Hydrogenase cluster biosynthesis: organometallic chemistry nature's way

Fundamentals and recent progress in bioelectrochemical system-assisted biohythane production

Biohythane, a balanced mixture of 10%-30% v/v of hydrogen and 70%-90% v/v of methane, could be the backbone of an all-purpose future energy supply. Recently, bioelectrochemical systems (BES) became a new sensation among environmental biotechnology processes with the potential to sustainably generate biohythane. Therefore, to unleash its full potential for scaling up, researchers are consistently improving microbial metabolic pathways, novel reactors, and electrode designs. This review presents a detailed analysis of recently discovered fundamental mechanisms and science and engineering intervention of different strategies to improve the biohythane composition and production rate from BES. However, several milestones are to be achieved, for instance, improving electrode kinetics using efficient catalysts, engineered microbial communities, and improved reactor configurations, for commercializing this sustainable technology. Thus, a future perspective section is included to recommend novel research lines, mainly focusing on the microbial communities and the efficient electrocatalysts, to enhance reactor performance.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H₂, N₂, CO₂, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N₂, CO₂, and CO and the production of H₂ require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N₂ fixation by nitrogenase and H₂ production by hydrogenase as well as CO₂ and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Carbon-Metal Bonds: Rare and Primordial in Metabolism

Submarine hydrothermal vents are rich in hydrogen (H₂), an ancient source of electrons and chemical energy for life. Geochemical H₂ stems from serpentinization, a process in which rock-bound iron reduces water to H₂. Reactions involving H₂ and carbon dioxide (CO₂) in hydrothermal systems generate abiotic methane and formate; these reactions resemble the core energy metabolism of methanogens and acetogens. These organisms are strict anaerobic autotrophs that inhabit hydrothermal vents and harness energy via H₂-dependent CO₂ reduction. Serpentinization also generates native metals, which can reduce CO₂ to formate and acetate in the laboratory. The enzymes that channel H₂, CO₂, and dinitrogen (N₂) into methanogen and acetogen metabolism are the backbone of the most ancient metabolic pathways. Their active sites share carbon-metal bonds which, although rare in biology, are conserved relics of primordial biochemistry present at the origin of life.

Simulating Serpentinization as It Could Apply to the Emergence of Life Using the JPL Hydrothermal Reactor

The molecules feeding life's emergence are thought to have been provided through the hydrothermal interactions of convecting carbonic ocean waters with minerals comprising the early Hadean oceanic crust. Few laboratory experiments have simulated ancient hydrothermal conditions to test this conjecture. We used the JPL hydrothermal flow reactor to investigate CO₂ reduction in simulated ancient alkaline convective systems over 3 days (T = 120°C, P = 100 bar, pH = 11). H₂-rich hydrothermal simulant and CO₂-rich ocean simulant solutions were periodically driven in 4-h cycles through synthetic mafic and ultramafic substrates and Fe>Ni sulfides. The resulting reductants included micromoles of HS^- and formate accompanied possibly by micromoles of acetate and intermittent minor bursts of methane as ascertained by isotopic labeling. The formate concentrations directly correlated with the CO₂ input as well as with millimoles of Mg²⁺ ions, whereas the acetate did not. Also, tens of micromoles of methane were drawn continuously from the reactor materials during what appeared to be the onset of serpentinization. These results support the hypothesis that formate may have been delivered directly to a branch of an emerging acetyl coenzyme-A pathway, thus obviating the need for the very first hydrogenation of CO₂ to be made in a hydrothermal mound. Another feed to early metabolism could have been methane, likely mostly leached from primary CH₄ present in the original Hadean crust or emanating from the mantle. That a small volume of methane was produced sporadically from the ¹³CO₂-feed, perhaps from transient occlusions, echoes the mixed results and interpretations from other laboratories. As serpentinization and hydrothermal leaching can occur wherever an ocean convects within anhydrous olivine- and sulfide-rich crust, these results may be generalized to other wet rocky planets and moons in our solar system and beyond.

Experimental and Simulation Efforts in the Astrobiological Exploration of Exooceans

The icy satellites of Jupiter and Saturn are perhaps the most promising places in the Solar System regarding habitability. However, the potential habitable environments are hidden underneath km-thick ice shells. The discovery of Enceladus' plume by the Cassini mission has provided vital clues in our understanding of the processes occurring within the interior of exooceans. To interpret these data and to help configure instruments for future missions, controlled laboratory experiments and simulations are needed. This review aims to bring together studies and experimental designs from various scientific fields currently investigating the icy moons, including planetary sciences, chemistry, (micro-)biology, geology, glaciology, etc. This chapter provides an overview of successful in situ, in silico, and in vitro experiments, which explore different regions of interest on icy moons, i.e. a potential plume, surface, icy shell, water and brines, hydrothermal vents, and the rocky core.

Triplet of cysteines - Coordinational riddle?

