Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

Myth and fact in the origins of cellular life on Earth

Myth and fact in the origins of cellular life on Earth BioscienceHorizons Volume 10 2017 10.1093/biohorizons/hzx017 ............................................................................................ ..................................................................... Review article Paul Jowett , Richard Rayne and Salvador Tomas Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK *Corresponding author: Thessaly Cottage, Foxcombe Lane, Boars Hill, Oxford OX1 5DH, UK. Tel: +44-1865 321107. Email: paul.jowett@ rolandberger.com Supervisor: Salvador Thomas, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK ............................................................................................ ..................................................................... Research into the origins of the first protocell is of a multidisciplinary nature. It draws evidence from what we know about the Earth’s early atmosphere and environment, and about the most ancient features of the cell’s structure and compos- ition. Such data provides the input for the hypothesis generation and experimental reconstruction necessary to mimic steps in the formation of the first protocell. While research into the origins of the first protocell is condemned to focus upon laboratory experiments, it should be guided by a detailed study of real evidence pertaining to the environment on Earth 4 billion years ago. In this review, we take stock of the research that has been performed to date across the main disciplines of earth sciences, biochemistry, and molecular biology. We seek to identify the progress made in laying down a sequence for the events that led up to the first protocell. We also assess the strengths and weaknesses of the experi- mental designs and suggest some future approaches. While the field has made many important advances, from the ori- ginal Stanley Miller experiment establishing ‘life from chemistry’ products such as amino acids, through to Deamer’s findings on fatty acid membranes and Szostack’s work on lipids, there is still a long and challenging journey ahead to understand how cellular life began. The experiments required to make more rapid progress in the field will likely be more elaborate, costly, and time consuming. Key words: abiogenesis, prebiotic, self-assembly, protocell, evolution, RNA Submitted on 14 November 2016; editorial decision on 6 October 2017 ............................................................................................ ..................................................................... of what constitutes the essentials for cellular life, and track Introduction progress made in mimicking the path by which cells came into existence. We will summarize some of the current theor- While at first sight the task of tracing the origins of primi- ies on how cellular life arose, examine the key experiments tive cellular life on Earth would appear to be the histor- that have yielded the best results to date, and take stock of ian’s domain, the lack of sources forces us to imagine and the current experimental designs and their limitations. then reconstruct the events that could have happened, approaches no historian would employ. The paucity of fos- We will also identify the challenges confronted in improving sil evidence makes it essential to follow the path of hypoth- our theories on the origins of the cell, which include: (1) the pos- esis generation and experimental reconstruction to shed sibility that many of the early nucleic and amino acids shaping light on the origins of the first protocell (see Schopf, 1978, the first protocell became extinct; (2) the obstacles to recon- 1993, 2006, for attempts to gain fossil evidence, Fig. 1 for structing the environment of 4–3.5 billion years ago and (3) the the putative results thereof, and see Brasier et al.,2002 for uncertainty over whether there was one original protocell, the a critique of what has been found). Our theories for how result of a unique sequence of events, or many different proto- life first evolved on Earth must be built upon laboratory cells, that developed spontaneously on many occasions once the research. This paper will review our current understanding appropriate environmental conditions were appropriate. ............................................................................................... .................................................................. © The Author 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. Figure 1. Putative timing of evolution. In his article in 1978, Schopf outlined the major events based on his and colleagues’ assessments of the fossil record and provided tentative estimates of the timing of major events in the evolution of life. P-M-C = Palaeozoic, Mesozoic, Cenozoic. Adapted from Schopf (1978) The evolution of the first cells. Scientific American 239(2):110–38 billion years ago (Fig. 2). Attention has focussed upon four Discussion critical processes: the formation of organic molecules such as amino and nucleic acids, the polymerization of these mole- The essentials for cellular life cules, the formation of membranes, and the development of While popular definitions of life, heavily influenced by metabolic networks for power. Competing theories exist for Darwin, centre on reproduction and the capacity for evolu- how each of these processes evolved, and in what sequence. tion, biologists in recent years have shifted their focus to the While there is a consensus that organic molecules came first, role played by autopoiesis, homoeostasis, cognition, and co- since nucleic and amino acids are the essential building blocks emergence. Autopoiesis is defined as the ability of the cell to of life, views differ over whether metabolism, polymerized replenish and renew itself. Homoeostasis is the ability of the molecules or membranes then followed. cell to maintain key parameters within the set boundaries Darwin originally suggested that life began in a ‘warm little required for function. Cognition implies that the cell is able to pond’ (Darwin, 1859), but it was Oparin in the early 20th sense its own needs within its surroundings. Co-emergence Century who conceived of a model whereby simple molecules, refers to the interplay between the cell and its environment. subjected to chemical reactions, became organic, underwent Current definitions of life as expressed by some biologists further reactions to assemble macromolecules and polymer assume that the cell is more than the sum of its parts: all of the complexes, and harnessed metabolic pathways to forge the cell’s components are dependent upon one another (Luisi, first cell (Oparin, 1924). The ‘life from chemistry’ model was 2014). This observation is particularly pertinent for the a vital first step in the formation of current views on the cell’s chicken-and-egg debate over the sequence of events leading to origins. the self-assembly and self-replication of the constituent com- ponents of the protocell: no self-replication of any cell compo- Both Oparin and Haldane independently hypothesized nent has ever been achieved in isolation, and the alternative that the Earth’s initial atmosphere was reductive, rather than may be that self-replication is impossible on a molecular self- oxidative as it is today and thus more likely to provide the sufficient basis, but rather dependent upon the interplay of metabolic basis for the formation of the organic chemicals disparate molecular assemblies (Segré and Lancet, 2000). essential for life. Oparin defined the term ‘primordial soup’ to describe the Archean ocean in which solar energy and a redu- The early hypotheses on the origins of the cing atmosphere created organic molecules (Oparin, 1924; protocell Haldane, 1929) (Fig. 3). The central hypothesis on the origin of the cell is that organic The debate over the order of the remaining three events molecules self-assembled to form the first protocell some 4 has been lively. Wächtershäuser, a German patent lawyer ............................................................................................... .................................................................. 2 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. Figure 2. Putative process of protocell development. In his review article of 2005, Pereto set out a scheme for a hypothetical transition from prebiotic chemistry to protocells. Pereto chose not to add a timescale to his scheme. Adapted, with key events defined by author, from Pereto (2005) Controversies on the origin of life. International Microbiology 8:23–31 Figure 3. Environmental influences relevant to protocell development. In their review article (2012) Pufahl and Hiatt collated a broad range of sources on environmental change that could impact the biosphere. They stress that the level of oxygenation immediately after the Great Oxidation Event is still largely unknown. Earth oxygenation is divided into three stages in their schema (1,2,3). PAL = present atmospheric levels, MIF = mass-independent fractionation. Adapted from Pufahl and Hiatt (2012) Oxygenation of the Earth’s atmosphere-ocean system: a review of physical and classical sedimentologic responses. Marine and Petroleum Geology 32:1–20 turned evolutionary biologist, argued that metabolism came And finally, Szostak, Deamer, and Luisi have put forward first with his ‘iron-sulphur world’ theory (Wächtershäuser, arguments for membranes being paramount, in part because 1990). Orgel and Gilbert argued equally passionately that the they provide the spatial localization necessary to promote polymerization of RNA took priority, putting the ‘RNA non-enzymatic polymerization (Szostak, Bartel, Luisi, 2001; World’ at the head of the pack (Orgel, 1968; Gilbert 1986). Luisi, 2014; Deamer, 2017). ............................................................................................... .................................................................. 3 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. experiments by Bernath and others using data from a Early experiments on the formation of Canadian satellite mission for sensing of the Earth’s atmos- organic molecules phere suggest that the Earth’s Hadean atmosphere could have The most significant experiment performed to date on the contained up to 40% hydrogen, a figure suggestive of an formation of organic molecules remains that of Miller and environment even more conducive of the formation of pre- Urey in 1952 when they sought to test the hypothesis of biotic organic molecules than the atmosphere used by Miller Oparin and Haldane that the organic building blocks of life in his earlier experiment (Bernath et al., 2005). emerged from a reducing atmosphere (Miller, 1953). Miller Extra-terrestrial influences on supply of filled a flask with the four gaseous elements of the reductive atmosphere: methane, ammonia, hydrogen and water. He organic molecules on Earth then passed electrical discharges through them to simulate Research into the Murchison meteorite, which fell to Earth in lightning. After 125 h of the experiment, using the equipment 1969 in Australia, has stimulated growth in the field of astro- available to him at the time, Miller identified several alpha biology, a field that studies how extra-terrestrial influences amino acids contained within the residues. could have played a role in the origins of life on Earth and Later analyses of the outputs of Miller’s experiment, using elsewhere in the universe. more advanced equipment conducted by Bada, revealed that A wide range of analyses have been made of the organic they included a much broader range of amino acids than had compounds contained in the Murchison meteorite (Yuen originally been detected (Bada, 2009). et al., 1984; Engel, Macko, Silfer, 1990; Pizzarello, Huang, Similar progress has been achieved in identifying paths to the Fuller, 2004; Huang et al., 2005), but perhaps the most com- formation of long chain fatty acids, such as seen in the work of prehensive and conclusive to date is that of a team led by McCollum, Ritter and Simoneit (1999) that used oxidation of Martins which used compound-specific carbon isotope data olivine in ultramaficrockbyaprocessof ‘serpentinization’ to to measure purine and pyrimidine compounds. Martins and reduce water to molecular hydrogen and subsequently combine others found that dicarboxylic acids were the most abundant it with CO via Fischer-Tropsch synthesis under high tempera- class of compounds contained within the Murchison meteor- tures (Segré et al. 2001). Potential examples of this process have ite, and many purines and pyrimidines were also found. The been found in the Rainbow hydrothermal field on the Mid- results for uracil and xanthine showed positive δ C values, Atlantic Ridge (Konn et al., 2015). uracil being abundant in modern biochemistry, while xan- thine is more limited, functioning as an intermediate in the By contrast, progress in explaining the formation of nucleic biosynthesis of guanosine and uric acid (Martins et al., 2008). acids is much less well advanced. Indeed Hud and Cafferty (2013) argue that given the failure of all attempts to mimic an Proponents of extra-terrestrial influences on prebiotic abiotic origin for RNA, they feel the evidence suggests that RNA development point to the carbonaceous meteorite in-falls dur- is the product of molecular ancestors, not their forebear. Hud ing the early Hadean phase of Earth’s history, and suggest and Cafferty base their views on a series of limiting factors influ- that nucleobases delivered together with sugar-related species encing the three distinct molecular units of RNA (the nucleobase, and amino acids may have played a critical role in the found- the ribose sugar, and the phosphate group). To these, they add ing of the RNA world (Engel, Macko, Silfer, 1990; Martins cations and solvent molecules as additional vital components. et al., 2008). The chemical building blocks for the ‘life from Each component faces severe abiotic challenges. Researchers chemistry’ thesis could have been formed on Earth, on extra- have grappled with the problem of how activated pyrimidine terrestrial planets and meteorites, or from a combination of ribonucleotides could have synthesized in prebiotically plausible the two. There are few current clues as to which source came conditions, most notably through the work of Powner, Gerland, ‘first’ or played the dominant role. What is remarkable, how- and Sutherland (Powner, Gerland, Sutherland, 2009). Powner ever, is that support for the ‘life from chemistry’ thesis is not et al. considered the formation of ribonucleotides from their con- restricted to Earth, giving first insights into the potential for stituent parts too difficult to replicate and advanced an alterna- life based on common building blocks beyond our planet. tive theory, validated by experiments, that ribonucleotides could undergo synthesis in a process that bypassed ribose. The ‘Metabolism First’ approach and the ‘Iron-Sulphur World’ Challenges not yet surmounted, such as the prebiotic route to ribose synthesis and the identity of the cations available in The ‘metabolism first’ or ‘iron-sulphur world’ model was ini- the atmosphere, have led Hud and Cafferty (2013) to postulate tially theorized without recourse to experimental testing. that RNA did not self-assemble but is rather the covalent merger Wächtershäuser conceived the hypothesis that the early steps of at least two different earlier polymers. Indeed it has been pro- towards polymerization and cell formation began in a hot posed that current RNA chemistry evolved from a complex (100 degrees centigrade) and high pressure (several kilometres ‘gemisch’ of nucleotide analogues (Segré and Lancet, 2000). under the sea) iron-sulphur hydrothermal environment, a Perhaps the best clues will continue to be better data on view very different from the warm pond model suggested by Earth’s early environment. For example, computer simulation Darwin. Wächtershäuser proposed that catalytic centres ............................................................................................... .................................................................. 