On the origin of biochemistry at an alkaline hydrothermal vent

Abstract

A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that focuses on the acetyl-CoA (Wood-Ljungdahl) pathway of CO2 fixation and central intermediary metabolism leading to the synthesis of the constituents of purines and pyrimidines. The idea that acetogenesis and methanogenesis were the ancestral forms of energy metabolism among the first free-living eubacteria and archaebacteria, respectively, stands in the foreground. The synthesis of formyl pterins, which are essential intermediates of the Wood-Ljungdahl pathway and purine biosynthesis, is found to confront early metabolic systems with steep bioenergetic demands that would appear to link some, but not all, steps of CO2 reduction to geochemical processes in or on the Earth's crust. Inorganically catalysed prebiotic analogues of the core biochemical reactions involved in pterin-dependent methyl synthesis of the modern acetyl-CoA pathway are considered. The following compounds appear as probable candidates for central involvement in prebiotic chemistry: metal sulphides, formate, carbon monoxide, methyl sulphide, acetate, formyl phosphate, carboxy phosphate, carbamate, carbamoyl phosphate, acetyl thioesters, acetyl phosphate, possibly carbonyl sulphide and eventually pterins. Carbon might have entered early metabolism via reactions hardly different from those in the modern Wood-Ljungdahl pathway, the pyruvate synthase reaction and the incomplete reverse citric acid cycle. The key energy-rich intermediates were perhaps acetyl thioesters, with acetyl phosphate possibly serving as the universal metabolic energy currency prior to the origin of genes. Nitrogen might have entered metabolism as geochemical NH3 via two routes: the synthesis of carbamoyl phosphate and reductive transaminations of alpha-keto acids. Together with intermediates of methyl synthesis, these two routes of nitrogen assimilation would directly supply all intermediates of modern purine and pyrimidine biosynthesis. Thermodynamic considerations related to formyl pterin synthesis suggest that the ability to harness a naturally pre-existing proton gradient at the vent-ocean interface via an ATPase is older than the ability to generate a proton gradient with chemistry that is specified by genes.

Figure 1

Acetogenesis and methanogenesis. (a) Biochemical cartoon of acetogenesis (i) as redrawn from Müller (2003) and methanogenesis (ii) as redrawn from Schönheit & Schäfer (1995) including the structures of the salient pterin cofactors (iii, iv) and their relevant chemical intermediates (v) as redrawn from Maden (2002) with a brown dot to indicate the relevant moieties of the intermediates with respect to the complete structures. Ion pumping portions of the pathways are indicated schematically with green shading, whereby the coupling sites are known in some detail in methanogens (Schönheit & Schäfer 1995), but are not known with certainty in acetogens (Müller 2003), although it is certain that acetogens depend upon chemiosmosis for H₂/CO₂-dependent growth (Fuchs 1986; Müller 2003). The homologous CODH/ACS enzymes are indicated with purple shading, the ATPase with blue. The initial energy investment required in both pathways to generate a formyl pterin, but provided by different means, is indicated. The dependence upon the MoCo in steps leading to the formation of formyl pterin is indicated. The PAT and ACK steps of the methanogen pathway, recently uncovered by Rother & Metcalf (2004) under particular growth conditions, are bracketed and labelled with a question mark, because it is uncertain whether that growth mode is sustainable through substrate level phosphorylation alone (see text). (b) Some biologically relevant pterins (see text), including MoCo.

Figure 2

The RNA world in early formulations (White 1976) as discussed by Penny (2005). This envisages RNA-like cofactors performing essential catalyses early, with continued utility as part of larger RNA molecules, and with the original RNA scaffold of the ribozyme being replaced piece-by-piece by proteins over evolutionary time, sometimes more than once independently, with the cofactor still doing the catalytic job, but with better positioning of substrates and intermediates within a handed catalytic site of a protein. Some cofactors representing the red dot are redrawn from Graham & White (2002) and Stryer (1975). Note the conspicuous absence of chiral centres in the catalytically active moieties of the cofactors. NAD, nicotinamide adenine dinucleotide; FAD, flavin adenine dinucleotide.

