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Jillian F Banfield - One of the best experts on this subject based on the ideXlab platform.
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Comparison of envIronmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms
BMC Genomics, 2014Co-Authors: Nicholas B Justice, Anders Norman, Christopher T Brown, Andrea Singh, Brian C Thomas, Jillian F BanfieldAbstract:Background Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage envIronments (AMD), acid-rock drainage envIronments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these envIronments, their role in biogeochemical cycling is poorly understood. Results Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans . We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of Nickel-Iron Hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate deHydrogenase complexes. Conclusions Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
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Comparison of envIronmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms.
BMC genomics, 2014Co-Authors: Nicholas B Justice, Anders Norman, Christopher T Brown, Andrea Singh, Brian C Thomas, Jillian F BanfieldAbstract:Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage envIronments (AMD), acid-rock drainage envIronments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these envIronments, their role in biogeochemical cycling is poorly understood. Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of Nickel-Iron Hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate deHydrogenase complexes. Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
Michael B. Hall - One of the best experts on this subject based on the ideXlab platform.
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Potential hydrogen bottleneck in Nickel-Iron Hydrogenase.
Inorganic chemistry, 2010Co-Authors: Jason M. Keith, Michael B. HallAbstract:The role of two-state reactivity at the enzyme active site with respect to binding of molecular H2 for the high- and low-spin of [NiFe] Hydrogenase (Ni−SI forms) is examined by density functional theory. In addition to examination of a single H2 molecule binding at either the Ni or Fe of the active site, the possibility that H2 binds simultaneously at each metal center in the active site of this enzyme is examined. The concurrent binding of two molecules of H2 suggests a potential hydrogen bottleneck in which high concentrations might lead to a decrease in the rate of hydrogen oxidation.
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theoretical characterization of the reaction intermediates in a model of the Nickel Iron Hydrogenase of desulfovibrio gigas
Journal of the American Chemical Society, 1999Co-Authors: Shuqiang Niu, And Lisa M. Thomson, Michael B. HallAbstract:The catalytic cycle for H2 oxidation in [NiFe] D. gigas Hydrogenase has been investigated through density functional theory (DFT) calculations on a wide variety of redox and protonated structures of the active site model, (CO)(CN)2Fe(μ-SMe)2Ni(SMe)2. DFT calculations on a series of known LFe(CO)(CN)(L‘)n- (L = Cp or Cp*, L‘ = CN, CO, CNCH3; n = 0, 1, 2) complexes are used to calibrate the calculated CO bond distances with the measured IR stretching frequency. By combining this calibration curve with the energy and CO bond distance of the DFT calculations on the active site model and the experimental IR frequencies on the enzyme, the redox states and structures of active site species have been determined: Ni-B is a Ni(III)−Fe(II) species, Ni-SI(a) is a Ni(II)−Fe(II) species, Ni-SI(b) has a protonated terminal sulfur (Ni bound), Ni-R is a Ni(II)−Fe(II) dihydrogen complex with H2 bound at Fe, and Ni-C is a Ni(III)−Fe(II) species with an Fe−H−Ni bridge. The latter species returns to Ni-SI through a Ni(I)−Fe(...
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Theoretical Characterization of the Reaction Intermediates in a Model of the Nickel−Iron Hydrogenase of Desulfovibrio gigas
Journal of the American Chemical Society, 1999Co-Authors: Shuqiang Niu, And Lisa M. Thomson, Michael B. HallAbstract:The catalytic cycle for H2 oxidation in [NiFe] D. gigas Hydrogenase has been investigated through density functional theory (DFT) calculations on a wide variety of redox and protonated structures of the active site model, (CO)(CN)2Fe(μ-SMe)2Ni(SMe)2. DFT calculations on a series of known LFe(CO)(CN)(L‘)n- (L = Cp or Cp*, L‘ = CN, CO, CNCH3; n = 0, 1, 2) complexes are used to calibrate the calculated CO bond distances with the measured IR stretching frequency. By combining this calibration curve with the energy and CO bond distance of the DFT calculations on the active site model and the experimental IR frequencies on the enzyme, the redox states and structures of active site species have been determined: Ni-B is a Ni(III)−Fe(II) species, Ni-SI(a) is a Ni(II)−Fe(II) species, Ni-SI(b) has a protonated terminal sulfur (Ni bound), Ni-R is a Ni(II)−Fe(II) dihydrogen complex with H2 bound at Fe, and Ni-C is a Ni(III)−Fe(II) species with an Fe−H−Ni bridge. The latter species returns to Ni-SI through a Ni(I)−Fe(...
