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Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.

Freyre-González JA, Manjarrez-Casas AM, Merino E, Martinez-Nuñez M, Perez-Rueda E, Gutiérrez-Ríos RM - BMC Syst Biol (2013)

Bottom Line: Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transcription factors, is the most extensively studied and the results, for a great number of model organisms, have been compiled making it possible the in silico construction of their corresponding transcriptional regulatory networks and the analysis of the biological relationships of the components of these intricate networks, that allows to elucidate the significant aspects of their organization and evolution.We confirm that the presence of paralogous proteins confers advantages to B. subtilis to adapt and select strategies to successfully face the extreme and changing environmental conditions in which it lives.The intricate organization is the product of a non-random network evolution that primarily follows a hierarchical organization based on the presence of transcription and σ factor, which is reflected in the connections that exist within and between modules.

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

ABSTRACT

Background: The regulation of gene expression at the transcriptional level is a fundamental process in prokaryotes. Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transcription factors, is the most extensively studied and the results, for a great number of model organisms, have been compiled making it possible the in silico construction of their corresponding transcriptional regulatory networks and the analysis of the biological relationships of the components of these intricate networks, that allows to elucidate the significant aspects of their organization and evolution.

Results: We present a thorough review of each regulatory element that constitutes the transcriptional regulatory network of Bacillus subtilis. For facilitating the discussion, we organized the network in topological modules. Our study highlight the importance of σ factors, some of them acting as master regulators which characterize modules by inter- or intra-connecting them and play a key role in the cascades that define relevant cellular processes in this organism. We discussed that some particular functions were distributed in more than one module and that some modules contained more than one related function. We confirm that the presence of paralogous proteins confers advantages to B. subtilis to adapt and select strategies to successfully face the extreme and changing environmental conditions in which it lives.

Conclusions: The intricate organization is the product of a non-random network evolution that primarily follows a hierarchical organization based on the presence of transcription and σ factor, which is reflected in the connections that exist within and between modules.

Show MeSH
B. subtilis presents different cell fates. TFs clustered in the cell differentiation module are devoted to different phenotypical subpopulations. Each color box emphasizes the group of TFs belonging to each related function.
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Figure 4: B. subtilis presents different cell fates. TFs clustered in the cell differentiation module are devoted to different phenotypical subpopulations. Each color box emphasizes the group of TFs belonging to each related function.

Mentions: Groups TFs involved in Cell differentiation, involving four master regulators: AbrB, DegU, ComK, and Spo0A [29], that coordinate in conjunction with other regulators the following well-defined cellular responses and fates: sporulation, competence, DNA protection, matrix and extracellular protein biogenesis, cannibalism, degradative enzyme synthesis, and nutritional limitation response (Figure 4 and Additional file 1: Table S3), that were clustered together in this module. In the Additional file 1, we discuss the direct and indirect influence of the master transcriptional regulators, on various differentiation processes and stress responses and its relationship with other TFs coordinating the above mention fates and cellular responses.


Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.

Freyre-González JA, Manjarrez-Casas AM, Merino E, Martinez-Nuñez M, Perez-Rueda E, Gutiérrez-Ríos RM - BMC Syst Biol (2013)

B. subtilis presents different cell fates. TFs clustered in the cell differentiation module are devoted to different phenotypical subpopulations. Each color box emphasizes the group of TFs belonging to each related function.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4225672&req=5

Figure 4: B. subtilis presents different cell fates. TFs clustered in the cell differentiation module are devoted to different phenotypical subpopulations. Each color box emphasizes the group of TFs belonging to each related function.
Mentions: Groups TFs involved in Cell differentiation, involving four master regulators: AbrB, DegU, ComK, and Spo0A [29], that coordinate in conjunction with other regulators the following well-defined cellular responses and fates: sporulation, competence, DNA protection, matrix and extracellular protein biogenesis, cannibalism, degradative enzyme synthesis, and nutritional limitation response (Figure 4 and Additional file 1: Table S3), that were clustered together in this module. In the Additional file 1, we discuss the direct and indirect influence of the master transcriptional regulators, on various differentiation processes and stress responses and its relationship with other TFs coordinating the above mention fates and cellular responses.

Bottom Line: Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transcription factors, is the most extensively studied and the results, for a great number of model organisms, have been compiled making it possible the in silico construction of their corresponding transcriptional regulatory networks and the analysis of the biological relationships of the components of these intricate networks, that allows to elucidate the significant aspects of their organization and evolution.We confirm that the presence of paralogous proteins confers advantages to B. subtilis to adapt and select strategies to successfully face the extreme and changing environmental conditions in which it lives.The intricate organization is the product of a non-random network evolution that primarily follows a hierarchical organization based on the presence of transcription and σ factor, which is reflected in the connections that exist within and between modules.

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. rmaria@ibt.unam.mx.

ABSTRACT

Background: The regulation of gene expression at the transcriptional level is a fundamental process in prokaryotes. Among the different kind of mechanisms modulating gene transcription, the one based on DNA binding transcription factors, is the most extensively studied and the results, for a great number of model organisms, have been compiled making it possible the in silico construction of their corresponding transcriptional regulatory networks and the analysis of the biological relationships of the components of these intricate networks, that allows to elucidate the significant aspects of their organization and evolution.

Results: We present a thorough review of each regulatory element that constitutes the transcriptional regulatory network of Bacillus subtilis. For facilitating the discussion, we organized the network in topological modules. Our study highlight the importance of σ factors, some of them acting as master regulators which characterize modules by inter- or intra-connecting them and play a key role in the cascades that define relevant cellular processes in this organism. We discussed that some particular functions were distributed in more than one module and that some modules contained more than one related function. We confirm that the presence of paralogous proteins confers advantages to B. subtilis to adapt and select strategies to successfully face the extreme and changing environmental conditions in which it lives.

Conclusions: The intricate organization is the product of a non-random network evolution that primarily follows a hierarchical organization based on the presence of transcription and σ factor, which is reflected in the connections that exist within and between modules.

Show MeSH