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Garcia SL, Mehrshad M, Buck M, Tsuji JM, Neufeld JD, McMahon KD, Bertilsson S, Greening C, Peura S. Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations. mSystems 2021; 6:e01196-20. [PMID: 33975970 PMCID: PMC8125076 DOI: 10.1128/msystems.01196-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/09/2021] [Indexed: 01/15/2023] Open
Abstract
Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or "species"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.
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Affiliation(s)
- Sarahi L Garcia
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Moritz Buck
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Jackson M Tsuji
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Madison, Wisconsin, USA
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
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Zorin NA, Starodubov AS, Tsygankov AA. Effect of Hg2+ on HydSL Hydrogenase of the Purple Sulfur Bacteria Thiocapsa roseopersicina BBS. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zorin NA, Zabelin AA, Shkuropatov AY, Tsygankov AA. Interaction of HydSL hydrogenase from Thiocapsa roseopersicina with cyanide leads to destruction of iron-sulfur clusters. J Inorg Biochem 2017; 177:190-197. [PMID: 28972933 DOI: 10.1016/j.jinorgbio.2017.09.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/18/2022]
Abstract
The effects of cyanide on enzymatic activity and absorption spectra in the visible and mid-IR (2150-1850cm-1) regions were characterized for purified HydSL hydrogenase from the purple sulfur bacterium Thiocapsa (T.) roseopersicina BBS. Prolonged incubation (over hours) of T. roseopersicina hydrogenase with exogenous cyanide was shown to result in an irreversible loss of activity of the enzyme in both the oxidized (as isolated) and H2-reduced states. The frequency position of the active site CO and CN- ligand stretching bands in the Fourier transform infrared (FTIR) spectrum of the oxidized form of hydrogenase was not influenced by cyanide treatment. The 410-nm absorption band characteristic of hydrogenase iron‑sulfur clusters showed a bleaching concomitantly with cyanide inactivation. A new band at 2038cm-1 was present in the FTIR spectrum of the cyanide-inactivated preparation, which band is assignable to ferrocyanide as a possible product of a destructive interaction of hydrogenase with cyanide. The results are interpreted in terms of a slow destruction of iron‑sulfur clusters of hydrogenase in the presence of cyanide accompanied by a release of iron ions in the form of ferrocyanide into the surrounding solution. Such a slow and irreversible cyanide-dependent inactivation seems to be complementary to a recently described rapid, reversible inhibitory reaction of cyanide with the active site of hydrogenases [S.V. Hexter, M.-W. Chung, K.A. Vincent, F.A. Armstrong, J. Am. Chem. Soc. 136 (2014) 10470-10477].
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Affiliation(s)
- Nikolay A Zorin
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
| | - Alexey A Zabelin
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
| | - Anatoly Ya Shkuropatov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation.
| | - Anatoly A Tsygankov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
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Cheng J, Liu M, Song W, Ding L, Liu J, Zhang L, Cen K. Enhanced hydrogen production of Enterobacter aerogenes mutated by nuclear irradiation. BIORESOURCE TECHNOLOGY 2017; 227:50-55. [PMID: 28013136 DOI: 10.1016/j.biortech.2016.12.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 06/06/2023]
Abstract
Nuclear irradiation was used for the first time to generate efficient mutants of hydrogen-producing bacteria Enterobacter aerogenes, which were screened with larger colour circles of more fermentative acid by-products. E. aerogenes cells were mutated by nuclear irradiation of 60Co γ-rays. The screened E. aerogenes ZJU1 mutant with larger colour circles enhanced the hydrogenase activity from 89.8 of the wild strain to 157.4mLH2/(gDWh). The hereditary stability of the E. aerogenes ZJU1 mutant was certified after over ten generations of cultivation. The hydrogen yield of 301mLH2/gglucose with the mutant was higher by 81.8% than that of 166mL/gglucose with the wild strain. The peak hydrogen production rate of 27.2mL/(L·h) with the mutant was higher by 40.9% compared with that of 19.3mL/(L·h) with the wild strain. The mutant produced more acetate and butyrate but less ethanol compared with the wild strain during hydrogen fermentation.
