N5, N10-methylenetetrahydromethanopterin dehydrogenase (H2-forming) from the extreme thermophile Methanopyrus kandleri

Heterologous Hydrogenase Overproduction Systems for Biotechnology-An Overview

Hydrogenases are complex metalloenzymes, showing tremendous potential as H2-converting redox catalysts for application in light-driven H2 production, enzymatic fuel cells and H2-driven cofactor regeneration. They catalyze the reversible oxidation of hydrogen into protons and electrons. The apo-enzymes are not active unless they are modified by a complicated post-translational maturation process that is responsible for the assembly and incorporation of the complex metal center. The catalytic center is usually easily inactivated by oxidation, and the separation and purification of the active protein is challenging. The understanding of the catalytic mechanisms progresses slowly, since the purification of the enzymes from their native hosts is often difficult, and in some case impossible. Over the past decades, only a limited number of studies report the homologous or heterologous production of high yields of hydrogenase. In this review, we emphasize recent discoveries that have greatly improved our understanding of microbial hydrogenases. We compare various heterologous hydrogenase production systems as well as in vitro hydrogenase maturation systems and discuss their perspectives for enhanced biohydrogen production. Additionally, activities of hydrogenases isolated from either recombinant organisms or in vivo/in vitro maturation approaches were systematically compared, and future perspectives for this research area are discussed.

Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments

Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.

The Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates

[Fe]-hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyl-tetrahydromethanopterin (methenyl-H₄ MPT⁺ ) with H₂ . H₄ MPT is a C1-carrier of methanogenic archaea. One bacterial genus, Desulfurobacterium, contains putative genes for the Hmd paralog, termed HmdII, and the HcgA-G proteins. The latter are required for the biosynthesis of the prosthetic group of Hmd, the iron-guanylylpyridinol (FeGP) cofactor. This finding is intriguing because Hmd and HmdII strictly use H₄ MPT derivatives that are absent in most bacteria. We identified the presence of the FeGP cofactor in D. thermolithotrophum. The bacterial HmdII reconstituted with the FeGP cofactor catalyzed the hydrogenation of derivatives of tetrahydrofolate, the bacterial C1-carrier, albeit with low enzymatic activities. The crystal structures show how Hmd recognizes tetrahydrofolate derivatives. These findings have an impact on future biotechnology by identifying a bacterial Hmd paralog.

Preparation of [Fe]-hydrogenase from methanogenic archaea

[Fe]-hydrogenase is one of the three types of hydrogenases. This enzyme is found in many hydrogenotrophic methanogenic archaea and catalyzes the reversible hydride transfer from H(2) to methenyl-H(4)MPT(+) in methanogenesis from H(2) and CO(2). The enzyme harbors a unique iron-guanylyl pyridinol (FeGP) cofactor as a prosthetic group. Here, we describe the purification of [Fe]-hydrogenase from Methanothermobacter marburgensis, the isolation of the FeGP cofactor from the native holoenzyme, and the reconstitution of [Fe]-hydrogenase from the isolated FeGP cofactor and the heterologously produced apoenzyme.

Carbon Monoxide as Intrinsic Ligand to Iron in the Active Site of [Fe]-Hydrogenase

Structural and spectroscopic studies on [Fe]-hydrogenase revealed an active site mononuclear low spin iron coordinated by the Cys176 sulfur, two CO, and the sp2 hybridized nitrogen of a 2-pyridinol compound with back bonding properties similar to those of cyanide. Thus, [Fe]-hydrogenases are endowed with an iron-ligation pattern related to that found in the active site of [NiFe]- and [FeFe]-hydrogenases although the three hydrogenases and the enzymes involved in their posttranslational maturation have evolved independently and although CO and cyanide ligands are not found in any other metallo-enzymes. Obviously, low-spin iron complexed with thiolate(s), CO, and cyanide or a cyanide functional analogue plays an essential role in H2 activation.

