Deletion of the hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough hampers hydrogen metabolism and low-redox-potential niche establishment

2000 ◽  
Vol 174 (3) ◽  
pp. 143-151 ◽  
Author(s):  
Alain Dolla ◽  
Brant K. J. Pohorelic ◽  
Johanna K. Voordouw ◽  
Gerrit Voordouw
Keyword(s):  
Redox Potential ◽  
Desulfovibrio Vulgaris ◽  
Hydrogen Metabolism

scholarly journals Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

2020 ◽  
Author(s):  
Vinicius Cruzeiro ◽  
Gustavo Troiano Feliciano ◽  
Adrian Roitberg
Keyword(s):  
Force Field ◽  
Redox Potential ◽  
Desulfovibrio Vulgaris ◽  
Cytochrome C3 ◽  
Computational Tools ◽  
Redox States ◽  
Computational Performance ◽  
Redox Active ◽  
Constant Ph ◽  
Experimental Findings

Coupled redox and pH-driven processes are at the core of many important biological mechanisms. As the distribution of protonation and redox states in a system is associated with the pH and redox potential of the solution, having efficient computational tools that can simulate under these conditions become very important. Such tools have the potential to provide information that complement and drive experiments. In previous publications we have presented the implementation of the constant pH and redox potential molecular dynamics (C(pH,E)MD) method in AMBER and we have shown how multidimensional replica exchange can be used to significantly enhance the convergence efficiency of our simulations. In the current work, after an improvement in our C(pH,E)MD approach that allows a given residue to be simultaneously pH- and redox-active, we have employed our methodologies to study five different systems of interest in the literature. We present results for: capped tyrosine dipeptide, two maquette systems containing one pH- and redox-active tyrosine (α3Y and peptide A), and two proteins that contain multiple heme groups (diheme cytochrome c from Rhodobacter sphaeroides and Desulfovibrio vulgaris Hildenborough cytochrome c3). We show that our results can provide new insights into previous theoretical and experimental findings by using a fully force field-based and GPUaccelerated approach, which allows the simulations to be executed with high computational performance.

scholarly journals Selenium Is Involved in Regulation of Periplasmic Hydrogenase Gene Expression in Desulfovibrio vulgaris Hildenborough

2006 ◽  
Vol 188 (9) ◽  
pp. 3228-3235 ◽  
Author(s):  
Filipa M. A. Valente ◽  
Cláudia C. Almeida ◽  
Isabel Pacheco ◽  
João Carita ◽  
Lígia M. Saraiva ◽  
...  
Keyword(s):  
Model Organism ◽  
Physiological Role ◽  
Major Effect ◽  
Electron Donors ◽  
Strong Increase ◽  
Desulfovibrio Vulgaris ◽  
Hydrogen Metabolism ◽  
Natural Habitats ◽  
Sulfate Reducing ◽  
Reducing Bacteria

ABSTRACT Desulfovibrio vulgaris Hildenborough is a good model organism to study hydrogen metabolism in sulfate-reducing bacteria. Hydrogen is a key compound for these organisms, since it is one of their major energy sources in natural habitats and also an intermediate in the energy metabolism. The D. vulgaris Hildenborough genome codes for six different hydrogenases, but only three of them, the periplasmic-facing [FeFe], [FeNi]1, and [FeNiSe] hydrogenases, are usually detected. In this work, we studied the synthesis of each of these enzymes in response to different electron donors and acceptors for growth as well as in response to the availability of Ni and Se. The formation of the three hydrogenases was not very strongly affected by the electron donors or acceptors used, but the highest levels were observed after growth with hydrogen as electron donor and lowest with thiosulfate as electron acceptor. The major effect observed was with inclusion of Se in the growth medium, which led to a strong repression of the [FeFe] and [NiFe]1 hydrogenases and a strong increase in the [NiFeSe] hydrogenase that is not detected in the absence of Se. Ni also led to increased formation of the [NiFe]1 hydrogenase, except for growth with H2, where its synthesis is very high even without Ni added to the medium. Growth with H2 results in a strong increase in the soluble forms of the [NiFe]1 and [NiFeSe] hydrogenases. This study is an important contribution to understanding why D. vulgaris Hildenborough has three periplasmic hydrogenases. It supports their similar physiological role in H2 oxidation and reveals that element availability has a strong influence in their relative expression.

