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ANRV413-BI79-18 ARI 27 April 2010 21:0 Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2 Storage Rudolf K. Thauer, Anne-Kristin Kaster, Meike Goenrich, Michael Schick, Takeshi Hiromoto, and Seigo Shima Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; email: [email protected] Annu. Rev. Biochem. 2010. 79:507–36 Key Words First published online as a Review in Advance on H2 activation, energy-converting hydrogenase, complex I of the March 17, 2010 respiratory chain, chemiosmotic coupling, electron bifurcation, The Annual Review of Biochemistry is online at reversed electron transfer biochem.annualreviews.org This article’s doi: Abstract 10.1146/annurev.biochem.030508.152103 Most methanogenic archaea reduce CO2 with H2 to CH4. For the Copyright c 2010 by Annual Reviews. activation of H2, they use different [NiFe]-hydrogenases, namely All rights reserved energy-converting [NiFe]-hydrogenases, heterodisulfide reductase- 0066-4154/10/0707-0507$20.00 associated [NiFe]-hydrogenase or methanophenazine-reducing by University of Texas - Austin on 06/10/13. For personal use only. [NiFe]-hydrogenase, and F420-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]- hydrogenase (instead of F420-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH2-, one S-CH2-, and a sp2-hybridized pyridinol nitrogen. Ligation of the iron is thus similar to that of the low-spin iron in the binuclear active-site metal center of [NiFe]- and [FeFe]-hydrogenases. Putative genes for the synthesis of the FeGP cofactor have been identified. The formation of methane from 4 H2 and CO2 catalyzed by methanogenic archaea is being discussed as an efficient means to store H2. 507 ANRV413-BI79-18 ARI 27 April 2010 21:0 The name hydrogenase was coined in 1931 by Contents Stephenson & Stickland (2, 3) for an activity in anaerobically grown Escherichia coli cells medi- INTRODUCTION .................. 508 ating the reversible reduction of dyes with H2. H2 AS AN INTERMEDIATE IN Dye reduction was reversibly inhibited by CO, CH4 FORMATION AND THE indicating the involvement of a transition metal ORGANISMS INVOLVED ....... 510 in H activation (4). The transition metal later HYDROGENASES FOUND 2 turned out to be nickel in a binuclear nickel- IN METHANOGENS AND iron center in the case of [NiFe]-hydrogenases THEIR FUNCTION ............. 511 (5–8), iron in a binuclear iron-iron center in the THE FOUR SUBTYPES case of [FeFe]-hydrogenases (9–11), and iron OF [NiFe]-HYDROGENASES in a mononuclear iron center in the case of IN METHANOGENS ............ 514 [Fe]-hydrogenase (12–14), which are the three Energy-Converting different types of hydrogenases known to date [NiFe]-Hydrogenases ........... 514 (Figure 1) (15, 16). Heterodisulfide From the work of Stephenson, it became Reductase-Associated evident that methane formation from biomass [NiFe]-Hydrogenase MvhADG. 517 in river sediments is at least in part the result Methanophenazine-Reducing of the syntrophic interaction of H -forming [NiFe]-Hydrogenase VhtACG . 520 2 bacteria such as E. coli and H2-consuming Coenzyme F420-Reducing methanogens. And indeed in later studies, it [NiFe]-Hydrogenases FrhABG . 521 turned out that interspecies hydrogen trans- Genes Involved in fer is a quantitatively important process in the [NiFe]-Hydrogenase carbon cycle despite the fact that for thermo- Maturation ..................... 522 dynamic and kinetic reasons the H concentra- Nickel Regulation.................. 523 2 tion in anaerobic habitats is generally very low [Fe]-HYDROGENASE (pH <10 Pa; E(H+/H ) =−300 mV) (17, 18). IN METHANOGENS 2 2 H (see the sidebar titled Properties of H ) (19, WITHOUT CYTOCHROMES . 524 2 2 20), even at low concentrations, is an ideal elec- Structural Properties ............... 