Nicholas B Justice - One of the best experts on this subject based on the ideXlab platform.
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Comparison of envIronmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms
BMC Genomics, 2014Co-Authors: Nicholas B Justice, Anders Norman, Christopher T Brown, Andrea Singh, Brian C Thomas, Jillian F BanfieldAbstract:Background Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage envIronments (AMD), acid-rock drainage envIronments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these envIronments, their role in biogeochemical cycling is poorly understood. Results Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans . We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of Nickel-Iron Hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate deHydrogenase complexes. Conclusions Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
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Comparison of envIronmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms.
BMC genomics, 2014Co-Authors: Nicholas B Justice, Anders Norman, Christopher T Brown, Andrea Singh, Brian C Thomas, Jillian F BanfieldAbstract:Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage envIronments (AMD), acid-rock drainage envIronments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these envIronments, their role in biogeochemical cycling is poorly understood. Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of Nickel-Iron Hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate deHydrogenase complexes. Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
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Analyzing Microbial Physiology and Nutrient Transformation in a Model, Acidophilic Microbial Community using Integrated `Omics' Technologies
2013Co-Authors: Nicholas B JusticeAbstract:Author(s): Justice, Nicholas Bruce | Advisor(s): Banfield, Jillian F | Abstract: Understanding how microorganisms contribute to nutrient transformations within their community is critical to prediction of overall ecosystem function, and thus is a major goal of microbial ecology. Communities of relatively tractable complexity provide a unique opportunity to study the distribution of metabolic characteristics amongst microorganisms and how those characteristics subscribe diverse ecological functions to co-occurring, and often closely related, species. The microbial communities present in the low-pH, metal-rich envIronment of the acid mine drainage (AMD) system in Richmond Mine at Iron Mountain, CA constitute a model microbial community due to their relatively low diversity and extensive characterization over the preceding fifteen years. Here, chemoautotrophic biofilms form at the air-solution interface of the AMD solution, and carbon is fixed using energy derived from the oxidation of Iron and sulfur species released from the dissolution of mineral sulfides. The chemoautotrophic microbial communities that develop at the air-solution interface sink to the underlying sediment and degrade under microaerobic and anaerobic conditions. A transition from Bacteria- to Archaea-dominated communities coincides with this event. The Archaea identified in sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. Comparative community proteomic analyses showed a persistence of bacterial proteins in sunken biofilms, and evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, hydrolyzed bacterial proteins were inferred to represent a population of lysed cells. These findings indicate dominance of acidophilic Archaea in degrading biofilms, and suggest that they play key roles in anaerobic nutrient cycling at low pH. Biofilm submersion was recapitulated in microcosm experiments in which floating AMD microbial biofilms were submerged, amended with either 15NH4+ or deuterium oxide (2H2O), and proteomic stable isotope probing (protein-SIP) used to trace isotope incorporation into newly synthesized proteins of different community members. In 15N-ammonia amended experiments, different 14N/15N atom% values reflect distinct modes of nitrogen acquisition, since 14N is ultimately derived from extant organic biomass and 15N is derived from inorganic ammonia provided in the media. There were relatively few 15N-enriched archaeal proteins and all showed low 15N atom% enrichment in anaerobic Iron-reducing, aerobic Iron-reducing, and aerobic Iron-oxidizing envIronments. These results are consistent with Archaea synthesizing protein using the 14N derived from recycled biomolecules. This conclusion is further supported by results of parallel experiments using 2H2O, in which extensive archaeal protein synthesis was detected. In contrast, the bacterial species showed little protein synthesis when incubated in 2H2O. The nearly exclusive ability of Archaea to synthesize proteins using 2H2O may be due to archaeal heterotrophy (whereby Archaea