Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reconstruction of the Mycobacterium tuberculosis Regulatory Network and Deconstruction of the Hypoxic Response

ABSTRACT: Expression data from hypoxic time course and transcription factor over expression experiments. (Abstract from paper will be appended after publication)

ORGANISM(S): Mycobacterium tuberculosis H37Rv

PROVIDER: GSE43466 | GEO | 2013/01/12

SECONDARY ACCESSION(S): PRJNA186476

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Reconstruction of the Mycobacterium tuberculosis Regulatory Network and Deconstruction of the Hypoxic Response

Project description:Expression data from hypoxic time course and transcription factor over expression experiments. (Abstract from paper will be appended after publication) Hypoxic time course experiments were done with a minimum of 3 replicates. TFOE are matched to the ChIP-seq experiment done simultaneously. This submission consists of the the gene expression component only.

2013-01-12 | E-GEOD-43466 | biostudies-arrayexpress

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

Project description:Expression data from transcription factor over expression experiments (Abstract from paper will be appended after publication)

2014-07-04 | GSE59086 | GEO

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

Project description:Expression data from transcription factor over expression experiments (Abstract from paper will be appended after publication) TFOE are matched to the ChIP-seq experiment done simultaneously.

2014-07-04 | E-GEOD-59086 | biostudies-arrayexpress

RNA-sequencing of hypoxic Mycobacterium tuberculosis treated with C10

Project description:We sought to identify which genes were dysregulated in hypoxic Mycobacterium tuberculosis upon treatment with C10. We cultured Mycobacterium tuberculosis in an air-tight vessel for 2 weeks in the presence of either DMSO or 50 μM C10, and used RNA-sequencing to compare transcriptional profiles.

2019-05-31 | GSE129830 | GEO

Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis

Project description:Unlike many pathogens that are overtly harmful to their hosts, Mycobacterium tuberculosis can persist for years within humans in a clinically latent state. Latency is often linked to hypoxic conditions within the host. Among M. tuberculosis genes induced by hypoxia is a putative transcription factor, Rv3133c/DosR. We performed targeted disruption of this locus followed by transcriptome analysis of wild-type and mutant bacilli. Nearly all the genes powerfully regulated by hypoxia require Rv3133c/DosR for their induction. Computer analysis identified a consensus motif, a variant of which is located upstream of nearly all M. tuberculosis genes rapidly induced by hypoxia. Further, Rv3133c/DosR binds to the two copies of this motif upstream of the hypoxic response gene alpha-crystallin. Mutations within the binding sites abolish both Rv3133c/DosR binding as well as hypoxic induction of a downstream reporter gene. Also, mutation experiments with Rv3133c/DosR confirmed sequence-based predictions that the C-terminus is responsible for DNA binding and that the aspartate at position 54 is essential for function. Together, these results demonstrate that Rv3133c/DosR is a transcription factor of the two-component response regulator class, and that it is the primary mediator of a hypoxic signal within M. tuberculosis. Keywords: strain or line design, genetic modification design and comparative genome hybridization design

2007-08-21 | GSE8829 | GEO

Gene expression profling of Mycobacterium tuberculosis H37Rv and H37RvΔdosSΔdosT in 0.2% glucose/acetate under aerobic/hypoxic conditions

Project description:The present study reports the gene expression data of Mycobacterium tuberculosis H37Rv and H37RvΔdosSΔdosT (DKO) grown on 0.2 % acetate/glucose under aerobic/hypoxic conditions. Acetate was reported to be present in granulomas of Mycobacterium tuberculosis infected guinea pigs which are also hypoxic. By exposing Mycobacterium tuberculosis H37Rv and H37RvΔdosSΔdosT to different combinations of granulomatous stresses (acetate/glucose and aerobic/hypoxic conditions) alongwith other experimental data, we were able to delineate a new signaling pathway that activates DevR (DosR) regulon through Acetyl phosphate. The presence of two pathways highlights the importance of targeting DevR and not DevS/DosT for intercepting DevRST signalling cascade.

2019-01-01 | GSE117428 | GEO

Transcription profiling of Mycobacterium tuberculosis wild type and Rv3133c/DosR mutants grown in hypoxic conditions

2007-09-29 | E-SMDB-4099 | biostudies-arrayexpress

Transcription profiling of Mycobacterium tuberculosis grown at reduced oxygen tension to identify regulators of the hypoxic response

Project description:Unlike many pathogens that are overtly toxic to their hosts, the primary virulence determinant of Mycobacterium tuberculosis appears to be its ability to persist for years or decades within humans in a clinically latent state. Since early in the 20th century latency has been linked to hypoxic conditions within the host, but the response of M. tuberculosis to a hypoxic signal remains poorly characterized. The M. tuberculosis alpha-crystallin (acr) gene is powerfully and rapidly induced at reduced oxygen tensions, providing us with a means to identify regulators of the hypoxic response. Using a whole genome microarray, we identified >100 genes whose expression is rapidly altered by defined hypoxic conditions. Numerous genes involved in biosynthesis and aerobic metabolism are repressed, whereas a high proportion of the induced genes have no known function. Among the induced genes is an apparent operon that includes the putative two-component response regulator pair Rv3133cy Rv3132c. When we interrupted expression of this operon by targeted disruption of the upstream gene Rv3134c, the hypoxic regulation of acr was eliminated. These results suggest a possible role for Rv3132cy3133cy3134c in mycobacterial latency.

2007-09-12 | E-TABM-312 | biostudies-arrayexpress

Sequence analysis of Mycobacterium tuberculosis

Project description:Study to perform RNAseq on the Mtb ?esx3 and complemented control including the non-coding RNAs.These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2015-06-23 | E-ERAD-355 | biostudies-arrayexpress

The enduring hypoxic response of Mycobacterium tuberculosis.

Project description:A significant body of evidence accumulated over the last century suggests a link between hypoxic microenvironments within the infected host and the latent phase of tuberculosis. Studies to test this correlation have identified the M. tuberculosis initial hypoxic response, controlled by the two-component response regulator DosR. The initial hypoxic response is completely blocked in a dosR deletion mutant.We show here that a dosR deletion mutant enters bacteriostasis in response to in vitro hypoxia with only a relatively mild decrease in viability. In the murine infection model, the phenotype of the mutant was indistinguishable from that of the parent strain. These results suggested that additional genes may be essential for entry into and maintenance of bacteriostasis. Detailed microarray analysis of oxygen starved cultures revealed that DosR regulon induction is transient, with induction of nearly half the genes returning to baseline within 24 hours. In addition, a larger, sustained wave of gene expression follows the DosR-mediated initial hypoxic response. This Enduring Hypoxic Response (EHR) consists of 230 genes significantly induced at four and seven days of hypoxia but not at initial time points. These genes include a surprising number of transcriptional regulators that could control the program of bacteriostasis. We found that the EHR is independent of the DosR-mediated initial hypoxic response, as EHR expression is virtually unaltered in the dosR mutant.Our results suggest a reassessment of the role of DosR and the initial hypoxic response in MTB physiology. Instead of a primary role in survival of hypoxia induced bacteriostasis, DosR may regulate a response that is largely optional in vitro and in mouse infections. Analysis of the EHR should help elucidate the key regulatory factors and enzymatic machinery exploited by M. tuberculosis for long-term bacteriostasis in the face of oxygen deprivation.

| S-EPMC2198943 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data