Polythiol binding of metal ions plays crucial role in the proper functioning of cysteine-rich proteins that are responsible for metal homeostasis and defending processes against metal toxicity (including heavy metals detoxification). The coordination properties of cysteine residues involved in specific sequencional patterns in proteins (like those present in e.g. metallothioneins) are interesting not only from a chemical point of view but may also lead to a better understanding of the purpose and allocation of metal ions in various biomolecules. In this study, the interaction of Zn²⁺, Cd²⁺ and Ni²⁺ ions with four peptides containing cysteine triplet motif were studied by potentiometric and spectroscopic methods. The main goal of this research was to answer the question how effectively three thiols, each being next to other, are able to bind single metal ion. Two of peptides contain additional, fourth cysteine residue, separated from triplet by two and three other amino acid residues. As results show, all three cysteine residues in the CCC motif are able to participate in the coordination of the metal ion (Cd²⁺, Zn²⁺). Except cysteine thiol groups, amide nitrogen atoms are also involved in the coordination of Ni²⁺.

Radionuclide-induced defect sites in iron-bearing minerals may have accelerated the emergence of life

The emergence of life on Earth (and elsewhere) must have occurred in a milieu that is far from equilibrium, such as at alkaline hydrothermal vents that would have harboured built-in gradients in temperature, redox potential and pH along with precipitated iron-bearing minerals capable of separating these gradients, concentrating reactants and catalysing requisite protobiotic reactions. Iron-bearing minerals such as mackinawite, greenalite and fougèrite have been investigated as catalysts for protobiotic reactions, including amino acid synthesis. In the field of heterogeneous catalysis, it is well known that defect sites in the crystal structure are often the most active sites for catalysis, and mineral catalysts that have been exposed to ionizing radiation are known to exhibit increased reactivity due to radiation-induced defect sites. In this work, we (i) review the literature on the radioactive environment of the Hadean era, (ii) highlight the role of radionuclide ionizing radiation from 238U, 232Th and 40K in generating defect sites with high catalytic activity for the chemical evolution of organic molecules, and (iii) hypothesize that these processes accelerated the emergence of life.

Geoelectrodes and Fuel Cells for Simulating Hydrothermal Vent Environments

Gradients generated in hydrothermal systems provide a significant source of free energy for chemosynthetic life and may play a role in present-day habitability on ocean worlds. Electron/proton/ion gradients, particularly in the context of hydrothermal chimney structures, may also be relevant to the origins of life on Earth. Hydrothermal vents are similar in some ways to typical fuel cell devices: redox/pH gradients between seawater and hydrothermal fluid are analogous to the fuel cell oxidant and fuel reservoirs; the porous chimney wall is analogous to a separator or ion-exchange membrane and is also a conductive path for electrons; and the hydrothermal minerals are analogous to electrode catalysts. The modular and scalable characteristics of fuel cell systems make for a convenient planetary geology test bed in which geologically relevant components may be assembled and investigated in a controlled simulation environment. We have performed fuel cell experiments and electrochemical studies to better understand the catalytic potential of seafloor minerals and vent chimneys, using samples from a black smoker vent chimney as an initial demonstration. In a fuel cell with Na⁺-conducting Nafion^® membranes and liquid fuel/oxidant reservoirs (simulating the vent environment), the black smoker mineral catalyst in the membrane electrode assembly was effective in reducing O₂ and oxidizing sulfide. In a H₂/O₂ polymer electrolyte membrane (PEM) fuel cell with H⁺-conducting Nafion membranes, the black smoker catalyst was effective in reducing O₂ but not in oxidizing H₂. These fuel cell experiments accurately simulated the redox reactions that could occur in a geological setting with this particular catalyst, and also tested whether the minerals are sufficiently active to replace a commercial fuel cell catalyst. Similar experiments with other geocatalysts could be utilized to test which redox reactions could be driven in other hydrothermal systems, including hypothesized vent systems on other worlds.

Green Rust: The Simple Organizing 'Seed' of All Life?

Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence FeII/FeIII oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.

Nitric oxide activation facilitated by cooperative multimetallic electron transfer within an iron-functionalized polyoxovanadate-alkoxide cluster

Cooperative multimetallic electron transfer to accommodate substrate binding.

A series of NO-bound, iron-functionalized polyoxovanadate–alkoxide (FePOV–alkoxide) clusters have been synthesized, providing insight into the role of multimetallic constructs in the coordination and activation of a substrate. Upon exposure of the heterometallic cluster to NO, the vanadium-oxide metalloligand is oxidized by a single electron, shuttling the reducing equivalent to the {FeNO} subunit to form a {FeNO}⁷ species. Four NO-bound clusters with electronic distributions ranging from [VV3VIV2]{FeNO}⁷ to [VIV5]{FeNO}⁷ have been synthesized, and characterized via¹H NMR, infrared, and electronic absorption spectroscopies. The ability of the FePOV–alkoxide cluster to store reducing equivalents in the metalloligand for substrate coordination and activation highlights the ultility of the metal-oxide scaffold as a redox reservoir.

