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Self-Organizing Biochemical Cycles

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Self-Organizing Biochemical Cycles Self-organizing biochemical cycles Leslie E. Orgel* Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037-1099 Contributed by Leslie E. Orgel, August 24, 2000 I examine the plausibility of theories that postulate the develop- of the first self-replicating molecules and perhaps to catalyze ment of complex chemical organization without requiring the their polymerization. The exact nature of the prior form of replication of genetic polymers such as RNA. One conclusion is that self-organization that is postulated differs from one scenario to theories that involve the organization of complex, small-molecule the next, but all scenarios have one feature in common: a metabolic cycles such as the reductive citric acid cycle on mineral self-organized cycle or network of chemical reactions that does surfaces make unreasonable assumptions about the catalytic prop- not depend directly or indirectly on a genetic polymer (8–11). In erties of minerals and the ability of minerals to organize sequences this paper, I will discuss chemical cycles with particular reference of disparate reactions. Another conclusion is that data in the to one of the best developed of these theories, that of Wa¨cht- Beilstein Handbook of Organic Chemistry that have been claimed ersha¨user (9, 12). to support the hypothesis that the reductive citric acid cycle originated as a self-organized cycle can more plausibly be inter- Nonenzymatic Metabolism preted in a different way. The monomeric components of the primary genetic system must have been available on the primitive earth. Those who claim that metabolic cycles ͉ reductive citric acid cycle ͉ Beilstein direct prebiotic synthesis of a suitable suite of monomers is impossible have to explain the indirect way in which they were he nature of the first genetic material and the prebiotic formed. Wa¨chtersha¨user argues that they were supplied via a Tchemistry that permitted its emergence are central themes in complex cycle of nonenzymatic chemical reactions that took discussions of the origins of life. The discovery of ribozymes and place on the surface of iron sulfide minerals, perhaps including the consequent rather general acceptance of the RNA world pyrites, FeS2 (9). Fig. 1 illustrates one of the cycles that is central hypothesis (1) pose an inescapable question: How were ribo- to his theory, the reverse citric acid cycle. I will concentrate on nucleotides first formed on the primitive earth? This is a very this cycle because it is also the subject of a recent paper and difficult problem. Stanley Miller’s synthesis of the amino acids by commentary in PNAS (13, 14). sparking a reducing atmosphere (2) was the paradigm for The reverse citric acid cycle is illustrated in Fig. 1 in the form prebiotic synthesis for many years, so at first, it was natural to adopted by Morowitz et al. (13). The input molecule is CO2, suppose that similar methods would meet with equal success in while the intermediates in the cycle include relatively compli- the nucleotide field. However, nucleotides are intrinsically more cated molecules such as citric acid and oxaloacetic acid. Re- complicated than amino acids, and it is by no means obvious that peated operation of the cycle would provide an autocatalytic they can be obtained in a few simple steps under prebiotic core mechanism for the synthesis of useful biochemicals from conditions. A remarkable synthesis of adenine (3) and more CO2 and H2 or some equivalent reducing agent (9, 13). or less plausible syntheses of the pyrimidine nucleoside bases (4) I begin by discussing nonenzymatic aqueous solution chem- have been reported, but the synthesis of ribose and the regio- istry that might throw some light on the likelihood of complex specific combination of the bases, ribose, and phosphate to give cycles self-organizing without the help of evolved catalysts. ␤-nucleotides remain problematical. The recent work of Eschen- Organic chemists interested in biochemical evolution have de- moser and his co-workers (5) has led to a specific synthesis of veloped a number of self-replicating systems (15–18). They can ribose 2,4-bisphosphate, but prebiotically plausible sequences of perhaps be considered as cycles of order one, that is, cycles with BIOCHEMISTRY steps to the precursors of this ribose derivative and from it to the a single intermediate (Fig. 2). This kind of cycle forms the standard nucleotides are not obvious. natural starting point for the design of a self-replicating polymer What are the alternatives if we tentatively agree that the direct in which the same kind of chemistry must be repeated time after prebiotic synthesis of standard nucleotides is implausible? time as in nucleic acid replication, but it could not be generalized Clearly, some complex chemistry must have ‘‘self-organized’’ on to give a metabolic cycle involving several different types of the primitive