525 tron carrier between organisms because it can Catalytic Properties ................ 525 freely diffuse through cytoplasmic membranes. Genes Involved in FeGP Estimates are that approximately 150 million Cofactor Biosynthesis ........... 526 tons of H2 are annually formed by microorgan- by University of Texas - Austin on 06/10/13. For personal use only. H2 STORAGE VIA CH4 isms and used to fuel methanogens (17). The FORMATION .................... 527 combustion of 150 million tons H2 yields 18 × Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org 1018 J, an energy amount that is 3.75% of the primary energy consumed in 2006 by the world INTRODUCTION population (455 × 1018 J). In 1933, Stephenson & Stickland (1) en- Today on Earth, most of the H2 used Black and white riched from river sediments methane-forming by methanogens is of biological origin. Only smokers: chimney- microorganisms that grow on H2 and CO2 some of the H that sustains the growth of like structures formed 2 (Reaction 1) and concluded that these around hydrothermal methanogens is geochemically generated, e.g., vents, where methanogens must contain hydrogenases that in black and white smokers. However, in the Ar- superheated mineral activate H2 (Reaction 2). chaeozoic (4 to 2.5 billion years back), when the rich water from below + → + different lineages of microbes on Earth evolved Earth’s crust comes 4H2 CO2 CH4 2H2O − and when the temperatures were much higher through the ocean G◦ =−131 kJ mol 1. 1. floor than today, geochemically formed H2 proba- − + + =− . H2 2e 2H Eo 414 mV 2. bly predominated that of biological origin and 508 Thauer et al. ANRV413-BI79-18 ARI 27 April 2010 21:0 Large Open subunit Cys N site C Cys S Cys S Ni S Fe CN S Fe Cys C S S Cys S O Cys Fe S 6 Å Cys Cys S S S Cys X Fe Fe S Open S S S Fe site 4Å S Fe S Fe Fe S Fe C CN S S N Fe S C C C Cys Cys Small O O O Cys S subunit [NiFe]-hydrogenase [FeFe]-hydrogenase Cys S O OC Fe N C O Open O site HO GMP [Fe]-hydrogenase Figure 1 The metal sites of the three types of hydrogenases involved in interspecies hydrogen transfer (see Figure 2) have unusual structural features in common, such as intrinsic CO ligands. Despite this fact, [NiFe]- hydrogenases (5–8), [FeFe]-hydrogenases (9–11), and [Fe]-hydrogenase (12–14) are not phylogenetically related at the level of their primary structure or at the level of the enzymes involved in their active-site biosynthesis (12). Abbreviation: GMP, guanylyl rest. fueled the growth of methanogens. Con- in Bacteria and lower Eukarya, have not yet sistently, among recent hydrogenotrophic been found in Archaea (15, 16). methanogens, there are many hyperther- mophiles, such as Methanopyrus kandleri (98◦C optimum growth temperature) and Methanocal- PROPERTIES OF H2 dococcus jannaschii (85◦C optimum growth tem- by University of Texas - Austin on 06/10/13. For personal use only. ◦ perature), and these hyperthermophiles branch H2 is a colorless gas with a boiling point at 22.28 K (−250.87 C). off the 16S phylogenetic tree relatively early. Its Bunsen coefficient α in water at 20◦C is 0.018 (0.8 mM at ◦ Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org This review highlights the properties of 1 bar), and its diffusion coefficient Dw in water at 20 C is near −9 2 −1 the five different hydrogenases found in 4 × 10 m s . The homolytic cleavage of H2 in the gas phase methanogens within the context of their func- is endergonic by +436 kJ mol−1, and the heterolytic cleavage in ◦ −1 tion in metabolism. Four of the enzymes water at 20 C is endergonic by about +200 kJ mol (pKa near −1 are [NiFe]-hydrogenases with some properties 35) (19). The combustion energy of H2 is 120 MJ kg . The similar and others dissimilar to those of