Methane: Fuel or Exhaust at the Emergence of Life?

As many of the methanogens first encountered at hydrothermal vents were thermophilic to hyperthermophilic and comprised one of the lower roots of the evolutionary tree, it has been assumed that methanogenesis was one of the earliest, if not the earliest, pathway to life. It being well known that hydrothermal springs associated with serpentinization also bore abiotic methane, it had been further assumed that emergent biochemistry merely adopted and quickened this supposed serpentinization reaction. Yet, recent hydrothermal experiments simulating serpentinization have failed to generate methane so far, thus casting doubt on this assumption. The idea that the inverse view is worthy of debate, that is, that methanotrophy was the earlier, is stymied by the "fact" that methanotrophy itself has been termed "reverse methanogenesis," so allotting the methanogens the founding pedigree. Thus, attempting to suggest instead that methanogenesis might be termed reverse methanotrophy would require "unlearning"-a challenge to the subconscious! Here we re-examine the "impossibility" of methanotrophy predating methanogenesis as in what we have termed the "denitrifying methanotrophic acetogenic pathway." Advantages offered by such thinking are that methane would not only be a fuel but also a ready source of reduced carbon to combine with formate or carbon monoxide-available in hydrothermal fluids-to generate acetate, a target molecule of the first autotrophs. And the nitrate/nitrite required for the putative oxidation of methane with activated NO would also be a ready source of fixed nitrogen for amination reactions. Theoretical conditions for such a putative pathway would be met in a hydrothermal green rust-bearing exhalative pile and associated chimneys subject to proton and electron counter gradients. This hypothesis could be put to test in a high-pressure hydrothermal reaction chamber in which a cool carbonate/nitrate/nitrite-bearing early acidulous ocean simulant is juxtaposed across a precipitate membrane to an alkaline solution of hydrogen and methane. Key Words: Green rust-Methanotrophy-Nitrate reduction-Emergence of life. Astrobiology 17, 1053-1066.

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides

Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.

A reduced 2Fe2S cluster probe of sulfur-hydrogen versus sulfur-gold interactions

The Ph3 PAu(+) cation, renowned as an isolobal analogue of H(+) , was found to serve as a proton surrogate and form a stable Au2 Fe2 complex, [(μ-SAuPPh3 )2 {Fe(CO)3 }2 ], analogous to the highly reactive dihydrosulfide [(μ-SH)2 {Fe(CO)3 }2 ]. Solid-state X-ray diffraction analysis found the two SAuPPh3 and SH bridges in anti configurations. VT NMR studies, supported by DFT computations, confirmed substantial barriers of approximately 25 kcal mol(-1) to intramolecular interconversion between the three stereoisomers of [(μ-SH)2 {Fe(CO)3 }2 ]. In contrast, the largely dative SAu bond in μ-SAuPPh3 facilitates inversion at S and accounts for the facile equilibration of the SAuPPh3 units, with an energy barrier half that of the SH analogue. The reactivity of the gold-protected sulfur atoms of [(μ-SAuPPh3 )2 {Fe(CO)3 }2 ] was accessed by release of the gold ligand with a strong acid to generate the [(μ-SH)2 {Fe(CO)3 }2 ] precursor of the [FeFe]H2 ase-active-site biomimetic [(μ2 -SCH2 (NR)CH2 S){Fe(CO)3 }2 ].

The drive to life on wet and icy worlds

This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, 308-343. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011 ) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999 ).

The fuel cell model of abiogenesis: a new approach to origin-of-life simulations

In this paper, we discuss how prebiotic geo-electrochemical systems can be modeled as a fuel cell and how laboratory simulations of the origin of life in general can benefit from this systems-led approach. As a specific example, the components of what we have termed the "prebiotic fuel cell" (PFC) that operates at a putative Hadean hydrothermal vent are detailed, and we used electrochemical analysis techniques and proton exchange membrane (PEM) fuel cell components to test the properties of this PFC and other geo-electrochemical systems, the results of which are reported here. The modular nature of fuel cells makes them ideal for creating geo-electrochemical reactors with which to simulate hydrothermal systems on wet rocky planets and characterize the energetic properties of the seafloor/hydrothermal interface. That electrochemical techniques should be applied to simulating the origin of life follows from the recognition of the fuel cell-like properties of prebiotic chemical systems and the earliest metabolisms. Conducting this type of laboratory simulation of the emergence of bioenergetics will not only be informative in the context of the origin of life on Earth but may help in understanding whether life might emerge in similar environments on other worlds.

Nickel-dependent metalloenzymes

This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.

Increasing the metabolic capacity of Escherichia coli for hydrogen production through heterologous expression of the Ralstonia eutropha SH operon

BACKGROUND

Fermentative hydrogen production is an attractive means for the sustainable production of this future energy carrier but is hampered by low yields. One possible solution is to create, using metabolic engineering, strains which can bypass the normal metabolic limits to substrate conversion to hydrogen. Escherichia coli can degrade a variety of sugars to hydrogen but can only convert electrons available at the pyruvate node to hydrogen, and is unable to use the electrons available in NADH generated during glycolysis.

