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Ge X, Vaccaro BJ, Thorgersen MP, Poole FL, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW. Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle. Environ Microbiol 2018; 21:152-163. [PMID: 30289197 DOI: 10.1111/1462-2920.14435] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/24/2018] [Accepted: 09/27/2018] [Indexed: 11/25/2022]
Abstract
Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO4 2- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.
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Affiliation(s)
- Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Erica L Majumder
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Kara B De León
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Ji Won Moon
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Charles J Paradis
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98495, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98495, USA
| | - Paul D Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
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Martinez-Pastor M, Lancaster WA, Tonner PD, Adams MWW, Schmid AK. A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea. Nucleic Acids Res 2017; 45:9990-10001. [PMID: 28973467 PMCID: PMC5737653 DOI: 10.1093/nar/gkx662] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023] Open
Abstract
Iron is required for key metabolic processes but is toxic in excess. This circumstance forces organisms across the tree of life to tightly regulate iron homeostasis. In hypersaline lakes dominated by archaeal species, iron levels are extremely low and subject to environmental change; however, mechanisms regulating iron homeostasis in archaea remain unclear. In previous work, we demonstrated that two transcription factors (TFs), Idr1 and Idr2, collaboratively regulate aspects of iron homeostasis in the model species Halobacterium salinarum. Here we show that Idr1 and Idr2 are part of an extended regulatory network of four TFs of the bacterial DtxR family that maintains intracellular iron balance. We demonstrate that each TF directly regulates at least one of the other DtxR TFs at the level of transcription. Dynamical modeling revealed interlocking positive feedback loop architecture, which exhibits bistable or oscillatory network dynamics depending on iron availability. TF knockout mutant phenotypes are consistent with model predictions. Together, our results support that this network regulates iron homeostasis despite variation in extracellular iron levels, consistent with dynamical properties of interlocking feedback architecture in eukaryotes. These results suggest that archaea use bacterial-type TFs in a eukaryotic regulatory network topology to adapt to harsh environments.
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Affiliation(s)
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Peter D Tonner
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA.,Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA.,Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
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Thorgersen MP, Lancaster WA, Ge X, Zane GM, Wetmore KM, Vaccaro BJ, Poole FL, Younkin AD, Deutschbauer AM, Arkin AP, Wall JD, Adams MWW. Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions. Front Microbiol 2017; 8:1529. [PMID: 28848534 PMCID: PMC5554334 DOI: 10.3389/fmicb.2017.01529] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/28/2017] [Indexed: 01/03/2023] Open
Abstract
Chromium and uranium are highly toxic metals that contaminate many natural environments. We investigated their mechanisms of toxicity under anaerobic conditions using nitrate-reducing Pseudomonas stutzeri RCH2, which was originally isolated from a chromium-contaminated aquifer. A random barcode transposon site sequencing library of RCH2 was grown in the presence of the chromate oxyanion (Cr[VI]O42−) or uranyl oxycation (U[VI]O22+). Strains lacking genes required for a functional nitrate reductase had decreased fitness as both metals interacted with heme-containing enzymes required for the later steps in the denitrification pathway after nitrate is reduced to nitrite. Cr[VI]-resistance also required genes in the homologous recombination and nucleotide excision DNA repair pathways, showing that DNA is a target of Cr[VI] even under anaerobic conditions. The reduced thiol pool was also identified as a target of Cr[VI] toxicity and psest_2088, a gene of previously unknown function, was shown to have a role in the reduction of sulfite to sulfide. U[VI] resistance mechanisms involved exopolysaccharide synthesis and the universal stress protein UspA. As the first genome-wide fitness analysis of Cr[VI] and U[VI] toxicity under anaerobic conditions, this study provides new insight into the impact of Cr[VI] and U[VI] on an environmental isolate from a chromium contaminated site, as well as into the role of a ubiquitous protein, Psest_2088.
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Affiliation(s)
- Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - Grant M Zane
- Department of Biochemistry, University of MissouriColumbia, MO, United States
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - Adam D Younkin
- Department of Biochemistry, University of MissouriColumbia, MO, United States
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Judy D Wall
- Department of Biochemistry, University of MissouriColumbia, MO, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
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King AJ, Preheim SP, Bailey KL, Robeson MS, Roy Chowdhury T, Crable BR, Hurt RA, Mehlhorn T, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole F, Watson DB, W Fields M, Chandonia JM, Alm EJ, Zhou J, Adams MWW, Hazen TC, Arkin AP, Elias DA. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environ Sci Technol 2017; 51:2879-2889. [PMID: 28112946 DOI: 10.1021/acs.est.6b04751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.
