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Gene Expression profiling of M. bovis BCG strain under hypoxia

ABSTRACT: Objective of the study is to find out the differentially regulated genes in Mycobacterium bovis BCG subjected to hypoxic condition. Gene expression profiling was carried out using Agilent microarray platform. Keywords: Hypoxia response

ORGANISM(S): Mycobacterium tuberculosis variant bovis BCG Mycobacterium tuberculosis H37Rv

PROVIDER: GSE10336 | GEO | 2009/08/06

SECONDARY ACCESSION(S): PRJNA105573

REPOSITORIES: GEO

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Gene Expression profiling of M. bovis BCG strain under hypoxia

Project description:Objective of the study is to find out the differentially regulated genes in Mycobacterium bovis BCG subjected to hypoxic condition. Gene expression profiling was carried out using Agilent microarray platform. Keywords: Hypoxia response Mycobacterium cells were lysed by bead beating in AL Buffer of Qiagenâs bacterial RNA kit. RNA was purified as per manufacturerâs instructions. RNA quality control was done using Agilent 2100 Bioanalyzer lab on a chip. Total RNA (500ng) of Mycobacterium under hypoxia and log phase were labelled with Cy3 and Cy5 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol. To eliminate dye bias, technical replicates were labelled in the reverse direction i.e log phase culture with Cy5 and hypoxia with Cy3. 825ng each of labeled control cRNA was mixed with 825ng of treated labelled cRNA, mixed with appropriate amount of blocking buffer and hybridization buffer (Agilent Technologies). The hybridization mix was applied on to the backings and hybridized to custom designed 60mer M.tuberculosis H37Rv microarray using sure hyb chambers at 65degC for 17 hours. Slides were washed with gene expression wash buffer 1 and 2 (Agilent Technologies) followed by Acetonitrile and scanned at 5 micron resolution using Agilent scanner. Automated feature extraction was done using Agilentâs Feature Extraction Software. Statistical analysis of microarray data was done using GeneSpring GX and Biological analysis of the differentially regulated genes were done using Genotypics Biointerpreter -Web based tool for biological interpretation of gene list in a click of mouse.

2010-05-15 | E-GEOD-10336 | biostudies-arrayexpress

M. bovis BCG PknG physiological substrates

Project description:Mycobacterial Ser/Thr kinases play a critical role in bacterial physiology and pathogenesis. Linking kinases to the substrates they phosphorylate in vivo, thereby elucidating their exact functions, is still a challenge. The aim of this work was to associate protein phosphorylation in mycobacteria with important subsequent macro cellular events by identifying the physiological substrates of PknG in Mycobacterium bovis BCG. The study compared the phosphoproteome dynamics during the batch growth of M. bovis BGC versus the respective PknG knock-out mutant (ΔPknG-BCG) strains.

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DosR-regulon genes induction in Mycobacterium bovis BCG under aerobic conditions

Project description:In this report we demonstrated that under aerobic conditions, Mycobacterium bovis BCG expressing an hsp60-driven second copy of the hypoxia-related transcriptional regulator DosR increased 2-fold or greater the expression of 38 out of the 48 genes belonging to the DosR regulon, including the latency antigens Rv1733c, Rv2029, Rv2627, and Rv2628. Expression of DosR under these conditions slightly delayed in vitro growth, but did not promote a non-replicating state as opposed to microaerobic and hypoxic adaptation. Our results suggest BCG producing DosR can be cultured under standard in vitro conditions, allowing evaluation of this strain as a latency-specific vaccine candidate. Set of arrays that are part of repeated experiments

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Project description:In the present study, we employed Affymetrix Mycobacterium bovis BCG GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Mycobacterium bovis BCG to hydrogen peroxide, which involved initial growth inhibition and metabolism. Keywords: Transcriptome study We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of hydrogen peroxide. We calculated fold change as the ratio between the signal averages of three untreated (control) and three hydrogen peroxide-treated (experimental) cultures for 0, 10 and 60 min exposures.

2010-05-06 | E-GEOD-14272 | biostudies-arrayexpress

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