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Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network


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Publication Date: 2015-01-09

Journal Title: Molecular BioSystems

Publisher: Royal Society of Chemistry

Volume: 11

Pages: 930-941

Language: English

Type: Article

Metadata: Show full item record

Citation: Kumar, S., Vendruscolo, M., Singh, A., Kumard, D., & Samal, A. (2015). Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network. Molecular BioSystems, 11 930-941.

Description: This is the author accepted manuscript. The final version is available from the Royal Society of Chemistry via http://dx.doi.org/10.1039/C4MB00298A

Abstract: The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these ‘transcriptional regulatory networks’ (TRNs) in bacteria have an inherently hierarchical architecture, although the design principles and the specific advantages offered by this type of organization have not yet been fully elucidated. In this study, we focussed on the hierarchical structure of the TRN of the gram-positive bacterium Bacillus subtilis and performed a comparative analysis with the TRN of the gram-negative bacterium Escherichia coli. Using a graph–theoretic approach, we organized the transcription factors (TFs) and σ-factors in the TRNs of B. subtilis and E. coli into three hierarchical levels (Top, Middle and Bottom) and studied several structural and functional properties across them. In addition to many similarities, we found also specific differences, explaining the majority of them with variations in the distribution of σ-factors across the hierarchical levels in the two organisms. We then investigated the control of target metabolic genes by transcriptional regulators to characterize the differential regulation of three distinct metabolic subsystems (catabolism, anabolism and central energy metabolism). These results suggest that the hierarchical architecture that we observed in B. subtilis represents an effective organization of its TRN to achieve flexibility in response to a wide range of diverse stimuli.

Sponsorship: SK acknowledges The Institute of Mathematical Sciences for hospitality, University Grants Commission (UGC) India for Senior Research Fellowship, and University of Delhi grant DRCH/R&D/2013–2014/4155 for infrastructural support.

Identifiers:

This record's URL: http://dx.doi.org/10.1039/C4MB00298Ahttp://www.repository.cam.ac.uk/handle/1810/248833





Author: Kumar, SanthustVendruscolo, MicheleSingh, AmitKumard, DhirajSamal, Areejit

Source: https://www.repository.cam.ac.uk/handle/1810/248833



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