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Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

OTHER RELATED OMICS DATASETS IN: PRJNA154013PRJNA141329PRJNA154015

ORGANISM(S): Nitratidesulfovibrio vulgaris str. Hildenborough

PROVIDER: GSE29560 | GEO | 2011/05/27

SECONDARY ACCESSION(S): PRJNA141329

REPOSITORIES: GEO

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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

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) One lane of sequence each for two different protocols applied to independently grown cells under similar conditions

2011-05-27 | E-GEOD-29559 | biostudies-arrayexpress

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

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

Project description: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. vulgaris prefers -10 and -35 boxes different from those preferred by Escherichia coli. A total of 549 transcripts ended at intrinsic (rho-independent) terminators, but most of the other transcripts seemed to have variable ends. We found low-level antisense expression of most genes, and the 5' ends of these transcripts mapped to promoter-like sequences. Because antisense expression was reduced for highly expressed genes, we suspect that elongation of nonspecific antisense transcripts is suppressed by transcription of the sense strand. Finally, we combined the transcript results with comparative analysis and proteomics data to make 505 revisions to the original annotation of 3,531 proteins: we removed 255 (7.5%) proteins, changed 123 (3.6%) start codons, and added 127 (3.7%) proteins that had been missed. Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available at http://genomics.lbl.gov/supplemental/DvHtranscripts2011/.

| S-EPMC3187205 | biostudies-literature

Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough

Project description:Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough

| PRJNA141329 | ENA

?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

Energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough

Project description:This SuperSeries is composed of the SubSeries listed below.

2008-04-05 | GSE8069 | GEO

Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility.

Project description:Sulfate-reducing bacteria such as Desulfovibrio vulgaris Hildenborough are often found in environments with limiting growth nutrients. Using lactate as the electron donor and carbon source, and sulfate as the electron acceptor, wild type D. vulgaris shows motility on soft agar plates. We evaluated this phenotype with mutants resulting from insertional inactivation of genes potentially related to motility. Our study revealed that the cheA3 (DVU2072) kinase mutant was impaired in the ability to form motility halos. Insertions in two other cheA loci did not exhibit a loss in this phenotype. The cheA3 mutant was also non-motile in capillary assays. Complementation with a plasmid-borne copy of cheA3 restores wild type phenotypes. The cheA3 mutant displayed a flagellum as observed by electron microscopy, grew normally in liquid medium, and was motile in wet mounts. In the growth conditions used, the D. vulgaris ΔfliA mutant (DVU3229) for FliA, predicted to regulate flagella-related genes including cheA3, was defective both in flagellum formation and in forming the motility halos. In contrast, a deletion of the flp gene (DVU2116) encoding a pilin-related protein was similar to wild type. We conclude that wild type D. vulgaris forms motility halos on solid media that are mediated by flagella-related mechanisms via the CheA3 kinase. The conditions under which the CheA1 (DVU1594) and CheA2 (DVU1960) kinase function remain to be explored.

| S-EPMC3944678 | biostudies-literature

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach.

Project description:The ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used by D. vulgaris to counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA helicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms.

| S-EPMC1482918 | biostudies-literature

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