The exchange activities of [Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases

[Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a low-spin iron carbonyl complex, albeit in a dinuclear metal center, is also involved in H2 activation. Like the [NiFe] and [FeFe] hydrogenases, [Fe] hydrogenase catalyzes an active exchange of H2 with protons of water; however, this activity is dependent on the presence of the hydride-accepting methenyl-H4MPT+. In its absence the exchange activity is only 0.01% of that in its presence. The residual activity has been attributed to the presence of traces of methenyl-H4MPT+ in the enzyme preparations, but it could also reflect a weak binding of H2 to the iron in the absence of methenyl-H4MPT+. To test this we reinvestigated the exchange activity with [Fe] hydrogenase reconstituted from apoprotein heterologously produced in Escherichia coli and highly purified iron-containing cofactor and found that in the absence of added methenyl-H4MPT+ the exchange activity was below the detection limit of the tritium method employed (0.1 nmol min(-1) mg(-1)). The finding reiterates that for H2 activation by [Fe] hydrogenase the presence of the hydride-accepting methenyl-H4MPT+ is essentially required. This differentiates [Fe] hydrogenase from [FeFe] and [NiFe] hydrogenases, which actively catalyze H2/H2O exchange in the absence of exogenous electron acceptors.

Carbon Monoxide as an Intrinsic Ligand to Iron in the Active Site of the Iron−Sulfur-Cluster-Free Hydrogenase H2-Forming Methylenetetrahydromethanopterin Dehydrogenase As Revealed by Infrared Spectroscopy

The iron-sulfur-cluster-free hydrogenase Hmd (H(2)-forming methylenetetrahydromethanopterin dehydrogenase) from methanogenic archaea has recently been found to contain one iron associated tightly with an extractable cofactor of yet unknown structure. We report here that Hmd contains intrinsic CO bound to the Fe. Chemical analysis of Hmd revealed the presence of 2.4 +/- 0.2 mol of CO/mol of iron. Fourier transform infrared spectra of the native enzyme showed two bands of almost equal intensity at 2011 and 1944 cm(-)(1), interpreted as the stretching frequencies of two CO molecules bound to the same iron in an angle of 90 degrees . We also report on the effect of extrinsic (12)CO, (13)CO, (12)CN(-), and (13)CN(-) on the IR spectrum of Hmd.

UV-A/blue-light inactivation of the 'metal-free' hydrogenase (Hmd) from methanogenic archaea

H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) is an unusual hydrogenase present in many methanogenic archaea. The homodimeric enzyme dubbed 'metal-free' hydrogenase does not contain iron-sulfur clusters or nickel and thus differs from [Ni-Fe] and [Fe-Fe] hydrogenases, which are all iron-sulfur proteins. Hmd preparations were found to contain up to 1 mol iron per 40 kDa subunit, but the iron was considered to be a contaminant as none of the catalytic and spectroscopic properties of the enzyme indicated that it was an essential component. Hmd does, however, harbour a low molecular mass cofactor of yet unknown structure. We report here that the iron found in Hmd is most probably functional after all. Further investigation was initiated by the discovery that Hmd is inactivated upon exposure to UV-A (320-400 nm) or blue-light (400-500 nm). Enzyme purified in the dark exhibited an absorption spectrum with a maximum at approximately 360 nm and which mirrored its sensitivity towards light. In UV-A/blue-light the enzyme was bleached. The cofactor extracted from active Hmd was also light sensitive. It showed an UV/visible spectrum similar to that of the active enzyme and was bleached upon exposure to light. Photobleached cofactor no longer had the ability to reconstitute active Hmd from the apoenzyme. When purified in the dark, Hmd consistently contained per monomer about one Fe, which was tightly bound to the cofactor. The iron was released from the enzyme and from the cofactor upon light inactivation. Hmd activity was inhibited by high concentrations of CO and CO protected the enzyme from light inactivation indicating that the iron in Hmd is of functional importance. Therefore, reference to Hmd as 'metal-free' hydrogenase is no longer appropriate.

