Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis.

Rinki Chauhan,Janani Ravi,Pratik Datta,Kevin E Bassler,Gábor Balázsi,Maria Laura Gennaro,Tianlong Chen,Dirk Schnappinger

doi:10.1038/ncomms11062

Abstract

Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Here we reconstruct the complete sigma factor regulatory network of the human pathogen Mycobacterium tuberculosis by an integrated approach. The approach combines identification of direct regulatory interactions between M. tuberculosis sigma factors in an E. coli model system, validation of selected links in M. tuberculosis, and extensive literature review. The resulting network comprises 41 direct interactions among all 13 sigma factors. Analysis of network topology reveals (i) a three-tiered hierarchy initiating at master regulators, (ii) high connectivity and (iii) distinct communities containing multiple sigma factors. These topological features are likely associated with multi-layer signal processing and specialized stress responses involving multiple sigma factors. Moreover, the identification of overrepresented network motifs, such as autoregulation and coregulation of sigma and anti-sigma factor pairs, provides structural information that is relevant for studies of network dynamics.

Highlights

Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments
Each M. tuberculosis sigma factor gene was expressed under an isopropyl beta-D-1-thiogalactopyranoside (IPTG)-inducible promoter
E. coli strains containing all combinations of donor–target pairs were tested for b-galactosidase activity in IPTG-treated cultures to determine the ability of each donor sigma factor to induce expression of each target sigma factor promoter

Summary

Introduction

Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Analysis of network topology reveals (i) a three-tiered hierarchy initiating at master regulators, (ii) high connectivity and (iii) distinct communities containing multiple sigma factors These topological features are likely associated with multi-layer signal processing and specialized stress responses involving multiple sigma factors. Expression of accessory sigma factors, which are found in all bacteria examined except Mycoplasma[8], leads to the reprogramming of RNA polymerase (RNAP) by a change in the sigma factor, the subunit that ensures specificity of the RNAP holoenzyme for specific promoter sequences and, initiation of transcription of particular gene sets[8]. The ‘housekeeping’ sigma factor typically directs RNAP to genes needed for essential functions in normal growth conditions, while accessory sigma factors reprogram RNAP to transcribe genes involved in stress responses. The regulatory connectivity among sigma factors has not been systematically investigated in M. tuberculosis

Methods

Results

Conclusion