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Omics score: 4

Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough (RNA-Seq)

ABSTRACT: 5' RNASeq of mRNA from DvH in defined lactate/sulfate media (LS4D) One lane of sequence each for two different protocols applied to independently grown cells under similar conditions

OTHER RELATED OMICS DATASETS IN: GSE29560PRJNA141329PRJNA154015PRJNA154013

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

SUBMITTER: Jennifer V Kuehl Adam P Arkin Adam M Deutschbauer Morgan N Price

PROVIDER: E-GEOD-29559 | ArrayExpress | 2011-05-27

SECONDARY ACCESSION(S): GSE29559SRP006901PRJNA154015

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Price Morgan N MN Deutschbauer Adam M AM Kuehl Jennifer V JV Liu Haichuan H Witkowska H Ewa HE Arkin Adam P AP

Journal of bacteriology 20110812 20

We used high-resolution tiling microarrays and 5' RNA sequencing to identify transcripts in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. We identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. Sequence analysis of these promoters showed that D. ...[more]

PMID: 21840973

Similar Datasets

Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough (tiling array)

Project description:High-resolution tiling analysis of the DvH transcriptome in lactate/sulfate media, both rich (LS) and defined (LS4D) Two replicates of rich media, one replicate of minimal media, and one “genomic control” array (genomic_control.ftr) hybridized to genomic DNA

2011-05-27 | E-GEOD-29556 | ArrayExpress

Co-culture stress in Desulfovibrio vulgaris Hildenborough

Project description:This set of microarray data was used to compare the effects of D. vulgaris grown syntrophically with a hydrogenotrophic methanogen versus D. vulgaris grown in sulfate-limited monoculture. Keywords: physiological response, one time point (stable continuous culture for both control and treated cells) Overall design: Comparison of cells treated with DvH + Mm co-culture + lactate only FC36, FC38, FC44 Co-culture to untreated cells at times of continuous culture at 24 hr retention time min.

2010-09-16 | GSE17831 | GEO

Single-Cell Analysis of Growth and Cell Division of the Anaerobe Desulfovibrio vulgaris Hildenborough.

Project description:Recent years have seen significant progress in understanding basic bacterial cell cycle properties such as cell growth and cell division. While characterization and regulation of bacterial cell cycle is quite well-documented in the case of fast growing aerobic model organisms, no data has been so far reported for anaerobic bacteria. This lack of information in anaerobic microorganisms can mainly be explained by the absence of molecular and cellular tools such as single cell microscopy and fluorescent probes usable for anaerobes and essential to study cellular events and/or subcellular localization of the actors involved in cell cycle. In this study, single-cell microscopy has been adapted to study for the first time, in real time, the cell cycle of a bacterial anaerobe, Desulfovibrio vulgaris Hildenborough (DvH). This single-cell analysis provides mechanistic insights into the cell division cycle of DvH, which seems to be governed by the recently discussed so-called incremental model that generates remarkably homogeneous cell sizes. Furthermore, cell division was reversibly blocked during oxygen exposure. This may constitute a strategy for anaerobic cells to cope with transient exposure to oxygen that they may encounter in their natural environment, thereby contributing to their aerotolerance. This study lays the foundation for the first molecular, single-cell assay that will address factors that cannot otherwise be resolved in bulk assays and that will allow visualization of a wide range of molecular mechanisms within living anaerobic cells.

2015-01-01 | S-EPMC4672049 | BioStudies

Effect of sulfide on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough

Project description:The effect of sulfide stress on Desulfovibrio vulgaris Hildenborough (DvH) gene expression was determined by comparing the gene expression profiles of DvH under conditions in which sulfide was allowed to accumulate (high sulfide, average concentration 10 mM) against DvH cells grown under conditions in which sulfide was removed by continuous gassing (low sulfide, average concentration 1 mM). High sulfide significantly decreased the instantaneous growth rate constant and final cell density of the culture indicating a decreased bioenergetic fitness. Changes in gene expression caused by exposure to high sulfide were determined using full-genome DvH microarrays. The transcription of ribosomal protein-encoding genes was decreased, in agreement with the lower growth rate of DvH under high sulfide conditions. Interestingly, expression of the gene for DsrD, located downstream of the genes for dissimilatory sulfite reductase (DsrAB) was also strongly down-regulated. In contrast, the expression of many genes involved in iron accumulation, stress response and proteolysis, and chemotaxis were increased. This indicates that high sulfide represents a significant stress condition, in which the bioavailability of metals like iron may be lowered and in which proteins (e.g. metalloenzymes) may need to be refolded, or proteolytically degraded. Overall this leads to a reduced growth rate and less efficient biomass production with available resources. For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

2010-05-06 | E-GEOD-15073 | ArrayExpress

Effect of THPS on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough

Project description:The effect of tetrakis (hydroxymethyl) phosphonium sulfate (THPS) stress on Desulfovibrio vulgaris Hildenborough (DvH) gene expression was determined by comparing the gene expression profiles of DvH with THPS added at mid-log phase against DvH grown without THPS. Low concentration THPS had little influence over instantaneous growth rate constant and final cell density of the culture. Changes in gene expression caused by exposure to THPS were determined using full-genome DvH microarrays. In comparison to Glutaraldehyde and BAC microarray results, not lot of gene expressions were altered by THPS. Keywords: THPS Stress Overall design: For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

2010-03-06 | GSE20657 | GEO

Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses.

