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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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M. tuberculosis transcriptional profile of delta pepD strain vs wild-type strain

ABSTRACT: pepD is regulated by a 2CS, MprAB, and impacts upon the regulation of sigE, an important M.tb sigma factor. Here we examine the global impact of gene regulation in a delta pepD mutant strain. Analysis compares total RNA from early log growth cultures of both wild-type and a delta pepD strain.

ORGANISM(S): Mycobacterium tuberculosis

SUBMITTER: Tom Zahrt

PROVIDER: E-GEOD-17587 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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PepD participates in the mycobacterial stress response mediated through MprAB and SigE.

White Mark J MJ He Hongjun H Penoske Renee M RM Twining Sally S SS Zahrt Thomas C TC

Journal of bacteriology 20100108 6

Currently, one-third of the world's population is believed to be latently infected with Mycobacterium tuberculosis. The mechanisms by which M. tuberculosis establishes latent infection remain largely undefined. mprAB encodes a two-component signal transduction system required by M. tuberculosis for aspects of persistent infection. MprAB regulates a large and diverse group of genetic determinants in response to membrane stress, including the extracytoplasmic function (ECF) sigma factor sigE and t ...[more]

PMID: 20061478

Similar Datasets

M. tuberculosis transcriptional profile of delta pepD strain vs wild-type strain

Project description:pepD is regulated by a 2CS, MprAB, and impacts upon the regulation of sigE, an important M.tb sigma factor. Here we examine the global impact of gene regulation in a delta pepD mutant strain.

2009-10-30 | GSE17587 | GEO

Comparison between V. cholerae MO10 delta PTS mutant and wild type strain grown as planktonic or surface-associated cells

Project description:The PTS system is a central regulatory cascade in bacteria. Here, Vibrio cholerae PTS role was investagated during biofilm formation Analysis used wild type MO10 cells as control samples for comparison to the delta PTS strain. Strains were grown as planktonic (sample 1) or surface attached cells (sample 2). Experiment was done in triplicate with dye swap, which represent 6 independent microarray hybridizations.

2012-12-10 | E-GEOD-42674 | biostudies-arrayexpress

Expression analysis of M.tb H37Rv after treatment with DTT (reduced) for 3 hrs

Project description:Effect of Thiol reductive stress (DTT 1mM) on M.tb Rv was studied. DTT reduced at 1 mM concentration was added to log pahse culture of M.tb H37Rv. After Three hours RNA was isolated and hybridization was done on HRI-UMNDJ Mycobacterium tuberculosis 4.8K CAG_Mtb microarrays.

2015-04-28 | E-GEOD-68350 | biostudies-arrayexpress

Sigma factor E of Mycobacterium tuberculosis controls the expression of bacterial components that modulate macrophages

Project description:Sigma factor E (SigE) controls the expression of genes that are essential for Mtb virulence. In this work, we have identified the SigE regulon during infection of macrophages Our results indicate that SigE regulates the expression of genes involved in the maintenance of Mtb cell envelope integrity and function (i.e., detoxification and secretion). Keywords: strains comparison We compared the global gene expression of the H37Rv strain and the sigE mutant strain of Mtb in different conditions: growing exponentially in liquid media; after 2h of incubation in RPMI; or after 24 hours of infection of human macrophage-like THP-1 cells.

2010-05-25 | E-GEOD-7962 | biostudies-arrayexpress

Bacillus subtilis W168, WT vs. delta-rocG delta-gudB

Project description:Transcriptional profile of the rocG gudB double null mutant during log growth phase in LB medium. Bacillus subtilis W168, WT vs. delta-rocG delta-gudB. The experiment was conducted two times using three independent total RNA preparations (biological triplicates). For each paried comparison, WT was labeled with Alexa Fluor 555 and the rocG gudB double mutant was with Alexa Fluor 647.

