Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

ABSTRACT: The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe], a [NiFeSe] and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1 and hyn2 genes, respectively. In order to understand their cellular functions the expression levels of these hydrogenases, along with the growth rate analysis of mutant strains, was determined during growth on defined media under 3 different conditions. These conditions incuded lactate or hydrogen at either 5% or 50% (vol/vol) used as the sole electron donor for sulfate reduction. Keywords: Electron donor change For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference. After total intensity normalization the SAM (significance analysis of microarrays) was used to find differentially expressed genes.

ORGANISM(S): Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough

SUBMITTER: Sean Caffrey

PROVIDER: E-GEOD-8137 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Caffrey Sean M SM Park Hyung-Soo HS Voordouw Johanna K JK He Zhili Z Zhou Jizhong J Voordouw Gerrit G

Journal of bacteriology 20070629 17

The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in def ...[more]

PMID: 17601789

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Project description:Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels. Systems analyses of such processes incorporating large-scale transcriptome or proteome profiling can be quite revealing. Although consistency between mRNA and proteins is often implicitly assumed in such studies, instances of divergent trends are frequently observed indicating the existence of post-transcriptional regulation. Here, we present a comparative transcriptome and proteome analysis of growth and stationary phase adaptation in Streptomyces coelicolor, taking the time-dynamics of process into consideration. These processes are of immense interest in streptomycetes as they encompass the physiological transformations eliciting biosynthesis of many naturally occurring therapeutic agents. A shotgun proteomics approach based on mass spectrometric analysis of isobaric stable isotope labeled peptides iTRAQ(TM) enabled identification and rapid quantification of approximately 14% of the theoretical proteome of S. coelicolor. Independent principal component analyses of this and DNA microarray-derived transcriptome data revealed that the prominent patterns in both protein and mRNA domains are surprisingly well correlated. Despite this general consensus, by employing a systematic concordance analysis we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends. Integrating this data with biological information, we discovered that certain groups of functionally related genes were co-regulated independently as mRNA and/or proteins despite observations of apparent mRNA-protein discordance. This clearly suggests that post-transcriptional regulatory mechanisms are prominent even amongst prokaryotes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level. Keywords: Time course Time-course study involved analysis of 8 samples (7h, 11h, 14h, 16h, 22h, 26h, 34h, 38h). Of these, 14h, 22h, 26h and 38h were analyzed in duplicate arrays. All arrays used cDNA labeled with Alexa647 and gDNA labeled with Cy3.

Dataset Information

Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

Publications

Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

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