Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network.

Publication Type:

Journal Article

Authors:

Rustad, Tige R; Minch, Kyle J; Ma, Shuyi; Winkler, Jessica K; Hobbs, Samuel; Hickey, Mark; Brabant, William; Turkarslan, Serdar; Price, Nathan D; Baliga, Nitin S; Sherman, David R

Source:

Genome Biol, Volume 15, Issue 11, p.502 (2014)

Keywords:

Cloning, Molecular, Gene Expression Regulation, Bacterial, Gene Regulatory Networks, Humans, Isoniazid, Mycobacterium tuberculosis, Promoter Regions, Genetic, Regulon, Transcription Factors, Transcription, Genetic, Transcriptome, Tuberculosis

Abstract:

BACKGROUND: Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription factors of M. tuberculosis, we have assayed the global transcriptional consequences of overexpressing each transcription factor from an inducible promoter.RESULTS: We cloned and overexpressed 206 transcription factors in M. tuberculosis to identify the regulatory signature of each. We identified 9,335 regulatory consequences of overexpressing each of 183 transcription factors, providing evidence of regulation for 70% of the M. tuberculosis genome. These transcriptional signatures agree well with previously described M. tuberculosis regulons. The number of genes differentially regulated by transcription factor overexpression varied from hundreds of genes to none, with the majority of expression changes repressing basal transcription. Exploring the global transcriptional maps of transcription factor overexpressing (TFOE) strains, we predicted and validated the phenotype of a regulator that reduces susceptibility to a first line anti-tubercular drug, isoniazid. We also combined the TFOE data with an existing model of M. tuberculosis metabolism to predict the growth rates of individual TFOE strains with high fidelity.CONCLUSION: This work has led to a systems-level framework describing the transcriptome of a devastating bacterial pathogen, characterized the transcriptional influence of nearly all individual transcription factors in M. tuberculosis, and demonstrated the utility of this resource. These results will stimulate additional systems-level and hypothesis-driven efforts to understand M. tuberculosis adaptations that promote disease.

Supplementary Files:

Attachment	Size
Supplementary Excel Files for Rustad et al. 2014	19.36 MB
TFOE Searchable Excel File	20.15 MB

Title	Gene	BioProject	GEO Series	Platform	Accession	Sample Method	Sample Type	References	Release Date	Repository
TFOE_2009_2359_A	Rv2359 Zinc uptake regulation protein ZUR	PRJNA254351	GSE59086	GPL14824	GSM1426820	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_4270_2359	Rv2359 Zinc uptake regulation protein ZUR	PRJNA254351	GSE59086	GPL14824	GSM1426821	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_7839_2359_B	Rv2359 Zinc uptake regulation protein ZUR	PRJNA254351	GSE59086	GPL14824	GSM1426822	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_8900_2359	Rv2359 Zinc uptake regulation protein ZUR	PRJNA254351	GSE59086	GPL14824	GSM1426823	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_2973_2374c	Rv2374c Heat-inducible transcription repressor HrcA	PRJNA254351	GSE59086	GPL14824	GSM1426824	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_9655_2374c	Rv2374c Heat-inducible transcription repressor HrcA	PRJNA254351	GSE59086	GPL14824	GSM1426825	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_5002_2324	Rv2324 Transcriptional regulator, AsnC family	PRJNA254351	GSE59086	GPL14824	GSM1426815	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_6902_2621c	Rv2621c Putative transcriptional regulatory protein	PRJNA254351	GSE59086	GPL14824	GSM1426840	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_5281_2710	Rv2710 RNA polymerase sigma factor SigB	PRJNA254351	GSE59086	GPL14824	GSM1426854	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_6068_2710	Rv2710 RNA polymerase sigma factor SigB	PRJNA254351	GSE59086	GPL14824	GSM1426855	Tiling Array	RNA	25232098	4-Jul-14	GEO