Activation of dihydrogen without transition metals

The metal-free hydrogenase from methanogenic archaea (Hmd) is a unique enzyme: it catalyzes the reaction of its substrate, methenyl-tetrahydromethanopterin, with molecular hydrogen without the aid of a transition metal. In other words, Hmd is currently the only example of a purely organic hydrogenation catalyst. Recent results from various fields have shed new light on this enzyme. In biochemistry, there is experimental proof that a tightly bound (and metal-free) cofactor exists. Ab initio calculations have revealed that the concerted action of the Lewis-acidic substrate and a Brønsted-base appears to induce facile heterolysis of the hydrogen molecule. In chemical model studies, a transition-metal-free hydrogenation of ketones was achieved in the presence of catalytic base. Taken together, the experimental results available to date point to an enzymatic mechanism in which the hydrogen molecule is heterolyzed by the joint action of the Lewis-acidic substrate methenyl-tetrahydromethanopterin and a Brønsted-base in the active site (i.e. by bifunctional catalysis).

Re-face stereospecificity of methylenetetrahydromethanopterin and methylenetetrahydrofolate dehydrogenases is predetermined by intrinsic properties of the substrate

Four different dehydrogenases are known that catalyse the reversible dehydrogenation of N5,N10-methylenetetrahydromethanopterin (methylene-H4MPT) or N5,N10-methylenetetrahydrofolate (methylene-H4F) to the respective N5,N10-methenyl compounds. Sequence comparison indicates that the four enzymes are phylogenetically unrelated. They all catalyse the Re-face-stereospecific removal of the pro-R hydrogen atom of the coenzyme's methylene group. The Re-face stereospecificity is in contrast to the finding that in solution the pro-S hydrogen atom of methylene-H4MPT and of methylene-H4F is more reactive to heterolytic cleavage. For a better understanding we determined the conformations of methylene-H4MPT in solution and when enzyme-bound by using NMR spectroscopy and semiempirical quantum mechanical calculations. For the conformation free in solution we find an envelope conformation for the imidazolidine ring, with the flap at N10. The methylene pro-S C-H bond is anticlinal and the methylene pro-R C-H bond is synclinal to the lone electron pair of N10. Semiempirical quantum mechanical calculations of heats of formation of methylene-H4MPT and methylene-H4F indicate that changing this conformation into an activated one in which the pro-S C-H bond is antiperiplanar, resulting in the preformation of the leaving hydride, would require a deltadeltaH(f) of +53 kJ mol-1 for methylene-H4MPT and of +51 kJ mol-1 for methylene-H4F. This is almost twice the energy required to force the imidazolidine ring in the enzyme-bound conformation of methylene-H4MPT (+29 kJ mol-1) or of methylene-H4F (+35 kJ mol-1) into an activated conformation in which the pro-R hydrogen atom is antiperiplanar to the lone electron pair of N10. The much lower energy for pro-R hydrogen activation thus probably predetermines the Re-face stereospecificity of the four dehydrogenases. Results are also presented explaining why the chemical reduction of methenyl-H4MPT+ and methenyl-H4F+ with NaBD4 proceeds Si-face-specific, in contrast to the enzyme-catalysed reaction.

Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability

Enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees C), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. These enzymes share the same catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, indicating that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, crystal structure comparisons, and mutagenesis experiments indicate that hyperthermophilic enzymes are, indeed, very similar to their mesophilic homologues. No single mechanism is responsible for the remarkable stability of hyperthermophilic enzymes. Increased thermostability must be found, instead, in a small number of highly specific alterations that often do not obey any obvious traffic rules. After briefly discussing the diversity of hyperthermophilic organisms, this review concentrates on the remarkable thermostability of their enzymes. The biochemical and molecular properties of hyperthermophilic enzymes are described. Mechanisms responsible for protein inactivation are reviewed. The molecular mechanisms involved in protein thermostabilization are discussed, including ion pairs, hydrogen bonds, hydrophobic interactions, disulfide bridges, packing, decrease of the entropy of unfolding, and intersubunit interactions. Finally, current uses and potential applications of thermophilic and hyperthermophilic enzymes as research reagents and as catalysts for industrial processes are described.

The metal-free hydrogenase from methanogenic archaea: evidence for a bound cofactor

The hmd gene, which encodes the metal-free hydrogenase in methanogenic archaea, was heterologously expressed in Escherichia coli. The overproduced enzyme was completely inactive. High activity could, however, be induced by the addition of ultrafiltrate from active enzyme denatured in 8 M urea. The active fraction in the ultrafiltrate was heat-labile and migrated on gel filtration columns with an apparent molecular mass well below 1000 Da.