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Affiliation(s)
- Andrew J King
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Sarah P Preheim
- Department of Environmental Health and Enginering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Kathryn L Bailey
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Michael S Robeson
- Fish, Wildlife and Conservation Biology, Colorado State University , Fort Collins, Colorado 80523, United States
| | - Taniya Roy Chowdhury
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Bryan R Crable
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Richard A Hurt
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Tonia Mehlhorn
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Kenneth A Lowe
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Tommy J Phelps
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Anthony V Palumbo
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Craig C Brandt
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Ping Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - David B Watson
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
| | - Matthew W Fields
- Department of Microbiology & Immunology, Montana State University , Bozeman, Montana 59717, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkley National Laboratory , Berkley, California 94720, United States
| | - Eric J Alm
- Civil and Environmental Engineering and Biological Engineering, Massachusets Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
| | - Terry C Hazen
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkley National Laboratory , Berkley, California 94720, United States
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
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Vaccaro BJ, Lancaster WA, Thorgersen MP, Zane GM, Younkin AD, Kazakov AE, Wetmore KM, Deutschbauer A, Arkin AP, Novichkov PS, Wall JD, Adams MWW. Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. Appl Environ Microbiol 2016; 82:6046-56. [PMID: 27474723 PMCID: PMC5038046 DOI: 10.1128/aem.01845-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/27/2016] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED Metal ion transport systems have been studied extensively, but the specificity of a given transporter is often unclear from amino acid sequence data alone. In this study, predicted Cu(2+) and Zn(2+) resistance systems in Pseudomonas stutzeri strain RCH2 are compared with those experimentally implicated in Cu(2+) and Zn(2+) resistance, as determined by using a DNA-barcoded transposon mutant library. Mutant fitness data obtained under denitrifying conditions are combined with regulon predictions to yield a much more comprehensive picture of Cu(2+) and Zn(2+) resistance in strain RCH2. The results not only considerably expand what is known about well-established metal ion exporters (CzcCBA, CzcD, and CusCBA) and their accessory proteins (CzcI and CusF), they also reveal that isolates with mutations in some predicted Cu(2+) resistance systems do not show decreased fitness relative to the wild type when exposed to Cu(2+) In addition, new genes are identified that have no known connection to Zn(2+) (corB, corC, Psest_3226, Psest_3322, and Psest_0618) or Cu(2+) resistance (Mrp antiporter subunit gene, Psest_2850, and Psest_0584) but are crucial for resistance to these metal cations. Growth of individual deletion mutants lacking corB, corC, Psest_3226, or Psest_3322 confirmed the observed Zn-dependent phenotypes. Notably, to our knowledge, this is the first time a bacterial homolog of TMEM165, a human gene responsible for a congenital glycosylation disorder, has been deleted and the resulting strain characterized. Finally, the fitness values indicate Cu(2+)- and Zn(2+)-based inhibition of nitrite reductase and interference with molybdenum cofactor biosynthesis for nitrate reductase. These results extend the current understanding of Cu(2+) and Zn(2+) efflux and resistance and their effects on denitrifying metabolism. IMPORTANCE In this study, genome-wide mutant fitness data in P. stutzeri RCH2 combined with regulon predictions identify several proteins of unknown function that are involved in resisting zinc and copper toxicity. For zinc, these include a member of the UPF0016 protein family that was previously implicated in Ca(2+)/H(+) antiport and a human congenital glycosylation disorder, CorB and CorC, which were previously linked to Mg(2+) transport, and Psest_3322 and Psest_0618, two proteins with no characterized homologs. Experiments using mutants lacking Psest_3226, Psest_3322, corB, corC, or czcI verified their proposed functions, which will enable future studies of these little-characterized zinc resistance determinants. Likewise, Psest_2850, annotated as an ion antiporter subunit, and the conserved hypothetical protein Psest_0584 are implicated in copper resistance. Physiological connections between previous studies and phenotypes presented here are discussed. Functional and mechanistic understanding of transport proteins improves the understanding of systems in which members of the same protein family, including those in humans, can have different functions.