RESULTS

Here, the heterologous expression of the soluble [NiFe] hydrogenase from Ralstonia eutropha H16 (the SH hydrogenase) was used to demonstrate the introduction of a pathway capable of deriving substantial hydrogen from the NADH generated by fermentation. Successful expression was demonstrated by in vitro assay of enzyme activity. Moreover, expression of SH restored anaerobic growth on glucose to adhE strains, normally blocked for growth due to the inability to re-oxidize NADH. Measurement of in vivo hydrogen production showed that several metabolically engineered strains were capable of using the SH hydrogenase to derive 2 mol H2 per mol of glucose consumed, close to the theoretical maximum.

CONCLUSION

Previous introduction of heterologous [NiFe] hydrogenase in E. coli led to NAD(P)H dependent activity, but hydrogen production levels were very low. Here we have shown for the first time substantial in vivo hydrogen production by a heterologously expressed [NiFe] hydrogenase, the soluble NAD-dependent H2ase of R. eutropha (SH hydrogenase). This hydrogenase was able to couple metabolically generated NADH to hydrogen production, thus rescuing an alcohol dehydrogenase (adhE) mutant. This enlarges the range of metabolism available for hydrogen production, thus potentially opening the door to the creation of greatly improved hydrogen production. Strategies for further increasing yields should revolve around making additional NADH available.

The inevitable journey to being

Life is evolutionarily the most complex of the emergent symmetry-breaking, macroscopically organized dynamic structures in the Universe. Members of this cascading series of disequilibria-converting systems, or engines in Cottrell's terminology, become ever more complicated-more chemical and less physical-as each engine extracts, exploits and generates ever lower grades of energy and resources in the service of entropy generation. Each one of these engines emerges spontaneously from order created by a particular mother engine or engines, as the disequilibrated potential daughter is driven beyond a critical point. Exothermic serpentinization of ocean crust is life's mother engine. It drives alkaline hydrothermal convection and thereby the spontaneous production of precipitated submarine hydrothermal mounds. Here, the two chemical disequilibria directly causative in the emergence of life spontaneously arose across the mineral precipitate membranes separating the acidulous, nitrate-bearing CO2-rich, Hadean sea from the alkaline and CH4/H2-rich serpentinization-generated effluents. Essential redox gradients-involving hydrothermal CH4 and H2 as electron donors, CO2 and nitrate, nitrite, and ferric iron from the ambient ocean as acceptors-were imposed which functioned as the original 'carbon-fixing engine'. At the same time, a post-critical-point (milli)voltage pH potential (proton concentration gradient) drove the condensation of orthophosphate to produce a high energy currency: 'the pyrophosphatase engine'.

On the antiquity of metalloenzymes and their substrates in bioenergetics

Many metalloenzymes that inject and extract reducing equivalents at the beginning and the end of electron transport chains involved in chemiosmosis are suggested, through phylogenetic analysis, to have been present in the Last Universal Common Ancestor (LUCA). Their active centres are affine with the structures of minerals presumed to contribute to precipitate membranes produced on the mixing of hydrothermal solutions with the Hadean Ocean ~4 billion years ago. These mineral precipitates consist of transition element sulphides and oxides such as nickelian mackinawite ([Fe>Ni]2S2), a nickel-bearing greigite (~FeSS[Fe3NiS4]SSFe), violarite (~NiSS[Fe2Ni2S4]SSNi), a molybdenum bearing complex (~Mo(IV/VI)2Fe3S(0/2-)9) and green rust or fougerite (~[Fe(II)Fe(III)(OH)4](+)[OH](-)). They may be respectively compared with the active centres of Ni-Fe hydrogenase, carbon monoxide dehydrogenase (CODH), acetyl coenzyme-A synthase (ACS), the complex iron-sulphur molybdoenzyme (CISM) superfamily and methane monooxygenase (MMO). With the look of good catalysts - a suggestion that gathers some support from prebiotic hydrothermal experimentation - and sequestered by short peptides, they could be thought of as the original building blocks of proto-enzyme active centres. This convergence of the makeup of the LUCA-metalloenzymes with mineral structure and composition of hydrothermal precipitates adds credence to the alkaline hydrothermal (chemiosmotic) theory for the emergence of life, specifically to the possibility that the first metabolic pathway - the acetyl CoA pathway - was initially driven from either end, reductively from CO2 to CO and oxidatively and reductively from CH4 through to a methane thiol group, the two entities assembled with the help of a further thiol on a violarite cluster sequestered by peptides. By contrast, the organic coenzymes were entirely a product of the first metabolic pathways. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