Enzymology of one-carbon metabolism in methanogenic pathways

Methanoarchaea, the largest and most phylogenetically diverse group in the Archaea domain, have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. All of the pathways have in common the two-electron reduction of methyl-coenzyme M to methane catalyzed by methyl-coenzyme M reductase but deviate in the source of the methyl group transferred to coenzyme M. Most of the methane produced in nature derives from acetate in a pathway where the activated substrate is cleaved by CO dehydrogenase/acetyl-CoA synthase and the methyl group is transferred to coenzyme M via methyltetrahydromethanopterin or methyltetrahydrosarcinapterin. Electrons for reductive demethylation of the methyl-coenzyme M originate from oxidation of the carbonyl group of acetate to carbon dioxide by the synthase. In the other major pathway, formate or H2 is oxidized to provide electrons for reduction of carbon dioxide to the methyl level and reduction of methyl-coenzyme to methane. Methane is also produced from the methyl groups of methanol and methylamines. In these pathways specialized methyltransferases transfer the methyl groups to coenzyme M. Electrons for reduction of the methyl-coenzyme M are supplied by oxidation of the methyl groups to carbon dioxide by a reversal of the carbon dioxide reduction pathway. Recent progress on the enzymology of one-carbon reactions in these pathways has raised the level of understanding with regard to the physiology and molecular biology of methanogenesis. These advances have also provided a foundation for future studies on the structure/function of these novel enzymes and exploitation of the recently completed sequences for the genomes from the methanoarchaea Methanobacterium thermoautotrophicum and Methanococcus jannaschii.

Thermozymes

Enzymes synthesized by thermophiles (organisms with optimal growth temperatures > 60 degrees C) and hyperthermophiles (optimal growth temperatures > 80 degrees C) are typically thermostable (resistant to irreversible inactivation at high temperatures) and thermophilic (optimally active at high temperatures, i.e., > 60 degrees C). These enzymes, called thermozymes, share catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, thermozymes usually retain their thermal properties, suggesting that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, and crystal structure comparisons indicate that thermozymes are, indeed, very similar to mesophilic enzymes. No obvious sequence or structural features account for enzyme thermostability and thermophilicity. Thermostability and thermophilicity molecular mechanisms are varied, differing from enzyme to enzyme. Thermostability and thermophilicity are usually caused by the accumulation of numerous subtle sequence differences. This review concentrates on the mechanisms involved in enzyme thermostability and thermophilicity. Their relationships with protein rigidity and flexibility and with protein folding and unfolding are discussed. Intrinsic stabilizing forces (e.g., salt bridges, hydrogen bonds, hydrophobic interactions) and extrinsic stabilizing factors are examined. Finally, thermozymes' potential as catalysts for industrial processes and specialty uses are discussed, and lines of development (through new applications, and protein engineering) are also proposed.

Characterization of nicotinamide mononucleotide adenylyltransferase from thermophilic archaea

The enzyme nicotinamide mononucleotide (NMN) adenylyltransferase (EC 2.7.7.1) catalyzes the synthesis of NAD+ and nicotinic acid adenine dinucleotide. It has been purified to homogeneity from cellular extracts of the thermophilic archaeon Sulfolobus solfataricus. Through a database search, a highly significant match was found between its N-terminal sequence and a hypothetical protein coded by the thermophilic archaeon Methanococcus jannaschii MJ0541 open reading frame (GenBank accession no. U67503). The MJ0541 gene was isolated, cloned into a T7-based vector, and expressed in Escherichia coli cells, yielding a high level of thermophilic NMN adenylyltransferase activity. The expressed protein was purified to homogeneity by a single-step chromatographic procedure. Both the subunit molecular mass and the N-terminal sequence of the pure recombinant protein were as expected from the deduced amino acid sequence of the MJ0541 open reading frame-encoded protein. Molecular and kinetic properties of the enzymes from both archaea are reported and compared with those already known for the mesophilic eukaryotic NMN adenylyltransferase.