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Affiliation(s)
- Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Adam D Younkin
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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McTernan PM, Chandrayan SK, Wu CH, Vaccaro BJ, Lancaster WA, Adams MWW. Engineering the respiratory membrane-bound hydrogenase of the hyperthermophilic archaeon Pyrococcus furiosus and characterization of the catalytically active cytoplasmic subcomplex. Protein Eng Des Sel 2015; 28:1-8. [PMID: 25476267 PMCID: PMC6373663 DOI: 10.1093/protein/gzu051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 11/14/2022] Open
Abstract
The archaeon Pyrococcus furiosus grows optimally at 100°C by converting carbohydrates to acetate, carbon dioxide and hydrogen gas (H2), obtaining energy from a respiratory membrane-bound hydrogenase (MBH). This conserves energy by coupling H2 production to oxidation of reduced ferredoxin with generation of a sodium ion gradient. MBH is classified as a Group 4 hydrogenase and is encoded by a 14-gene operon that contains hydrogenase and Na(+)/H(+) antiporter modules. Herein a His-tagged 4-subunit cytoplasmic subcomplex of MBH (C-MBH) was engineered and expressed in P. furiosus by differential transcription of the MBH operon. It was purified under anaerobic conditions by affinity chromatography without detergent. Purified C-MBH had a Fe : Ni ratio of 14 : 1, similar to the predicted value of 13 : 1. The O2 sensitivities of C-MBH and the 14-subunit membrane-bound version were similar (half-lives of ∼15 h in air), but C-MBH was more thermolabile (half-lives at 90°C of 8 and 25 h, respectively). C-MBH evolved H2 with the physiological electron donor, reduced ferredoxin, optimally at 60°C. This is the first report of the engineering and characterization of a soluble catalytically active subcomplex of a membrane-bound respiratory hydrogenase.
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Affiliation(s)
- Patrick M McTernan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
| | - Sanjeev K Chandrayan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
| | - Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
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Lancaster WA, Menon AL, Scott I, Poole FL, Vaccaro BJ, Thorgersen MP, Geller J, Hazen TC, Hurt RA, Brown SD, Elias DA, Adams MWW. Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization. Metallomics 2014; 6:1004-13. [PMID: 24706256 DOI: 10.1039/c4mt00050a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although as many as half of all proteins are thought to require a metal cofactor, the metalloproteomes of microorganisms remain relatively unexplored. Microorganisms from different environments are likely to vary greatly in the metals that they assimilate, not just among the metals with well-characterized roles but also those lacking any known function. Herein we investigated the metal utilization of two microorganisms that were isolated from very similar environments and are of interest because of potential roles in the immobilization of heavy metals, such as uranium and chromium. The metals assimilated and their concentrations in the cytoplasm of Desulfovibrio vulgaris strain Hildenborough (DvH) and Enterobacter cloacae strain Hanford (EcH) varied dramatically, with a larger number of metals present in Enterobacter. For example, a total of 9 and 19 metals were assimilated into their cytoplasmic fractions, respectively, and DvH did not assimilate significant amounts of zinc or copper whereas EcH assimilated both. However, bioinformatic analysis of their genome sequences revealed a comparable number of predicted metalloproteins, 813 in DvH and 953 in EcH. These allowed some rationalization of the types of metal assimilated in some cases (Fe, Cu, Mo, W, V) but not in others (Zn, Nd, Ce, Pr, Dy, Hf and Th). It was also shown that U binds an unknown soluble protein in EcH but this incorporation was the result of extracellular U binding to cytoplasmic components after cell lysis.
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Affiliation(s)
- W Andrew Lancaster
- Department of Biochemistry & Molecular Biology, University of Georgia, Life Sciences Bldg., Athens, GA 30602-7229, USA.