4 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. supported pathways to autocatalytic carbon fixation in a promoting polymerization of amino acids into oligopeptides primitive sulphur-dependent version of the citric acid cycle was demonstrated by Forsyth et al. (2015). The three major (Wächtershäuser, 1990). Wächtershäuser’s theory gained advantages which have emerged from research to date in sup- support after the discovery of sub-ocean hydrothermal vents, port of the hydrothermal fields theory are: (1) the wet–dry and Koonin and Martin proposed a variant on Wächtershäuser’s, cycles allow for increasingly complex interactions; (2) the by which energy is supplied by proton gradients within small confines of the rock pools permit product accumulation and inorganic cavities deep on the ocean floor (Koonin and Martin, (3) light is a potential source of energy, and makes possible a 2005). role for light-absorbing-pigments to power the reactions. MacLeod et al. (1994) have proposed that iron sulphide Such counter-intuitive ideas of life beginning in very hot bubbles containing alkaline emerging from hydrothermal conditions, rather than in the typical temperatures of life vents could have inflated hydrostatically, as witnessed at the today, gained further support through Woese’s research in Lost City hydrothermal vents near the Mid-Atlantic ridge. the 1970s, which identified archaea as a distinct domain, now Schock (1990); Schock, McCollum, Schulte (1998) have con- found in extreme environments which may reflect its origins ducted experiments on the chemical equilibrium of H /CO (Woese, 1967). 2 2 which provides conditions for the synthesis of reduced carbon compounds such as methanogens and acetogens. These are The ‘Polymerization of RNA First’ approach critical given their role in synthesizing adenosine triphosphate with the help of the Wood-Ljungdahl acetyl-CoA pathway of and the ‘RNA World’ CO fixation (Fuchs, 1986). The ‘polymerization of RNA first’ thesis has also attracted Russell and Hall (1997), Russell and Martin (2004) argue many proponents. Oparin in his early model assumed that the that microporous cavities within the hydrothermal vents formation of macromolecules and polymer complexes would could provide the spatial localization necessary to permit follow directly from the spawning of organic molecules on early product accumulation and concentration, both vital for self- Earth. Orgel and others hypothesized that RNA preceded both replication systems to arise. They also suggest that the bases DNA and proteins before the formation of a membrane in the which make up RNA could have functioned as catalysts with development of the first cell, although such compartments need co-factors such as FeS for methyl synthesis, a role subse- not have been mineral in nature (Orgel, 2004; Ralser, 2014). quently played by proteins. Research has followed focusing Deamer and Szostak have shown that proton gradients arise on experiments with a wide variety of inorganic catalysering readily in lipid vesicles (Deamer, 1992; Chen and Szostak, co-factors that could accept electrons in the reduction of CO 2004). The work of Cech and Altman identifying the enzymatic into carbon compounds. property of RNA in the ribozyme triggered Gilbert to see a role for RNA in self-replication (Gilbert, 1986; Westheimer, 1986; Despite the support gathered by the hydrothermal vents the- Cech, 2002). Debates have since centred on: (a) whether RNA ory, the ‘concentration problem’ (never fully resolved by the was preceded by some other nucleic acid easier to polymerize; microporous inorganic cavities model) coupled with the chal- (b) whether RNA or its predecessor could have polymerized in lenges of molecule formation and polymerization occurring in an unenclosed environment and (c) how RNA could spontan- salt water, led to an alternative school of thought gaining trac- eously arise at all (Robertson and Joyce, 2012). tion which locates the site of activity in clay-lined fresh-water pools of volcanic land masses (frequently referred to as hydro- While the hypothesis that cellular life began from an ‘RNA thermal fields) (Deamer and Georgiou, 2015). Whereas the World’ is widely held for key steps in the origins of the cell metabolism theories of the proponents of sub-ocean hydrother- sequence, all experiments have so far failed to mimic the poly- mal vents focus upon a single interface between the solid min- merization of nucleotides to form RNA. Groups like those led eral surface of inorganic cavities and the aqueous ocean, the by Orgel, Eschenmoser, Szostak and others have resorted to hydrothermal field supporters see advantages in more complex experimenting with alternative nucleotides to examine interfaces between atmosphere/water, atmosphere/mineral and whether more reactive molecules could achieve a better per- mineral/water, which can leverage dehydration/rehydration formance without the aid of enzymes. Indeed, as previously (DH–RH) cycles to power molecule formation and polymeriza- mentioned, a school of thought holds that RNA had predeces- tion (Rajamani et al., 2008; Deamer, 2017). sors, and is itself a product of evolution. Experimental designs to test the hydrothermal vent theor- The pre-requisite for polymerized oligonucleotides is that a ies have been hampered by the challenges of simulating high prebiotic stock of random sequence RNAs was available. pressures and temperatures in the laboratory. By contrast, Should one of these be a triple stem-loop structure of some fewer challenges have stood in the way of laboratory simula- 40–60 nucleotides, it might function as a replicase ribozyme, tion of hydrothermal fields, and research to establish the and if this replicase ribozyme is capable of replicating itself impacts of evaporation and precipitation upon the processes with about 90% fidelity, a plausible pathway for RNA evolu- of molecular self-assembly has been more fruitful. For tion might be found (Robertson and Joyce, 2012). Such evi- example, the role of wet–dry cycles at high temperatures in dence, however, is sparse, and it is currently a very optimistic ............................................................................................... .................................................................. 5 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. view that RNA replicase could emerge from a random stock credible evidence therefore that a transition was possible from of oligonucleotides. The question also remains of whether a a PNA to an RNA world. It would require more information replicase could act on sequences similar to itself while ignor- about the compounds available on primitive Earth to deter- ing unrelated sequences. Researchers have attempted to mine whether p-RNA, TNA, GNA, PNA, ANA, tPNA or address these challenges by experimenting with the segrega- some other analogue is the best candidate to precede RNA tion of specific molecules or clonal lines by aligning them (Robertson and Joyce, 2012). along the grains of mineral clay surfaces or on the surface of Despite the many seemingly insuperable obstacles to valid- fatty acid or lipid membranes. For example, Ferris has ating the theory, the ‘RNA World’ school has continued to pointed to a potential role for montmorillonite clay in catalys- attract significant research interest over the years, supported ing the formation of RNA, having demonstrated that artifi- by the likes of Gilbert, Crick, Woese and others. cially activated nucleotides do polymerize on certain clays, a process considered likely to have taken place before lipid The ‘Membranes First’ approach and the membranes, but potentially within inorganic ‘cells’ (Ferris ‘Lipid World’ et al., 1996; Ferris, 2006). Brasier has suggested pumice as being a rival substrate for life (Brasier et al., 2011). Many theories concerning the polymerization of RNA consider Bartel and Szostak (1993) succeeded in evolving an RNA spatial localization to play a key role. The hypothesis that spa- ligase ribozyme from a large population of random sequence tial localization was provided initially by inorganic cavities in RNAs. But pessimists point to the fact that there is no known hydrothermal vents commanded much early attention, but in polymerase ribozyme that can sustain its own replication, and recent years proponents of the ‘membrane first’ school have argue that therefore no such ribozyme is possible (Robertson expanded this hypothesis to include a role for lipid vesicles, and Joyce, 2012). Nevertheless, researchers have demon- shifting the focus to hydrothermal fields as the more likely loca- strated a robust reaction system for RNA-catalysed RNA rep- tion of molecular formation and polymerization. lication using a pair of cross-replicating ligase ribozymes The key factors underpinning the view that the membrane (Lincoln and Joyce, 2009). Rajamani and others showed that came first in the evolution of the protocell include: (a) the unactivated mononucleotides polymerize when dried in the requirement for spatial localization to achieve product accu- presence of a lipid although the conditions cause some loss of mulation and concentration; (b) the benefits for prebiotic the bases (Rajamani et al., 2008; Mungi and Rajamani, non-enzymatic polymerization of monomers trapped within 2015). The solution may once again be that no single oligo- multi-lamellar sandwiches of lipid layers; (c) the potential for nucleotide prevailed in RNA evolution, but rather that RNA rate enhancing chemical reactions enhanced by the presence evolution is the result of a complex interplay of many inter- of certain lipid vesicles referred to by Segré et al. (2001) as dependent oligonucleotides, none of which could function lipozymes (Fendler and Fendler, 1975; Cuccovia, Quina, alone (Kaufman, 1993; Higgs and Lehman, 2015). Even Chaimovich, 1982; Luisi, Walde, Oberholzer, 1999); (d) the assuming such polymerase/ligase activity could have evolved advantages for condensation cycles, involving the loss of independently from cells, there remains the question of how water molecules, of separating molecules by means of a mem- sufficient feedstock would have been available from the start- brane from an aqueous environment; (e) the protection also ing materials abundant on Earth 4 billion years ago. afforded to growing polymers from hydrolysis; (f) the barriers The lack of progress in polymerizing RNA in isolation may to free diffusion of monovalent cations afforded by mem- be evidence that RNA was not the first nucleotide in the form- branes, permitting their capture and use in the catalysis of ation of the cell, and indeed the notion of the ‘RNA World’ polymerization; and (g) the selection advantages that would has been described by Bernhardt as ‘the worst theory of the accrue to protocells that develop machinery for influencing early evolution of life (except for all the others)’ (Bernhardt, transmembrane transport of molecules (Deamer, 2017). 2012). Many candidates have been proposed as alternatives While hydrothermal fields dominate current research into to RNA for the feedstock of oligonucleotide polymerization the role of membranes, not all proponents of the primacy of experiments. Eschenmoser (1999) and others have performed lipid membranes have dismissed a role for hydrothermal studies on an extensive range of nucleic acid analogues. Their vents. Grochmal et al. have postulated that porous fatty acid findings suggested that pyranosyl RNA made a good candi- walls could develop within vent pours which would permit date, given its reaction properties, but this candidacy was absorption of nucleotides and/or peptides and promote non- short-lived given its inability to base pair with RNA enzymatic oligomerisation reactions (Grochmal et al., 2015). (Robertson and Joyce, 2012). Threose nucleotides (TNAs) Lane argues that lipids might have formed within the vent were found to pair with RNA, and the ability for an analogue pours lining them with leaky lipid membranes (Lane, 2012). to base-pair with RNA has since become an important selec- tion criteria. Orgel (1989) and others have worked on peptide Without a membrane, it is difficult to conceive of an nucleic acid (PNA) which has a backbone held together by autonomous cell, and given that amphiphilic lipids automatic- amide bonds, and can transfer information from PNA to ally self-assemble into vesicles when placed in water, it is easy RNA or vice versa in template-directed reactions. There is to imagine them providing a viable membrane to the first ............................................................................................... .................................................................. 6 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. protocells. The first protocell walls were likely porous, com- that early genetics was largely the province of RNA. Szostak posed of simple single-chain fatty acids capable of being both (2012) has divided the ‘RNA World’ into two phases, the first synthesized in the environment and transported to Earth on centring on the prebiotic synthesis of ribonucleotides, and the meteorites. Budin and Szostak have investigated the evolu- second encompassing template-directed replication of RNA tionary importance of lipid membranes in establishing select- molecules within replicating protocells. The Sutherland lab ive advantages. Their theory is that the first RNA machinery helped define ways in which the first phase could have been may have produced phospholipids, which when added to the achieved (Powner, Gerland, Sutherland, 2009), but progress fatty acids in the membrane reduced membrane permeability. on the second phase is much slower and more challenging. For this reason they believe the second stage of RNA evolu- The principle hypothesis currently being tested is that the tion included the development of transmembrane transport second phase involved non-enzymatic RNA replication with machinery (Budin and Szostak, 2011). the implication that the first heritable RNA might have been a metabolic ribozyme that conferred enhanced protocell repro- The earliest protocells will have had very little functionality duction or survival (Szostak, 2011). This is a minimalist of any kind, and instead responded largely passively to environ- approach to reproduction, as it assumes no machinery is put mental influences for their operation. Fatty acid membranes are in place to improve replication, and that the fidelity of replica- highly permeable, which is consistent with a heterotrophic mod- tion may be very poor. el by which chemical building blocks synthesized outside the protocell are diffused passively across the cell membrane to con- Szostak (2012) has defined an eight-fold path to non- tribute to functions that confer selective advantages. Any enzymatic RNA replication in his blueprint for the design of increase in the sophistication of the membrane wall, permitting experimental reconstructions which could prove the efficacy of the cell to retain internally synthesized metabolites, would be chemically driven RNA replication. But despite the neat division dependent upon an increase in the sophistication of the machin- of the challenges into categories, he himself highlights the inter- ery established within the protocell. Szostak (2011) and his col- dependence and interaction between the potential solutions to laborators have shown that selective advantages are given to each challenge, making RNA replication a truly ‘systems chem- fatty acid protocell membranes surrounding RNA as they istry’ problem, in which every aspect of a complex system must absorb fatty acid monomers from other empty membranes or be considered as part and parcel of the whole. micelles. In their most recent work they found that small The principle obstacle non-enzymatic template-directed repli- increases in phospholipid content lead to a cascade of additional cation needs to overcome is the outperformance of strand re- selective pressures for transmembrane transport machinery that annealing relative to non-enzymatic template copying (Jia et al., might be produced by primitive acyltransferase ribozymes. The 2016). The RNA duplex produced by non-enzymatic copying early transporters are thought to have been formed by short must denature to supply templates for subsequent replication, peptides or nucleic acid assemblies (Szostak, 2011). and research has focussed on mechanisms to identify: (a) prop- The development of lipid membranes is highly synergistic erties that would facilitate strand separation and (b) properties with the development of early catalysts such as phospho- and which permit non-enzymatic RNA replication to out-compete acyltransferases, which once established could quickly be re-annealing of the duplex RNA strands. A further challenge is adapted for use in metabolic tasks such as sugar catabolism that functional RNA sequences need to be able to self-replicate and peptide synthesis (Budin and Szostak, 2011). Furthermore, before they degrade. Many in the Szostak lab and elsewhere the increasing phospholipid content of the membrane would have attempted to overcome these challenges, currently without enable the emerging protocell to utilize transmembrane ion gra- material success. Jia et al. (2016) did believe that the solution to dients, the basis for the chemiosmosis vital for metabolism in the re-annealing problem might be found in arginine-rich oligo- all extant cells (Szostak, Bartel, Luisi, 2001). peptides that could function as primers both promoting copying and inhibiting re-annealing, but this thesis was quickly with- drawn (Szostak, 2017). More progress has been made in achiev- Template-directed non-enzymatic ing non-enzymatic copying of RNA templates containing all replication and reproduction four nucleotides (A,C,G,T) through catalysis of activated oligo- The model of the first protocell, in which little machinery is nucleotides (Prywes et al., 2016; Wachowius, Attwater, present and the protocell responds passively to environmental Holliger, 2017). The challenges faced for non-enzymatic replica- influences for its function, sits poorly with a major role being tion of RNA through requirements for high concentrations of 2+ given to template-directed replication and reproduction Mg (or other divalent) ions and their destructive power over (Deamer, 2008), particularly in comparison with the much fatty acid membranes, were resolved when Adamala and more simple role of compositional information contained in Szostak (2013) demonstrated that the presence of citrate could assemblies of amphiphilic molecules (Segré et al., 2001). For inhibit this destructive influence. A possible solution to the evolutionarily selective advantages to be established it is problem of the high melting point of RNA has been suggested essential that protocells be able to divide and pass on their which would imply that the RNA backbone may have con- information and structures to their daughters. While DNA- tained both 2’ and 3’ linkages, which requires less fidelity in coded protein synthesis is now the basis of replication and reproduction (Bernhardt, 2012). It has also been suggested that reproduction, considerable evidence supports the hypothesis the environment played a major role in supporting the ............................................................................................... .................................................................. 