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Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules.

Williams, KJ; Bryant, WA; Jenkins, VA; Barton, GR; Witney, AA; Pinney, JW; Robertson, BD (2013) Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules. BMC Genomics, 14 (436). ISSN 1471-2164 https://doi.org/10.1186/1471-2164-14-436
SGUL Authors: Witney, Adam Austin

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Abstract

Background The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. Results A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. Conclusions Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments.

Item Type: Article
Additional Information: PubMed ID: 23819599. © 2013 Williams et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Science & Technology, Life Sciences & Biomedicine, Biotechnology & Applied Microbiology, Genetics & Heredity, Nitrogen Stress, Mycobacteria, Gene Expression, Metabolic Network, GENOME-WIDE ANALYSIS, STREPTOMYCES-COELICOLOR, GENE-EXPRESSION, CORYNEBACTERIUM-GLUTAMICUM, ESCHERICHIA-COLI, STATIONARY-PHASE, METABOLISM, TUBERCULOSIS, GLNR, BACTERIA
SGUL Research Institute / Research Centre: Academic Structure > Infection and Immunity Research Institute (INII)
Journal or Publication Title: BMC Genomics
ISSN: 1471-2164
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Dates:
DateEvent
2 July 2013Published
Web of Science ID: WOS:000321564300001
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URI: http://sgultest.da.ulcc.ac.uk/id/eprint/102236
Publisher's version: https://doi.org/10.1186/1471-2164-14-436

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