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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

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

SUBMITTER: Morgan Price

PROVIDER: E-GEOD-29559 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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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

2010-03-06 | GSE20657 | GEO

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 | biostudies-arrayexpress

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

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.

2009-08-18 | GSE15073 | GEO

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

2010-05-06 | E-GEOD-15073 | biostudies-arrayexpress

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

Project description:5' RNASeq of mRNA from DvH in defined lactate/sulfate media (LS4D)

2011-05-27 | GSE29559 | GEO

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)

2011-05-27 | GSE29556 | GEO

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 | biostudies-arrayexpress

?54-dependent regulome in Desulfovibrio vulgaris Hildenborough.

Project description:The ?(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown.To characterize the ?(54)-dependent regulome of D. vulgaris Hildenborough, we identified EBP binding motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of ?(54)-dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the ?(54) regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by ?(54)-dependent regulators.The ?(54)-dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of ?(54)-dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.

| S-EPMC4641369 | biostudies-literature

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

Project description:The syntrophic growth of strain 195 with Desulfovibrio vulgaris Hildenborough (DVH) and/or Methanobacterium congolense (MC) enhanced TCE dechlorination process by faster dechlorination rate and more robust growth. Transcriptomes of strain 195 grown in isolation, co- and tri-cultures were obtained by microarray experiments to find out the differential expressed genes corresponding to the syntrophic growth. Thus we can better understand the role of DVH and MC within this syntrophy.

2011-08-01 | GSE26815 | GEO

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