7 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. replication process. Varying extremes of temperature would allow for the renewal of individual components. Miller and provide an ideal environment for different steps, with cold Gulbis consider the lack of reproductive capacity renders a environments hosting template copying and hot ones strand simplified protocell unworthy of the label ‘life’ form. Yet at separation and the influx of nutrients and nucleotides (Budin the dawn of the cell’s origins replication may have been and Szostak, 2010). achieved through the interplay between protocells and their environment. While we are still a long way from achieving a successful experimental reconstruction of early RNA replication, prom- The role of the environment in early ising work has been done on both strand separation, and the protocell formation fidelity of the replication process. Recognition that amino acid, nucleic acid and protein extinc- tions may pose one of our biggest challenges to protocell ori- The extinction of proteins and implications gins research brings to the fore the most crucial areas for for their role in the protocell future experiments. The best clues we have currently as to One of the biggest challenges faced in considering the role which organic molecules and proteins played an early role in played by proteins in the emergence of the protocell is the the cell’s origins are to be found in the environment in which high probability that many of them may have been lost due to they evolved. Advances in our knowledge will depend on top selective pressure from environmental changes. The single down approaches, such as molecular phylogeny, and bottom biggest change likely to have caused protein extinction is the up approaches, such as palaeobiochemistry (Fig. 4). Oparin Great Oxidation Event, when Earth moved from a reductive and Miller demonstrated the power of combining theories to an oxidative atmosphere around 2.5 billion years ago about the conditions on Earth 4 billion years ago with experi- (Holland, 2002; Sessions et al., 2009; Shields-Zhou, 2011; ments that mimic those conditions. In the absence of cell- Pufahl and Hiatt, 2012). specific fossils, we must rely upon clues concerning their environment. Such evidence may yet be found under the beds To date, the theory of parsimonious conservation, by which of deep oceans (Russell and Martin, 2004; Keller, Turchyn, evolution occurs with the lowest possible number of changes, Ralser, 2014; Ralser, 2014), or in rock formations under the has had a big influence on consideration of the role played by polar caps. Such sources may also be found in today’s deep proteins in the protocell, partly because of its convenience as a biosphere, in conditions analogous to those found on the pla- hypothesis. The overwhelming challenge posed by rejecting net’s early days. Or the evidence may lie in meteorites, and this theory, and accepting that most if not all primordial pro- samples from other planets. The more light we can cast on the teins are now extinct, is that the ratio of potential proteins to conditions existing on Earth 4 billion years ago, the more known proteins is so large. Even after taking into consideration hope we have of understanding the early steps in life (Fig. 3). the arguments proposed by Chiarabelli and De Lucrezia on the By narrowing down the range of conditions, we may be able one hand, who consider the frequency of stable folds being to find credible candidates for the first nucleotide and peptide likely to reduce the potential number, and Marsh on the other, combinations. These candidates should also, of course, who argues evolution could not have taken place on the basis undergo back-solving analyses from current cells, and this is of an unbiased selection, the number of proteins which could an area where sequencing may be of great assistance. have evolved and then been lost is enormous (Chiarabelli and De Lucrezia, 2007; Marsh, 2013). Rediscovering extinct pro- Current assumptions on the Earth’s early environment are teins, and the enzymatic functions they held, is a formidable focusing our attention on halophilic archaea, which inhabit challenge. Even if we discover potential protein candidates for extreme environments exposed to heat, salt, and highly acidic the cell’s early development, it will be impossible to prove that or alkaline environments (Woese, Kandler, Wheelis, 1990; they either existed or played a role. Caetano-Anollés, Kim, Mittenthal, 2007; Ellis, Bizzoco, Kelley, 2008). Such archaea occupy an environment similar Despite the very great challenges of identifying the proteins to the hydrothermal vents on the ocean floor. Thermoplasma involved in protocell development, our ability to practice and Ferroplasma are archaea lacking cell walls, living in hot experimental reconstruction in the development of proteins acidic soils. They are considered to have parallels with the has advanced by leaps and bounds. Miller and Gulbis have protocell functioning within inorganic walls. The fact that reviewed the growing tool-kit now available to researchers, these organisms can exist in anaerobic conditions, and power including the ability to clone, modify, express, reconstitute themselves with chemical energy from hydrogen protons, sul- and recombine an extensive range of proteins (Miller and phur and iron is considered particularly relevant. Gulbis, 2015). Researchers are also developing technologies that could assist with building protocells de novo. Complex Some of the most promising research conducted recently protocell designs may soon be able to incorporate machinery has examined ways in which protocells might have travelled for product synthesis, energy generation, protein transcrip- from one environment, such as hydrothermal vents under the tion, translation machinery and the capacity for replication. sea, to another, such as trapped clay-lined pools on land. While simpler versions may dispense with replication cap- Ellis, Bizzoco, and Kelley experimented with new techniques acity, they would likely retain template-guided processes that to overcome the challenges facing collection of sufficient ............................................................................................... .................................................................. 8 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. Figure 4. Multi-disciplinary approaches to origins of cellular life research. In their perspective article (2008) Patrick Forterre and Simonetta Gribaldo produced a schematic highlighting the bottom-up and top-down approaches tackling origins of life research and detailing the contribution of different disciplines to the research. Adapted from Forterre and Gribaldo (2008) The origin of modern terrestrial life. Human Frontier Science Program Journal 1(3):156–68. quantities of steam water from hydrothermal vents to exam- Given that viruses depend upon cells for their reproduction, they ine archaea migration. Their success using a novel portable cannot predate cellular life, but current consensus views are that steam collector enabled them to deduce that considerable they emerged simultaneously with cells, and played an important quantities of microbes from such events could disperse over role in their genetic exchange (Filee, Forterre, Laurent, 2003; great distances along with the steam water. This work has Claverie, 2006; Koonin, Senkevich, Dolja, 2006). been very influential in underpinning the hypothesis that pro- Future directions in research tocells supported by hydrogen sulphide contained in deep faults and fractures could populate broader regions of the pla- Future research will build on what has already been tried and net through air-based dispersion (Ellis, Bizzoco, Kelley, tested. The hypotheses which have received most attention will 2008). It forms a vital connection between the contrasting continue to be the focus of activity including the theories that: environments of hydrothermal vents and hydrothermal fields. (a) organic molecules including amino acids may have formed The metabolic variety of archaea gives scope for multiple in a reductive atmosphere; (b) dicarboxylic acids, purines and origins of the cell. The fact that cells may have emerged only pyrimidines may have been delivered to Earth via carbon- 700 million years after the planet was formed is held by many aceous meteorite in-falls; (c) carbon fixation may have occurred to be proof that they evolved ‘as soon as they could’, and sug- in a primitive sulphur-dependent version of the citric acid cycle; gests: (a) an inevitability of life emerging in that environment (d) long chain fatty acids may have formed in ultramaficrocks and (b) life emerging many times rather than once at a unique by a process of serpentinization; (e) organic molecules pro- confluence of events. These insights suggest that in looking at duced in sub-sea hydrothermal vents may have been trans- the conditions of life on Earth 4 billion years ago our search ported to volcanic land masses through clouds of steam; (f) should not be restricted to a single environment or event. nucleotide analogues may have formed either on clay or There is sufficient probability that protocells and their compo- trapped between multi-lamellar sandwiches of lipid layers; (g) nents emerged in multiple environments, i.e. both hydrother- amino acids may have polymerized into oligopeptides through mal vents and hydrothermal fields, and that these early cells DH–RH cycles in hydrothermal fields; (h) selective advantages exchanged genetic material by means of lateral transfer both may have been given to fatty acid membranes which sur- within and between species. Such views challenge a long- rounded nucleotides, particularly in absorbing other fatty acid standing Tree of Life dogma, by which all life stems from a monomers; (i) phospholipids may have been one of the first cat- single root. In its place a ‘web of life’ theory has emerged as alysed products of the protocell acting to limit membrane per- an alternative (McInerney, Cotton, Pisani, 2008; O’Malley, meability; and (j) the emergence of primitive transmembrane Martin, Dupre, 2010). We must face the prospect that the machinery based upon short peptides or nucleic acid assemblies objective of our pursuit is not a single original cell from one may have paved the way to the first chemiosmotic metabolism environment, but multiple original cells from many locations. capable of autotrophic powering of the protocell. The role played by lateral gene transfer in the origin of proto- Future experiments designed to test these and other hypoth- cells is also supported by what we now know about viruses. eses will likely require more resources devoted to recreating the ............................................................................................... .................................................................. 9 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. early environments in which protocells evolved. To date, the Recent advances in mapping the evolution of the first pro- environments used for prebiotic reconstruction experiments tocell have seen us gain an understanding of how organic have been constrained to laboratory conditions recognized as molecules formed prior to cellular life. In the next decade, unconducive for the cultivation of most bacteria. Future experi- advances may be made in explaining more definitively how ments will need not only to mimic the environmental conditions these early organic molecules polymerized. in hydrothermal vents and hydrothermal fields of 4 billion The best support for our account of how cellular life began years ago, but also to link them, in order that the products of may well rest upon our ability to create some level of cellular one may freely migrate to mix with the products of the other. life de novo. From the contemporary standpoint, achievement The extent to which different organisms are interdependent is of this goal still seems distant, but underpinned by the recent frequently underestimated, and in attempting to recreate condi- advances in protein engineering it is possible that more ambi- tions on primitive Earth, it will be beneficial to facilitate some tious, expensive, and interdisciplinary experiments on the one degree of interdependence within the modelled prebiotic hand, and massive whole genome mapping of all extant spe- environment. cies on the other, may bring this goal closer. Ideally the experimental design should be so constructed to A review of the authors sourced in this paper reveals that ensure that the DH–RH cycle and other processes can be 44% are biologists, 40% are geologists, and 16% are chemists. accelerated to achieve results in years rather than millennia. Narrowing this analysis down to more specific disciplines brings To maximize the chances of achieving a successful result, the earth sciences to pole position (17%), followed by biochemistry experimental design should also be constructed in a modular (17%), chemistry (15%), and molecular biology (13%). A hol- fashion to permit many different variants to be processed sim- istic approach to the origins of the cell is by definition a multi- ultaneously as a form of high throughput testing. The moni- disciplinary activity and will continue to be so, as the design of toring mechanism will also ideally be real-time in order to experiments becomes larger and more complex. Only a multi- ensure that positive results in any experiment can be identified disciplinary approach will capture fully the interplay between immediately, and learnings quickly applied to new experi- environment and biosphere, the fossil record and experimental mental designs. reconstruction, the terrestrial and extra-terrestrial sources of Experiments in the future will likely become more multi- information. Only by treating the origins of the cell enquiry as a disciplinary and more costly, potentially requiring infrastruc- ‘systems’ exercise can progress be made on all fronts, and at a ture on the scale of the large Hadron collider at CERN. One speed that will yield results in our lifetime. experimental design might be to reconstruct a slice of the Archaean