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Affiliation(s)
- Jun Cheng
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China.
| | - Min Liu
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China
| | - Wenlu Song
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China; Department of Life Science and Engineering, Jining University, Jining 273155, China
| | - Lingkan Ding
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China
| | - Jianzhong Liu
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China
| | - Li Zhang
- Shandong Botong New Energy Company, Jining 272000, China
| | - Kefa Cen
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China
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Zadvorny OA, Barrows AM, Zorin NA, Peters JW, Elgren TE. High level of hydrogen production activity achieved for hydrogenase encapsulated in sol–gel material doped with carbon nanotubes. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b922296k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Optimization of metabolic capacity and flux through environmental cues to maximize hydrogen production by the cyanobacterium "Arthrospira (Spirulina) maxima". Appl Environ Microbiol 2008; 74:6102-13. [PMID: 18676712 DOI: 10.1128/aem.01078-08] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental and nutritional conditions that optimize the yield of hydrogen (H(2)) from water using a two-step photosynthesis/fermentation (P/F) process are reported for the hypercarbonate-requiring cyanobacterium "Arthrospira maxima." Our observations lead to four main conclusions broadly applicable to fermentative H(2) production by bacteria: (i) anaerobic H(2) production in the dark from whole cells catalyzed by a bidirectional [NiFe] hydrogenase is demonstrated to occur in two temporal phases involving two distinct metabolic processes that are linked to prior light-dependent production of NADPH (photosynthetic) and dark/anaerobic production of NADH (fermentative), respectively; (ii) H(2) evolution from these reductants represents a major pathway for energy production (ATP) during fermentation by regenerating NAD(+) essential for glycolysis of glycogen and catabolism of other substrates; (iii) nitrate removal during fermentative H(2) evolution is shown to produce an immediate and large stimulation of H(2), as nitrate is a competing substrate for consumption of NAD(P)H, which is distinct from its slower effect of stimulating glycogen accumulation; (iv) environmental and nutritional conditions that increase anaerobic ATP production, prior glycogen accumulation (in the light), and the intracellular reduction potential (NADH/NAD(+) ratio) are shown to be the key variables for elevating H(2) evolution. Optimization of these conditions and culture age increases the H(2) yield from a single P/F cycle using concentrated cells to 36 ml of H(2)/g (dry weight) and a maximum 18% H(2) in the headspace. H(2) yield was found to be limited by the hydrogenase-mediated H(2) uptake reaction.
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Serebriakova LT, Sheremet'eva ME. Characterization of catalytic properties of hydrogenase isolated from the unicellular cyanobacterium Gloeocapsa alpicola CALU 743. BIOCHEMISTRY (MOSCOW) 2007; 71:1370-6. [PMID: 17223791 DOI: 10.1134/s0006297906120133] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The main catalytic properties of the Hox type hydrogenase isolated from the Gloeocapsa alpicola cells have been studied. The enzyme effectively catalyzes reactions of oxidation and evolution of H2 in the presence of methyl viologen (MV) and benzyl viologen (BV). The rates of these reactions in the interaction with the physiological electron donor/acceptor NADH/NAD+ are only 3-8% of the MV(BV)-dependent values. The enzyme interacts with NADP+ and NADPH, but is more specific to NAD+ and NADH. Purification of the hydrogenase was accompanied by destruction of its multimeric structure and the loss of ability to interact with pyridine nucleotides with retained activity of the hydrogenase component (HoxYH). To show the catalytic activity, the enzyme requires reductive activation, which occurs in the presence of H2, and NADH accelerates this process. The final hydrogenase activity depends on the redox potential of the activation medium (E(h)). At pH 7.0, the enzyme activity in the MV-dependent oxidation of H2 increased with a decrease in E(h) from -350 mV and reached the maximum at E(h) of about -390 mV. However, the rate of H2 oxidation in the presence of NAD+ in the E(h) range under study was virtually constant and equal to 7-8% of the maximal rate of H2 oxidation in the presence of MV.
