Hyperthermophilic redox chemistry: a re-evaluation

Bioenergetic constraints on the origin of autotrophic metabolism

Autotrophs form the base of all complex food webs and seemingly have done so since early in Earth history. Phylogenetic evidence suggests that early autotrophs were anaerobic, used CO₂ as both an oxidant and carbon source, were dependent on H₂ as an electron donor, and used iron-sulfur proteins (termed ferredoxins) as a primary electron carrier. However, the reduction potential of H₂ is not typically low enough to efficiently reduce ferredoxin. Instead, in modern strictly anaerobic and H₂-dependent autotrophs, ferredoxin reduction is accomplished using one of several recently evolved enzymatic mechanisms, including electron bifurcating and coupled ion translocating mechanisms. These observations raise the intriguing question of why anaerobic autotrophs adopted ferredoxins as central electron carriers only to have to evolve complex machinery to reduce them. Here, we report calculated reduction potentials for H₂ as a function of observed environmental H₂ concentration, pH and temperature. Results suggest that a combination of alkaline pH and high H₂ concentration yield H₂ reduction potentials low enough to efficiently reduce ferredoxins. Hyperalkaline, H₂ rich environments have existed in discrete locations throughout Earth history where ultramafic minerals are undergoing hydration through the process of serpentinization. These results suggest that serpentinizing systems, which would have been common on early Earth, naturally produced conditions conducive to the emergence of H₂-dependent autotrophic life. The primitive process of hydrogenotrophic methanogenesis is used to examine potential changes in methanogenesis and Fd reduction pathways as these organisms diversified away from serpentinizing environments. This article is part of a discussion meeting issue 'Serpentinite in the earth system'.

Integrated thermodynamic analysis of electron bifurcating [FeFe]-hydrogenase to inform anaerobic metabolism and H2 production

Electron bifurcating, [FeFe]-hydrogenases are recently described members of the hydrogenase family and catalyze a combination of exergonic and endergonic electron exchanges between three carriers (2 ferredoxin_red^- + NAD(P)H + 3 H⁺ = 2 ferredoxin_ox + NAD(P)⁺ + 2 H₂). A thermodynamic analysis of the bifurcating, [FeFe]-hydrogenase reaction, using electron path-independent variables, quantified potential biological roles of the reaction without requiring enzyme details. The bifurcating [FeFe]-hydrogenase reaction, like all bifurcating reactions, can be written as a sum of two non-bifurcating reactions. Therefore, the thermodynamic properties of the bifurcating reaction can never exceed the properties of the individual, non-bifurcating, reactions. The bifurcating [FeFe]-hydrogenase reaction has three competitive properties: 1) enabling NAD(P)H-driven proton reduction at pH₂ higher than the concurrent operation of the two, non-bifurcating reactions, 2) oxidation of NAD(P)H and ferredoxin simultaneously in a 1:1 ratio, both are produced during typical glucose fermentations, and 3) enhanced energy conservation (~10 kJ mol^-1 H₂) relative to concurrent operation of the two, non-bifurcating reactions. Our analysis demonstrated ferredoxin E°' largely determines the sensitivity of the bifurcating reaction to pH₂, modulation of the reduced/oxidized electron carrier ratios contributed less to equilibria shifts. Hydrogenase thermodynamics data were integrated with typical and non-typical glycolysis pathways to evaluate achieving the 'Thauer limit' (4 H₂ per glucose) as a function of temperature and pH₂. For instance, the bifurcating [FeFe]-hydrogenase reaction permits the Thauer limit at 60 °C if pH ₂ ≤ ~10 mbar. The results also predict Archaea, expressing a non-typical glycolysis pathway, would not benefit from a bifurcating [FeFe]-hydrogenase reaction; interestingly, no Archaea have been observed experimentally with a [FeFe]-hydrogenase enzyme.

