comparing growth in LB+G to that in LB. Genes displaying higher and lower transcript levels, due to the presence of glucose are shown in red and green respectively. Abbreviations: AcCoA, acetyl coenzyme-A; Ac~P, acetyl phosphate; AKG, α-ketoglutarate; CIT, citrate; F1,6BP, fructose-1,6-bisphosphate; F6P, fructose-6-phosphate; FUM, fumarate; G3P, glycerol-3-phosphate; G6P, glucose-6-phosphate; ICIT, isocitrate; MAL, malate;OAA, oxaloacetate; PEP, phosphoenolpyruvate; PYR, pyruvate; SUC, succinate; SUCCoA, succinyl-CoA;. G2P 2-phospho-glycerate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2749860&req=5

Figure 1: A metabolic view of the transcriptome profile of B. subtilis, comparing growth in LB+G to that in LB. Genes displaying higher and lower transcript levels, due to the presence of glucose are shown in red and green respectively. Abbreviations: AcCoA, acetyl coenzyme-A; Ac~P, acetyl phosphate; AKG, α-ketoglutarate; CIT, citrate; F1,6BP, fructose-1,6-bisphosphate; F6P, fructose-6-phosphate; FUM, fumarate; G3P, glycerol-3-phosphate; G6P, glucose-6-phosphate; ICIT, isocitrate; MAL, malate;OAA, oxaloacetate; PEP, phosphoenolpyruvate; PYR, pyruvate; SUC, succinate; SUCCoA, succinyl-CoA;. G2P 2-phospho-glycerate.
Mentions: We performed an analysis of transcriptome data obtained from previous reports of experiments, employing B. subtilis [8]. Following the procedure described in the methods section, 504 genes were found to display significant differential expression, when grown in either the absence or presence of glucose and these were compared (see Additional File 1: Table 1SM). In figure 1, we present the genes with known functions, where transcription was found to consist of a response to the presence of glucose in LB medium (LB+G). Among this set of genes, we found those induced in the presence of glucose, to be related to transport and metabolism, for example the general PTS protein enzyme I and the glucose-specific IICBGlc permease, as well as the pgk, pgm, eno and pdhC genes, which encode enzymes from the glycolytic pathway. The transcriptional activation of the aforementioned genes is expected to increase the cellular glucose capacity for transport and catabolism. On the other hand, down-regulation was observed in the case of genes encoding most of the enzymes from the TCA cycle and the glyoxylate bypass [7].

Bottom Line: In terms of topological functional units in both these bacteria, we found interconnected modules that cluster together genes relating to heat shock, respiratory functions, carbon and peroxide metabolism.Interestingly, B. subtilis functions not found in E. coli, such as sporulation and competence were shown to be interconnected, forming modules subject to catabolic repression at the level of transcription.Our results demonstrate that the response to glucose is partially conserved in model organisms E. coli and B. subtilis, including genes encoding basic functions such as transcription, translation, replication and genes involved in the central carbon metabolism.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamentos de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, Postal 510-3, Cuernavaca, Morelos 62250, México. cvazquez@ibt.unam.mx

ABSTRACT

Background: Glucose is the preferred carbon and energy source for Bacillus subtilis and Escherichia coli. A complex regulatory network coordinates gene expression, transport and enzymatic activities, in response to the presence of this sugar. We present a comparison of the cellular response to glucose in these two model organisms, using an approach combining global transcriptome and regulatory network analyses.

Results: Transcriptome data from strains grown in Luria-Bertani medium (LB) or LB+glucose (LB+G) were analyzed, in order to identify differentially transcribed genes in B. subtilis. We detected 503 genes in B. subtilis that change their relative transcript levels in the presence of glucose. A similar previous study identified 380 genes in E. coli, which respond to glucose. Catabolic repression was detected in the case of transport and metabolic interconversion activities for both bacteria in LB+G. We detected an increased capacity for de novo synthesis of nucleotides, amino acids and proteins. A comparison between orthologous genes revealed that global regulatory functions such as transcription, translation, replication and genes relating to the central carbon metabolism, presented similar changes in their levels of expression. An analysis of the regulatory network of a subset of genes in both organisms revealed that the set of regulatory proteins responsible for similar physiological responses observed in the transcriptome analysis are not orthologous. An example of this observation is that of transcription factors mediating catabolic repression for most of the genes that displayed reduced transcript levels in the case of both organisms. In terms of topological functional units in both these bacteria, we found interconnected modules that cluster together genes relating to heat shock, respiratory functions, carbon and peroxide metabolism. Interestingly, B. subtilis functions not found in E. coli, such as sporulation and competence were shown to be interconnected, forming modules subject to catabolic repression at the level of transcription.

Conclusion: Our results demonstrate that the response to glucose is partially conserved in model organisms E. coli and B. subtilis, including genes encoding basic functions such as transcription, translation, replication and genes involved in the central carbon metabolism.

Show MeSH
Related in: MedlinePlus