2011-12-13 | E-GEOD-34383 | biostudies-arrayexpress

GRO analysis of topoisomerase mutants

Project description:Genomic Run-on analysis of topoisomerase mutants (top1-delta/top2ts or top2ts) has been conducted at reference temperature for wt strain and at non-permissive temperature for wt and mutant strains. Keywords: Genomic Run On The analysis includes 3 repeats of the wild type strain (JCW25) at 30ÂºC and 3 more at 37ÂºC, 3 repeats of the top2ts mutant (JCW26) at 37ÂºC and 3 repeats of the double top1 (delta) top2ts mutant at 37ÂºC. A single genomic DNA hybridization on one of the filters can be used for normalization between gene probes if needed.

2010-06-24 | E-GEOD-16673 | biostudies-arrayexpress

Comparative genomic hybridization of Streptococcus pneumoniae clinical isolates that differ in strain and/or serotype

Project description:identification of genetic differences and similarities between clinical isolates of s.pneumonie of the same sequence type and /or serotype

2008-08-04 | E-TABM-278 | biostudies-arrayexpress

Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures

Project description:Specific growth rate dependent gene expression changes of Escherichia coli K12 MG1655 were determined by microarray and real time PCR analyses. The bacteria were cultivated on glucose limited minimal medium using the accelerostat method (A-stat), where starting from steady state conditions in a chemostat culture, dilution rate is constantly increased. At specific growth rate (Î¼) 0.47 h-1, E. coli had focused its metabolism to glucose utilization by down-regulation of alternative substrate transporters expression compared to Î¼ = 0.3 h-1. It was found that acetic acid accumulation began at Î¼ = 0.34 Â± 0.01 h-1 and two acetate synthesis pathways (phosphotransacetylase-acetate kinase (pta-ackA) and pyruvate oxidase (poxB)) contributed to the synthesis at the beginning of overflow metabolism, i.e. onset of acetate excretion. On the other hand, poxB, pta and ackA expression patterns suggest that pyruvate oxidase may be the only enzyme synthesizing acetate at Î¼ = 0.47 h-1. Down-regulation of acs-yjcH-actP operon, the resulting loss of glucose and acetate co-utilization between specific growth rates 0.3 h-1 â 0.42 h-1 and acetic acid accumulation from Î¼ = 0.34 Â± 0.01 h-1 allows one to surmise that the acetate utilization operon expression might play an important role in overflow metabolism. DNA microarray analysis was performed from three A-stat cultivations, for which one has a technical replicate.

2010-05-22 | E-GEOD-18183 | biostudies-arrayexpress

Transcription profiling of Yersinia pestis overexpressing phoP

Project description:Microarrays were used to identify Y. pestis genes that are differentially regulated under conditions of phoP overexpression. RNA samples were isolated from cultures of two isogenic Y. pestis strains, one overexpressing phoP (KIM10+phoP(delta)/PhoP) and the other not (KIM10+phoP(delta)/MMB67EH), and their gene expression profiles were compared.

2006-07-01 | E-MEXP-712 | biostudies-arrayexpress

Roles of relSpn in Stringent Response, Global Regulation, and Virulence of Serotype 2 Streptococcus pneumoniae D39

Project description:Transcriptome analysis of D39 rel+Spn and delta-relSpn strains treated with mupirocin revealed relSpn-independent (translation stress), relSpn-dependent (stringent response), and delta-relSpn-dependent changes suggesting that relSpn and (p)ppGpp amount play wide-ranging homeostatic roles in pneumococcal physiology, besides adjusting macromolecular synthesis and transport in response to nutrient availability. Wildtype and rel deletion mutant (Delta rel) bacteria were grown statically in BHI broth at 37C in an atmosphere of 5% CO2. Cultures were divided in two upon reaching a density of OD620 ~0.1, and lithium mupirocin was added to one culture (t=0) to a final concentration of 100 ng per mL. Treated and untreated cultures were harvested after 20 min further incubation and RNA was extracted by a hot lysis-acid phenol protocol. We performed the following comparisons: Wildtype + mupirocin versus Wildtype untreated (reference); Delta rel + mupirocin versus Delta rel untreated (reference); Delta rel untreated versus Wildtype untreated (reference); Delta rel + mupirocin versus Wildtype + mupirocin (reference). For each comparison, microarray data were obtained from three independent biological replicates and included one dye swap.

2010-05-15 | E-GEOD-14750 | biostudies-arrayexpress

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