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Affiliation(s)
- L T Serebriakova
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142292, Russia.
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Tsygankov AA, Minakov EA, Zorin NA, Gosteva KS, Voronin OG, Karyakin AA. Measuring the pH dependence of hydrogenase activities. BIOCHEMISTRY (MOSCOW) 2007; 72:968-73. [PMID: 17922655 DOI: 10.1134/s0006297907090076] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- A A Tsygankov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
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9
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Zadvorny OA, Zorin NA, Gogotov IN. Transformation of metals and metal ions by hydrogenases from phototrophic bacteria. Arch Microbiol 2005; 184:279-85. [PMID: 16283252 DOI: 10.1007/s00203-005-0040-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 08/25/2005] [Accepted: 08/30/2005] [Indexed: 10/25/2022]
Abstract
The ability of hydrogenases isolated from Thiocapsa roseopersicina and Lamprobacter modestohalophilus to reduce metal ions and oxidize metals has been studied. Hydrogenases from both phototrophic bacteria oxidized metallic Fe, Cd, Zn and Ni into their ionic forms with simultaneous evolution of molecular hydrogen. The metal oxidation rate decreased in the series Zn > Fe > Cd > Ni and depended on the pH. The presence of methyl viologen in the reaction system accelerated this process. T. roseopersicina and L. modestohalophilus cells and their hydrogenases reduced Ni(II), Pt(IV), Pd(II) or Ru(III) to their metallic forms under H2 atmosphere. These results suggest that metals or metal ions can serve as electron donors or acceptors for hydrogenases from phototrophic bacteria.
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Affiliation(s)
- Oleg A Zadvorny
- Institute of Basic Biological Problems of RAS, 142290 Pushchino, Russia
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Antal TK, Lindblad P. Production of H2 by sulphur-deprived cells of the unicellular cyanobacteria Gloeocapsa alpicola and Synechocystis sp. PCC 6803 during dark incubation with methane or at various extracellular pH. J Appl Microbiol 2005; 98:114-20. [PMID: 15610423 DOI: 10.1111/j.1365-2672.2004.02431.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To examine sulphur (S) deprivation in combination with the presence of methane (CH4) and changes in extracellular pH as a method to enhance in situ hydrogen (H2) generation during fermentation in the unicellular non-diazotrophic cyanobacteria Gloeocapsa alpicola and Synechocystis PCC 6803. METHODS AND RESULTS The level of H2 production, measured using a gas chromatography, was determined in S-deprived cells of G. alpicola and Synechocystis PCC 6803 during fermentation. Starvation on S enhanced the rate of H2 production by more than fourfold in both strains. S-deprived cyanobacteria were able to maintain maximum rate of H2 production during at least 8 h of fermentation representing the entire dark period of a day. Increased H2 production was observed during dark anoxic incubation with a gas phase of 100% CH4 (up to four times) at lower pH of the medium (5.0-5.5). CONCLUSIONS S-deprivation in combination with CH4, added or maybe produced by another micro-organisms, and changes in the pH of the media can be used to further increase the specific capacity of unicellular non-N2-fixing cyanobacteria to produce H2 during fermentation with the overall aim of applying it for outdoor photobiological H2 production. SIGNIFICANCE AND IMPACT OF THE STUDY S-deprivation with respect to H2 production is well studied in the green algae Chlamydomonas reinhardtii while its application for H2 production in cyanobacteria is novel. Similarly, the stimulation of H2 generation in the presence of CH4 opens up new possibilities to increase the H2 production. Natural gas enriched with H2 seems to be a perspective fuel and may be an intermediate step on the pathway to the exploitation of pure biohydrogen.