Figure 3

Schematic summary of some core reactions of carbon and energy metabolism relevant to modern biochemistry and possibly relevant to prebiotic chemistry. The names of the enzymes that catalyse the reactions labelled as I–VI interconnecting pyruvate, PEP and oxalacetate, as modified from O'Brien et al. (1977), are: I, pyruvate carboxylase; II, oxalacetate decarboxylase; III, PEP synthase (or alternatively pyruvate:orthophosphate dikinase); IV, pyruvate kinase (or alternatively pyruvate:orthophosphate dikinase); V, PEP carboxylase; VI, PEP carboxykinase. Reactions that are coupled to phosphoanhydride hydrolysis in GTP (or ATP) in the modern enzymatic reactions are labelled with a small red star. The exclamation point at formyl pterin involvement points to the bioenergetic problem of energy investment at the formyl pterin synthesis step of the Wood–Ljungdahl pathway as shown in figure 1 and as elaborated in §16. The ‘D!’ and ‘L!’ symbols indicate the points at which product chirality sets in among organisms that use the Wood–Ljungdahl pathway (see text). The references to Fuchs, de Duve and Morowitz in the figure underscore that we are merging mutually compatible aspects concerning early biochemistry that they have stressed previously into a common framework. The split from combined energy and carbon metabolism involving thioester formation from CO₂ and H₂ into committed energy and carbon metabolism for early biochemical evolution, both starting from the thioester acetyl-CoA (and simpler thiol analogues, such as acetyl methyl sulphide) is indicated (see text). PGA, phosphoglycerate; TCA cycle, tricarboxylic acid cycle. X, Y and Z indicate any substrate that can be phosphorylated by the acyl phosphate bond in acetyl phosphate. The isocitrate and glyoxylate steps in the modern incomplete reverse TCA cycle are apparently missing (see text). The box at right indicates aqueous equilibria in the triose phosphate system (Noltmann 1972).

Figure 4

Pterins, purines and pyrimidines. (a) Schematic of the interdependence between GTP and pterin synthesis. (b) The origin of the atoms in the purine and pyrimidine rings, slightly modified from Stryer (1975) as it relates to microbes (Kappock et al. 2000), and including formyl phosphate-dependent reactions summarized by Ownby et al. (2005). H₄F, tetrahydrofolate. (c) The substrate, intermediates and product of the GTP cyclohydrolase reaction initiating pterin synthesis, redrawn from Wuebbens & Rajagopalan (1995).

Figure 5

Chicken-and-egg synthesis and chirality loss. (a) Schematic of the circumstance that in some micro-organisms TPP (thiamine pyrophosphate) and PLP are required for their own synthesis (see text), but also positively feedback into their own synthesis in the sense of a chemical hypercycle (Hordijk & Steel 2004). (b) Disappearance of chiral centres through aromatization in PLP biosynthesis by PdxA and PdxJ according to the mechanism proposed by Laber et al. (1999), see also Eubanks & Poulter (2003). The chiral carbon atoms a–d in substrates and products are labelled. GA3P, glyceraldehyde-3-phosphate; DX5P, 1-deoxy-xylulose-5-phosphate; 4PH-Thr, 4-(phosphohydroxy)-threonine; glu, glutamate; αkg, α-ketoglutarate; E4P, erythrose-4-phosphate; PNP, pyridoxine phosphate.

Figure 6

Speculations about early biochemistry. (a) Possible routes of nitrogen incorporation into metabolism, energetically feasible with acetyl phosphate owing to its higher energy of hydrolysis (table 2) than ATP, which is the modern phosphoryl donor in the enzymes today. Oxalacetate (oxa), pyruvate (pyr), glyoxylate (gox) and α-ketoglutarate (αkg) also occur on the left-hand side of figure 3. ‘Pyranose’ (Eschenmoser 2004) indicates that we do not specify the ancestral kind of sugar phosphate in the backbone of RNA-like polymers. The blue star indicates that we have not specified a mechanism of sugar phosphate formation here, although we suspect it to have proceeded via PEP and PGA, via the enolase reaction (figure 3). ‘DL’ indicates that pyranosyl (or other sugar) phosphate synthesis probably occurred without stereospecificity at first, and that a chemical hypercyclic feedback loop into a handed precursor of the enolase reaction as sketched in figure 7 tipped the homochirality scale for sugars. (b) A reminder that we are suggesting the synthesis of thioesters that are the ‘food’ for an autocatalytic chemical cycle (Hordijk & Steel 2004) to have been continuous and stable and to have proceeded initially with inorganic catalysts only. R indicates a simple aliphatic residue. (c) Structures of some of the simple reactive compounds that are central to the considerations in this paper. The Lewis structures for COS are from Luther (2004).