Field-Control, Phase-Transitions, and Life's Emergence

Instances of critical-like characteristics in living systems at each organizational level (bio-molecules to ecosystems) as well as the spontaneous emergence of computation (Langton), do suggest the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life's origins, brings up a paradox: how could simple organics - lacking the "soft-matter" response properties of today's complex bio-molecules - have dissipated energy from primordial reactions (eventually reducing CO(2)) in a controlled manner for their "ordering"? Nevertheless, a causal link of life's macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the "functional-takeover" of a soft magnetic scaffold by organics (c.f. Cairns-Smith's "crystal-scaffold"). A field-controlled structure offers a mechanism for boot-strapping - bottom-up assembly with top-down control: its super-paramagnetic colloidal components obey reversible dynamics, but its dissipation of magnetic (H)-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic dipolar network's capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically oriented system (trimming the phase-space via sterically coupled organics) toward a series of phase-transitions with appropriate organic replacements "taking-over" its functions. Where available, experiments are cited in support of these speculations and for designing appropriate tests.

On the universal core of bioenergetics

Living cells are able to harvest energy by coupling exergonic electron transfer between reducing and oxidising substrates to the generation of chemiosmotic potential. Whereas a wide variety of redox substrates is exploited by prokaryotes resulting in very diverse layouts of electron transfer chains, the ensemble of molecular architectures of enzymes and redox cofactors employed to construct these systems is stunningly small and uniform. An overview of prominent types of electron transfer chains and of their characteristic electrochemical parameters is presented. We propose that basic thermodynamic considerations are able to rationalise the global molecular make-up and functioning of these chemiosmotic systems. Arguments from palaeogeochemistry and molecular phylogeny are employed to discuss the evolutionary history leading from putative energy metabolisms in early life to the chemiosmotic diversity of extant organisms. Following the Occam's razor principle, we only considered for this purpose origin of life scenarios which are contiguous with extant life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.

Biomineralization: a proposed evolutionary origin for inorganic cofactors of enzymes

In this paper, three different reactions of nanoparticles and proteins are explained. As a model system, the interactions of birnessite, which is a common manganese oxide in the environment, and bovine serum albumin, as a protein that has a strong affinity for a variety of inorganic molecules, are studied. The author proposes that the cofactor-formation in particular enzymes may be considered as a biomineralization in the presence of the protein. One of the numerous and very small nanoparticles produced in the presence of protein could be formed in an appropriate location in proteins and be used as a primitive inorganic core (cofactor) of enzyme.

Peptide and RNA contributions to iron-sulphur chemical gardens as life's first inorganic compartments, catalysts, capacitors and condensers

Hydrothermal chimneys and compartments comprising transition metal sulphides and associated minerals have been proposed as likely locations for the beginnings of life. In laboratory simulations of off-axis alkaline springs, it is shown that the interaction of a simulated alkaline sulphide-bearing submarine vent solution with a primeval anoxic iron-bearing ocean leads to the formation of chimney structures reminiscent of chemical gardens. These chimneys display periodicity in their deposition and exhibit diverse morphologies and mineralogies, affording the possibilities of catalysis and molecular sequestration. The addition of peptides and RNA to the alkaline solution modifies the elemental stoichiometry of the chimneys-perhaps indicating the very initial stage of the organic takeover on the way to living cells by charged organic polymers potentially synthesized in this same environment.

Emerging paradigms for complex iron-sulfur cofactor assembly and insertion

[FeFe]-hydrogenses and molybdenum (Mo)-nitrogenase are evolutionarily unrelated enzymes with unique complex iron-sulfur cofactors at their active sites. The H cluster of [FeFe]-hydrogenases and the FeMo cofactor of Mo-nitrogenase require specific maturation machinery for their proper synthesis and insertion into the structural enzymes. Recent insights reveal striking similarities in the biosynthetic pathways of these complex cofactors. For both systems, simple iron-sulfur cluster precursors are modified on assembly scaffolds by the activity of radical S-adenosylmethionine (SAM) enzymes. Radical SAM enzymes are responsible for the synthesis and insertion of the unique nonprotein ligands presumed to be key structural determinants for their respective catalytic activities. Maturation culminates in the transfer of the intact cluster assemblies to a cofactor-less structural protein recipient. Required roles for nucleotide binding and hydrolysis have been implicated in both systems, but the specific role for these requirements remain unclear. In this review, we highlight the progress on [FeFe]-hydrogenase H cluster and nitrogenase FeMo-cofactor assembly in the context of these emerging paradigms.

Radical AdoMet enzymes in complex metal cluster biosynthesis

Radical S-adenosylmethionine (AdoMet) enzymes comprise a large superfamily of proteins that engage in a diverse series of biochemical transformations through generation of the highly reactive 5'-deoxyadenosyl radical intermediate. Recent advances into the biosynthesis of unique iron-sulfur (FeS)-containing cofactors such as the H-cluster in [FeFe]-hydrogenase, the FeMo-co in nitrogenase, as well as the iron-guanylylpyridinol (FeGP) cofactor in [Fe]-hydrogenase have implicated new roles for radical AdoMet enzymes in the biosynthesis of complex inorganic cofactors. Radical AdoMet enzymes in conjunction with scaffold proteins engage in modifying ubiquitous FeS precursors into unique clusters, through novel amino acid decomposition and sulfur insertion reactions. The ability of radical AdoMet enzymes to modify common metal centers to unusual metal cofactors may provide important clues into the stepwise evolution of these and other complex bioinorganic catalysts. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.