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Affiliation(s)
- T K Antal
- Department of Physiological Botany, EBC, Uppsala University, Uppsala, Sweden
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Léger C, Dementin S, Bertrand P, Rousset M, Guigliarelli B. Inhibition and aerobic inactivation kinetics of Desulfovibrio fructosovorans NiFe hydrogenase studied by protein film voltammetry. J Am Chem Soc 2005; 126:12162-72. [PMID: 15382953 DOI: 10.1021/ja046548d] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used protein film voltammetry to study the NiFe hydrogenase from Desulfovibrio fructosovorans. We show how measurements of transient activity following the addition in the electrochemical cell of H(2), CO, or O(2) allow simple and virtually instantaneous determinations of the Michaelis constant, inhibition constant, or rate of inactivation, respectively, thus opening new opportunities to study the active site of NiFe hydrogenases. The binding and release of CO occur within a fraction of a second, and we determine and discuss how its affinity for the active site changes as the driving force for the H(+)/H(2) reaction is continuously varied. Inactivation by O(2) is a slow, bimolecular process (with pH-independent rate constant approximately 3 x 10(4) s(-1) M(-1) at 40 degrees C, under one atm of H(2)) that leads to a mixture of fully oxidized states, and unlike the case of CO inhibition, the active site is not fully protected by H(2). This experimental approach could be used to study the reaction of other multicentered metalloenzymes with their gaseous substrates or inhibitors.
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Affiliation(s)
- Christophe Léger
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie, CNRS UPR9036 et Université de Provence, 31, chemin Joseph Aiguier, 13402, Marseille, France.
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Laurinavichene TV, Tsygankov AA. H2 consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors. FEMS Microbiol Lett 2001; 202:121-4. [PMID: 11506918 DOI: 10.1111/j.1574-6968.2001.tb10790.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Hydrogen uptake in the presence of various terminal electron acceptors was examined in Escherichia coli mutants synthesizing either hydrogenase 1 or hydrogenase 2. Both hydrogenases mediated nitrate-dependent H2 consumption but neither of them was coupled with nitrite. Unlike hydrogenase 2, hydrogenase 1 demonstrated poor activity with electron acceptors of low midpoint redox potential. Oxygen-linked H2 uptake via hydrogenase 1 was observed over a wide range of air concentrations. Hydrogenase 2 catalyzed this reaction only at low air concentrations. Thus, hydrogenase 1 works in cells at higher redox potential, being more tolerant to oxygen than hydrogenase 2.
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Affiliation(s)
- T V Laurinavichene
- Institute of Basic Biological Problems, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
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Nedoluzhko AI, Shumilin IA, Mazhorova LE, Popov VO, Nikandrov VV. Enzymatic oxidation of cadmium and lead metals photodeposited on cadmium sulfide. Bioelectrochemistry 2001; 53:61-71. [PMID: 11206926 DOI: 10.1016/s0302-4598(00)00094-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cadmium and lead metals deposited on CdS particles are shown to act as substrates--electron donors for enzymes, hydrogenase from Thiocapsa roseopersicina (HG), NAD-dependent hydrogenase from Alcaligenes eutrophus (NLH), and ferredoxin:NADP oxidoreductase (FNR) from Chlorella in the formation of hydrogen, NADH and NADPH, respectively. Adsorption of the enzyme on the surface of the metallized CdS particle is required for enzymatic oxidation of metal. The maximum rates for the formation of hydrogen and NADH catalyzed by hydrogenase and NAD-dependent hydrogenase with metals as electron donors are comparable with the rates obtained for these enzymes using soluble substrates. Kinetic analysis of the enzymatic oxidation of cadmium metal has revealed that the rate decreases mainly due to the formation of a solid product, which is supposed to be Cd(OH)2. The deceleration of lead oxidation catalyzed by hydrogenase proceeds at the expense of the inhibitory effect of the formed Pb2+. The enzymatic oxidation of electrochemically prepared cadmium metal is also shown. Based on these results, a new mechanism of action of the enzymes involved in anaerobic biocorrosion is proposed. By this mechanism, the enzyme accelerates the process of metal dissolution through a mediatorless catalysis of the reduction of the enzyme substrate.