EPR monitored redox titration of the cofactors of Saccharomyces cerevisiae Nar1

Electron Paramagnetic Resonance (EPR) monitored redox titrations are a powerful method to determine the midpoint potential of cofactors in proteins and to identify and quantify the cofactors in their detectable redox state. The technique is complementary to direct electrochemistry (voltammetry) approaches, as it does not offer information on electron transfer rates, but does establish the identity and redox state of the cofactors in the protein under study. The technique is widely applicable to any protein containing an electron paramagnetic resonance (EPR) detectable cofactor. A typical titration requires 2 ml protein with a cofactor concentration in the range of 1-100 µM. The protein is titrated with a chemical reductant (sodium dithionite) or oxidant (potassium ferricyanide) in order to poise the sample at a certain potential. A platinum wire and a Ag/AgCl reference electrode are connected to a voltmeter to measure the potential of the protein solution A set of 13 different redox mediators is used to equilibrate between the redox cofactors of the protein and the electrodes. Samples are drawn at different potentials and the Electron Paramagnetic Resonance spectra, characteristic for the different redox cofactors in the protein, are measured. The plot of the signal intensity versus the sample potential is analyzed using the Nernst equation in order to determine the midpoint potential of the cofactor.

The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications

Hydrogen production is a vital metabolic process for many anaerobic organisms, and the enzyme responsible, hydrogenase, has been studied since the 1930s. A novel subfamily with unique properties was recently recognized, represented by the 14-subunit membrane-bound [NiFe] hydrogenase from the archaeon Pyrococcus furiosus. This so-called energy-converting hydrogenase links the thermodynamically favorable oxidation of ferredoxin with the formation of hydrogen and conserves energy in the form of an ion gradient. It is therefore a simple respiratory system within a single complex. This hydrogenase shows a modular composition represented by a Na(+)/H(+) antiporter domain (Mrp) and a [NiFe] hydrogenase domain (Mbh). An analysis of the large number of microbial genome sequences available shows that homologs of Mbh and Mrp tend to be clustered within the genomes of a limited number of archaeal and bacterial species. In several instances, additional genes are associated with the Mbh and Mrp gene clusters that encode proteins that catalyze the oxidation of formate, CO or NAD(P)H. The Mbh complex also shows extensive homology to a number of subunits within the NADH quinone oxidoreductase or complex I family. The respiratory-type membrane-bound hydrogenase complex appears to be closely related to the common ancestor of complex I and [NiFe] hydrogenases in general.

Mutational Analyses of the Enzymes Involved in the Metabolism of Hydrogen by the Hyperthermophilic Archaeon Pyrococcus furiosus

Pyrococcus furiosus grows optimally near 100°C by fermenting carbohydrates to produce hydrogen (H₂) or, if elemental sulfur (S⁰) is present, hydrogen sulfide instead. It contains two cytoplasmic hydrogenases, SHI and SHII, that use NADP(H) as an electron carrier and a membrane-bound hydrogenase (MBH) that utilizes the redox protein ferredoxin. We previously constructed deletion strains lacking SHI and/or SHII and showed that they exhibited no obvious phenotype. This study has now been extended to include biochemical analyses and growth studies using the ΔSHI and ΔSHII deletion strains together with strains lacking a functional MBH (ΔmbhL). Hydrogenase activity in cytoplasmic extracts of various strains demonstrate that SHI is responsible for most of the cytoplasmic hydrogenase activity. The ΔmbhL strain showed no growth in the absence of S⁰, confirming the hypothesis that, in the absence of S⁰, MBH is the only enzyme that can dispose of reductant (in the form of H₂) generated during sugar oxidation. Under conditions of limiting sulfur, a small but significant amount of H₂ was produced by the ΔmbhL strain, showing that SHI can produce H₂ from NADPH in vivo, although this does not enable growth of ΔmbhL in the absence of S⁰. We propose that the physiological function of SHI is to recycle H₂ and provide a link between external H₂ and the intracellular pool of NADPH needed for biosynthesis. This likely has a distinct energetic advantage in the environment, but it is clearly not required for growth of the organism under the usual laboratory conditions. The function of SHII, however, remains unknown.