Purification, properties and primary structure of H2-forming N5 ,N10 -methylenetetrahydromethanopterin dehydrogenase from Methanococcus thermolithotrophicus

H2-Forming N5,N10 -methylenetetrahydromethanopterin dehydrogenase (Hmd) is a novel type of hydrogenase found in methanogenic Achaea that contains neither nickel nor iron-sulfur clusters. The enzyme has previously been characterized from Methanobacterium thermoautotrophicum and from Methanopyrus kandleri. We report here on the purification and properties of the enzyme from Methanococcus thermolithotrophicus. The hmd gene was cloned and sequenced. The results indicate that the enzyme from Mc. thermolithotrophicus is functionally and structurally closely related to the H2-forming methylene tetrahydromethanopterin dehydrogenase from Mb. thermoautotrophicum and Mp. kandleri. From amino acid sequence comparisons of the three enzymes, a phylogenetic tree was deduced that shows branching orders similar to those derived from sequence comparisons of the 16S rRNA of the orders Methanococcales, Methanobacteriales, and Methanopyrales.

Different structure and expression of the operons encoding the membrane-bound hydrogenases from Methanosarcina mazei Gö1

The expression of the vho and vht operons from Methanosarcina mazei Gö1, which each encode a membrane-bound hydrogenase and a cytochrome b, was analyzed under various growth conditions. Synthesis of both hydrogenases was induced at the level of transcription during methanogenesis from H2/CO2 or methanol. Transcripts of the vho operon were also detected when Ms. mazei Gö1 was grown on acetate, indicating that this operon is constitutively expressed. In contrast, mRNA from the vht operon was not found in acetate-grown cells. Downstream of the structural genes vhtG and vhtA and the cytochrome-b-encoding gene vhtC, an additional open reading frame (vhtD; 486 bp) was identified. vhtD is followed by six tandem repeats of an 11-bp sequence, which is probably a termination site of transcription. Northern blots revealed that vhtD is part of the vht operon. In the vho operon, a vhtD-like gene and a terminator composed of tandem repeats could not be identified. The physiological function of two genetically distinct, membrane-bound hydrogenases from Ms. mazei Gö1 is discussed.

Hydrogen isotope effects in the reactions catalyzed by H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea

H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from methanogenic Archaea, which is a novel hydrogenase containing neither nickel nor iron-sulfur clusters, catalyzes the reversible reduction of N5,N10-methenyltetrahydomethanopterin (CH identical to H4MPT+) with H2 to N5,N10-methylenetetrahydromethanopterin (CH2 = H4MPT) and a proton (delta G degree' = -5.5 kJ/mol). The enzyme also catalyzes a CH identical to H4MPT(+)-dependent H2/H+ exchange. We report here on kinetic deuterium isotope effects in these reactions. When CH identical to H4MPT+ reduction was performed with D2 instead of H2, Vmax and the Km did not change. A primary isotope effect of 1 was found at all pH and temperatures tested and independent of whether H2O or D2O was the solvent. The findings indicate that a step other than the activation of H2 was rate-determining in CH identical to H4MPT+ reduction with H2. This was substantiated by the observation that also the CH identical to H4MPT(+)-dependent H2/H+ exchange reaction did not exhibit an appreciable deuterium isotope effect. Vmax for CH2 = H4MPT dehydrogenation to CH identical to H4MPT+ and H2 was only 2-3 times higher than for CD2 = H4MPT dehydrogenation to CD identical to H4MPT+ and HD. Such a small primary isotope effect indicates that the breakage of the C-H bond in the methylene group of CH2 = H4MPT was only rate-limiting when hydrogen was substituted by a deuterium.

Formylmethanofuran:tetrahydromethanopterin formyltransferase (Ftr) from the hyperthermophilic Methanopyrus kandleri. Cloning, sequencing and functional expression of the ftr gene and one-step purification of the enzyme overproduced in Escherichia coli