re- activation of H2 is mechanistically challenging, and the catalytic lated [NiFe]-hydrogenases in bacteria. It was mechanism is of considerable interest. The H2 generated, e.g., in methanogens that nickel was first found to by electrolysis or photolysis of water, is presently discussed as an be required for hydrogenase activity (21, 22). environmentally clean energy carrier for use in fuel cell-powered The fifth enzyme is a [Fe]-hydrogenase (23) electrical cars. Before H2 can be used in fuel cells, cheap catalysts that is unique to methanogens and functional still have to be developed, and it is hoped that the active-site in these only under conditions of nickel limi- structure of hydrogenases will show how to proceed (20). tation. [FeFe]-hydrogenases, which are present www.annualreviews.org • Hydrogenases from Methanogens 509 ANRV413-BI79-18 ARI 27 April 2010 21:0 Anoxic environments CH4 Atmosphere Freshwater and marine sediments, (1.8 ppm) wetlands, swamps, intestinal tracts of ruminants and termites, 0.4 Gt per year hot springs, hydrothermal vents Methanogenic archaea with cytochromes Oxic [NiFe] environments Acetate- Aerobic + H+ bacteria Rate- CO2 limiting Propionate 0.6 Gt per year step Butyrate Acetogenic bacteria CO2 + CH4 Biomass Monomers Lactate CO2 [FeFe] and [NiFe] ~1 Gt per year (~2% NPP) Ethanol Anaerobic H2 + CO2 archaea and (pH2 < 10 Pa) bacteria Bacteria [FeFe] and [NiFe] Protozoa [FeFe] H2 + CO2 Fungi [FeFe] Archaea [NiFe] Methanogenic archaea without cytochromes [NiFe] and [Fe] Geochemical Methane hydrates Reactions H2 (>10,000 Gt methane) Diffusion Figure 2 Approximately 2% of the net primary production (NPP) of plants, algae, and cyanobacteria are fermented in anoxic environments by a syntrophic association of anaerobic microorganisms with methane, in a process that involves interspecies H2 transfer.
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  • Composition of the Coenzyme F420-Dependent Formate Dehydrogenase from Methanobacterium Formicicum NEIL L

    Composition of the Coenzyme F420-Dependent Formate Dehydrogenase from Methanobacterium Formicicum NEIL L

    JOURNAL OF BACTERIOLOGY, Feb. 1986, p. 405-411 Vol. 165, No. 2 0021-9193/86/020405-07$02.00/0 Copyright (C 1986, American Society for Microbiology Composition of the Coenzyme F420-Dependent Formate Dehydrogenase from Methanobacterium formicicum NEIL L. SCHAUERt AND JAMES G. FERRY* Department of Anaerobic Microbiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 Received 16 August 1985/Accepted 19 November 1985 The coenzyme F420-dependent formate dehydrogenase from Methanobacterium formicicum was purified to electrophoretic homogeneity by anoxic procedures which included the addition o(f azide, flavin adenine dinucleotide (FAD), glycerol, and 2-mercaptoethanol to all buffer solutions to stabilize iictivity. The enzyme contains, in approximate miolar ratios, 1 FAD molecule and 1 molybdenum, 2 zinc, 21 to 24 iron, and 25 to 29 Downloaded from inorganic sulfur atoms. Denaturation of the enzyme released a molybdopterin cofactor. The enzyme has a molecular weight of 177,000 and consists of one each of two different subunits, giving the composition olol. The molecular weight of the a-subunit is 85,000, and that of the ,-subunit is 53,000. The UV-visible spectrum is typical of nonheme iron-sulfur flavoprotein. Reduction of the enzyme facilitated dissociation of FAD, and the FAD-depleted enzyme was unable to reduce coenzyme F420. Preincubation of the FAD-depleted enzyme with FAD restored coenzyme F420-dependent activity. The methanogenic bacteria are phylogenetically distant Cells were harvested in the late log phase at an optical density from eubacteria and eucaryotes (10). Consistent with this of 3.0 to 4.5 (550 nm, 1-cm light path).