atmosphere, hermetically sealed from our own, Author biography including both landmass and a portion of reconstructed ocean. The time-frame of such an experiment would necessar- Paul Jowett completed a BSc in Biomedicine at Birkbeck, ily be long, involving many collaborative groups dedicated to University of London, before moving on to the MSc pro- different parts of the evolutionary puzzle. gramme in Genomic Medicine at Barts and the London Despite all the obstacles placed in our way, including the School of Medicine & Dentistry. He originally studied for a possibility of mass extinctions of nucleotides, amino acids, BA in History and Politics at Queen Mary, University of and proteins, we must not lose sight of the forensic nature of London, before researching for a D. Phil in Politics at our investigation into the past: any clues might help. Rather Nuffield College, University of Oxford. He is keen to discover like the work that took place in producing the periodic table, ways in which genomics and proteomics can help shed light our ability to advance knowledge on protocell origins may on the earliest origins of life on Earth. Paul manages the depend upon identifying more precisely the gaps that exist in London office of Roland Berger, a strategy consultancy, and our knowledge. is the author (with Francoise Jowett) of Private Equity: The German Experience, along with four other business and polit- ics books published by Palgrave Macmillan. Conclusion Much work is left to be done to: understand how cellular life Acknowledgements began; achieve an approximation of the protocell’s develop- ment; and establish a theory which is both consistent with the I would like to thank Dr Salvador Tomas of Birkbeck, conditions of Earth’s early environment and with the evolu- University of London for his support and feedback while tionary outcome. The end result will be a hypothesis that will developing and writing this paper. I would also like to very likely be popularized into a new evidence-based myth on thank Professor Jack Szostak of Harvard Medical School, how life began on Earth. The extent to which this hypothesis Professor Gerald Marsh of the Argonne National Laboratory becomes dogma may depend upon what it teaches us about at the University of Chicago, and Geraldine Jowett of King’s cellular life today. College London for feedback on earlier drafts of this paper. ............................................................................................... .................................................................. 10 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. Darwin, C. (1859) The origin of species by means of natural selection, Funding John Murray, London. This research received no specific grant from any funding Deamer, D. W. (1992) Polycyclic aromatic hydrocarbons: primitive pig- agency in the public, commercial or not-for-profit sectors. ment systems in the prebiotic environment, Advances in Space Research: The Official Journal of the Committee on Space Research (COSPAR), 12 (4), 183–189. References Deamer, D. W. (2008) How leaky were primitive cells? Nature, 454, 37–38. Deamer, D. W. and Georgiou, C. D. (2015) Hydrothermal conditions and Adamala, K. and Szostak, J. W. (2013) Nonenzymatic template-directed the origins of cellular life, Astrobiology, 15 (12), 1091–1095. RNA synthesis inside model protocells, Science (New York, N.Y.), 342 (6162), 1098–1180. Deamer, D. W. (2017) The role of lipid membranes in life’s origin, Life (Chicago, IL: 1978), 7 (5), 1–17. Bada, J., (2009) The results of the re-visiting of the Miller-Urey experi- ment were broadcast by the BBC in ‘The spark of life’, a television Ellis, D. G., Bizzoco, R. W. and Kelley, S. T. (2008) Halophilic archaea documentary. BBC 4, 26 August 2009. determined from geothermal steam vent aerosols, Environmental Microbiology, 10 (6), 1582–1590. Bartel, D. P. and Szostak, J. W. (1993) Isolation of new ribozymes from a large pool of random sequences, Science (New York, N.Y.), 261, Engel, M. H., Macko, S. A. and Silfer, J. A. (1990) Carbon isotope compos- 1411–1418. ition of individual amino acids in the Murchison meteorite, Nature, 348, 47–49. Bernath, P. F., McElroy, C. T., Abrams, M. C. et al. (2005) Atmospheric chemistry experiment (ACE): mission overview, Geophysical Eschenmoser, A. (1999) Chemical etiology of nucleic acid structure, Research Letters, 32 (L15S01), 1–5. Science (New York, N.Y.), 284, 2118–2124. Bernhardt, H. S. (2012) The RNA world hypothesis, the worst theory of Fendler, J. D. and Fendler, E. J. (1975) Catalysis in Micellar and the early evolution of life, except for all the rest, Biology Direct,7 Macromolecular Systems, Academic Press, New York. (23), 1–10. Ferris, J. P., Hill, A. R., Liu, R. and Orgel, L. E. (1996) Synthesis of long pre- Brasier, M. D., Green, O. R., Jephcoat, A. P. et al. (2002) Questioning the biotic oligomers on mineral surfaces, Nature, 381, 59–62. evidence for Earth’s oldest fossils, Nature, 416 (6876), 76–81. Ferris, J. P. (2006) Montmorillonite-catalysed formation of RNA oligo- Brasier, M. D., Matthewman, R., McMahon, S. et al. (2011) Pumice as a mers: the possible role of catalysis in the origins of life, remarkable substrate for the origin of life, Astrobiology, 11, Philosophical Transactions of the Royal Society B: Biological Sciences, 725–735. 361 (1474), 1777–1786. Budin, I. and Szostak, J. W. (2010) Expanding roles for diverse physical Filee, J., Forterre, P. and Laurent, J. (2003) The role played by viruses in phenomena during the origin of life, Annual Review of Biophysics, the evolution of their hosts: a view based on informational protein 39, 245–246. phylogenies, Research in Microbiology, 154, 237–243. Budin, I. and Szostak, J. S. (2011) Physical effects underlying the trans- Forsyth, J. G., Yu, S. S., Mamajanov, I. et al. (2015) Ester-mediated amide ition from primitive to modern cell membranes, Proceedings of the bond formation driven by wet-dry cycles: a possible path to poly- National Academy of Sciences, 108 (13), 5249–5254. peptides on the prebiotic Earth, Angewandte Chemie International Edition, 54, 9871–9875. Caetano-Anollés, G., Kim, H. S. and Mittenthal, J. E. (2007) The origin of modern metabolic networks inferred from phylogenomic analysis Forterre, P. and Gribaldo, S. (2008) The origin of modern terrestrial life, of protein architecture, Proceedings of the National Academy of Human Frontier Science Program Journal, 1 (3), 156–168. Science, 104 (22), 9358–9363. Fuchs, G. (1986) CO fixation in acetogenic bacteria: variations on a Chen, I. A. and Szostak, J. W. (2004) Membrane growth can generate a theme, FEMS Microbiology Review, 39, 181–213. transmembrane pH gradient in fatty acid vesicles, PNAS, 101 (21), 7965–7970. Gilbert, W. (1986) The RNA World, Nature, 319, 618. Chiarabelli, C. and De Lucrezia, D. (2007) Question 3: the worlds of the Grochmal, A., Prout, L., Makin-Taylor, R., Prohens, R. and Tomas, S. prebiotic and never born proteins, Origins of Life and Evolution of (2015) Modulation of reactivity in the cavity of liposomes promotes Biospheres, 37, 357–361. the formation of peptide bonds, Journal of the American Chemical Society, 137 (38), 12269–12275. Claverie, J. M., (2006) Virus evolution, from neglect to centre stage, amidst some confusion. Structural & Genomic Information Haldane, J. B. S., (1929) The origin of life. The Rationalist Annual for the Laboratory CNRS-UPR2589 IBSM: 1–10. Year 1929, edited by Charles A Watts: 3–10. Cuccovia, L. M., Quina, F. H. and Chaimovich, H. (1982) A remarkable Higgs,P.G.and Lehman,N.(2015) The RNA World: molecular enhancement of the rate of ester thiolysis by synthetic and amphi- cooperation at the origins of life, Nature Reviews: Genetics,16, phile vesicles, Tetrahedron, 38 (7), 917–920. 7–17. ............................................................................................... .................................................................. 11 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. Holland, H. D. (2002) Volcanic gases, black smokers, and the Great Miller, D. S. and Gulbis, J. M. (2015) Engineering protocells: prospects for Oxidation Event, Geochimica et Cosmochimica Acta, 66 (21), self-assembly and nanoscale production lines, Life (Chicago, Ill: 3811–3826. 1978), 5, 1019–1053. Huang, Y., Wang, Y., Alexandre, M. R., Lee, T., Rose-Petruck, C., Fuller, M. Miller, S. (1953) A production of amino acids under possible primitive and Pizzarello, S. (2005) Molecular and compound-specific isotopic Earth conditions, Science (New York, N.Y.), New Series 117 (3046), characterization of monocarboxylic acids in carbonaceous meteor- 528–529. ites, Geochimica et Cosmochimica Acta, 69, 1073–1084. Mungi, C. V. and Rajamani, S. (2015) Characteristics of RNA-like oligo- Hud, N. V. and Cafferty, B. J. (2013) The origin of RNA and ‘My mers from lipid-assisted non-enzymatic synthesis: implications for Grandfather’s Axe’, Chemistry & Biology, 20, 466–474. origins of informational molecules on early Earth, Life (Chicago, Ill: 1978),5,65–84. Jia, T. Z., Fahrenbach, A. C., Kamat, N. P. et al. (2016) Oligoarinine pep- tides slow strand annealing and assist non-enzymatic RNA replica- O’Malley, M. A., Martin, W. and Dupre, J. (2010) The tree of life: introduc- tion, Nature Chemistry, 8 (10), 915–921. tion to an evolutionary debate, Biology and Philosophy, 25, 441–453. Kaufman, S. A. (1993) The Origins of Order – Self Organisation and Oparin, A. I. (1924) The origin of life. Translation by Anne Synge, pub- Selection Evolution, Oxford University Press, New York, Oxford. lished on-line via valencia.edu. Keller, A. K., Turchyn, A. V. and Ralser, M. (2014) Non-enzymatic glycoly- Orgel, L. E. (1968) Evolution of the genetic apparatus, Journal of sis and pentose phosphate pathway-like reactions in a plausible Molecular Biology, 38 (3), 381–393. Archaean ocean, Molecular Systems Biology, 10 (725), 1–12. Orgel, L. E. (1989) The origin of polynucleotide-directed protein synthe- Koonin, E. V. and Martin, W. (2005) On the origin of genomes and cells sis, Journal of Molecular Evolution, 29 (6), 465–474. within inorganic compartments, Trends in Genetics, 21 (12), Orgel, L. E. (2004) Prebiotic chemistry and the origin of the RNA world, 647–654. Critical Reviews in Biochemistry and Molecular Biology, 39, 99–123. Koonin, E. V., Senkevich, T. G. and Dolja, V. V. (2006) The ancient virus Pereto, J. (2005) Controversies on the origin of life, International world and evolution of cells, Biology Direct, 19, 1–29. Microbiology,8,23–31. Konn, C., Charlou, J. L., Holm, N. G. et al.. (2015) The production of methane, Pizzarello, S., Huang, Y. and Fuller, P. (2004) The carbon isotopic distri- hydrogen, and organic compounds in ultramafic-hosted hydrothermal bution of Murchison amino acids, Geochimica et Cosmochimica vents of the Mid-Atlantic Ridge, Astrobiology, 15 (5), 381–399. Acta, 68, 4963–4969. Lane, N. (2012) Life – inevitable or fluke, New Scientist, 23, 32–37. Powner, M. W., Gerland, B. and Sutherland, J. D. (2009) Synthesis of acti- Lincoln, T. A. and Joyce, G. F. (2009) Self-sustained replication of an vated pyrimidine ribonucleotides in prebiotically plausible condi- RNA enzyme, Science, 323 (5918), 1229–1232. tions, Nature, 459, 239–242. Luisi, P. L., Walde, P. and Oberholzer, T. (1999) Lipid vesicles as possible Prywes, N., Blain, J. C., Del Frate, F. and Szostak, J. W. (2016) Non- intermediates in the origin of life, Current Opinions in Colloid & enzymatic copying of RNA templates containing all four letters is Interface Science,4,33–39. catalysed by activated oligonucleotides, eLIFE, 17756, 1–14. Luisi, P. L. (2014) The Emergence of Life: From Chemical Origins to Pufahl, P. K. and Hiatt, E. E. (2012) Oxygenation of the Earth’s Synthetic Biology, Cambridge University Press, Cambridge, UK. atmosphere-ocean system: a review of physical and chemical sedi- mentologic responses, Marine and Petroleum Geology, 32, 1–20. MacLeod, G., McKeown, C., Hall, A. J. et al.. (1994) Hydrothermal and oceanic pH conditions of possible relevance to the origin of life, Rajamani, S., Vlassov, A, Benner, S et al. (2008) Lipid-assisted synthesis Origins of Life and Evolution of the Biosphere, 24 (1), 19–41. of RNA-like polymers from mononucleotides, Origins of Life & Evolution of Biospheres, 38, 57–74. Marsh, G. (2013) The problem of the ‘prebiotic and never born pro- teins’, International Journal of Astrobiology, 12 (1), 94–98. Ralser, M. (2014) The RNA world and the origin of metabolic enzymes, Biochemical Society Transactions, 42, 985–988. Martins, Z., Botta, O., Fogel, M. L. et al. (2008) Extra-terrestrial nucleo- bases in the Murchison meteorite, Earth and Planetary Science Robertson, M. P. and Joyce, G. F. (2012) The origins of the RNA world, Letters, 270, 130–136. Cold Spring Harbour Perspectives on Biology,4, 1–23. McCollum, C., Ritter, G. and Simoneit, B. R. T. (1999) Lipid synthesis Russell, M. J. and Martin, W. (2004) The rocky roots of the acetyl-CoA under hydrothermal conditions by Fischer-Tropsch-type reactions, pathway, Trends in Biochemical Sciences, 29 (7), 358–363. Origins of Life and Evolution of the Biosphere, 29 (2), 153–166. Russell, M. J. and Hall, A. J. (1997) The emergence of life from iron McInerney, J. O., Cotton, J. A. and Pisani, D. (2008) The prokaryotic tree monosulfide bubbles at submarine hydrothermal redox and of life: past, present… and future? Trends in Ecology and Evolution, pH front, Journal of the Geological Society of London,154, 23 (5), 281. 377–402. ............................................................................................... .................................................................. 12 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. Schock, E. L. (1990) Geochemical constraints on the origin of organic Szostak, J. W. (2012) The eightfold path to non-enzymatic RNA replica- compounds in hydrothermal systems, Origins of Life and Evolution tion, Journal of Systems Chemistry, 3 (2), 1–14. of Biospheres, 20, 331–367. Szostak, J. W., (2017) Unpublished correspondence between Jack Schock, E. L., McCollum, T. and Schulte, M. D. (1998) The emergence of Szostak and Paul Jowett on 9th September 2017. metabolism from within hydrothermal systems, in Wiegel J. and Szostak, J. W., Bartel, D. P. and Luisi, P. L. (2001) Synthesizing life, Adams M.W.W. (eds), Thermophiles: The Keys to Molecular Evolution Nature, 409, 387–390. and the Origins of Life, Taylor & France, London UK, pp. 59–76. Wachowius, F., Attwater, J. and Holliger, P. (2017) Nucleic acids: func- Schopf, J. W. (1978) The evolution of the first cells, Scientific American, tion and potential for abiogenesis, Quarterly Review of Biophysics, 239 (3), 110–138. 50 (e4), 1–37. Schopf,J.W.(1993) Microfossils of the early Archaean apex chert: new evi- Wächtershäuser, G. (1990) Evolution of the first metabolic cycles, dence of the antiquity of life, Science (New York, N.Y.), 260, 640–646. Proceedings of the National Academy of Sciences, 87, 200–204. Schopf, J. W. (2006) The first billion years: when did life emerge? Westheimer, F. H. (1986) Polyribonucleic acids as enzymes, Nature, Elements, 2, 229–233. 319, 534. Segré, D., Ben-Eli, D., Deamer, D. W. and Lancet, D. (2001) The lipid Woese, C. R. (1967) The Genetic Code: The Molecular Basis for Genetic world, Origins of Life and Evolution of the Biosphere, 31, 119–145. Expression, Harper & Row, New York. Segré, D. and Lancet, D. (2000) Composing life, EMBO Reports, 1 (3), 217–222. Woese, C. R., Kandler, O. and Wheelis, M. (1990) Towards a natural sys- Sessions, A. L., Doughty, D. M., Welander, P. V. et al. (2009) The continuing tem of organisms: proposal for the domains Archaea, Bacteria, and puzzle of the Great Oxidation Event, Current Biology, 19 (14), 567–574. Eucarya, Proceedings of the National Academy of Sciences, 87 (12), 4576–4579. Shields-Zhou, G. (2011) Biogeochemistry toxic Cambrian oceans, Nature, 469 (7328), 42–43. Yuen, G., Blair, N., Des Marais, D. J. and Chang, S. (1984) Carbon iso- tope composition of low molecular weight hydrocarbons and Szostak, J. W. (2011) An optimal degree of physical and chemical het- monocarboxylic acids from Murchison meteorite, Nature, 307, erogeneity for the origin of life? Philosophical Transactions of the 252–254. Royal Society B, 366, 2894–2901. ............................................................................................... .................................................................. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioscience Horizons Oxford University Press

Myth and fact in the origins of cellular life on Earth

Loading next page...