Temperature dependent electrochemistry--a versatile tool for investigations of biology related topics

Temperature dependent electrochemistry can be efficiently used to determine very different properties of the investigated system, such as thermodynamic parameters of redox processes (especially the entropy), the degeneration temperature of a protein or kinetic parameters, for instance activation energy. It can even be used in biotechnology for improved catalysis and detection of substances. This perspective describes a selection of different experiments that used temperature dependent electrochemistry in order to determine these different values or achieve an enhancement of biotechnological applications, respectively, and hence gives an overview of its versatile use in studies aimed at biological issues.

Voltammetry of Pyrococcus furiosus ferritin: dependence of iron release rate on mediator potential

The electrocatalytic iron release from P. furiosus ferritin upon reduction with a series of electron mediators was studied. The observed iron release rate as a function of mediator midpoint potentials is described by a two-step model, in which electron transfer from the mediator to ferritin is rate limiting at low driving force, and the protein's overall catalytic rate of k(cat)= 701 electrons per s is limiting at high driving force (low mediator potentials). The upper limit of the mediator potential at which the reductive iron release activity of P. furiosus ferritin has been observed in the electrochemical cell is -47 mV vs. SHE.

Redox chemistry of tungsten and iron–sulfur prosthetic groups in Pyrococcus furiosus formaldehyde ferredoxin oxidoreductase

Formaldehyde oxidoreductase (FOR) is one of the tungstopterin iron-sulfur enzymes of the five-membered family of aldehyde oxidoreductases in the hyperthermophilic archaeon Pyrococcus furiosus. In dye-mediated equilibrium redox titrations, the tungsten in active P. furiosus FOR is a two-electron acceptor, W(VI/IV). The intermediate, paramagnetic W(V) state can be trapped only by reduction with substrate, with consecutive one-electron intraprotein electron transfer to the single [4Fe-4S](2+;+) cluster and partial comproportionation of the tungsten over W(IV, V, VI); this is a stable state in the absence of an external electron acceptor. Electron paramagnetic resonance (EPR) spectroscopy reveals a single "low-potential" W(V) spectrum with gxyz values 1.847, 1.898, and 1.972, and a [4Fe-4S]+ cubane in a spin mixture of S = 1/2 (10%) and S = 3/2 (90%) of intermediate rhombicity (E/D = 0.21, greal = 1.91). The development of this intermediate in vitro is slow even at elevated temperature and with a nominal 50:1 excess of substrate over enzyme presumably owing to the very unfavorable hydration equilibrium of the formaldehyde/methylene glycol couple with KD approximately 10(3). Rapid intermediate formation of enzyme at concentrations suitable for EPR spectroscopy (200 microM) is only obtained with extremely high nominal substrate concentration (1 M formaldehyde) and is followed by a slower phase of denaturation. The premise that the free formaldehyde, and not the methylene glycol, is the enzyme's substrate implies that KM for formaldehyde is 3 orders of magnitude less that the previously reported value.

Pyrococcus furiosus ferredoxin is a functional dimer

Pyrococcus furiosus ferredoxin is subject to a monomer/dimer equilibrium as a function of ionic strength. At physiological ionic strength, approximately 0.35 M NaCl, the protein is very predominantly homodimer. The monomeric form exhibits impaired electron transfer on glassy carbon; it also has a decreased S=3/2 over S=1/2 ratio as shown by electron paramagnetic resonance spectroscopy. Even following sterilization at 121 degrees C the dimer is stable in denaturing gel electrophoresis.