Iron-sulfide-bearing chimneys as potential catalytic energy traps at life's emergence

The concept that life emerged where alkaline hydrogen-bearing submarine hot springs exhaled into the most ancient acidulous ocean was used as a working hypothesis to investigate the nature of precipitate membranes. Alkaline solutions at 25-70°C and pH between 8 and 12, bearing HS(-)±silicate, were injected slowly into visi-jars containing ferrous chloride to partially simulate the early ocean on this or any other wet and icy, geologically active rocky world. Dependent on pH and sulfide content, fine tubular chimneys and geodal bubbles were generated with semipermeable walls 4-100 μm thick that comprised radial platelets of nanometric mackinawite [FeS]±ferrous hydroxide [∼Fe(OH)(2)], accompanied by silica and, at the higher temperature, greigite [Fe(3)S(4)]. Within the chimney walls, these platelets define a myriad of micropores. The interior walls of the chimneys host iron sulfide framboids, while, in cases where the alkaline solution has a pH>11 or relatively low sulfide content, their exteriors exhibit radial flanges with a spacing of ∼4 μm that comprise microdendrites of ferrous hydroxide. We speculate that this pattern results from outward and inward radial flow through the chimney walls. The outer Fe(OH)(2) flanges perhaps precipitate where the highly alkaline flow meets the ambient ferrous iron-bearing fluid, while the intervening troughs signal where the acidulous iron-bearing solutions could gain access to the sulfidic and alkaline interior of the chimneys, thereby leading to the precipitation of the framboids. Addition of soluble pentameric peptides enhances membrane durability and accentuates the crenulations on the chimney exteriors. These dynamic patterns may have implications for acid-base catalysis and the natural proton motive force acting through the matrix of the porous inorganic membrane. Thus, within such membranes, steep redox and pH gradients would bear across the nanometric platelets and separate the two counter-flowing solutions, a condition that may have led to the onset of an autotrophic metabolism through the reduction of carbon dioxide.

Insights into [FeFe]-hydrogenase structure, mechanism, and maturation

Hydrogenases are metalloenzymes that are key to energy metabolism in a variety of microbial communities. Divided into three classes based on their metal content, the [Fe]-, [FeFe]-, and [NiFe]-hydrogenases are evolutionarily unrelated but share similar nonprotein ligand assemblies at their active site metal centers that are not observed elsewhere in biology. These nonprotein ligands are critical in tuning enzyme reactivity, and their synthesis and incorporation into the active site clusters require a number of specific maturation enzymes. The wealth of structural information on different classes and different states of hydrogenase enzymes, biosynthetic intermediates, and maturation enzymes has contributed significantly to understanding the biochemistry of hydrogen metabolism. This review highlights the unique structural features of hydrogenases and emphasizes the recent biochemical and structural work that has created a clearer picture of the [FeFe]-hydrogenase maturation pathway.

Protein interactions and localization of the Escherichia coli accessory protein HypA during nickel insertion to [NiFe] hydrogenase

Nickel delivery during maturation of Escherichia coli [NiFe] hydrogenase 3 includes the accessory proteins HypA, HypB, and SlyD. Although the isolated proteins have been characterized, little is known about how they interact with each other and the hydrogenase 3 large subunit, HycE. In this study the complexes of HypA and HycE were investigated after modification with the Strep-tag II. Multiprotein complexes containing HypA, HypB, SlyD, and HycE were observed, consistent with the assembly of a single nickel insertion cluster. An interaction between HypA and HycE did not require the other nickel insertion proteins, but HypB was not found with the large subunit in the absence of HypA. The HypA-HycE complex was not detected in the absence of the HypC or HypD proteins, involved in the preceding iron insertion step, and this interaction is enhanced by nickel brought into the cell by the NikABCDE membrane transporter. Furthermore, without the hydrogenase 1, 2, and 3 large subunits, complexes between HypA, HypB, and SlyD were observed. These results support the hypothesis that HypA acts as a scaffold for assembly of the nickel insertion proteins with the hydrogenase precursor protein after delivery of the iron center. At different stages of the hydrogenase maturation process, HypA was observed at or near the cell membrane by using fluorescence confocal microscopy, as was HycE, suggesting membrane localization of the nickel insertion event.