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Affiliation(s)
- A I Nedoluzhko
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow
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14
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Serebryakova L, Sheremetieva M, Tsygankov A. Reversible hydrogenase activity of Gloeocapsa alpicola in continuous culture. FEMS Microbiol Lett 1998. [DOI: 10.1111/j.1574-6968.1998.tb13187.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Nedoluzhko AI, Shumilin IA, Nikandrov VV. Coupled Action of Cadmium Metal and Hydrogenase in Formate Photodecomposition Sensitized by CdS. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp9613807] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aleksey I. Nedoluzhko
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr., 33, Moscow 117071, Russian Federation
| | - Igor A. Shumilin
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr., 33, Moscow 117071, Russian Federation
| | - Vitaly V. Nikandrov
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr., 33, Moscow 117071, Russian Federation
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Zorin NA, Dimon B, Gagnon J, Gaillard J, Carrier P, Vignais PM. Inhibition by iodoacetamide and acetylene of the H-D-exchange reaction catalyzed by Thiocapsa roseopersicina hydrogenase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 241:675-81. [PMID: 8917471 DOI: 10.1111/j.1432-1033.1996.00675.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The kinetics of H-D isotope exchange catalyzed by the thermostable hydrogenase from Thiocapsa roseopersicina have been studied by analysis of the exchange between D2 and H2O. The pH dependence of the exchange reaction was examined between pH 2.5 and pH 11. Over the whole pH range, HD was produced at a higher initial velocity than H2, with a marked optimum at pH 5.5; a second peak in the pH profile was observed at around pH 8.5. The rapid formation of H2 with respect to HD in the D2/H2O system is consistent with a heterolytic cleavage of D2 into D+ and an enzyme hydride that can both exchange with the solvent. The H-D-exchange activity was lower in the H2/D2O system than in the D2/H2O system. The other reactions catalyzed by the hydrogenase, H2 oxidation and H2 evolution, are pH dependent; the optimal pH were 9.5 for H2 uptake and 4.0 for H2 production. Treatment of the active form of hydrogenase by iodoacetamide led to a slow and irreversible inhibition of the H-D exchange. When iodo[1-14C]acetamide was incubated with hydrogenase, the radioactive labeling of the large subunit was higher for the enzyme activated under H2 than for the inactive oxidized form. Cysteine residues were identified as the alkylated derivative by amino acid analysis. Acetylene, which inhibits H-D exchange and abolishes the Ni-C EPR signal, protected the enzyme from irreversible inhibition by iodoacetamide. These data indicate that iodoacetamide can reach the active site of the H2-activated hydrogenase from T. roseopersicina. This was not found to be the case with the seleno hydrogenase from Desulfovibrio baculatus (now Desulfomicrobium baculatus). Cysteine modification by iodoacetamide upon activation of the enzyme concomitant with loss of H-D exchange indicates that reductive activation makes at least one Cys residue of the active site available for alkylation.
