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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
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 gluco...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749860/ https://www.ncbi.nlm.nih.gov/pubmed/19703276 http://dx.doi.org/10.1186/1471-2180-9-176 |
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author | Vázquez, Carlos Daniel Freyre-González, Julio A Gosset, Guillermo Loza, José Antonio Gutiérrez-Ríos, Rosa María |
author_facet | Vázquez, Carlos Daniel Freyre-González, Julio A Gosset, Guillermo Loza, José Antonio Gutiérrez-Ríos, Rosa María |
author_sort | Vázquez, Carlos Daniel |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2749860 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-27498602009-09-24 Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli Vázquez, Carlos Daniel Freyre-González, Julio A Gosset, Guillermo Loza, José Antonio Gutiérrez-Ríos, Rosa María BMC Microbiol Research article 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. BioMed Central 2009-08-24 /pmc/articles/PMC2749860/ /pubmed/19703276 http://dx.doi.org/10.1186/1471-2180-9-176 Text en Copyright ©2009 Vázquez et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research article Vázquez, Carlos Daniel Freyre-González, Julio A Gosset, Guillermo Loza, José Antonio Gutiérrez-Ríos, Rosa María Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli |
title | Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli |
title_full | Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli |
title_fullStr | Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli |
title_full_unstemmed | Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli |
title_short | Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli |
title_sort | identification of network topological units coordinating the global expression response to glucose in bacillus subtilis and its comparison to escherichia coli |
topic | Research article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749860/ https://www.ncbi.nlm.nih.gov/pubmed/19703276 http://dx.doi.org/10.1186/1471-2180-9-176 |
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