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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.

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Related in: MedlinePlus

Cross-talk between modules. Master regulators (hubs) interconnect functional modules. At the higher levels, each master regulator is indicated. The color of each TF relates it to the module to which it belongs. We also show (top left) four disconnected groups that represent modules that are not interconnected by master regulators.
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Figure 2: Cross-talk between modules. Master regulators (hubs) interconnect functional modules. At the higher levels, each master regulator is indicated. The color of each TF relates it to the module to which it belongs. We also show (top left) four disconnected groups that represent modules that are not interconnected by master regulators.

Mentions: In a posterior step, we extracted a sub-network consisting of only the regulatory interactions of all known B. subtilis TFs and σ factors (54 and 16, respectively). We excluded σA interactions from this sub-network because, as a housekeeping factor, σA is tightly connected to almost every node of the network (with an outcoming connectivity of 782, connecting 46.5% of the genes in the network), generating a mega-module that encompasses all the basic physiological functions described in B. subtilis. Our resulting TRN was composed of 71 nodes and 81 edges and is supported by strong experimental evidence. The data were used as input to perform a hierarchical agglomerative average linkage clustering. This analysis revealed nine discrete modules (Additional file 1: Figure S1) whose genes clearly correlate with a metabolic or specific function (Figure 2), as reported for E. coli and M. tuberculosis[6,11,12].


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)

Cross-talk between modules. Master regulators (hubs) interconnect functional modules. At the higher levels, each master regulator is indicated. The color of each TF relates it to the module to which it belongs. We also show (top left) four disconnected groups that represent modules that are not interconnected by master regulators.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Cross-talk between modules. Master regulators (hubs) interconnect functional modules. At the higher levels, each master regulator is indicated. The color of each TF relates it to the module to which it belongs. We also show (top left) four disconnected groups that represent modules that are not interconnected by master regulators.
Mentions: In a posterior step, we extracted a sub-network consisting of only the regulatory interactions of all known B. subtilis TFs and σ factors (54 and 16, respectively). We excluded σA interactions from this sub-network because, as a housekeeping factor, σA is tightly connected to almost every node of the network (with an outcoming connectivity of 782, connecting 46.5% of the genes in the network), generating a mega-module that encompasses all the basic physiological functions described in B. subtilis. Our resulting TRN was composed of 71 nodes and 81 edges and is supported by strong experimental evidence. The data were used as input to perform a hierarchical agglomerative average linkage clustering. This analysis revealed nine discrete modules (Additional file 1: Figure S1) whose genes clearly correlate with a metabolic or specific function (Figure 2), as reported for E. coli and M. tuberculosis[6,11,12].

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
Related in: MedlinePlus