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Affiliation(s)
- N A Zorin
- CEA/Grenoble, Laboratoire de Biochimie Microbienne (CNRS URA 1130 alliée à I'INSERM), Département de Biologie Moléculaire et Structurale, Grenoble, France
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Serebryakova LT, Medina M, Zorin NA, Gogotov IN, Cammack R. Reversible hydrogenase of Anabaena variabilis ATCC 29413: catalytic properties and characterization of redox centres. FEBS Lett 1996; 383:79-82. [PMID: 8612797 DOI: 10.1016/0014-5793(96)00228-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The catalytic and spectroscopic properties of the reversible hydrogenase from the cyanobacterium Anabaena variabilis have been examined. The hydrogenase required reductive activation in order to elicit hydrogen-oxidation activity. Carbon monoxide was a weak (Ki=35 microM), reversible and competitive inhibitor. A flavin with the chromatographic properties of FMN, and nickel were detected in the purified enzyme. A. variabilis hydrogenase exhibited electron paramagnetic resonance (EPR) spectra in its hydrogen-reduced state, indicative of [2Fe-2S] and [4Fe-4S] clusters. Although no EPR signals due to nickel were detected, the results are consistent with the enzyme being a flavin-containing hydrogenase of the nickel-iron type.
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Affiliation(s)
- L T Serebryakova
- Institute of Soil Science and Photosynthesis, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Goldman CM, Mascharak PK. Reactions of H2with the Nickel Site(s) of the [FeNi] and [FeNiSe] Hydrogenases: What Do the Model Complexes Suggest? COMMENT INORG CHEM 1995. [DOI: 10.1080/02603599508033861] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Albracht SP. Nickel hydrogenases: in search of the active site. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1188:167-204. [PMID: 7803444 DOI: 10.1016/0005-2728(94)90036-1] [Citation(s) in RCA: 341] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- S P Albracht
- E.C. Slater Institute, BioCentrum Amsterdam, University of Amsterdam, The Netherlands
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Localization of hydrogenase in the purple sulphur bacterium Thiocapsa roseopersicina. Arch Microbiol 1993. [DOI: 10.1007/bf00288709] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kovács KL, Bagyinka C. Structural properties, functional states and physiological roles of hydrogenase in photosynthetic bacteria. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb04945.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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van der Zwaan JW, Coremans JM, Bouwens EC, Albracht SP. Effect of 17O2 and 13CO on EPR spectra of nickel in hydrogenase from Chromatium vinosum. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1041:101-10. [PMID: 2176104 DOI: 10.1016/0167-4838(90)90051-g] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Oxygen, either molecular oxygen or a reduction adduct, can tightly bind in the vicinity of the two forms of trivalent nickel occurring in hydrogenase from Chromatium vinosum, as evident from studies with 17O-enriched O2. This oxygen is not in the first coordination sphere of nickel. As has been reported earlier for hydrogenase from Desulfovibrio gigas (Fernandez, V.M., Hatchikian, A.C., Patil, D.S. and Cammack, R. (1986) Biochim. Biophys. Acta 883, 145-154), also the relative activity of the C.vinosum enzyme correlates well with the presence of only one of the two Ni(III) forms in the oxidized preparation. These results make it less likely that a specific oxygenation of only one of the Ni(III) forms would be the reason for the reversible inactivation of nickel hydrogenases by oxygen. Reaction of H2-reduced enzyme with 13CO now demonstrated beyond doubt that: (i) One 13CO molecule is a direct ligand to nickel in axial position; and (ii) hydrogen binds at the same coordination site as CO. It can also be concluded that hydrogen is not bound as a hydride ion, but presumably as molecular hydrogen. A simple way to explain the EPR spectra from the 13CO-adduct of the enzyme is to assume a monovalent state for the nickel.