Methanopyrus kandleri is a methanogenic Archaeon that grows on H2 and CO2 at a temperature optimum of 98 degrees C. The gene ftr encoding the formylmethanofuran:tetrahydromethanopterin formyltransferase, an enzyme involved in CO2 reduction to methane, has been cloned, sequenced, and overexpressed in Escherichia coli. The overproduced enzyme could be purified in yields above 90% by simply heating the cell extract to 90 degrees C in 1.5 M K2HPO4 pH 8.0 for 30 min. From 1 g wet cells (70 mg protein) approximately 14 mg formyltransferase was obtained. The purified enzyme showed essentially the same catalytic properties as that purified from M. kandleri cells. The primary structure and properties of the formyltransferase are compared with those of the enzyme from Methanobacterium thermoautotrophicum (growth temperature optimum 65 degrees C) and Methanothermus fervidus (83 degrees C). Of the three enzymes that from M. kandleri had the lowest isoelectric point (4.2) and the lowest hydrophobicity of the amino acid composition. The enzyme from M. kandleri had the relatively highest content in alanine, glutamate and glutamine and the relatively lowest content in isoleucine, leucine and lysine. These properties, some of which are unusual for enzymes from other hyperthermophilic organisms, may reflect that the formyltransferase from M. kandleri is adapted to both hyperthermophilic and halophilic conditions.

Two N5,N10-methylenetetrahydromethanopterin dehydrogenases in the extreme thermophile Methanopyrus kandleri: characterization of the coenzyme F420-dependent enzyme

It was recently reported that the extreme thermophile Methanopyrus kandleri contains only a H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase which uses protons as electron acceptor. We describe here the presence in this Archaeon of a second N5,N10-methylenetetrahydromethanopterin dehydrogenase which is coenzyme F420-dependent. This enzyme was purified and characterized. The enzyme was colourless, had an apparent molecular mass of 300 kDa, an isoelectric point of 3.7 +/- 0.2 and was composed of only one type of subunit of apparent molecular mass of 36 kDa. The enzyme activity increased to an optimum with increasing salt concentrations. Optimal salt concentrations were e.g. 2 M (NH4)2SO4, 2 M Na2HPO4, 1.5 M K2HPO4, and 2 M NaCl. In the absence of salts the enzyme exhibited almost no activity. The salts affected mainly the Vmax rather than the Km of the enzyme. The catalytic mechanism of the dehydrogenase was determined to be of the ternary complex type, in agreement with the finding that the enzyme lacked a chromophoric prosthetic group. In the presence of 1 M (NH4)2SO4 the Vmax was 4000 U/mg (kcat = 2400 s-1) and the Km for N5,N10-methylenetetrahydromethanopterin and for coenzyme F420 were 80 microM and 20 microM, respectively. The enzyme was relatively heat-stable and lost no activity when incubated anaerobically in 50 mM K2HPO4 at 90 degrees C for one hour. The N-terminal amino acid sequence was found to be similar to that of the F420-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum, Methanosarcina barkeri, and Archaeoglobus fulgidus.

Purification and characterization of an extremely thermostable beta-glucosidase from the hyperthermophilic archaeon Pyrococcus furiosus

Cell-free extracts of cellobiose-grown cells of the hyperthermophile Pyrococcus furiosus contain very high activities (19.8 U/mg) of a beta-glucosidase. The cytoplasmic enzyme was purified 22-fold to apparent homogeneity, indicating that the enzyme comprises nearly 5% of the total cell protein. The native beta-glucosidase has a molecular mass of 230 +/- 20 kDa, composed of 58 +/- 2-kDa subunits. The enzyme has a pI of 4.40. Thiol groups are not essential for activity, nor is the enzyme dependent on divalent cations or a high ionic strength. The enzyme shows optimum activity at pH 5.0 and 102-105 degrees C. From Lineweaver-Burk plots, Vmax values of 470 U/mg and 700 U/mg were found for cellobiose (Km = 20 mM) and p-nitrophenyl-beta-D-glucopyranoside (Km = 0.15 mM), respectively. The purified enzyme also exhibits high beta-galactosidase activity and beta-xylosidase activity, but shows no activity towards alpha-linked disaccharides or beta-linked polymers, like cellulose. The purified beta-glucosidase shows a remarkable thermostability with a half life of 85 h at 100 degrees C and 13 h at 110 degrees C.