Enzymes of hydrogen metabolism in Pyrococcus furiosus

The genome of Pyrococcus furiosus contains the putative mbhABCDEFGHIJKLMN operon for a 14-subunit transmembrane complex associated with a Ni-Fe hydrogenase. Ten ORFs (mbhA-I and mbhM) encode hydrophobic, membrane-spanning subunits. Four ORFs (mbhJKL and mbhN) encode putative soluble proteins. Two of these correspond to the canonical small and large subunit of Ni-Fe hydrogenase, however, the small subunit can coordinate only a single iron-sulfur cluster, corresponding to the proximal [4Fe-4S] cubane. The structural genes for the small and the large subunits, mbhJ and mbhL, are separated in the genome by a third ORF, mbhK, encoding a protein of unknown function without Fe/S binding. The fourth ORF, mbhN, encodes a 2[4Fe-4S] protein. With P. furiosus soluble [4Fe-4S] ferredoxin as the electron donor the membranes produce H2, and this activity is retained in an extracted core complex of the mbh operon when solubilized and partially purified under mild conditions. The properties of this membrane-bound hydrogenase are unique. It is rather resistant to inhibition by carbon monoxide. It also exhibits an extremely high ratio of H2 evolution to H2 uptake activity compared with other hydrogenases. The activity is sensitive to inhibition by dicyclohexylcarbodiimide, an inhibitor of NADH dehydrogenase (complex I). EPR of the reduced core complex is characteristic for interacting iron-sulfur clusters with Em approximately -0.33 V. The genome contains a second putative operon, mbxABCDFGHH'MJKLN, for a multisubunit transmembrane complex with strong homology to the mbh operon, however, with a highly unusual putative binding motif for the Ni-Fe-cluster in the large hydrogenase subunit. Kinetic studies of membrane-bound hydrogenase, soluble hydrogenase and sulfide dehydrogenase activities allow the formulation of a comprehensive working hypothesis of H2 metabolism in P. furiosus in terms of three pools of reducing equivalents (ferredoxin, NADPH, H2) connected by devices for transduction, transfer, recovery and safety-valving of energy.

Temperature dependence of the formal reduction potential of putidaredoxin

Putidaredoxin (Pdx), a [2Fe-2S] redox protein of size M(r) 11,600, transfers two electrons in two separate steps from the flavin containing putidaredoxin reductase to the heme protein, cytochrome CYP101 in the P450cam catalytic cycle. It has recently come to light, through NMR measurements, that there can be appreciable differences in the Pdx conformational dynamics between its reduced and oxidized states. The redox reaction entropy, deltaS(0')rc = (S(0')Pdx(r)-S(0')Pdx(0)), as determined from measurements of the variation in formal potential with temperature, E0'(T), provides a measure of the strength of this influence on Pdx function. We designed a spectroelectrochemical cell using optically transparent tin oxide electrodes, without fixed or diffusible mediators, to measure E0'(T) over the temperature range 0-40 degrees C. The results indicate that the redox reaction entropy for Pdx is biphasic, decreasing from -213 +/- 27 J mol(-1) K(-1) over 0-27 degrees C, to -582 +/- 150 J mol(-1) K (-1) over 27-40 degrees C. These redox reaction entropy changes are significantly more negative than the changes reported for most cytochromes, although our measurement over the temperature interval 0-27 degrees C is in the range reported for other iron-sulfur proteins. This suggests that Pdx (and other ferredoxins) is a less rigid system than monohemes, and that redox-linked changes in conformation, and/or conformational dynamics, impart to these proteins the ability to interact with a number of redox partners.

Pyrococcus furiosus glyceraldehyde 3-phosphate oxidoreductase has comparable W(6+/5+) and W(5+/4+) reduction potentials and unusual [4Fe-4S] EPR properties

Pyrococcus furiosus glyceraldehyde 3-phosphate oxidoreductase has been characterized using EPR-monitored redox titrations. Two different W signals were found. W(1)(5+) is an intermediate species in the catalytic cycle, with the midpoint potentials E(m)(W(6+/5+))=-507 mV and E(m)(W(5+/4+))=-491 mV. W(2)(5+) represents an inactivated species with E(m)(W(6+/5+))=-329 mV. The cubane cluster exhibits both S=3/2 and S=1/2 signals with the same midpoint potential: E(m)([4Fe-4S](2+/1+))=-335 mV. The S=1/2 EPR signal is unusual with all g values below 2.0. The titration results combined with catalytic voltammetry data are consistent with electron transfer from glyceraldehyde 3-phosphate first to the tungsten center, then to the cubane cluster and finally to the ferredoxin.