Project description:Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0±0.01 ?mol per day for the co-culture and 10.1±0.3 ?mol per day for the tri-culture) compared with DE195 grown alone (3.8±0.1 ?mol per day). Cell yield of DE195 was enhanced in the co-culture (9.0±0.5 × 10(7) cells per ?mol Cl(-) released, compared with 6.8±0.9 × 10(7) cells per ?mol Cl(-) released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3±1.8 × 10(7) cells per ?mol Cl(-) released). The transcriptome of DE195 grown in the co-culture was analyzed using a whole-genome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H(2) and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.

1000-01-01 | S-EPMC3260503 | BioStudies

Effect of glutaraldehyde (Glut) on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough

Project description:The effect of glutaraldehyde stress on Desulfovibrio vulgaris Hildenborough (DvH) gene expression was determined by comparing the gene expression profiles of DvH with glutaraldehyde added at mid-log phase against DvH grown without glutaraldehdyde. Low concentration glutaraldehyde had little influence over instantaneous growth rate constant and final cell density of the culture. Changes in gene expression caused by exposure to glutaraldehyde were determined using full-genome DvH microarrays. A lot of gene expressions were altered by glutaraldehyde. Keywords: Glutaraldehyde Stress Overall design: For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

2010-03-06 | GSE20656 | GEO

Effect of sulfide on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough

Project description:The effect of sulfide stress on Desulfovibrio vulgaris Hildenborough (DvH) gene expression was determined by comparing the gene expression profiles of DvH under conditions in which sulfide was allowed to accumulate (high sulfide, average concentration 10 mM) against DvH cells grown under conditions in which sulfide was removed by continuous gassing (low sulfide, average concentration 1 mM). High sulfide significantly decreased the instantaneous growth rate constant and final cell density of the culture indicating a decreased bioenergetic fitness. Changes in gene expression caused by exposure to high sulfide were determined using full-genome DvH microarrays. The transcription of ribosomal protein-encoding genes was decreased, in agreement with the lower growth rate of DvH under high sulfide conditions. Interestingly, expression of the gene for DsrD, located downstream of the genes for dissimilatory sulfite reductase (DsrAB) was also strongly down-regulated. In contrast, the expression of many genes involved in iron accumulation, stress response and proteolysis, and chemotaxis were increased. This indicates that high sulfide represents a significant stress condition, in which the bioavailability of metals like iron may be lowered and in which proteins (e.g. metalloenzymes) may need to be refolded, or proteolytically degraded. Overall this leads to a reduced growth rate and less efficient biomass production with available resources. Overall design: For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

2009-08-18 | GSE15073 | GEO

Isotopic Fractionation Associated With Sulfate Import and Activation by Desulfovibrio vulgaris str. Hildenborough.

Project description:The use of stable isotopes to trace biogeochemical sulfur cycling relies on an understanding of how isotopic fractionation is imposed by metabolic networks. We investigated the effects of the first two enzymatic steps in the dissimilatory sulfate reduction (DSR) network - sulfate permease and sulfate adenylyl transferase (Sat) - on the sulfur and oxygen isotopic composition of residual sulfate. Mutant strains of Desulfovibrio vulgaris str. Hildenborough (DvH) with perturbed expression of these enzymes were grown in batch culture, with a subset grown in continuous culture, to examine the impact of these enzymatic steps on growth rate, cell specific sulfate reduction rate and isotopic fractionations in comparison to the wild type strain. Deletion of several permease genes resulted in only small (?1‰) changes in sulfur isotope fractionation, a difference that approaches the uncertainties of the measurement. Mutants that perturb Sat expression show higher fractionations than the wild type strain. This increase probably relates to an increased material flux between sulfate and APS, allowing an increase in the expressed fractionation of rate-limiting APS reductase. This work illustrates that flux through the initial steps of the DSR pathway can affect the fractionation imposed by the overall pathway, even though these steps are themselves likely to impose only small fractionations.

2020-01-01 | S-EPMC7531388 | BioStudies

Identification of transcript starts in Desulfovibrio alaskensis G20

Project description:5' RNASeq of mRNA from G20 in defined lactate/sulfate media (LS4D) 5' RNASeq of a single sample

2013-08-03 | E-GEOD-49484 | ArrayExpress