N5,N10-methenyltetrahydromethanopterin cyclohydrolase from the extremely thermophilic sulfate reducing Archaeoglobus fulgidus: comparison of its properties with those of the cyclohydrolase from the extremely thermophilic Methanopyrus kandleri

Archaeoglobus fulgidus and Methanopyrus kandleri are both extremely thermophilic Archaea with a growth temperature optimum at 83 degrees C and 98 degrees C, respectively. Both Archaea contain an active N5,N10-methenyltetrahydromethanopterin cyclohydrolase. The enzyme from M. kandleri has recently been characterized. We describe here the purification and properties of the enzyme from A. fulgidus. The cyclohydrolase from A. fulgidus was purified 180-fold to apparent homogeneity and its properties were compared with those recently published for the cyclohydrolase from M. kandleri. The two cytoplasmic enzymes were found to have very similar molecular and catalytic properties. They differed, however, significantly with respect of the effect of K2HPO4 and of other salts on the activity and the stability. The cyclohydrolase from A. fulgidus required relatively high concentrations of K2HPO4 (1 M) for optimal thermostability at 90 degrees C but did not require salts for activity. Vice versa, the enzyme from M. kandleri was dependent on high K2HPO4 concentrations (1.5 M) for optimal activity but not for thermostability. Thus the activity and structural stability of the two thermophilic enzymes depend in a completely different way on the concentration of inorganic salts. The molecular basis for these differences are discussed.

H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum. Studies of the catalytic mechanism of H2 formation using hydrogen isotopes

H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase is a novel hydrogenase found in most methanogenic archaea. It catalyzes the reversible conversion of N5,N10-methylenetetrahydromethanopterin (CH2 = H4MPT) to N5,N10-methenyltetrahydromethanopterin (CH identical to H4MPT+) and dihydrogen; CH2 = H4MPT + H+<-->CH identical to H4MPT(+) + H2; delta G degrees ' = + 5 kJ/mol. In the following investigation, the formation of H2, HD and D2 was studied in experiments in which either the methylene group of CH2 = H4MPT or water were deuterium labelled. In the case of CD2 = H4MPT and H2O, the dihydrogen formed immediately after the start of the reaction was composed of approximately 50% HD and 50% of H2 at all pH tested. In the case of CH2 = H4MPT and D2O, the dihydrogen generated was composed of approximately 50% HD and 50% D2 at pD 5.7 and of approximately 85% HD and 15% D2 at pD 7.0. Evidence is presented that the enzyme catalyzes a CH identical to H4MPT(+)-dependent isotopic exchange between HD and H2O and between HD and D2O, yielding H2 and D2, respectively. A catalytic mechanism aimed to explain these findings is discussed.

Salt dependence, kinetic properties and catalytic mechanism of N-formylmethanofuran:tetrahydromethanopterin formyltransferase from the extreme thermophile Methanopyrus kandleri

N-Formylmethanofuran(CHO-MFR):tetrahydromethanopterin(H4MPT) formyltransferase (formyltransferase) from the extremely thermophilic Methanopyrus kandleri was purified over 100-fold to apparent homogeneity with a 54% yield. The monomeric enzyme had an apparent molecular mass of 35 kDa. The N-terminal amino acid sequence of the polypeptide was determined. The formyltransferase was found to be absolutely dependent on the presence of phosphate or sulfate salts for activity. The ability of salts to activate the enzyme decreased in the order K2HPO4 > (NH4)2SO4 > K2SO4 > Na2SO4 > Na2HPO4. The salts KCl, NaCl and NH4Cl did not activate the enzyme. The dependence of activity on salt concentration showed a sigmoidal curve. For half-maximal activity, 1 M K2HPO4 and 1.2 M (NH4)2SO4 were required. A detailed kinetic analysis revealed that phosphates and sulfates both affected the Vmax rather than the Km for CHO-MFR and H4MPT. At the optimal salt concentration and at 65 degrees C, the Vmax was 2700 U/mg (1 U = 1 mumol/min), the Km for CHO-MFR was 50 microM and the Km for H4MPT was 100 microM. At 90 degrees C, the temperature optimum of the enzyme, the Vmax was about 2.5-fold higher than at 65 degrees C. Thermostability as well as activity of formyltransferase was dramatically increased in the presence of salts, 1.5 M being required for optimal stabilization. The efficiency of salts in protecting formyltransferase from heat inactivation at 90 degrees C decreased in the order K2HPO4 = (NH4)2SO4 >> KCl = NH4Cl = NaCl >> Na2SO4 > Na2HPO4. The catalytic mechanism of formyltransferase was determined to be of the ternary-complex type. The properties of the enzyme from M. kandleri are compared with those of formyltransferase from Methanobacterium thermoautotrophicum, Methanosarcina barkeri and Archaeoglobus fulgidus.