Speculation on quantum mechanics and the operation of life giving catalysts

The origin of life necessitated the formation of catalytic functionalities in order to realize a number of those capable of supporting reactions that led to the proliferation of biologically accessible molecules and the formation of a proto-metabolic network. Here, the discussion of the significance of quantum behavior on biological systems is extended from recent hypotheses exploring brain function and DNA mutation to include origins of life considerations in light of the concept of quantum decoherence and the transition from the quantum to the classical. Current understandings of quantum systems indicate that in the context of catalysis, substrate-catalyst interaction may be considered as a quantum measurement problem. Exploration of catalytic functionality necessary for life's emergence may have been accommodated by quantum searches within metal sulfide compartments, where catalyst and substrate wave function interaction may allow for quantum based searches of catalytic phase space. Considering the degree of entanglement experienced by catalytic and non catalytic outcomes of superimposed states, quantum contributions are postulated to have played an important role in the operation of efficient catalysts that would provide for the kinetic basis for the emergence of life.

Communication between the zinc and nickel sites in dimeric HypA: metal recognition and pH sensing

Helicobacter pylori , a pathogen that colonizes the human stomach, requires the nickel-containing metalloenzymes urease and NiFe-hydrogenase to survive this low pH environment. The maturation of both enzymes depends on the metallochaperone, HypA. HypA contains two metal sites, an intrinsic zinc site and a low-affinity nickel binding site. X-ray absorption spectroscopy (XAS) shows that the structure of the intrinsic zinc site of HypA is dynamic and able to sense both nickel loading and pH changes. At pH 6.3, an internal pH that occurs during acid shock, the zinc site undergoes unprecedented ligand substitutions to convert from a Zn(Cys)(4) site to a Zn(His)(2)(Cys)(2) site. NMR spectroscopy shows that binding of Ni(II) to HypA results in paramagnetic broadening of resonances near the N-terminus. NOEs between the beta-CH(2) protons of Zn cysteinyl ligands are consistent with a strand-swapped HypA dimer. Addition of nickel causes resonances from the zinc binding motif and other regions to double, indicating more than one conformation can exist in solution. Although the structure of the high-spin, 5-6 coordinate Ni(II) site is relatively unaffected by pH, the nickel binding stoichiometry is decreased from one per monomer to one per dimer at pH = 6.3. Mutation of any cysteine residue in the zinc binding motif results in a zinc site structure similar to that found for holo-WT-HypA at low pH and is unperturbed by the addition of nickel. Mutation of the histidines that flank the CXXC motifs results in a zinc site structure that is similar to holo-WT-HypA at neutral pH (Zn(Cys)(4)) and is no longer responsive to nickel binding or pH changes. Using an in vitro urease activity assay, it is shown that the recombinant protein is sufficient for recovery of urease activity in cell lysate from a HypA deletion mutant, and that mutations in the zinc-binding motif result in a decrease in recovered urease activity. The results are interpreted in terms of a model wherein HypA controls the flow of nickel traffic in the cell in response to nickel availability and pH.

Design, fabrication, and test of a hydrothermal reactor for origin-of-life experiments

We describe a continuous high-pressure flow reactor designed to simulate the unforced convective interaction of hydrothermal solutions and ocean waters with submarine crust on early Earth-conditions appropriate to those that may have led to the onset of life. The experimental operating conditions are appropriate for investigating kinetic hydrothermal processes in the early history of any sizable wet, rocky planet. Beyond the description of the fabrication, we report an initial experiment that tested the design and investigated the feasibility of sulfide and silica dissolution in alkaline solution from iron sulfide and basaltic rock, and their possible subsequent transport as HS(-) and H(2)SiO(2-)(4) in hot alkaline solutions. Delivery of hydrogen sulfide and dihydrogen silicate ions would have led to the precipitation of ferrous hydroxide, hydroxysilicates, and iron sulfides as integral mineral components of an off-ridge compartmentalized hydrothermal mound in the Hadean. Such a mound could, we contend, have acted as a natural chemical and electrochemical reactor and, ultimately, as the source of all biochemistry on our planet. In the event, we show that an average of ∼1 mM/kg of both sulfide and silica were released throughout, though over 10 mM/kg of HS(-) was recorded for ∼100 minutes in the early stages of the experiment. This alkaline effluent from the reactor was injected into a reservoir of a simulacrum of ferrous iron-bearing "Hadean Ocean" water in an experiment that demonstrated the capacity of such fluids to generate hydrothermal chimneys and a variety of contiguous inorganic microgeode precipitates bearing disseminations of discrete metal sulfides. Comparable natural composite structures may have acted as hatcheries for emergent life in the Hadean.

Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG)

Complex enzymes containing Fe-S clusters are ubiquitous in nature, where they are involved in a number of fundamental processes including carbon dioxide fixation, nitrogen fixation and hydrogen metabolism. Hydrogen metabolism is facilitated by the activity of three evolutionarily and structurally unrelated enzymes: the [NiFe]-hydrogenases, [FeFe]-hydrogenases and [Fe]-hydrogenases (Hmd). The catalytic core of the [FeFe]-hydrogenase (HydA), termed the H-cluster, exists as a [4Fe-4S] subcluster linked by a cysteine thiolate to a modified 2Fe subcluster with unique non-protein ligands. The 2Fe subcluster and non-protein ligands are synthesized by the hydrogenase maturation enzymes HydE, HydF and HydG; however, the mechanism, synthesis and means of insertion of H-cluster components remain unclear. Here we show the structure of HydA(DeltaEFG) (HydA expressed in a genetic background devoid of the active site H-cluster biosynthetic genes hydE, hydF and hydG) revealing the presence of a [4Fe-4S] cluster and an open pocket for the 2Fe subcluster. The structure indicates that H-cluster synthesis occurs in a stepwise manner, first with synthesis and insertion of the [4Fe-4S] subcluster by generalized host-cell machinery and then with synthesis and insertion of the 2Fe subcluster by specialized hydE-, hydF- and hydG-encoded maturation machinery. Insertion of the 2Fe subcluster presumably occurs through a cationically charged channel that collapses following incorporation, as a result of conformational changes in two conserved loop regions. The structure, together with phylogenetic analysis, indicates that HydA emerged within bacteria most likely from a Nar1-like ancestor lacking the 2Fe subcluster, and that this was followed by acquisition in several unicellular eukaryotes.

Wiring photosystem I for direct solar hydrogen production

The generation of H(2) by the use of solar energy is a promising way to supply humankind's energy needs while simultaneously mitigating environmental concerns that arise due to climate change. The challenge is to find a way to connect a photochemical module that harnesses the sun's energy to a catalytic module that generates H(2) with high quantum yields and rates. In this review, we describe a technology that employs a "molecular wire" to connect a terminal [4Fe-4S] cluster of Photosystem I directly to a catalyst, which can be either a Pt nanoparticle or the distal [4Fe-4S] cluster of an [FeFe]- or [NiFe]-hydrogenase enzyme. The keys to connecting these two moieties are surface-located cysteine residues, which serve as ligands to Fe-S clusters and which can be changed through site-specific mutagenesis to glycine residues, and the use of a molecular wire terminated in sulfhydryl groups to connect the two modules. The sulfhydryl groups at the end of the molecular wire form a direct chemical linkage to a suitable catalyst or can chemically rescue a [4Fe-4S] cluster, thereby generating a strong coordination bond. Specifically, the molecular wire can connect the F(B) iron-sulfur cluster of Photosystem I either to a Pt nanoparticle or, by using the same type of genetic modification, to the differentiated iron atom of the distal [4Fe-4S].(Cys)(3)(Gly) cluster of hydrogenase. When electrons are supplied by a sacrificial donor, this technology forms the cathode of a photochemical half-cell that evolves H(2) when illuminated. If such a device were connected to the anode of a photochemical half-cell that oxidizes water, an in vitro solar energy converter could be realized that generates only O(2) and H(2) in the light. A similar methodology can be used to connect Photosystem I to other redox proteins that have surface-located [4Fe-4S] clusters. The controlled light-driven production of strong reductants by such systems can be used to produce other biofuels or to provide mechanistic insights into enzymes catalyzing multielectron, proton-coupled reactions.

Hydrothermal focusing of chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo/W, Co, S and Se, forced life to emerge

Energised by the protonmotive force and with the intervention of inorganic catalysts, at base Life reacts hydrogen from a variety of sources with atmospheric carbon dioxide. It seems inescapable that life emerged to fulfil the same role (i.e., to hydrogenate CO(2)) on the early Earth, thus outcompeting the slow geochemical reduction to methane. Life would have done so where hydrothermal hydrogen interfaced a carbonic ocean through inorganic precipitate membranes. Thus we argue that the first carbon-fixing reaction was the molybdenum-dependent, proton-translocating formate hydrogenlyase system described by Andrews et al. (Microbiology 143:3633-3647, 1997), but driven in reverse. Alkaline on the inside and acidic and carbonic on the outside - a submarine chambered hydrothermal mound built above an alkaline hydrothermal spring of long duration - offered just the conditions for such a reverse reaction imposed by the ambient protonmotive force. Assisted by the same inorganic catalysts and potential energy stores that were to evolve into the active centres of enzymes supplied variously from ocean or hydrothermal system, the formate reaction enabled the rest of the acetyl coenzyme-A pathway to be followed exergonically, first to acetate, then separately to methane. Thus the two prokaryotic domains both emerged within the hydrothermal mound-the acetogens were the forerunners of the Bacteria and the methanogens were the forerunners of the Archaea.

Identification and characterization of a novel member of the radical AdoMet enzyme superfamily and implications for the biosynthesis of the Hmd hydrogenase active site cofactor

The genetic context, phylogeny, and biochemistry of a gene flanking the H(2)-forming methylene-H(4)-methanopterin dehydrogenase gene (hmdA), here designated hmdB, indicate that it is a new member of the radical S-adenosylmethionine enzyme superfamily. In contrast to the characteristic CX(3)CX(2)C or CX(2)CX(4)C motif defining this family, HmdB contains a unique CX(5)CX(2)C motif.