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Affiliation(s)
- J W van der Zwaan
- E.C. Slater Institute for Biochemical Research, University of Amsterdam, The Netherlands
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Abstract
Hydrogenases devoid of nickel and containing only Fe-S clusters have been found so far only in some strictly anaerobic bacteria. Four Fe-hydrogenases have been characterized: from Megasphaera elsdenii, Desulfovibrio vulgaris (strain Hildenborough), and two from Clostridium pasteurianum. All contain two or more [4Fe-4S]1+,2+ or F clusters and a unique type of Fe-S center termed the H cluster. The H cluster appears to be remarkably similar in all the hydrogenases, and is proposed as the site of H2 oxidation and H2 production. The F clusters serve to transfer electrons between the H cluster and the external electron carrier. In all of the hydrogenases the H cluster is comprised of at least three Fe atoms, and possibly six. In the oxidized state it contains two types of magnetically distinct Fe atoms, has an S = 1/2 spin state, and exhibits a novel rhombic EPR signal. The reduced cluster is diamagnetic (S = 0). The oxidized H cluster appears to undergo a conformation change upon reduction with H2 with an increase in Fe-Fe distances of about 0.5 A. Studies using resonance Raman, magnetic circular dichroism and electron spin echo spectroscopies suggest that the H cluster has significant non-sulfur coordination. The H cluster has two binding sites for CO, at least one of which can also bind O2. Binding to one site changes the EPR properties of the cluster and gives a photosensitive adduct, but does not affect catalytic activity. Binding to the other site, which only becomes exposed during the catalytic cycle, leads to loss of catalytic activity. Mechanisms of H2 activation and electron transfer are proposed to explain the effects of CO binding and the ability of one of the hydrogenases to preferentially catalyze H2 oxidation.
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Affiliation(s)
- M W Adams
- Department of Biochemistry, University of Georgia, Athens 30602
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Cammack R, Bagyinka C, Kovacs KL. Spectroscopic characterization of the nickel and iron-sulphur clusters of hydrogenase from the purple photosynthetic bacterium Thiocapsa roseopersicina. 1. Electron spin resonance spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 182:357-62. [PMID: 2544424 DOI: 10.1111/j.1432-1033.1989.tb14838.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The thermostable hydrogenase from Thiocapsa roseopersicina was examined by low-temperature ESR spectroscopy. Two types of signals were detected, from an oxidized iron-sulphur cluster and a nickel centre (Ni-A). In the oxidized protein additional signals were observed due to spin-spin interaction between the two paramagnetic centres. This interaction could be reversibly abolished by reduction to a redox potential below 105 mV. This implies that an additional redox centre is involved in the interaction, for which an Fe3+ ion is suggested. Reduction with hydrogen induced a second type of nickel ESR signal (Ni-C), corresponding to an intermediate redox state seen in other nickel hydrogenases. The Ni-C species was light-sensitive at cryogenic temperatures. At temperatures near to 4.2 K the Ni-C signal showed evidence of interaction with another paramagnetic centre, presumably a second iron-sulphur cluster. On reoxidation a signal due to a third Ni(III) species, Ni-B, increased in amplitude. These results establish that metal centres in the hydrogenase from T. roseopersicina are closely similar to those of the well-studied hydrogenase from Chromatium vinosum.
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Affiliation(s)
- R Cammack
- Department of Biochemistry, King's College, London, England
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Petrov RR, Utkin IB, Munilla R, Fernandez VM, Popov VO. Effect of redox potential on the catalytic properties of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1. Arch Biochem Biophys 1989; 268:306-13. [PMID: 2536263 DOI: 10.1016/0003-9861(89)90592-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The effect of redox potential on the catalytic activities of the soluble hydrogenase from the hydrogen bacterium Alcaligenes eutrophus Z1 was studied. Several transitions were observed on the enzyme catalytic activity vs potential profiles. The coenzyme-dependent activities of the hydrogenase, its diaphorase activity and activity toward NAD, are controlled by the Em -300 mV, while the process of hydrogen evolution from reduced methyl viologen is governed by the midpoint redox potential of -435 mV. This value of Em was independent of pH in the range 5 to 8. The redox potential of the medium appears to be one of the major factors determining the hydrogenase activation, inactivation, and catalytic properties. It is suggested that a change in the redox state of the enzyme electron transport chain is followed by structural rearrangements within the protein affecting both the hydrogenase catalytic activity and stability. The probable mechanism of enzyme activity regulation is discussed.
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Affiliation(s)
- R R Petrov
- A.N. Bach Institute of Biochemistry, USSR Academy of Sciences, Moscow
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