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McTernan PM, Chandrayan SK, Wu CH, Vaccaro BJ, Lancaster WA, Yang Q, Fu D, Hura GL, Tainer JA, Adams MWW. Intact functional fourteen-subunit respiratory membrane-bound [NiFe]-hydrogenase complex of the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 2014; 289:19364-72. [PMID: 24860091 PMCID: PMC4094048 DOI: 10.1074/jbc.m114.567255] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/15/2014] [Indexed: 11/06/2022] Open
Abstract
The archaeon Pyrococcus furiosus grows optimally at 100 °C by converting carbohydrates to acetate, CO2, and H2, obtaining energy from a respiratory membrane-bound hydrogenase (MBH). This conserves energy by coupling H2 production to oxidation of reduced ferredoxin with generation of a sodium ion gradient. MBH is encoded by a 14-gene operon with both hydrogenase and Na(+)/H(+) antiporter modules. Herein a His-tagged MBH was expressed in P. furiosus and the detergent-solubilized complex purified under anaerobic conditions by affinity chromatography. Purified MBH contains all 14 subunits by electrophoretic analysis (13 subunits were also identified by mass spectrometry) and had a measured iron:nickel ratio of 15:1, resembling the predicted value of 13:1. The as-purified enzyme exhibited a rhombic EPR signal characteristic of the ready nickel-boron state. The purified and membrane-bound forms of MBH both preferentially evolved H2 with the physiological donor (reduced ferredoxin) as well as with standard dyes. The O2 sensitivities of the two forms were similar (half-lives of ∼ 15 h in air), but the purified enzyme was more thermolabile (half-lives at 90 °C of 1 and 25 h, respectively). Structural analysis of purified MBH by small angle x-ray scattering indicated a Z-shaped structure with a mass of 310 kDa, resembling the predicted value (298 kDa). The angle x-ray scattering analyses reinforce and extend the conserved sequence relationships of group 4 enzymes and complex I (NADH quinone oxidoreductase). This is the first report on the properties of a solubilized form of an intact respiratory MBH complex that is proposed to evolve H2 and pump Na(+) ions.
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Affiliation(s)
- Patrick M McTernan
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - Sanjeev K Chandrayan
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - Chang-Hao Wu
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - Brian J Vaccaro
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - W Andrew Lancaster
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - Qingyuan Yang
- the Department of Physiology, John Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - Dax Fu
- the Department of Physiology, John Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - Greg L Hura
- the Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - John A Tainer
- the Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael W W Adams
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229,
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Lancaster WA, Praissman JL, Poole FL, Cvetkovic A, Menon AL, Scott JW, Jenney FE, Thorgersen MP, Kalisiak E, Apon JV, Trauger SA, Siuzdak G, Tainer JA, Adams MWW. A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data. BMC Bioinformatics 2011; 12:64. [PMID: 21356119 PMCID: PMC3058030 DOI: 10.1186/1471-2105-12-64] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Accepted: 02/28/2011] [Indexed: 12/02/2022] Open
Abstract
Background Metal-containing proteins comprise a diverse and sizable category within the proteomes of organisms, ranging from proteins that use metals to catalyze reactions to proteins in which metals play key structural roles. Unfortunately, reliably predicting that a protein will contain a specific metal from its amino acid sequence is not currently possible. We recently developed a generally-applicable experimental technique for finding metalloproteins on a genome-wide scale. Applying this metal-directed protein purification approach (ICP-MS and MS/MS based) to the prototypical microbe Pyrococcus furiosus conclusively demonstrated the extent and diversity of the uncharacterized portion of microbial metalloproteomes since a majority of the observed metal peaks could not be assigned to known or predicted metalloproteins. However, even using this technique, it is not technically feasible to purify to homogeneity all metalloproteins in an organism. In order to address these limitations and complement the metal-directed protein purification, we developed a computational infrastructure and statistical methodology to aid in the pursuit and identification of novel metalloproteins. Results We demonstrate that our methodology enables predictions of metal-protein interactions using an experimental data set derived from a chromatography fractionation experiment in which 870 proteins and 10 metals were measured over 2,589 fractions. For each of the 10 metals, cobalt, iron, manganese, molybdenum, nickel, lead, tungsten, uranium, vanadium, and zinc, clusters of proteins frequently occurring in metal peaks (of a specific metal) within the fractionation space were defined. This resulted in predictions that there are from 5 undiscovered vanadium- to 13 undiscovered cobalt-containing proteins in Pyrococcus furiosus. Molybdenum and nickel were chosen for additional assessment producing lists of genes predicted to encode metalloproteins or metalloprotein subunits, 22 for nickel including seven from known nickel-proteins, and 20 for molybdenum including two from known molybdo-proteins. The uncharacterized proteins are prime candidates for metal-based purification or recombinant approaches to validate these predictions. Conclusions We conclude that the largely uncharacterized extent of native metalloproteomes can be revealed through analysis of the co-occurrence of metals and proteins across a fractionation space. This can significantly impact our understanding of metallobiochemistry, disease mechanisms, and metal toxicity, with implications for bioremediation, medicine and other fields.
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Affiliation(s)
- W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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