A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

Eliza J R Peterson, David J. Reiss, Serdar Turkarslan, Kyle J. Minch, Tige Rustad, Christopher Plaisier, William J R Longabaugh, David R. Sherman, Nitin S. Baliga

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

The resilience of Mycobacterium tuberculosis (MTB) is largely due to its ability to effectively counteract and even take advantage of the hostile environments of a host. In order to accelerate the discovery and characterization of these adaptive mechanisms, we have mined a compendium of 2325 publicly available transcriptome profiles of MTB to decipher a predictive, systems-scale gene regulatory network model. The resulting modular organization of 98% of all MTB genes within this regulatory network was rigorously tested using two independently generated datasets: a genome-wide map of 7248 DNA-binding locations for 143 transcription factors (TFs) and global transcriptional consequences of overexpressing 206 TFs. This analysis has discovered specific TFs that mediate conditional co-regulation of genes within 240 modules across 14 distinct environmental contexts. In addition to recapitulating previously characterized regulons, we discovered 454 novel mechanisms for gene regulation during stress, cholesterol utilization and dormancy. Significantly, 183 of these mechanisms act uniquely under conditions experienced during the infection cycle to regulate diverse functions including 23 genes that are essential to host-pathogen interactions. These and other insights underscore the power of a rational, model-driven approach to unearth novel MTB biology that operates under some but not all phases of infection.

Original languageEnglish (US)
Pages (from-to)11291-11303
Number of pages13
JournalNucleic Acids Research
Volume42
Issue number18
DOIs
StatePublished - Oct 13 2014
Externally publishedYes

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Mycobacterium tuberculosis
Transcription Factors
Gene Regulatory Networks
Genes
Host-Pathogen Interactions
Regulon
Essential Genes
Infection
Transcriptome
Statistical Factor Analysis
Cholesterol
Genome
DNA

ASJC Scopus subject areas

  • Genetics
  • Medicine(all)

Cite this

Peterson, E. J. R., Reiss, D. J., Turkarslan, S., Minch, K. J., Rustad, T., Plaisier, C., ... Baliga, N. S. (2014). A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. Nucleic Acids Research, 42(18), 11291-11303. https://doi.org/10.1093/nar/gku777

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. / Peterson, Eliza J R; Reiss, David J.; Turkarslan, Serdar; Minch, Kyle J.; Rustad, Tige; Plaisier, Christopher; Longabaugh, William J R; Sherman, David R.; Baliga, Nitin S.

In: Nucleic Acids Research, Vol. 42, No. 18, 13.10.2014, p. 11291-11303.

Research output: Contribution to journalArticle

Peterson, EJR, Reiss, DJ, Turkarslan, S, Minch, KJ, Rustad, T, Plaisier, C, Longabaugh, WJR, Sherman, DR & Baliga, NS 2014, 'A high-resolution network model for global gene regulation in Mycobacterium tuberculosis', Nucleic Acids Research, vol. 42, no. 18, pp. 11291-11303. https://doi.org/10.1093/nar/gku777
Peterson, Eliza J R ; Reiss, David J. ; Turkarslan, Serdar ; Minch, Kyle J. ; Rustad, Tige ; Plaisier, Christopher ; Longabaugh, William J R ; Sherman, David R. ; Baliga, Nitin S. / A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. In: Nucleic Acids Research. 2014 ; Vol. 42, No. 18. pp. 11291-11303.
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