 
/lp/oxford-university-press/myth-and-fact-in-the-origins-of-cellular-life-on-earth-ULhWmQJTEX

References (97)

Publisher
Oxford University Press
Copyright
© The Author 2017. Published by Oxford University Press.
eISSN
1754-7431
DOI
10.1093/biohorizons/hzx017
Publisher site
See Article on Publisher Site

Abstract

BioscienceHorizons Volume 10 2017 10.1093/biohorizons/hzx017 ............................................................................................ ..................................................................... Review article Paul Jowett , Richard Rayne and Salvador Tomas Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK *Corresponding author: Thessaly Cottage, Foxcombe Lane, Boars Hill, Oxford OX1 5DH, UK. Tel: +44-1865 321107. Email: paul.jowett@ rolandberger.com Supervisor: Salvador Thomas, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK ............................................................................................ ..................................................................... Research into the origins of the first protocell is of a multidisciplinary nature. It draws evidence from what we know about the Earth’s early atmosphere and environment, and about the most ancient features of the cell’s structure and compos- ition. Such data provides the input for the hypothesis generation and experimental reconstruction necessary to mimic steps in the formation of the first protocell. While research into the origins of the first protocell is condemned to focus upon laboratory experiments, it should be guided by a detailed study of real evidence pertaining to the environment on Earth 4 billion years ago. In this review, we take stock of the research that has been performed to date across the main disciplines of earth sciences, biochemistry, and molecular biology. We seek to identify the progress made in laying down a sequence for the events that led up to the first protocell. We also assess the strengths and weaknesses of the experi- mental designs and suggest some future approaches. While the field has made many important advances, from the ori- ginal Stanley Miller experiment establishing ‘life from chemistry’ products such as amino acids, through to Deamer’s findings on fatty acid membranes and Szostack’s work on lipids, there is still a long and challenging journey ahead to understand how cellular life began. The experiments required to make more rapid progress in the field will likely be more elaborate, costly, and time consuming. Key words: abiogenesis, prebiotic, self-assembly, protocell, evolution, RNA Submitted on 14 November 2016; editorial decision on 6 October 2017 ............................................................................................ ..................................................................... of what constitutes the essentials for cellular life, and track Introduction progress made in mimicking the path by which cells came into existence. We will summarize some of the current theor- While at first sight the task of tracing the origins of primi- ies on how cellular life arose, examine the key experiments tive cellular life on Earth would appear to be the histor- that have yielded the best results to date, and take stock of ian’s domain, the lack of sources forces us to imagine and the current experimental designs and their limitations. then reconstruct the events that could have happened, approaches no historian would employ. The paucity of fos- We will also identify the challenges confronted in improving sil evidence makes it essential to follow the path of hypoth- our theories on the origins of the cell, which include: (1) the pos- esis generation and experimental reconstruction to shed sibility that many of the early nucleic and amino acids shaping light on the origins of the first protocell (see Schopf, 1978, the first protocell became extinct; (2) the obstacles to recon- 1993, 2006, for attempts to gain fossil evidence, Fig. 1 for structing the environment of 4–3.5 billion years ago and (3) the the putative results thereof, and see Brasier et al.,2002 for uncertainty over whether there was one original protocell, the a critique of what has been found). Our theories for how result of a unique sequence of events, or many different proto- life first evolved on Earth must be built upon laboratory cells, that developed spontaneously on many occasions once the research. This paper will review our current understanding appropriate environmental conditions were appropriate. ............................................................................................... .................................................................. © The Author 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. Figure 1. Putative timing of evolution. In his article in 1978, Schopf outlined the major events based on his and colleagues’ assessments of the fossil record and provided tentative estimates of the timing of major events in the evolution of life. P-M-C = Palaeozoic, Mesozoic, Cenozoic. Adapted from Schopf (1978) The evolution of the first cells. Scientific American 239(2):110–38 billion years ago (Fig. 2). Attention has focussed upon four Discussion critical processes: the formation of organic molecules such as amino and nucleic acids, the polymerization of these mole- The essentials for cellular life cules, the formation of membranes, and the development of While popular definitions of life, heavily influenced by metabolic networks for power. Competing theories exist for Darwin, centre on reproduction and the capacity for evolu- how each of these processes evolved, and in what sequence. tion, biologists in recent years have shifted their focus to the While there is a consensus that organic molecules came first, role played by autopoiesis, homoeostasis, cognition, and co- since nucleic and amino acids are the essential building blocks emergence. Autopoiesis is defined as the ability of the cell to of life, views differ over whether metabolism, polymerized replenish and renew itself. Homoeostasis is the ability of the molecules or membranes then followed. cell to maintain key parameters within the set boundaries Darwin originally suggested that life began in a ‘warm little required for function. Cognition implies that the cell is able to pond’ (Darwin, 1859), but it was Oparin in the early 20th sense its own needs within its surroundings. Co-emergence Century who conceived of a model whereby simple molecules, refers to the interplay between the cell and its environment. subjected to chemical reactions, became organic, underwent Current definitions of life as expressed by some biologists further reactions to assemble macromolecules and polymer assume that the cell is more than the sum of its parts: all of the complexes, and harnessed metabolic pathways to forge the cell’s components are dependent upon one another (Luisi, first cell (Oparin, 1924). The ‘life from chemistry’ model was 2014). This observation is particularly pertinent for the a vital first step in the formation of current views on the cell’s chicken-and-egg debate over the sequence of events leading to origins. the self-assembly and self-replication of the constituent com- ponents of the protocell: no self-replication of any cell compo- Both Oparin and Haldane independently hypothesized nent has ever been achieved in isolation, and the alternative that the Earth’s initial atmosphere was reductive, rather than may be that self-replication is impossible on a molecular self- oxidative as it is today and thus more likely to provide the sufficient basis, but rather dependent upon the interplay of metabolic basis for the formation of the organic chemicals disparate molecular assemblies (Segré and Lancet, 2000). essential for life. Oparin defined the term ‘primordial soup’ to describe the Archean ocean in which solar energy and a redu- The early hypotheses on the origins of the cing atmosphere created organic molecules (Oparin, 1924; protocell Haldane, 1929) (Fig. 3). The central hypothesis on the origin of the cell is that organic The debate over the order of the remaining three events molecules self-assembled to form the first protocell some 4 has been lively. Wächtershäuser, a German patent lawyer ............................................................................................... .................................................................. 2 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. Figure 2. Putative process of protocell development. In his review article of 2005, Pereto set out a scheme for a hypothetical transition from prebiotic chemistry to protocells. Pereto chose not to add a timescale to his scheme. Adapted, with key events defined by author, from Pereto (2005) Controversies on the origin of life. International Microbiology 8:23–31 Figure 3. Environmental influences relevant to protocell development. In their review article (2012) Pufahl and Hiatt collated a broad range of sources on environmental change that could impact the biosphere. They stress that the level of oxygenation immediately after the Great Oxidation Event is still largely unknown. Earth oxygenation is divided into three stages in their schema (1,2,3). PAL = present atmospheric levels, MIF = mass-independent fractionation. Adapted from Pufahl and Hiatt (2012) Oxygenation of the Earth’s atmosphere-ocean system: a review of physical and classical sedimentologic responses. Marine and Petroleum Geology 32:1–20 turned evolutionary biologist, argued that metabolism came And finally, Szostak, Deamer, and Luisi have put forward first with his ‘iron-sulphur world’ theory (Wächtershäuser, arguments for membranes being paramount, in part because 1990). Orgel and Gilbert argued equally passionately that the they provide the spatial localization necessary to promote polymerization of RNA took priority, putting the ‘RNA non-enzymatic polymerization (Szostak, Bartel, Luisi, 2001; World’ at the head of the pack (Orgel, 1968; Gilbert 1986). Luisi, 2014; Deamer, 2017). ............................................................................................... .................................................................. 3 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. experiments by Bernath and others using data from a Early experiments on the formation of Canadian satellite mission for sensing of the Earth’s atmos- organic molecules phere suggest that the Earth’s Hadean atmosphere could have The most significant experiment performed to date on the contained up to 40% hydrogen, a figure suggestive of an formation of organic molecules remains that of Miller and environment even more conducive of the formation of pre- Urey in 1952 when they sought to test the hypothesis of biotic organic molecules than the atmosphere used by Miller Oparin and Haldane that the organic building blocks of life in his earlier experiment (Bernath et al., 2005). emerged from a reducing atmosphere (Miller, 1953). Miller Extra-terrestrial influences on supply of filled a flask with the four gaseous elements of the reductive atmosphere: methane, ammonia, hydrogen and water. He organic molecules on Earth then passed electrical discharges through them to simulate Research into the Murchison meteorite, which fell to Earth in lightning. After 125 h of the experiment, using the equipment 1969 in Australia, has stimulated growth in the field of astro- available to him at the time, Miller identified several alpha biology, a field that studies how extra-terrestrial influences amino acids contained within the residues. could have played a role in the origins of life on Earth and Later analyses of the outputs of Miller’s experiment, using elsewhere in the universe. more advanced equipment conducted by Bada, revealed that A wide range of analyses have been made of the organic they included a much broader range of amino acids than had compounds contained in the Murchison meteorite (Yuen originally been detected (Bada, 2009). et al., 1984; Engel, Macko, Silfer, 1990; Pizzarello, Huang, Similar progress has been achieved in identifying paths to the Fuller, 2004; Huang et al., 2005), but perhaps the most com- formation of long chain fatty acids, such as seen in the work of prehensive and conclusive to date is that of a team led by McCollum, Ritter and Simoneit (1999) that used oxidation of Martins which used compound-specific carbon isotope data olivine in ultramaficrockbyaprocessof ‘serpentinization’ to to measure purine and pyrimidine compounds. Martins and reduce water to molecular hydrogen and subsequently combine others found that dicarboxylic acids were the most abundant it with CO via Fischer-Tropsch synthesis under high tempera- class of compounds contained within the Murchison meteor- tures (Segré et al. 2001). Potential examples of this process have ite, and many purines and pyrimidines were also found. The been found in the Rainbow hydrothermal field on the Mid- results for uracil and xanthine showed positive δ C values, Atlantic Ridge (Konn et al., 2015). uracil being abundant in modern biochemistry, while xan- thine is more limited, functioning as an intermediate in the By contrast, progress in explaining the formation of nucleic biosynthesis of guanosine and uric acid (Martins et al., 2008). acids is much less well advanced. Indeed Hud and Cafferty (2013) argue that given the failure of all attempts to mimic an Proponents of extra-terrestrial influences on prebiotic abiotic origin for RNA, they feel the evidence suggests that RNA development point to the carbonaceous meteorite in-falls dur- is the product of molecular ancestors, not their forebear. Hud ing the early Hadean phase of Earth’s history, and suggest and Cafferty base their views on a series of limiting factors influ- that nucleobases delivered together with sugar-related species encing the three distinct molecular units of RNA (the nucleobase, and amino acids may have played a critical role in the found- the ribose sugar, and the phosphate group). To these, they add ing of the RNA world (Engel, Macko, Silfer, 1990; Martins cations and solvent molecules as additional vital components. et al., 2008). The chemical building blocks for the ‘life from Each component faces severe abiotic challenges. Researchers chemistry’ thesis could have been formed on Earth, on extra- have grappled with the problem of how activated pyrimidine terrestrial planets and meteorites, or from a combination of ribonucleotides could have synthesized in prebiotically plausible the two. There are few current clues as to which source came conditions, most notably through the work of Powner, Gerland, ‘first’ or played the dominant role. What is remarkable, how- and Sutherland (Powner, Gerland, Sutherland, 2009). Powner ever, is that support for the ‘life from chemistry’ thesis is not et al. considered the formation of ribonucleotides from their con- restricted to Earth, giving first insights into the potential for stituent parts too difficult to replicate and advanced an alterna- life based on common building blocks beyond our planet. tive theory, validated by experiments, that ribonucleotides could undergo synthesis in a process that bypassed ribose. The ‘Metabolism First’ approach and the ‘Iron-Sulphur World’ Challenges not yet surmounted, such as the prebiotic route to ribose synthesis and the identity of the cations available in The ‘metabolism first’ or ‘iron-sulphur world’ model was ini- the atmosphere, have led Hud and Cafferty (2013) to postulate tially theorized without recourse to experimental testing. that RNA did not self-assemble but is rather the covalent merger Wächtershäuser conceived the hypothesis that the early steps of at least two different earlier polymers. Indeed it has been pro- towards polymerization and cell formation began in a hot posed that current RNA chemistry evolved from a complex (100 degrees centigrade) and high pressure (several kilometres ‘gemisch’ of nucleotide analogues (Segré and Lancet, 2000). under the sea) iron-sulphur hydrothermal environment, a Perhaps the best clues will continue to be better data on view very different from the warm pond model suggested by Earth’s early environment. For example, computer simulation Darwin. Wächtershäuser proposed that catalytic centres ............................................................................................... .................................................................. 