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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 discussed that some particular functions were distributed in more than one module and that some modules contained more than one related function.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.

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Respiratory functions. Regulatory cascade associated with the gene induction under low oxygen conditions (dark green circles). As described in the text, other TFs (light green circles) were also clustered in this module, for which functions in the adaptation to respiratory stress have been described.
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Figure 3: Respiratory functions. Regulatory cascade associated with the gene induction under low oxygen conditions (dark green circles). As described in the text, other TFs (light green circles) were also clustered in this module, for which functions in the adaptation to respiratory stress have been described.

Mentions: Or Respiration module includes all the TFs that are required for switching between aerobic and anaerobic growth (see Additional file 1: Table S2). The TFs belonging to this module are ArfM, HrcA, FNR, NsrR, ResD, and PhoP, which are highly inter-regulated in a hierarchical order (see Figures 2 and 3). The complex regulation of this module correlates with the fact that B. subtilis grows either by fermentation or anaerobically, using nitrate or nitrite as terminal electron acceptors [22].


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)

Respiratory functions. Regulatory cascade associated with the gene induction under low oxygen conditions (dark green circles). As described in the text, other TFs (light green circles) were also clustered in this module, for which functions in the adaptation to respiratory stress have been described.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Respiratory functions. Regulatory cascade associated with the gene induction under low oxygen conditions (dark green circles). As described in the text, other TFs (light green circles) were also clustered in this module, for which functions in the adaptation to respiratory stress have been described.
Mentions: Or Respiration module includes all the TFs that are required for switching between aerobic and anaerobic growth (see Additional file 1: Table S2). The TFs belonging to this module are ArfM, HrcA, FNR, NsrR, ResD, and PhoP, which are highly inter-regulated in a hierarchical order (see Figures 2 and 3). The complex regulation of this module correlates with the fact that B. subtilis grows either by fermentation or anaerobically, using nitrate or nitrite as terminal electron acceptors [22].

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 discussed that some particular functions were distributed in more than one module and that some modules contained more than one related function.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
Related in: MedlinePlus