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_3630_3488	Rv3488 Transcriptional regulator, PadR family	PRJNA254351	GSE59086	GPL14824	GSM1427002	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_9539_3405c	Rv3405c Transcriptional regulator, TetR family	PRJNA254351	GSE59086	GPL14824	GSM1426992	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_1352_3414c	Rv3414c RNA polymerase sigma-70 factor	PRJNA254351	GSE59086	GPL14824	GSM1426993	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_1523_3414c	Rv3414c RNA polymerase sigma-70 factor	PRJNA254351	GSE59086	GPL14824	GSM1426994	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_7743_3414c	Rv3414c RNA polymerase sigma-70 factor	PRJNA254351	GSE59086	GPL14824	GSM1426995	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_2558_3416	Rv3416 Sporulation regulatory protein WhiD	PRJNA254351	GSE59086	GPL14824	GSM1426996	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_6695_3416	Rv3416 Sporulation regulatory protein WhiD	PRJNA254351	GSE59086	GPL14824	GSM1426997	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_8067_3416	Rv3416 Sporulation regulatory protein WhiD	PRJNA254351	GSE59086	GPL14824	GSM1426998	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_2895_3417c	Rv3417c Heat shock protein 60 family chaperone GroEL	PRJNA254351	GSE59086	GPL14824	GSM1426999	Tiling Array	RNA	25232098	4-Jul-14	GEO
TFOE_6616_3301c	Rv3301c Phosphate transport system regulatory protein PhoU	PRJNA254351	GSE59086	GPL14824	GSM1426980	Tiling Array	RNA	25232098	4-Jul-14	GEO