4 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. supported pathways to autocatalytic carbon fixation in a promoting polymerization of amino acids into oligopeptides primitive sulphur-dependent version of the citric acid cycle was demonstrated by Forsyth et al. (2015). The three major (Wächtershäuser, 1990). Wächtershäuser’s theory gained advantages which have emerged from research to date in sup- support after the discovery of sub-ocean hydrothermal vents, port of the hydrothermal fields theory are: (1) the wet–dry and Koonin and Martin proposed a variant on Wächtershäuser’s, cycles allow for increasingly complex interactions; (2) the by which energy is supplied by proton gradients within small confines of the rock pools permit product accumulation and inorganic cavities deep on the ocean floor (Koonin and Martin, (3) light is a potential source of energy, and makes possible a 2005). role for light-absorbing-pigments to power the reactions. MacLeod et al. (1994) have proposed that iron sulphide Such counter-intuitive ideas of life beginning in very hot bubbles containing alkaline emerging from hydrothermal conditions, rather than in the typical temperatures of life vents could have inflated hydrostatically, as witnessed at the today, gained further support through Woese’s research in Lost City hydrothermal vents near the Mid-Atlantic ridge. the 1970s, which identified archaea as a distinct domain, now Schock (1990); Schock, McCollum, Schulte (1998) have con- found in extreme environments which may reflect its origins ducted experiments on the chemical equilibrium of H /CO (Woese, 1967). 2 2 which provides conditions for the synthesis of reduced carbon compounds such as methanogens and acetogens. These are The ‘Polymerization of RNA First’ approach critical given their role in synthesizing adenosine triphosphate with the help of the Wood-Ljungdahl acetyl-CoA pathway of and the ‘RNA World’ CO fixation (Fuchs, 1986). The ‘polymerization of RNA first’ thesis has also attracted Russell and Hall (1997), Russell and Martin (2004) argue many proponents. Oparin in his early model assumed that the that microporous cavities within the hydrothermal vents formation of macromolecules and polymer complexes would could provide the spatial localization necessary to permit follow directly from the spawning of organic molecules on early product accumulation and concentration, both vital for self- Earth. Orgel and others hypothesized that RNA preceded both replication systems to arise. They also suggest that the bases DNA and proteins before the formation of a membrane in the which make up RNA could have functioned as catalysts with development of the first cell, although such compartments need co-factors such as FeS for methyl synthesis, a role subse- not have been mineral in nature (Orgel, 2004; Ralser, 2014). quently played by proteins. Research has followed focusing Deamer and Szostak have shown that proton gradients arise on experiments with a wide variety of inorganic catalysering readily in lipid vesicles (Deamer, 1992; Chen and Szostak, co-factors that could accept electrons in the reduction of CO 2004). The work of Cech and Altman identifying the enzymatic into carbon compounds. property of RNA in the ribozyme triggered Gilbert to see a role for RNA in self-replication (Gilbert, 1986; Westheimer, 1986; Despite the support gathered by the hydrothermal vents the- Cech, 2002). Debates have since centred on: (a) whether RNA ory, the ‘concentration problem’ (never fully resolved by the was preceded by some other nucleic acid easier to polymerize; microporous inorganic cavities model) coupled with the chal- (b) whether RNA or its predecessor could have polymerized in lenges of molecule formation and polymerization occurring in an unenclosed environment and (c) how RNA could spontan- salt water, led to an alternative school of thought gaining trac- eously arise at all (Robertson and Joyce, 2012). tion which locates the site of activity in clay-lined fresh-water pools of volcanic land masses (frequently referred to as hydro- While the hypothesis that cellular life began from an ‘RNA thermal fields) (Deamer and Georgiou, 2015). Whereas the World’ is widely held for key steps in the origins of the cell metabolism theories of the proponents of sub-ocean hydrother- sequence, all experiments have so far failed to mimic the poly- mal vents focus upon a single interface between the solid min- merization of nucleotides to form RNA. Groups like those led eral surface of inorganic cavities and the aqueous ocean, the by Orgel, Eschenmoser, Szostak and others have resorted to hydrothermal field supporters see advantages in more complex experimenting with alternative nucleotides to examine interfaces between atmosphere/water, atmosphere/mineral and whether more reactive molecules could achieve a better per- mineral/water, which can leverage dehydration/rehydration formance without the aid of enzymes. Indeed, as previously (DH–RH) cycles to power molecule formation and polymeriza- mentioned, a school of thought holds that RNA had predeces- tion (Rajamani et al., 2008; Deamer, 2017). sors, and is itself a product of evolution. Experimental designs to test the hydrothermal vent theor- The pre-requisite for polymerized oligonucleotides is that a ies have been hampered by the challenges of simulating high prebiotic stock of random sequence RNAs was available. pressures and temperatures in the laboratory. By contrast, Should one of these be a triple stem-loop structure of some fewer challenges have stood in the way of laboratory simula- 40–60 nucleotides, it might function as a replicase ribozyme, tion of hydrothermal fields, and research to establish the and if this replicase ribozyme is capable of replicating itself impacts of evaporation and precipitation upon the processes with about 90% fidelity, a plausible pathway for RNA evolu- of molecular self-assembly has been more fruitful. For tion might be found (Robertson and Joyce, 2012). Such evi- example, the role of wet–dry cycles at high temperatures in dence, however, is sparse, and it is currently a very optimistic ............................................................................................... .................................................................. 5 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. view that RNA replicase could emerge from a random stock credible evidence therefore that a transition was possible from of oligonucleotides. The question also remains of whether a a PNA to an RNA world. It would require more information replicase could act on sequences similar to itself while ignor- about the compounds available on primitive Earth to deter- ing unrelated sequences. Researchers have attempted to mine whether p-RNA, TNA, GNA, PNA, ANA, tPNA or address these challenges by experimenting with the segrega- some other analogue is the best candidate to precede RNA tion of specific molecules or clonal lines by aligning them (Robertson and Joyce, 2012). along the grains of mineral clay surfaces or on the surface of Despite the many seemingly insuperable obstacles to valid- fatty acid or lipid membranes. For example, Ferris has ating the theory, the ‘RNA World’ school has continued to pointed to a potential role for montmorillonite clay in catalys- attract significant research interest over the years, supported ing the formation of RNA, having demonstrated that artifi- by the likes of Gilbert, Crick, Woese and others. cially activated nucleotides do polymerize on certain clays, a process considered likely to have taken place before lipid The ‘Membranes First’ approach and the membranes, but potentially within inorganic ‘cells’ (Ferris ‘Lipid World’ et al., 1996; Ferris, 2006). Brasier has suggested pumice as being a rival substrate for life (Brasier et al., 2011). Many theories concerning the polymerization of RNA consider Bartel and Szostak (1993) succeeded in evolving an RNA spatial localization to play a key role. The hypothesis that spa- ligase ribozyme from a large population of random sequence tial localization was provided initially by inorganic cavities in RNAs. But pessimists point to the fact that there is no known hydrothermal vents commanded much early attention, but in polymerase ribozyme that can sustain its own replication, and recent years proponents of the ‘membrane first’ school have argue that therefore no such ribozyme is possible (Robertson expanded this hypothesis to include a role for lipid vesicles, and Joyce, 2012). Nevertheless, researchers have demon- shifting the focus to hydrothermal fields as the more likely loca- strated a robust reaction system for RNA-catalysed RNA rep- tion of molecular formation and polymerization. lication using a pair of cross-replicating ligase ribozymes The key factors underpinning the view that the membrane (Lincoln and Joyce, 2009). Rajamani and others showed that came first in the evolution of the protocell include: (a) the unactivated mononucleotides polymerize when dried in the requirement for spatial localization to achieve product accu- presence of a lipid although the conditions cause some loss of mulation and concentration; (b) the benefits for prebiotic the bases (Rajamani et al., 2008; Mungi and Rajamani, non-enzymatic polymerization of monomers trapped within 2015). The solution may once again be that no single oligo- multi-lamellar sandwiches of lipid layers; (c) the potential for nucleotide prevailed in RNA evolution, but rather that RNA rate enhancing chemical reactions enhanced by the presence evolution is the result of a complex interplay of many inter- of certain lipid vesicles referred to by Segré et al. (2001) as dependent oligonucleotides, none of which could function lipozymes (Fendler and Fendler, 1975; Cuccovia, Quina, alone (Kaufman, 1993; Higgs and Lehman, 2015). Even Chaimovich, 1982; Luisi, Walde, Oberholzer, 1999); (d) the assuming such polymerase/ligase activity could have evolved advantages for condensation cycles, involving the loss of independently from cells, there remains the question of how water molecules, of separating molecules by means of a mem- sufficient feedstock would have been available from the start- brane from an aqueous environment; (e) the protection also ing materials abundant on Earth 4 billion years ago. afforded to growing polymers from hydrolysis; (f) the barriers The lack of progress in polymerizing RNA in isolation may to free diffusion of monovalent cations afforded by mem- be evidence that RNA was not the first nucleotide in the form- branes, permitting their capture and use in the catalysis of ation of the cell, and indeed the notion of the ‘RNA World’ polymerization; and (g) the selection advantages that would has been described by Bernhardt as ‘the worst theory of the accrue to protocells that develop machinery for influencing early evolution of life (except for all the others)’ (Bernhardt, transmembrane transport of molecules (Deamer, 2017). 2012). Many candidates have been proposed as alternatives While hydrothermal fields dominate current research into to RNA for the feedstock of oligonucleotide polymerization the role of membranes, not all proponents of the primacy of experiments. Eschenmoser (1999) and others have performed lipid membranes have dismissed a role for hydrothermal studies on an extensive range of nucleic acid analogues. Their vents. Grochmal et al. have postulated that porous fatty acid findings suggested that pyranosyl RNA made a good candi- walls could develop within vent pours which would permit date, given its reaction properties, but this candidacy was absorption of nucleotides and/or peptides and promote non- short-lived given its inability to base pair with RNA enzymatic oligomerisation reactions (Grochmal et al., 2015). (Robertson and Joyce, 2012). Threose nucleotides (TNAs) Lane argues that lipids might have formed within the vent were found to pair with RNA, and the ability for an analogue pours lining them with leaky lipid membranes (Lane, 2012). to base-pair with RNA has since become an important selec- tion criteria. Orgel (1989) and others have worked on peptide Without a membrane, it is difficult to conceive of an nucleic acid (PNA) which has a backbone held together by autonomous cell, and given that amphiphilic lipids automatic- amide bonds, and can transfer information from PNA to ally self-assemble into vesicles when placed in water, it is easy RNA or vice versa in template-directed reactions. There is to imagine them providing a viable membrane to the first ............................................................................................... .................................................................. 6 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. protocells. The first protocell walls were likely porous, com- that early genetics was largely the province of RNA. Szostak posed of simple single-chain fatty acids capable of being both (2012) has divided the ‘RNA World’ into two phases, the first synthesized in the environment and transported to Earth on centring on the prebiotic synthesis of ribonucleotides, and the meteorites. Budin and Szostak have investigated the evolu- second encompassing template-directed replication of RNA tionary importance of lipid membranes in establishing select- molecules within replicating protocells. The Sutherland lab ive advantages. Their theory is that the first RNA machinery helped define ways in which the first phase could have been may have produced phospholipids, which when added to the achieved (Powner, Gerland, Sutherland, 2009), but progress fatty acids in the membrane reduced membrane permeability. on the second phase is much slower and more challenging. For this reason they believe the second stage of RNA evolu- The principle hypothesis currently being tested is that the tion included the development of transmembrane transport second phase involved non-enzymatic RNA replication with machinery (Budin and Szostak, 2011). the implication that the first heritable RNA might have been a metabolic ribozyme that conferred enhanced protocell repro- The earliest protocells will have had very little functionality duction or survival (Szostak, 2011). This is a minimalist of any kind, and instead responded largely passively to environ- approach to reproduction, as it assumes no machinery is put mental influences for their operation. Fatty acid membranes are in place to improve replication, and that the fidelity of replica- highly permeable, which is consistent with a heterotrophic mod- tion may be very poor. el by which chemical building blocks synthesized outside the protocell are diffused passively across the cell membrane to con- Szostak (2012) has defined an eight-fold path to non- tribute to functions that confer selective advantages. Any enzymatic RNA replication in his blueprint for the design of increase in the sophistication of the membrane wall, permitting experimental reconstructions which could prove the efficacy of the cell to retain internally synthesized metabolites, would be chemically driven RNA replication. But despite the neat division dependent upon an increase in the sophistication of the machin- of the challenges into categories, he himself highlights the inter- ery established within the protocell. Szostak (2011) and his col- dependence and interaction between the potential solutions to laborators have shown that selective advantages are given to each challenge, making RNA replication a truly ‘systems chem- fatty acid protocell membranes surrounding RNA as they istry’ problem, in which every aspect of a complex system must absorb fatty acid monomers from other empty membranes or be considered as part and parcel of the whole. micelles. In their most recent work they found that small The principle obstacle non-enzymatic template-directed repli- increases in phospholipid content lead to a cascade of additional cation needs to overcome is the outperformance of strand re- selective pressures for transmembrane transport machinery that annealing relative to non-enzymatic template copying (Jia et al., might be produced by primitive acyltransferase ribozymes. The 2016). The RNA duplex produced by non-enzymatic copying early transporters are thought to have been formed by short must denature to supply templates for subsequent replication, peptides or nucleic acid assemblies (Szostak, 2011). and research has focussed on mechanisms to identify: (a) prop- The development of lipid membranes is highly synergistic erties that would facilitate strand separation and (b) properties with the development of early catalysts such as phospho- and which permit non-enzymatic RNA replication to out-compete acyltransferases, which once established could quickly be re-annealing of the duplex RNA strands. A further challenge is adapted for use in metabolic tasks such as sugar catabolism that functional RNA sequences need to be able to self-replicate and peptide synthesis (Budin and Szostak, 2011). Furthermore, before they degrade. Many in the Szostak lab and elsewhere the increasing phospholipid content of the membrane would have attempted to overcome these challenges, currently without enable the emerging protocell to utilize transmembrane ion gra- material success. Jia et al. (2016) did believe that the solution to dients, the basis for the chemiosmosis vital for metabolism in the re-annealing problem might be found in arginine-rich oligo- all extant cells (Szostak, Bartel, Luisi, 2001). peptides that could function as primers both promoting copying and inhibiting re-annealing, but this thesis was quickly with- drawn (Szostak, 2017). More progress has been made in achiev- Template-directed non-enzymatic ing non-enzymatic copying of RNA templates containing all replication and reproduction four nucleotides (A,C,G,T) through catalysis of activated oligo- The model of the first protocell, in which little machinery is nucleotides (Prywes et al., 2016; Wachowius, Attwater, present and the protocell responds passively to environmental Holliger, 2017). The challenges faced for non-enzymatic replica- influences for its function, sits poorly with a major role being tion of RNA through requirements for high concentrations of 2+ given to template-directed replication and reproduction Mg (or other divalent) ions and their destructive power over (Deamer, 2008), particularly in comparison with the much fatty acid membranes, were resolved when Adamala and more simple role of compositional information contained in Szostak (2013) demonstrated that the presence of citrate could assemblies of amphiphilic molecules (Segré et al., 2001). For inhibit this destructive influence. A possible solution to the evolutionarily selective advantages to be established it is problem of the high melting point of RNA has been suggested essential that protocells be able to divide and pass on their which would imply that the RNA backbone may have con- information and structures to their daughters. While DNA- tained both 2’ and 3’ linkages, which requires less fidelity in coded protein synthesis is now the basis of replication and reproduction (Bernhardt, 2012). It has also been suggested that reproduction, considerable evidence supports the hypothesis the environment played a major role in supporting the ............................................................................................... .................................................................. 