Figure 7

Suggestion for the origin of homochirality (see text) via an autocatalytic cycle in the sense of Hordijk & Steel (2004). From a mixture of l and d amino acids, only those of one α-carbon configuration are incorporated into protein by virtue of the chance stereochemistry of the initial peptidyl transferase reaction catalysed by a protoribosome. Handed peptides (also possible to synthesize initially by chance, owing to the complexity of racemates with many chiral centres, see text) with some enolase activity produce more d sugars, possibly as pyranose (pyr), leading to more stereoselective peptide synthesis at the peptidyl transferase site of the ribosome as redrawn from Steitz (2005), because only activated amino acids of one configuration will polymerize. This is schematically indicated by the fit of an activated l-amino acid into the modern peptidyl transferase site (centre), where the α-amino group of the next amino acid to be polymerized is coordinated by the active site so as to attack the C-terminal carbonyl carbon of the tRNA-bound growing peptide chain, whereas the d-configuration (left) leaves the amino group in the wrong spot (arrow) for peptidyl transfer. While the translation process can filter one configuration into peptides, it cannot synthesize the l-configuration. But handed peptides with PLP-dependent transaminase activities can (arrows leading to l), feeding back into the autocatalytic cycle by promoting more of both the stereochemically homogeneous enolase and the transaminase activity. Note that the autocatalytic cycle requires a sustained source of new precursors (‘food’) in order to operate (Hordijk & Steel 2004).

Figure 8

Hydrothermal starting conditions for biochemical origins. (a) Redox gradient in the early ocean, with (i) CO₂ from volcanoes meeting hydrothermal sulphide and (ii) H₂ at an alkaline vent with acetate production (Russell & Martin 2004) The red circle indicates a hydrothermal mound. (b) A metal sulphide orebody with botryoids (bubbles) of FeS owing to inflation of freshly precipitated FeS by vent water, the arrow indicating a small chimney in cross-section (Russell & Hall 1997). (c)–(e) Electron micrographs through botryoids (see Russell & Hall 1997). (f) Electron micrograph of a section from the Lost City alkaline vent (Kelley et al. 2001), kindly provided by Deborah Kelley.

Figure 9

Possible stages in the early evolution of carbon and energy metabolism. (a) Carbon assimilation from methyl sulphide and CO₂ to acetyl thioesters and energy metabolism through acetyl phosphate via substrate level phosphorylation. This could, in principle, fuel the evolution of self-replicating systems into the world of genes and proteins. (b) Hypothetical biochemical map of early biochemistry at a stage that is still dependent on geochemically reduced C1 compounds. AA, amino acids; R, purines; Y, pyrimidines; P_i, inorganic phosphate; ∼P, organic phosphate. Reducing power from H₂ is required at almost all steps (not shown). (c) With the advent of protein synthesis, harnessing the pre-existing proton gradient at the vent via simple proteins that conserve energy permits the use of pterin-dependent CO₂ fixation as in the modern Wood–Ljungdahl pathway (see text). The energy conserving reaction X→Y is kept general, because it can indicate pyrophosphate synthesis, ATP synthesis or Ech-type energy conservation (Hedderich 2004) as in formyl-MF dehydrogenase (see text). (d) Hypothetical biochemical map of early biochemistry at a stage that is independent of geochemically reduced C1 compounds by virtue of chemiosmotic energy harnessing. MoFe indicates the Mo-Fe-S centre of nitrogenase. Abbreviations as in (b). (e) With the advent of proteins that catalyse membrane-associated electron transport coupled to proton pumping, chemiosmotic potential can be generated autogenously, a prerequisite for the free-living lifestyle among autotrophs. Proton-pumping systems like Ech, that operate as a single, membrane-associated complex, without the help of quinones or analogues, such as methanophenazine, would possibly precede cytochrome-type (Schütz et al. 2000) proton-pumping systems. (f) Autotrophy equates to achieving independence from reduced carbon and nitrogen species supplied geochemically by serpentinization, and requires mechanisms for both autogenous proton pumping and chemiosmotic energy harnessing.

Figure 10

Quinones, quinone analogues and lipids. Structures from Berry (2002) and Lengeler et al. (1999). (a) Compounds common among or specific to eubacteria (with the exception of ubiquinone). (b) Compounds specific to archaebacteria. Note the difference in glycerol configuration (Koga et al. 1998). There has been a claim that archaebacteria synthesize eubacterial-type phospholipids (Pereto et al. 2004), but reading of the original literature behind that claim (Gattinger et al. 2002) reveals that the archaebacteria in question were grown on yeast extract and/or with fatty acid supplements; the methanogens contained the lipids (Gattinger et al. 2002), the inference that they synthesized them (Pereto et al. 2004) is tenuous.

Figure 11

Cutting loose. Escape from the vent was only possible when genetically encoded lipid synthesis and cell wall synthesis had been achieved, and when autogenous formyl pterin synthesis as well as ab initio ion-pumping mechanisms had been developed for bioenergetic reasons relating to energy conservation efficiency (see text), but in independent lineages of energetically sustainable and genetically replicating ensembles within the network of FeS compartments (see also Russell & Hall 1997; Martin & Russell 2003; Koonin & Martin 2005). The ancestral state of eubacterial physiology would be acetogenesis and that of archaebacterial physiology would be methanogenesis, followed by anaerobic microbial communities (Schink 1997) utilizing H₂, acetate, methane and similar small organic compounds.