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Modern Metabolism As a Palimpsest of the RNA World STEVEN A Proc. Nati. Acad. Sci. USA Vol. 86, pp. 7054-7058, September 1989 Evolution Modern metabolism as a palimpsest of the RNA world STEVEN A. BENNER*, ANDREW D. ELLINGTONt, AND ANDREAS TAUER *Laboratory for Organic Chemistry, Eidgen6ssische Technische Hochschule, CH-8092 Zurich, Switzerland; and tDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114 Communicated by F. H. Westheimer, May 15, 1989 ABSTRACT An approach is developed for constructing origin of translation, and other events that occurred in the models of ancient organisms using data from metabolic path- RNA world. ways, genetic organization, chemical structure, and enzymatic If several descendants of an ancient organism can be reaction mechanisms found in contemporary organisms. This inspected, a rule of "parsimony" can be used to model the approach is illustrated by a partial reconstruction of a model biochemistry ofthe ancestral organism by extrapolation from for the "breakthrough organism," the last organism to use the biochemistry of the descendant organisms. The most RNA as the sole genetically encoded biological catalyst. As parsimonious model is one that explains the diversity in the reconstructed here, this organism had a complex metabolism modem descendants by a minimum number of independent that included dehydrogenations, transmethylations, carbon- evolutionary events. For the progenote, three independent carbon bond-forming reactions, and an energy metabolism lineages of descendants are known (archaebacteria, eubac- based on phosphate esters. Furthermore, the breakthrough teria, and eukaryotes). Thus, a biochemical trait present in all organism probably used DNA to store genetic information, three can be assigned to the progenote. The assignment is biosynthesized porphyrins, and used terpenes as its major lipid strongest when (i) the trait is found in several representative component. This model differs significandy from prevailing organisms from each of the three kingdoms; (ii) assignments models based primarily on genetic data. of homology in various branches of the progenotic pedigree are supported by high information content (preferably se- Since the discovery of self-splicing RNA (1), molecular quence data); and (iii) aspects of the trait serve no selected biology has become the central focus of speculation concern- function in the modem world.b Such assignments are not ing early forms of life. Many of these speculations consider absolute; if only some criteria are fulfilled, a weaker assign- genetic structure to the exclusion of most other biochemical ment can be proposed. data in modeling the "RNA world" (2-5). As discussed Parsimony cannot be similarly used to decide which traits elsewhere, this narrow focus leads to interesting but often in the progenote are vestiges of the breakthrough organism, chemically and biologically implausible models (6-10). as a biochemical description is possible for only a single We develop here an alternative approach for generating descendant of the breakthrough organism (the progenote). experimentally testable models of the RNA world, based on Thus, chemical criteria are needed. A biochemical trait ofthe metabolic, structural, and mechanistic data from contempo- progenote can be assigned to the breakthrough organism rary organisms. Several specific "paradigms," problem so- most strongly when (i) RNA is involved in the trait, (itk) the lutions covering individual topics in biochemical evolution, involvement does not reflect the intrinsic chemistry of RNA, are constructed by this approach. These paradigms demon- and (iii) substitution of another structural unit for the RNA strate the utility ofthis broader view and provide elements of unit could, on chemical grounds, provide similar or better a framework for interpreting the "historical" component of biochemical performance.' modern biochemistry (11). Using these rules, rRNA can be reliably placed in the We begin by assuming that life on earth passed through progenote and from there in the breakthrough organism. three episodes (Fig. 1) (12). In the first (the RNA world) (13), Likewise, RNA cofactors (NAD', S-adenosylmethionine, RNA was the only genetically encoded component of bio- CoA, ATP, FAD) all contain fragments of RNA that are logical catalysts. The second episode began with the inven- present in all lineages descendant from the progenote (20- tion of translation-based synthesis of proteins in a "break- 22); these RNA cofactors can be assigned to the progenote. through organism," the first organism to contain a genetically However, the RNA portions ofthe cofactors are not intrinsic encoded messenger RNA that directed the synthesis of a to the chemical performance of the cofactor.c Thus, on protein selectable