7 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. replication process. Varying extremes of temperature would allow for the renewal of individual components. Miller and provide an ideal environment for different steps, with cold Gulbis consider the lack of reproductive capacity renders a environments hosting template copying and hot ones strand simplified protocell unworthy of the label ‘life’ form. Yet at separation and the influx of nutrients and nucleotides (Budin the dawn of the cell’s origins replication may have been and Szostak, 2010). achieved through the interplay between protocells and their environment. While we are still a long way from achieving a successful experimental reconstruction of early RNA replication, prom- The role of the environment in early ising work has been done on both strand separation, and the protocell formation fidelity of the replication process. Recognition that amino acid, nucleic acid and protein extinc- tions may pose one of our biggest challenges to protocell ori- The extinction of proteins and implications gins research brings to the fore the most crucial areas for for their role in the protocell future experiments. The best clues we have currently as to One of the biggest challenges faced in considering the role which organic molecules and proteins played an early role in played by proteins in the emergence of the protocell is the the cell’s origins are to be found in the environment in which high probability that many of them may have been lost due to they evolved. Advances in our knowledge will depend on top selective pressure from environmental changes. The single down approaches, such as molecular phylogeny, and bottom biggest change likely to have caused protein extinction is the up approaches, such as palaeobiochemistry (Fig. 4). Oparin Great Oxidation Event, when Earth moved from a reductive and Miller demonstrated the power of combining theories to an oxidative atmosphere around 2.5 billion years ago about the conditions on Earth 4 billion years ago with experi- (Holland, 2002; Sessions et al., 2009; Shields-Zhou, 2011; ments that mimic those conditions. In the absence of cell- Pufahl and Hiatt, 2012). specific fossils, we must rely upon clues concerning their environment. Such evidence may yet be found under the beds To date, the theory of parsimonious conservation, by which of deep oceans (Russell and Martin, 2004; Keller, Turchyn, evolution occurs with the lowest possible number of changes, Ralser, 2014; Ralser, 2014), or in rock formations under the has had a big influence on consideration of the role played by polar caps. Such sources may also be found in today’s deep proteins in the protocell, partly because of its convenience as a biosphere, in conditions analogous to those found on the pla- hypothesis. The overwhelming challenge posed by rejecting net’s early days. Or the evidence may lie in meteorites, and this theory, and accepting that most if not all primordial pro- samples from other planets. The more light we can cast on the teins are now extinct, is that the ratio of potential proteins to conditions existing on Earth 4 billion years ago, the more known proteins is so large. Even after taking into consideration hope we have of understanding the early steps in life (Fig. 3). the arguments proposed by Chiarabelli and De Lucrezia on the By narrowing down the range of conditions, we may be able one hand, who consider the frequency of stable folds being to find credible candidates for the first nucleotide and peptide likely to reduce the potential number, and Marsh on the other, combinations. These candidates should also, of course, who argues evolution could not have taken place on the basis undergo back-solving analyses from current cells, and this is of an unbiased selection, the number of proteins which could an area where sequencing may be of great assistance. have evolved and then been lost is enormous (Chiarabelli and De Lucrezia, 2007; Marsh, 2013). Rediscovering extinct pro- Current assumptions on the Earth’s early environment are teins, and the enzymatic functions they held, is a formidable focusing our attention on halophilic archaea, which inhabit challenge. Even if we discover potential protein candidates for extreme environments exposed to heat, salt, and highly acidic the cell’s early development, it will be impossible to prove that or alkaline environments (Woese, Kandler, Wheelis, 1990; they either existed or played a role. Caetano-Anollés, Kim, Mittenthal, 2007; Ellis, Bizzoco, Kelley, 2008). Such archaea occupy an environment similar Despite the very great challenges of identifying the proteins to the hydrothermal vents on the ocean floor. Thermoplasma involved in protocell development, our ability to practice and Ferroplasma are archaea lacking cell walls, living in hot experimental reconstruction in the development of proteins acidic soils. They are considered to have parallels with the has advanced by leaps and bounds. Miller and Gulbis have protocell functioning within inorganic walls. The fact that reviewed the growing tool-kit now available to researchers, these organisms can exist in anaerobic conditions, and power including the ability to clone, modify, express, reconstitute themselves with chemical energy from hydrogen protons, sul- and recombine an extensive range of proteins (Miller and phur and iron is considered particularly relevant. Gulbis, 2015). Researchers are also developing technologies that could assist with building protocells de novo. Complex Some of the most promising research conducted recently protocell designs may soon be able to incorporate machinery has examined ways in which protocells might have travelled for product synthesis, energy generation, protein transcrip- from one environment, such as hydrothermal vents under the tion, translation machinery and the capacity for replication. sea, to another, such as trapped clay-lined pools on land. While simpler versions may dispense with replication cap- Ellis, Bizzoco, and Kelley experimented with new techniques acity, they would likely retain template-guided processes that to overcome the challenges facing collection of sufficient ............................................................................................... .................................................................. 8 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. Figure 4. Multi-disciplinary approaches to origins of cellular life research. In their perspective article (2008) Patrick Forterre and Simonetta Gribaldo produced a schematic highlighting the bottom-up and top-down approaches tackling origins of life research and detailing the contribution of different disciplines to the research. Adapted from Forterre and Gribaldo (2008) The origin of modern terrestrial life. Human Frontier Science Program Journal 1(3):156–68. quantities of steam water from hydrothermal vents to exam- Given that viruses depend upon cells for their reproduction, they ine archaea migration. Their success using a novel portable cannot predate cellular life, but current consensus views are that steam collector enabled them to deduce that considerable they emerged simultaneously with cells, and played an important quantities of microbes from such events could disperse over role in their genetic exchange (Filee, Forterre, Laurent, 2003; great distances along with the steam water. This work has Claverie, 2006; Koonin, Senkevich, Dolja, 2006). been very influential in underpinning the hypothesis that pro- Future directions in research tocells supported by hydrogen sulphide contained in deep faults and fractures could populate broader regions of the pla- Future research will build on what has already been tried and net through air-based dispersion (Ellis, Bizzoco, Kelley, tested. The hypotheses which have received most attention will 2008). It forms a vital connection between the contrasting continue to be the focus of activity including the theories that: environments of hydrothermal vents and hydrothermal fields. (a) organic molecules including amino acids may have formed The metabolic variety of archaea gives scope for multiple in a reductive atmosphere; (b) dicarboxylic acids, purines and origins of the cell. The fact that cells may have emerged only pyrimidines may have been delivered to Earth via carbon- 700 million years after the planet was formed is held by many aceous meteorite in-falls; (c) carbon fixation may have occurred to be proof that they evolved ‘as soon as they could’, and sug- in a primitive sulphur-dependent version of the citric acid cycle; gests: (a) an inevitability of life emerging in that environment (d) long chain fatty acids may have formed in ultramaficrocks and (b) life emerging many times rather than once at a unique by a process of serpentinization; (e) organic molecules pro- confluence of events. These insights suggest that in looking at duced in sub-sea hydrothermal vents may have been trans- the conditions of life on Earth 4 billion years ago our search ported to volcanic land masses through clouds of steam; (f) should not be restricted to a single environment or event. nucleotide analogues may have formed either on clay or There is sufficient probability that protocells and their compo- trapped between multi-lamellar sandwiches of lipid layers; (g) nents emerged in multiple environments, i.e. both hydrother- amino acids may have polymerized into oligopeptides through mal vents and hydrothermal fields, and that these early cells DH–RH cycles in hydrothermal fields; (h) selective advantages exchanged genetic material by means of lateral transfer both may have been given to fatty acid membranes which sur- within and between species. Such views challenge a long- rounded nucleotides, particularly in absorbing other fatty acid standing Tree of Life dogma, by which all life stems from a monomers; (i) phospholipids may have been one of the first cat- single root. In its place a ‘web of life’ theory has emerged as alysed products of the protocell acting to limit membrane per- an alternative (McInerney, Cotton, Pisani, 2008; O’Malley, meability; and (j) the emergence of primitive transmembrane Martin, Dupre, 2010). We must face the prospect that the machinery based upon short peptides or nucleic acid assemblies objective of our pursuit is not a single original cell from one may have paved the way to the first chemiosmotic metabolism environment, but multiple original cells from many locations. capable of autotrophic powering of the protocell. The role played by lateral gene transfer in the origin of proto- Future experiments designed to test these and other hypoth- cells is also supported by what we now know about viruses. eses will likely require more resources devoted to recreating the ............................................................................................... .................................................................. 9 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. early environments in which protocells evolved. To date, the Recent advances in mapping the evolution of the first pro- environments used for prebiotic reconstruction experiments tocell have seen us gain an understanding of how organic have been constrained to laboratory conditions recognized as molecules formed prior to cellular life. In the next decade, unconducive for the cultivation of most bacteria. Future experi- advances may be made in explaining more definitively how ments will need not only to mimic the environmental conditions these early organic molecules polymerized. in hydrothermal vents and hydrothermal fields of 4 billion The best support for our account of how cellular life began years ago, but also to link them, in order that the products of may well rest upon our ability to create some level of cellular one may freely migrate to mix with the products of the other. life de novo. From the contemporary standpoint, achievement The extent to which different organisms are interdependent is of this goal still seems distant, but underpinned by the recent frequently underestimated, and in attempting to recreate condi- advances in protein engineering it is possible that more ambi- tions on primitive Earth, it will be beneficial to facilitate some tious, expensive, and interdisciplinary experiments on the one degree of interdependence within the modelled prebiotic hand, and massive whole genome mapping of all extant spe- environment. cies on the other, may bring this goal closer. Ideally the experimental design should be so constructed to A review of the authors sourced in this paper reveals that ensure that the DH–RH cycle and other processes can be 44% are biologists, 40% are geologists, and 16% are chemists. accelerated to achieve results in years rather than millennia. Narrowing this analysis down to more specific disciplines brings To maximize the chances of achieving a successful result, the earth sciences to pole position (17%), followed by biochemistry experimental design should also be constructed in a modular (17%), chemistry (15%), and molecular biology (13%). A hol- fashion to permit many different variants to be processed sim- istic approach to the origins of the cell is by definition a multi- ultaneously as a form of high throughput testing. The moni- disciplinary activity and will continue to be so, as the design of toring mechanism will also ideally be real-time in order to experiments becomes larger and more complex. Only a multi- ensure that positive results in any experiment can be identified disciplinary approach will capture fully the interplay between immediately, and learnings quickly applied to new experi- environment and biosphere, the fossil record and experimental mental designs. reconstruction, the terrestrial and extra-terrestrial sources of Experiments in the future will likely become more multi- information. Only by treating the origins of the cell enquiry as a disciplinary and more costly, potentially requiring infrastruc- ‘systems’ exercise can progress be made on all fronts, and at a ture on the scale of the large Hadron collider at CERN. One speed that will yield results in our lifetime. experimental design might be to reconstruct a slice of the Archaean atmosphere, hermetically sealed from our own, Author biography including both landmass and a portion of reconstructed ocean. The time-frame of such an experiment would necessar- Paul Jowett completed a BSc in Biomedicine at Birkbeck, ily be long, involving many collaborative groups dedicated to University of London, before moving on to the MSc pro- different parts of the evolutionary puzzle. gramme in Genomic Medicine at Barts and the London Despite all the obstacles placed in our way, including the School of Medicine & Dentistry. He originally studied for a possibility of mass extinctions of nucleotides, amino acids, BA in History and Politics at Queen Mary, University of and proteins, we must not lose sight of the forensic nature of London, before researching for a D. Phil in Politics at our investigation into the past: any clues might help. Rather Nuffield College, University of Oxford. He is keen to discover like the work that took place in producing the periodic table, ways in which genomics and proteomics can help shed light our ability to advance knowledge on protocell origins may on the earliest origins of life on Earth. Paul manages the depend upon identifying more precisely the gaps that exist in London office of Roland Berger, a strategy consultancy, and our knowledge. is the author (with Francoise Jowett) of Private Equity: The German Experience, along with four other business and polit- ics books published by Palgrave Macmillan. Conclusion Much work is left to be done to: understand how cellular life Acknowledgements began; achieve an approximation of the protocell’s develop- ment; and establish a theory which is both consistent with the I would like to thank Dr Salvador Tomas of Birkbeck, conditions of Earth’s early environment and with the evolu- University of London for his support and feedback while tionary outcome. The end result will be a hypothesis that will developing and writing this paper. I would also like to very likely be popularized into a new evidence-based myth on thank Professor Jack Szostak of Harvard Medical School, how life began on Earth. The extent to which this hypothesis Professor Gerald Marsh of the Argonne National Laboratory becomes dogma may depend upon what it teaches us about at the University of Chicago, and Geraldine Jowett of King’s cellular life today. College London for feedback on earlier drafts of this paper. ............................................................................................... .................................................................. 