scholarly journals The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

2004 ◽  
Vol 22 (5) ◽  
pp. 554-559 ◽  
Author(s):  
John F Heidelberg ◽  
Rekha Seshadri ◽  
Shelley A Haveman ◽  
Christopher L Hemme ◽  
Ian T Paulsen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Desulfovibrio Vulgaris ◽  
Sulfate Reducing ◽  
Desulfovibrio Vulgaris Hildenborough

Functional characterization of the early steps of tetrapyrrole biosynthesis and modification in Desulfovibrio vulgaris Hildenborough

2009 ◽  
Vol 420 (2) ◽  
pp. 317-326 ◽  
Author(s):  
Susana A. L. Lobo ◽  
Amanda Brindley ◽  
Martin J. Warren ◽  
Lígia M. Saraiva
Keyword(s):  
Functional Characterization ◽  
Desulfovibrio Vulgaris ◽  
Decarboxylase Activity ◽  
Sulfate Reducing ◽  
Porphobilinogen Synthase ◽  
Desulfovibrio Vulgaris Hildenborough ◽  
The Individual ◽  
Individual Enzyme ◽  
Relevant Gene

The biosynthesis of the tetrapyrrole framework has been investigated in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough by characterization of the enzymes required for the transformation of aminolaevulinic acid into sirohydrochlorin. PBG (porphobilinogen) synthase (HemB) was found to be a zinc-dependent enzyme that exists in its native state as a homohexamer. PBG deaminase (HemC) was shown to contain the dipyrromethane cofactor. Uroporphyrinogen III synthase is found fused with a uroporphyrinogen III methyltransferase (HemD-CobA). Both activities could be demonstrated in this amalgamated protein and the individual enzyme activities were separated by dissecting the relevant gene to allow the production of two distinct proteins. A gene annotated in the genome as a bifunctional precorrin-2 dehydrogenase/sirohydrochlorin ferrochelatase was in fact shown to act only as a dehydrogenase and is simply capable of synthesizing sirohydrochlorin rather than sirohaem. Genome analysis also reveals a lack of any uroporphyrinogen III decarboxylase, an enzyme necessary for the classical route to haem synthesis. However, the genome does encode some predicted haem d1 biosynthetic enzymes even though the bacterium does not contain the cd1 nitrite reductase. We suggest that sirohydrochlorin acts as a substrate for haem synthesis using a novel pathway that involves homologues of the d1 biogenesis system. This explains why the uroporphyrinogen III synthase is found fused with the methyltransferase, bypassing the need for uroporphyrinogen III decarboxylase activity.

scholarly journals Evidence-Based Annotation of Transcripts and Proteins in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

2011 ◽  
Vol 193 (20) ◽  
pp. 5716-5727 ◽  
Author(s):  
M. N. Price ◽  
A. M. Deutschbauer ◽  
J. V. Kuehl ◽  
H. Liu ◽  
H. E. Witkowska ◽  
...  
Keyword(s):  
Desulfovibrio Vulgaris ◽  
Evidence Based ◽  
Sulfate Reducing ◽  
Desulfovibrio Vulgaris Hildenborough

Effects of biocides on gene expression in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

2010 ◽  
Vol 87 (3) ◽  
pp. 1109-1118 ◽  
Author(s):  
Meng-Hsin Phoebe Lee ◽  
Sean M. Caffrey ◽  
Johanna K. Voordouw ◽  
Gerrit Voordouw
Keyword(s):  
Gene Expression ◽  
Desulfovibrio Vulgaris ◽  
Sulfate Reducing ◽  
Desulfovibrio Vulgaris Hildenborough

scholarly journals Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

2021 ◽  
Vol 10 (11) ◽  
Author(s):  
Judy D. Wall ◽  
Grant M. Zane ◽  
Thomas R. Juba ◽  
Jennifer V. Kuehl ◽  
Jayashree Ray ◽  
...  
Keyword(s):  
Research Collaboration ◽  
Research Community ◽  
Desulfovibrio Vulgaris ◽  
Deletion Mutants ◽  
Content Type ◽  
Sulfate Reducing ◽  
Desulfovibrio Vulgaris Hildenborough ◽  
Genetic Constructs ◽  
Protein Constructs

ABSTRACT The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community.

scholarly journals Development of genome-wide genetic assays in Desulfovibrio vulgaris Hildenborough

2015 ◽  
Author(s):  
◽  
Samuel R. Fels
Keyword(s):  
De Novo ◽  
Genetic System ◽  
Desulfovibrio Vulgaris ◽  
Biologically Relevant ◽  
Sulfate Reducing ◽  
Rna Transcripts ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
New Type ◽  
Desulfovibrio Vulgaris Hildenborough

Illumina sequencing and other massively-parallel, short read sequencing technologies have become prevalent methods for querying the genetic systems of organisms. This trend was initially driven by the demand for general de novo and resequencing applications in eukaryotes, but uses for these instruments have recently grown in scope to also include more specific assays and methods intended for use in prokaryotic systems. This thesis seeks to develop two such assays for use in the sulfate reducing bacteria type species Desulfovibrio vulgaris Hildenborough. These novel assays continue advances made in other bacteria, and the use of this environmentally relevant obligate anaerobe will ensure their extension to other bacteria outside the easily-manipulated groups studied previously. The first assay is a variation on existing transposon sequencing (Tn-seq) assays, which seek to determine gene fitness profiles and essential genes by simultaneous analyses of whether the absence of each gene product alters the growth kinetics of the bacterium. Here we modify the standard Tn-seq procedure by including delivery of the transposon through conjugation and liquid culture enrichment of the mutant pool, creating transposon liquid enrichment sequencing (TnLE-seq). This simplifies and shortens the process, and also reduces barriers to application of the technique in microbes lacking a facile genetic system. The second assay provides a means of mapping consensus 3' end sites of RNA transcripts across a reference genome. This method is known as 3' RNA-seq and compliments an established technique for determining 5' start sites of transcripts. Together these facilitate the application of current sequencing technology to a wider array of microbes and a new type of biologically relevant genetic data.

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

2007 ◽  
Vol 189 (17) ◽  
pp. 6159-6167 ◽  
Author(s):  
Sean M. Caffrey ◽  
Hyung-Soo Park ◽  
Johanna K. Voordouw ◽  
Zhili He ◽  
Jizhong Zhou ◽  
...  
Keyword(s):  
Electron Donor ◽  
Molecular Hydrogen ◽  
Desulfovibrio Vulgaris ◽  
Rate Data ◽  
Wild Type ◽  
Cellular Functions ◽  
Lower Affinity ◽  
Sulfate Reducing ◽  
Defined Media ◽  
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] 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 defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen > 50% hydrogen > lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase.

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