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

Kumar, Santhust and Vendruscolo, Michele and Singh, Amit and Kumar, Dhiraj and Samal, Areejit (2015) Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network. In: MOLECULAR BIOSYSTEMS, 11 (3). pp. 930-941.

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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 sigma-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 s-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.

Item Type:	Journal Article
Publication:	MOLECULAR BIOSYSTEMS
Publisher:	ROYAL SOC CHEMISTRY
Additional Information:	Copy right for this article belongs to the ROYAL SOC CHEMISTRY, THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND
Keywords:	ESCHERICHIA-COLI K-12; BACILLUS-SUBTILIS; COMPLEX NETWORKS; GENOMIC ANALYSIS; BIOLOGICAL NETWORKS; OPERON ORGANIZATION; E. COLI; EVOLUTION; DATABASE; INFORMATION
Department/Centre:	Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited:	20 Apr 2015 07:42
Last Modified:	20 Apr 2015 07:42
URI:	http://eprints.iisc.ac.in/id/eprint/51265

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