earth (or wherever else terrestrial life originated, if reaction. It is instructive to notice how much synthetic skill is the panspermia hypothesis is correct) and facilitated the appear- needed to develop even the simplest cycles (15–17). It will be a ance of the RNA world. But what was it like? A popular long time before organic chemists can match the reductive citric hypothesis supposes that there was an earlier ‘‘genetic system,’’ acid cycle in a single-pot reaction system! based on monomers that are more easily formed under prebiotic The formose reaction is the only familiar chemical system that conditions than nucleotides, and that this primary genetic system I am aware of that comes at all close to a metabolic cycle. The ‘‘learned’’ to synthesize the nucleotides (1). This is the simplest formation of sugars from formaldehyde under alkaline condi- form of the hypothesis, but the route to the RNA world could tions in the presence of divalent metal ions is preceded by an have passed through more than one transitional ‘‘genetic sys- induction period and is clearly autocatalytic. It has been studied tem.’’ Possible transitional systems might have been based, for intensively, and the complexity of the product mixture is noto- example, on pRNA, an isomer of RNA involving the pyranose rious (19). Nonetheless, the core reactions clearly constitute a form of ribose (6), or PNA, a molecule like RNA but with a cycle, or more correctly, a family of interconnected cycles (20). peptide backbone (7). The basis of the above hypothesis is the belief that there is a *E-mail: [email protected]. suite of monomers simple enough to form directly under prim- The publication costs of this article were defrayed in part by page charge payment. This itive-earth conditions, but still able to form the self-replicating article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. polymers of a primary genetic system. This belief has, with good §1734 solely to indicate this fact. reason, been challenged repeatedly. It is claimed that some other Article published online before print: Proc. Natl. Acad. Sci. USA, 10.1073͞pnas.220406697. form of self-organization was needed to supply the components Article and publication date are at www.pnas.org͞cgi͞doi͞10.1073͞pnas.220406697 PNAS ͉ November 7, 2000 ͉ vol. 97 ͉ no. 23 ͉ 12503–12507 Downloaded by guest on October 2, 2021 Fig. 1. The reductive (reverse) citric acid cycle adapted from the scheme in Morowitz et al. (13). The nature of the chemical steps is indicated as follows: 1a, introduction of CO2 and reduction to give an ␣-ketoacid; 1b, introduction of CO2 to give a ␤-ketoacid; 2a, reduction of a carbonyl group; 2b, reduction of a double bond; 3, reversible hydration͞dehydration; and 4, cleavage of citrate to acetate and oxaloacetate. Under the conditions of the formose reaction, redistilled form- Ca2ϩ or Pb2ϩ (23). My first observation then is that each step of aldehyde does not yield sugars (21, 22). The addition of glyco- a proposed cycle must proceed at a reasonable rate, and that this laldehyde, glyceraldehyde, etc. initiates an autocatalytic cycle will often depend on the availability of a suitable catalyst. If one based on sequential additions of formaldehyde followed by of the component reactions of a proposed cycle does not proceed reverse aldol reactions. An oversimplified version of the simplest spontaneously or under the influence of a plausibly prebiotic of the possible cycles is illustrated in Fig. 3. The reactions catalyst, some additional hypothesis will be needed to maintain illustrated in the scheme would constitute a simple autocatalytic the relevance of the cycle to the origins of life. If several of the metabolic cycle if they could be accomplished with sufficient reactions need ‘‘help,’’ desperate measures will be called for. efficiency to permit exponential growth; the input is formalde- One possible saving hypothesis is that the molecules that are hyde, the intermediates are glycolaldehyde, glyceraldehyde, di- the carriers of the cycle are also catalysts for the difficult hydroxyacetone, and tetrose sugars. A closer look at this over- reactions of the cycle. Unfortunately, catalytic reactions of the simplified version of the simplest model of the formose reaction required kind in aqueous solution are virtually unknown; there will reveal the formidable difficulties facing the development of is no reason to believe, for example, that any intermediate of the a complex, nonenzymatic metabolic cycle in homogeneous aque- citric acid cycle would specifically catalyze any reaction of the ous solution. citric acid cycle. The explanation of this is simple: noncovalent The formose reaction does not proceed at an appreciable rate interactions between small molecules in aqueous solution are under neutral conditions, and even at high pH, is inefficient in generally too weak to permit large and regiospecific catalytic the absence of a catalyst such as a divalent metal ion, for example accelerations.
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