offset deleterious effects of 2H by accessing 1H generated by respiration of organic compounds) or differences in how archaeal versus bacterial membranes (and their associated mechanisms of energy conservation) respond to 2H2O. In biofilms incubated with 15N-ammonium, bacteria synthesized proteins to different extents, with Sulfobacillus spp. synthesizing protein almost exclusively under Iron-reducing conditions whereas Leptospirillum spp. synthesized protein in all conditions, with a clear emphasis on Iron-oxidation metabolisms in the presence of Fe2+ and oxygen. These findings highlight distinct roles for Sulfobacillus vs. Leptospirillum in Iron cycling. The greatest extent of 15N atom incorporation was detected in proteins of Leptospirillum, whereas Sulfobacillus proteins had a low extent of 15N incorporation, consistent with an autotrophic metabolism for Leptospirillum and heterotrophic metabolism for Sulfobacillus. The role of Sulfobacillus organisms in biogeochemical cycling is poorly understood. The diversity of energy conservation and central carbon metabolism within this genus was analyzed using published Sulfobacillus genomes as well as five draft genomes of Sulfobacillus reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (AMDSBA1-5). Three of the newly sequenced species (AMDSBA1, AMDSBA2, and AMDSBA3) have no cultured representatives, and AMDSBA5 and AMDSBA4 represent strains of S. thermosulfidooxidans and S. benefaciens, respectively. Genomes were replete with pathways of sulfur oxidation, however the presence of enzymes involved with these pathways (and their copy numbers) varied considerably across the genus. Furthermore, several enzymes with putative sulfur and sulfur-compound reduction were identified, perhaps lending previously unknown anaerobic sulfur reduction capacity to Sulfobacillus species. Central carbon degradation pathways in Sulfobacillus lineages varied, with S. thermosulfidooxidans likely favoring the pentose phosphate pathway and lineages of S. acidophilus, AMDSBA1, AMDSBA2, AMDSBA3, and AMDSBA4 capable of using the semi-phosporylative Entner-Doudoroff pathway. Proteins involved in dissimilatory nitrate reduction were limited to AMDSBA3, and amongst AMDSBA genomes, only AMDSBA5 encoded Nickel-Iron Hydrogenase proteins. AMDSBA4 (S. benefaciens) is unusual in that its electron transport chain includes a bc complex, a unique cytochrome c oxidase, and an additional succinate deHydrogenase. It is also the only Sulfobacillus species with putative carboxysome proteins. Overall, the results demonstrate diverse ecological strategies for species of Sulfobacillus within the Richmond Mine.Metabolomics methods lag behind other omics technologies due to a wide range of experimental complexities often associated with the envIronmental matrix. We identified key metabolites associated with acidophilic and metal-tolerant microorganisms using stable isotope labeling coupled with untargeted, high-resolution mass spectrometry. Initially, g3,500 metabolic features were observed in extracts of AMD biofilms, although the molecular identity of these features remained unclear. Stable isotope labeling improved chemical formula prediction by g50% for larger metabolites (g250 atomic mass units), many of which were unrepresented in metabolic databases and may represent novel compounds. Taurine and hydroxyectoine were identified and likely provide protection from osmotic stress in the biofilms. Community genomic, transcriptomic and proteomic data were integrated to implicate fungi in taurine metabolism. Leptospirillum group II bacteria decrease production of ectoine and hydroxyectoine as biofilms mature, suggesting that biofilm structure provides some resistance to high metal and proton concentrations. The combination of taurine, ectoine, and hydroxyectoine may also constitute a sulfur, nitrogen, and carbon currency in the communities. The genomic, proteomic, and metabolomic characterizations of the Richmond Mine microbial communities not only further our understanding of the physiology of acidophilic organisms but also help elucidate their functional roles within the ecosystem as a whole. Archaea dominate in anaerobic, submerged biofilms, where they synthesize protein using organic nitrogen derived from the degrading biofilm. Sulfobacillus are implicated in sulfur transformations, and encode diverse complements of proteins involved in sulfur, nitrate and hydrogen metabolisms, suggesting key niche differentiation within this genus. Metabolites that likely serve as organic nutrient sources for a variety of organisms were identified though use of stable istope labeling techniques. The development and integration of novel ‘omics’ based technologies extends our knowledge of the Richmond Mine microbial communities and will ultimately help illuminate microbial contributions to ecosystem function in more complex envIronments.