H2-forming methylenetetrahydromethanopterin dehydrogenase, a novel type of hydrogenase without iron-sulfur clusters in methanogenic archaea

A novel hydrogenase has recently been found in methanogenic archaea. It catalyzes the reversible dehydrogenation of methylenetetrahydromethanopterin (CH2 = H4MPT) to methenyltetrahydromethanopterin (CH identical to H4MPT+) and H2 and was therefore named H2-forming methylenetetrahydromethanopterin dehydrogenase. The hydrogenase, which is composed of only one polypeptide with an apparent molecular mass of 43 kDa, does not mediate the reduction of viologen dyes with either H2 or CH2 = H4MPT. We report here that the purified enzyme from Methanobacterium thermoautotrophicum exhibits the following other unique properties: (a) the colorless protein with a specific activity of 2000 U/mg (Vmax) did not contain iron-sulfur clusters, nickel, or flavins; (b) the activity was not inhibited by carbon monoxide, acetylene, nitrite, cyanide, or azide; (c) the enzyme did not catalyze an isotopic exchange between 3H2 and 1H+; (d) the enzyme catalyzed the reduction of CH identical to H4MPT+ with 3H2 generating [methylene-3H]CH2 = H4MPT; and (e) the primary structure contained at most four conserved cysteines as revealed by a comparison of the DNA-deduced amino acid sequence of the proteins from M. thermoautotrophicum and Methanopyrus kandleri. None of the four cysteines were closely spaced as would be indicative for a (NiFe) hydrogenase or a ferredoxin-type iron-sulfur protein. Properties of the H2-forming methylenetetrahydromethanopterin dehydrogenase from Methanobacterium wolfei are also described indicating that the enzyme from this methanogenic archaeon is very similar to the enzyme from M. thermoautotrophicum with respect both to molecular and catalytic properties.

Biochemistry of methanogenesis

Methane is a product of the energy-yielding pathways of the largest and most phylogenetically diverse group in the Archaea. These organisms have evolved three pathways that entail a novel and remarkable biochemistry. All of the pathways have in common a reduction of the methyl group of methyl-coenzyme M (CH3-S-CoM) to CH4. Seminal studies on the CO2-reduction pathway have revealed new cofactors and enzymes that catalyze the reduction of CO2 to the methyl level (CH3-S-CoM) with electrons from H2 or formate. Most of the methane produced in nature originates from the methyl group of acetate. CO dehydrogenase is a key enzyme catalyzing the decarbonylation of acetyl-CoA; the resulting methyl group is transferred to CH3-S-CoM, followed by reduction to methane using electrons derived from oxidation of the carbonyl group to CO2 by the CO dehydrogenase. Some organisms transfer the methyl group of methanol and methylamines to CH3-S-CoM; electrons for reduction of CH3-S-CoM to CH4 are provided by the oxidation of methyl groups to CO2.

Hydrogen-forming and coenzyme-F420-reducing methylene tetrahydromethanopterin dehydrogenase are genetically distinct enzymes in Methanobacterium thermoautotrophicum (Marburg)

A coenzyme-F420-reducing and an H2-forming methylenetetrahydromethanopterin dehydrogenase have been isolated from Methanobacterium thermoautotrophicum (Marburg). Indirect evidence suggested that the former enzyme (32 kDa) might be derived from the latter enzyme (42 kDa) by proteolysis. To test this hypothesis the gene sequence of the H2-forming dehydrogenase was determined and compared with the N-terminal amino acid sequence of the F420-reducing dehydrogenase. No corresponding sequences were found indicating that the two dehydrogenases are genetically distinct enzymes. With purified enzyme preparations it is shown that the activity of the F420-reducing dehydrogenase is inhibited in the presence of the H2-forming enzyme. This finding is discussed in terms of substrate competition.