10 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. Darwin, C. (1859) The origin of species by means of natural selection, Funding John Murray, London. This research received no specific grant from any funding Deamer, D. W. (1992) Polycyclic aromatic hydrocarbons: primitive pig- agency in the public, commercial or not-for-profit sectors. ment systems in the prebiotic environment, Advances in Space Research: The Official Journal of the Committee on Space Research (COSPAR), 12 (4), 183–189. References Deamer, D. W. (2008) How leaky were primitive cells? Nature, 454, 37–38. Deamer, D. W. and Georgiou, C. D. (2015) Hydrothermal conditions and Adamala, K. and Szostak, J. W. (2013) Nonenzymatic template-directed the origins of cellular life, Astrobiology, 15 (12), 1091–1095. RNA synthesis inside model protocells, Science (New York, N.Y.), 342 (6162), 1098–1180. Deamer, D. W. (2017) The role of lipid membranes in life’s origin, Life (Chicago, IL: 1978), 7 (5), 1–17. Bada, J., (2009) The results of the re-visiting of the Miller-Urey experi- ment were broadcast by the BBC in ‘The spark of life’, a television Ellis, D. G., Bizzoco, R. W. and Kelley, S. T. (2008) Halophilic archaea documentary. BBC 4, 26 August 2009. determined from geothermal steam vent aerosols, Environmental Microbiology, 10 (6), 1582–1590. Bartel, D. P. and Szostak, J. W. (1993) Isolation of new ribozymes from a large pool of random sequences, Science (New York, N.Y.), 261, Engel, M. H., Macko, S. A. and Silfer, J. A. (1990) Carbon isotope compos- 1411–1418. ition of individual amino acids in the Murchison meteorite, Nature, 348, 47–49. Bernath, P. F., McElroy, C. T., Abrams, M. C. et al. (2005) Atmospheric chemistry experiment (ACE): mission overview, Geophysical Eschenmoser, A. (1999) Chemical etiology of nucleic acid structure, Research Letters, 32 (L15S01), 1–5. Science (New York, N.Y.), 284, 2118–2124. Bernhardt, H. S. (2012) The RNA world hypothesis, the worst theory of Fendler, J. D. and Fendler, E. J. (1975) Catalysis in Micellar and the early evolution of life, except for all the rest, Biology Direct,7 Macromolecular Systems, Academic Press, New York. (23), 1–10. Ferris, J. P., Hill, A. R., Liu, R. and Orgel, L. E. (1996) Synthesis of long pre- Brasier, M. D., Green, O. R., Jephcoat, A. P. et al. (2002) Questioning the biotic oligomers on mineral surfaces, Nature, 381, 59–62. evidence for Earth’s oldest fossils, Nature, 416 (6876), 76–81. Ferris, J. P. (2006) Montmorillonite-catalysed formation of RNA oligo- Brasier, M. D., Matthewman, R., McMahon, S. et al. (2011) Pumice as a mers: the possible role of catalysis in the origins of life, remarkable substrate for the origin of life, Astrobiology, 11, Philosophical Transactions of the Royal Society B: Biological Sciences, 725–735. 361 (1474), 1777–1786. Budin, I. and Szostak, J. W. (2010) Expanding roles for diverse physical Filee, J., Forterre, P. and Laurent, J. (2003) The role played by viruses in phenomena during the origin of life, Annual Review of Biophysics, the evolution of their hosts: a view based on informational protein 39, 245–246. phylogenies, Research in Microbiology, 154, 237–243. Budin, I. and Szostak, J. S. (2011) Physical effects underlying the trans- Forsyth, J. G., Yu, S. S., Mamajanov, I. et al. (2015) Ester-mediated amide ition from primitive to modern cell membranes, Proceedings of the bond formation driven by wet-dry cycles: a possible path to poly- National Academy of Sciences, 108 (13), 5249–5254. peptides on the prebiotic Earth, Angewandte Chemie International Edition, 54, 9871–9875. Caetano-Anollés, G., Kim, H. S. and Mittenthal, J. E. (2007) The origin of modern metabolic networks inferred from phylogenomic analysis Forterre, P. and Gribaldo, S. (2008) The origin of modern terrestrial life, of protein architecture, Proceedings of the National Academy of Human Frontier Science Program Journal, 1 (3), 156–168. Science, 104 (22), 9358–9363. Fuchs, G. (1986) CO fixation in acetogenic bacteria: variations on a Chen, I. A. and Szostak, J. W. (2004) Membrane growth can generate a theme, FEMS Microbiology Review, 39, 181–213. transmembrane pH gradient in fatty acid vesicles, PNAS, 101 (21), 7965–7970. Gilbert, W. (1986) The RNA World, Nature, 319, 618. Chiarabelli, C. and De Lucrezia, D. (2007) Question 3: the worlds of the Grochmal, A., Prout, L., Makin-Taylor, R., Prohens, R. and Tomas, S. prebiotic and never born proteins, Origins of Life and Evolution of (2015) Modulation of reactivity in the cavity of liposomes promotes Biospheres, 37, 357–361. the formation of peptide bonds, Journal of the American Chemical Society, 137 (38), 12269–12275. Claverie, J. M., (2006) Virus evolution, from neglect to centre stage, amidst some confusion. Structural & Genomic Information Haldane, J. B. S., (1929) The origin of life. The Rationalist Annual for the Laboratory CNRS-UPR2589 IBSM: 1–10. Year 1929, edited by Charles A Watts: 3–10. Cuccovia, L. M., Quina, F. H. and Chaimovich, H. (1982) A remarkable Higgs,P.G.and Lehman,N.(2015) The RNA World: molecular enhancement of the rate of ester thiolysis by synthetic and amphi- cooperation at the origins of life, Nature Reviews: Genetics,16, phile vesicles, Tetrahedron, 38 (7), 917–920. 7–17. ............................................................................................... .................................................................. 11 Review article Bioscience Horizons � Volume 10 2017 ............................................................................................... .................................................................. Holland, H. D. (2002) Volcanic gases, black smokers, and the Great Miller, D. S. and Gulbis, J. M. (2015) Engineering protocells: prospects for Oxidation Event, Geochimica et Cosmochimica Acta, 66 (21), self-assembly and nanoscale production lines, Life (Chicago, Ill: 3811–3826. 1978), 5, 1019–1053. Huang, Y., Wang, Y., Alexandre, M. R., Lee, T., Rose-Petruck, C., Fuller, M. Miller, S. (1953) A production of amino acids under possible primitive and Pizzarello, S. (2005) Molecular and compound-specific isotopic Earth conditions, Science (New York, N.Y.), New Series 117 (3046), characterization of monocarboxylic acids in carbonaceous meteor- 528–529. ites, Geochimica et Cosmochimica Acta, 69, 1073–1084. Mungi, C. V. and Rajamani, S. (2015) Characteristics of RNA-like oligo- Hud, N. V. and Cafferty, B. J. (2013) The origin of RNA and ‘My mers from lipid-assisted non-enzymatic synthesis: implications for Grandfather’s Axe’, Chemistry & Biology, 20, 466–474. origins of informational molecules on early Earth, Life (Chicago, Ill: 1978),5,65–84. Jia, T. Z., Fahrenbach, A. C., Kamat, N. P. et al. (2016) Oligoarinine pep- tides slow strand annealing and assist non-enzymatic RNA replica- O’Malley, M. A., Martin, W. and Dupre, J. (2010) The tree of life: introduc- tion, Nature Chemistry, 8 (10), 915–921. tion to an evolutionary debate, Biology and Philosophy, 25, 441–453. Kaufman, S. A. (1993) The Origins of Order – Self Organisation and Oparin, A. I. (1924) The origin of life. Translation by Anne Synge, pub- Selection Evolution, Oxford University Press, New York, Oxford. lished on-line via valencia.edu. Keller, A. K., Turchyn, A. V. and Ralser, M. (2014) Non-enzymatic glycoly- Orgel, L. E. (1968) Evolution of the genetic apparatus, Journal of sis and pentose phosphate pathway-like reactions in a plausible Molecular Biology, 38 (3), 381–393. Archaean ocean, Molecular Systems Biology, 10 (725), 1–12. Orgel, L. E. (1989) The origin of polynucleotide-directed protein synthe- Koonin, E. V. and Martin, W. (2005) On the origin of genomes and cells sis, Journal of Molecular Evolution, 29 (6), 465–474. within inorganic compartments, Trends in Genetics, 21 (12), Orgel, L. E. (2004) Prebiotic chemistry and the origin of the RNA world, 647–654. Critical Reviews in Biochemistry and Molecular Biology, 39, 99–123. Koonin, E. V., Senkevich, T. G. and Dolja, V. V. (2006) The ancient virus Pereto, J. (2005) Controversies on the origin of life, International world and evolution of cells, Biology Direct, 19, 1–29. Microbiology,8,23–31. Konn, C., Charlou, J. L., Holm, N. G. et al.. (2015) The production of methane, Pizzarello, S., Huang, Y. and Fuller, P. (2004) The carbon isotopic distri- hydrogen, and organic compounds in ultramafic-hosted hydrothermal bution of Murchison amino acids, Geochimica et Cosmochimica vents of the Mid-Atlantic Ridge, Astrobiology, 15 (5), 381–399. Acta, 68, 4963–4969. Lane, N. (2012) Life – inevitable or fluke, New Scientist, 23, 32–37. Powner, M. W., Gerland, B. and Sutherland, J. D. (2009) Synthesis of acti- Lincoln, T. A. and Joyce, G. F. (2009) Self-sustained replication of an vated pyrimidine ribonucleotides in prebiotically plausible condi- RNA enzyme, Science, 323 (5918), 1229–1232. tions, Nature, 459, 239–242. Luisi, P. L., Walde, P. and Oberholzer, T. (1999) Lipid vesicles as possible Prywes, N., Blain, J. C., Del Frate, F. and Szostak, J. W. (2016) Non- intermediates in the origin of life, Current Opinions in Colloid & enzymatic copying of RNA templates containing all four letters is Interface Science,4,33–39. catalysed by activated oligonucleotides, eLIFE, 17756, 1–14. Luisi, P. L. (2014) The Emergence of Life: From Chemical Origins to Pufahl, P. K. and Hiatt, E. E. (2012) Oxygenation of the Earth’s Synthetic Biology, Cambridge University Press, Cambridge, UK. atmosphere-ocean system: a review of physical and chemical sedi- mentologic responses, Marine and Petroleum Geology, 32, 1–20. MacLeod, G., McKeown, C., Hall, A. J. et al.. (1994) Hydrothermal and oceanic pH conditions of possible relevance to the origin of life, Rajamani, S., Vlassov, A, Benner, S et al. (2008) Lipid-assisted synthesis Origins of Life and Evolution of the Biosphere, 24 (1), 19–41. of RNA-like polymers from mononucleotides, Origins of Life & Evolution of Biospheres, 38, 57–74. Marsh, G. (2013) The problem of the ‘prebiotic and never born pro- teins’, International Journal of Astrobiology, 12 (1), 94–98. Ralser, M. (2014) The RNA world and the origin of metabolic enzymes, Biochemical Society Transactions, 42, 985–988. Martins, Z., Botta, O., Fogel, M. L. et al. (2008) Extra-terrestrial nucleo- bases in the Murchison meteorite, Earth and Planetary Science Robertson, M. P. and Joyce, G. F. (2012) The origins of the RNA world, Letters, 270, 130–136. Cold Spring Harbour Perspectives on Biology,4, 1–23. McCollum, C., Ritter, G. and Simoneit, B. R. T. (1999) Lipid synthesis Russell, M. J. and Martin, W. (2004) The rocky roots of the acetyl-CoA under hydrothermal conditions by Fischer-Tropsch-type reactions, pathway, Trends in Biochemical Sciences, 29 (7), 358–363. Origins of Life and Evolution of the Biosphere, 29 (2), 153–166. Russell, M. J. and Hall, A. J. (1997) The emergence of life from iron McInerney, J. O., Cotton, J. A. and Pisani, D. (2008) The prokaryotic tree monosulfide bubbles at submarine hydrothermal redox and of life: past, present… and future? Trends in Ecology and Evolution, pH front, Journal of the Geological Society of London,154, 23 (5), 281. 377–402. ............................................................................................... .................................................................. 12 Bioscience Horizons � Volume 10 2017 Review article ............................................................................................... .................................................................. Schock, E. L. (1990) Geochemical constraints on the origin of organic Szostak, J. W. (2012) The eightfold path to non-enzymatic RNA replica- compounds in hydrothermal systems, Origins of Life and Evolution tion, Journal of Systems Chemistry, 3 (2), 1–14. of Biospheres, 20, 331–367. Szostak, J. W., (2017) Unpublished correspondence between Jack Schock, E. L., McCollum, T. and Schulte, M. D. (1998) The emergence of Szostak and Paul Jowett on 9th September 2017. metabolism from within hydrothermal systems, in Wiegel J. and Szostak, J. W., Bartel, D. P. and Luisi, P. L. (2001) Synthesizing life, Adams M.W.W. (eds), Thermophiles: The Keys to Molecular Evolution Nature, 409, 387–390. and the Origins of Life, Taylor & France, London UK, pp. 59–76. Wachowius, F., Attwater, J. and Holliger, P. (2017) Nucleic acids: func- Schopf, J. W. (1978) The evolution of the first cells, Scientific American, tion and potential for abiogenesis, Quarterly Review of Biophysics, 239 (3), 110–138. 50 (e4), 1–37. Schopf,J.W.(1993) Microfossils of the early Archaean apex chert: new evi- Wächtershäuser, G. (1990) Evolution of the first metabolic cycles, dence of the antiquity of life, Science (New York, N.Y.), 260, 640–646. Proceedings of the National Academy of Sciences, 87, 200–204. Schopf, J. W. (2006) The first billion years: when did life emerge? Westheimer, F. H. (1986) Polyribonucleic acids as enzymes, Nature, Elements, 2, 229–233. 319, 534. Segré, D., Ben-Eli, D., Deamer, D. W. and Lancet, D. (2001) The lipid Woese, C. R. (1967) The Genetic Code: The Molecular Basis for Genetic world, Origins of Life and Evolution of the Biosphere, 31, 119–145. Expression, Harper & Row, New York. Segré, D. and Lancet, D. (2000) Composing life, EMBO Reports, 1 (3), 217–222. Woese, C. R., Kandler, O. and Wheelis, M. (1990) Towards a natural sys- Sessions, A. L., Doughty, D. M., Welander, P. V. et al. (2009) The continuing tem of organisms: proposal for the domains Archaea, Bacteria, and puzzle of the Great Oxidation Event, Current Biology, 19 (14), 567–574. Eucarya, Proceedings of the National Academy of Sciences, 87 (12), 4576–4579. Shields-Zhou, G. (2011) Biogeochemistry toxic Cambrian oceans, Nature, 469 (7328), 42–43. Yuen, G., Blair, N., Des Marais, D. J. and Chang, S. (1984) Carbon iso- tope composition of low molecular weight hydrocarbons and Szostak, J. W. (2011) An optimal degree of physical and chemical het- monocarboxylic acids from Murchison meteorite, Nature, 307, erogeneity for the origin of life? Philosophical Transactions of the 252–254. Royal Society B, 366, 2894–2901. ............................................................................................... ..................................................................

Journal

Bioscience HorizonsOxford University Press

Published: Dec 5, 2017

There are no references for this article.