Neil A. Burton - One of the best experts on this subject based on the ideXlab platform.
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how are the ready and unready states of Nickel Iron Hydrogenase activated by h2 a density functional theory study
Physical Chemistry Chemical Physics, 2006Co-Authors: Prabha Jayapal, Mahesh Sundararajan, Ian H. Hillier, Neil A. BurtonAbstract:We have explored possible mechanisms for the formation of the catalytically active Nia–S state of the enzyme, Nickel Iron Hydrogenase, from the Ni*r (ready) or Ni*u (unready) state, by reaction with H2, using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an –OH bridge, the rate determining step is the cleavage of H2 at the Ni3+ centre with a barrier of ∼15 kcal mol−1. We take the unready state to have a –OOH bridge, and find that reaction with H2 to form the Nir–S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of ∼19 kcal mol−1. The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.
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How are the ready and unready states of Nickel–Iron Hydrogenase activated by H2? A density functional theory study
Physical chemistry chemical physics : PCCP, 2006Co-Authors: Prabha Jayapal, Mahesh Sundararajan, Ian H. Hillier, Neil A. BurtonAbstract:We have explored possible mechanisms for the formation of the catalytically active Nia–S state of the enzyme, Nickel Iron Hydrogenase, from the Ni*r (ready) or Ni*u (unready) state, by reaction with H2, using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an –OH bridge, the rate determining step is the cleavage of H2 at the Ni3+ centre with a barrier of ∼15 kcal mol−1. We take the unready state to have a –OOH bridge, and find that reaction with H2 to form the Nir–S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of ∼19 kcal mol−1. The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.
Prabha Jayapal - One of the best experts on this subject based on the ideXlab platform.
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High level ab initio and DFT calculations of models of the catalytically active Ni–Fe Hydrogenases
Physical chemistry chemical physics : PCCP, 2008Co-Authors: Prabha Jayapal, Mahesh Sundararajan, Ian H. Hillier, David Robinson, Joseph J. W. McdouallAbstract:Multi-reference Moller-Plesset calculations of a model of the Ni-SI state of Nickel-Iron Hydrogenase predict a singlet rather than a triplet state for this species, and show that it is better described with a BP86 rather than a B3LYP functional.
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how are the ready and unready states of Nickel Iron Hydrogenase activated by h2 a density functional theory study
Physical Chemistry Chemical Physics, 2006Co-Authors: Prabha Jayapal, Mahesh Sundararajan, Ian H. Hillier, Neil A. BurtonAbstract:We have explored possible mechanisms for the formation of the catalytically active Nia–S state of the enzyme, Nickel Iron Hydrogenase, from the Ni*r (ready) or Ni*u (unready) state, by reaction with H2, using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an –OH bridge, the rate determining step is the cleavage of H2 at the Ni3+ centre with a barrier of ∼15 kcal mol−1. We take the unready state to have a –OOH bridge, and find that reaction with H2 to form the Nir–S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of ∼19 kcal mol−1. The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.
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How are the ready and unready states of Nickel–Iron Hydrogenase activated by H2? A density functional theory study
Physical chemistry chemical physics : PCCP, 2006Co-Authors: Prabha Jayapal, Mahesh Sundararajan, Ian H. Hillier, Neil A. BurtonAbstract:We have explored possible mechanisms for the formation of the catalytically active Nia–S state of the enzyme, Nickel Iron Hydrogenase, from the Ni*r (ready) or Ni*u (unready) state, by reaction with H2, using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an –OH bridge, the rate determining step is the cleavage of H2 at the Ni3+ centre with a barrier of ∼15 kcal mol−1. We take the unready state to have a –OOH bridge, and find that reaction with H2 to form the Nir–S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of ∼19 kcal mol−1. The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.