for its catalytic activity. The third episode comprises the divergent evolution of the "progenote," the Abbreviation: RNR, ribonucleotide reductase. most recent common ancestor of all modern forms of life.a aAs rRNA and tRNA molecules are homologous in all kingdoms, and as rRNA must have been present in the breakthrough organism, the This model views modern macromolecular catalysis as a progenote must have been a descendant (or perhaps a contempo- "palimpsest" of an earlier metabolic state, with features that rary) of the breakthrough organism. arose recently ("derived traits") superimposed upon features bA chemically unique solution to a particular biochemical problem that are remnants of ancient life ("primitive traits"). (A can arise independently more than once. Further, assignments must palimpsest is a parchment that has been inscribed two or recognize the possibility of lateral transfer of genetic information more times, with the previous texts imperfectly erased and between members of divergent branches of an evolutionary tree, a process that occurs with unknown frequency (14-17). therefore still partially legible.) To describe the biochemistry CRNA serving a role that could be better performed by proteins is of these ancient organisms, we must first examine contem- unlikely to arise in a world with proteins; RNA performing roles for porary biochemical traits to distinguish ancient information which it is intrinsically chemically suited could arise at any time. To from information added later. These descriptions are prereq- evaluate the "intrinsic chemical suitability" of RNA for solving a uisites for descriptions ofthe development ofmetabolism, the particular biochemical problem, alternative solutions not involving RNA are compared by using a degree of chemical intuition. For example, pyrophosphate is as good a phosphoryl donor as the RNA The publication costs of this article were defrayed in part by page charge cofactor ATP in several kinases (18); S,S-dimethylthioacetate is as payment. This article must therefore be hereby marked "advertisement" good a methyl donor in enzymes evolved to accept it as the RNA in accordance with 18 U.S.C. §1734 solely to indicate this fact. cofactor S-adenosylmethionine (19). 7054 Downloaded by guest on October 1, 2021 Evolution: Benner et al. Proc. Natl. Acad. Sci. USA 86 (1989) 7055 FIRST ORGANISM A model for the breakthrough organism consists of a Contained an RNA-directed RNA polymerase that collection of statements about it, statements that can be was an RNA molecule, and no other genetically examined for internal consistency and that suggest experi- encoded catalytic molecules mentally testable predictions. The considerations described Simple extrapolation from modern above allow us to begin to construct a model that biochemistry is Impossible; assigns RNA WORLD Deductions based on organic biochemical traits to the breakthrough organism. At the very chemistry and the deduced metabolism least, the presence of many cofactors in the breakthrough of the breakthrough organism organism implies that the breakthrough organism was meta- BREAKTHROUGH ORGANISM bolically complex and contained ribonucleotide enzymes that First organism to synthesize proteins by translation catalyzed redox reactions, transmethylations, carbon-carbon First organism with genetically encoded message bond formation, an energy metabolism based on Complex metabolism, including reactions dependent phosphate on NADH, FAD, coenzyme A, S-adenosylmethionine, ATP anhydrides, and carbon-carbon bond forming and breaking All of the genetically encoded portions of the reactions. [This is not chemically unreasonable; almost any catalysts are RNA molecules functionalized macromolecule catalyzes reactions at some Extrapolation from biochemistry of progenote, together with rate, although RNA is undoubtedly a poorer catalyst than assumptions inherent in the proteins for most reactions (8).] RNA-world model We now develop specific arguments that describe in PROGENOTE greater detail the metabolism ofthe last organism to use RNA Most recent common ancestor of modern life forms Existence after the breakthrough secure, as all as the sole genetically encoded biological catalyst ("riboor- ribosomes from modern organisms are homologous ganism"). Extrapolation from The Breakthrough Organism Used DNA modern biochemical data using the rule of parsimony We consider the following facts, together with implications drawn from these facts: (t) Several DNA-dependent enzymes can be reliably as- signed to the progenote. In particular, archaebacteria, eu- bacteria, and eukaryotes contain DNA-dependent RNA poly- Animals Fungi Plants Eubacteria Archaebacteria merases that are quite possibly homologous (30). This implies that the progenote contained a
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