scholarly journals Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

2020 ◽  
Author(s):  
Vinicius Cruzeiro ◽  
Gustavo Troiano Feliciano ◽  
Adrian Roitberg
Keyword(s):  
Force Field ◽  
Redox Potential ◽  
Desulfovibrio Vulgaris ◽  
Cytochrome C3 ◽  
Computational Tools ◽  
Redox States ◽  
Computational Performance ◽  
Redox Active ◽  
Constant Ph ◽  
Experimental Findings

Coupled redox and pH-driven processes are at the core of many important biological mechanisms. As the distribution of protonation and redox states in a system is associated with the pH and redox potential of the solution, having efficient computational tools that can simulate under these conditions become very important. Such tools have the potential to provide information that complement and drive experiments. In previous publications we have presented the implementation of the constant pH and redox potential molecular dynamics (C(pH,E)MD) method in AMBER and we have shown how multidimensional replica exchange can be used to significantly enhance the convergence efficiency of our simulations. In the current work, after an improvement in our C(pH,E)MD approach that allows a given residue to be simultaneously pH- and redox-active, we have employed our methodologies to study five different systems of interest in the literature. We present results for: capped tyrosine dipeptide, two maquette systems containing one pH- and redox-active tyrosine (α3Y and peptide A), and two proteins that contain multiple heme groups (diheme cytochrome c from Rhodobacter sphaeroides and Desulfovibrio vulgaris Hildenborough cytochrome c3). We show that our results can provide new insights into previous theoretical and experimental findings by using a fully force field-based and GPUaccelerated approach, which allows the simulations to be executed with high computational performance.

Redox potential of the small intestine lumer in a model of experimental hemorrhage in rats

2001 ◽  
Vol 120 (5) ◽  
pp. A195-A195
Author(s):  
J PAULA ◽  
E SPINEDI ◽  
A DUBIN ◽  
D BUSTOS ◽  
J DAVOLOS
Keyword(s):  
Small Intestine ◽  
Redox Potential

Unravelling a microbial synergy to boost caproate production via carboxylates chain elongation with ethanol

2019 ◽  
Vol 26 (2) ◽  
pp. 63-71
Author(s):  
Ling Leng ◽  
Ying Wang ◽  
Peixian Yang ◽  
Takashi Narihiro ◽  
Masaru Konishi Nobu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Volatile Fatty Acids ◽  
Microbial Consortia ◽  
Chain Elongation ◽  
Desulfovibrio Vulgaris ◽  
Rrna Gene ◽  
Selective Enrichment ◽  
Microbial Network ◽  
Cost Efficient ◽  
Rrna Gene Sequencing

Chain elongation of volatile fatty acids for medium chain fatty acids production (e.g. caproate) is an attractive approach to treat wastewater anaerobically and recover resource simultaneously. Undefined microbial consortia can be tailored to achieve chain elongation process with selective enrichment from anaerobic digestion sludge, which has advantages over pure culture approach for cost-efficient application. Whilst the metabolic pathway of the dominant caproate producer, Clostridium kluyveri, has been annotated, the role of other coexisting abundant microbiomes remained unclear. To this end, an ethanol-acetate fermentation inoculated with fresh digestion sludge at optimal conditions was conducted. Also, physiological study, thermodynamics and 16 S rRNA gene sequencing to elucidate the biological process by linking the system performance and dominant microbiomes were integrated. Results revealed a possible synergistic network in which C. kluyveri and three co-dominant species, Desulfovibrio vulgaris, Fusobacterium varium and Acetoanaerobium sticklandii coexisted. D. vulgaris and A. sticklandii (F. varium) were likely to boost the carboxylates chain elongation by stimulating ethanol oxidation and butyrate production through a syntrophic partnership with hydrogen (H2) serving as an electron messenger. This study unveils a synergistic microbial network to boost caproate production in mixed culture carboxylates chain elongation.

Comparison of two methods of measuring the depth of the redox potential discontinuity in intertidal mudflat sediments

2013 ◽  
Vol 487 ◽  
pp. 7-13 ◽  
Author(s):  
TG Gerwing ◽  
AMA Gerwing ◽  
D Drolet ◽  
DJ Hamilton ◽  
MA Barbeau
Keyword(s):  
Redox Potential ◽  
Intertidal Mudflat ◽  
Mudflat Sediments
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