7 Imperfect RNA synthesis via model prebiotic reactions and consequences for functional RNAs

Contemporary life synthesizes RNA of homogeneous length and regioisomer composition via sophisticated enzymatic catalysis. Before such catalysts existed, RNA could have been produced only via simpler, non-enzymatic means, which model prebiotic systems have shown produce pools of products that are similar, but varied (e.g. in regioisomer composition). Recently, we have demonstrated that functional RNAs (ribozymes and aptamers) containing mixed-regioisomer backbones (i.e. 2′–5′ vs. 3′–5′ linkages) retain function. This observation, coupled with the well-known fact that mixed-regioisomer RNAs exhibit depressed melting temperatures relative to native RNA, suggests that mixed-regioisomer backbones could actually be adaptive in an RNA (or pre-RNA) world. In this poster, we will show our recent work with functional RNAs representative of those produced in non-enzymatic polymerization reactions and their behaviours as catalysts and receptors.     

Lethal mutants and truncated selection together solve a paradox of the origin of life

Background

Many attempts have been made to describe the origin of life, one of which is Eigen''s cycle of autocatalytic reactions [Eigen M (1971) Naturwissenschaften 58, 465–523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, the information carrier (either RNA or DNA or their precursor) must be transmitted to the next generation with a minimal number of misprints. In Eigen''s theory, the maximum chain length that could be maintained is restricted to nucleotides, while for the most primitive genome the length is around . This is the famous error catastrophe paradox. How to solve this puzzle is an interesting and important problem in the theory of the origin of life.

Methodology/Principal Findings

We use methods of statistical physics to solve this paradox by carefully analyzing the implications of neutral and lethal mutants, and truncated selection (i.e., when fitness is zero after a certain Hamming distance from the master sequence) for the critical chain length. While neutral mutants play an important role in evolution, they do not provide a solution to the paradox. We have found that lethal mutants and truncated selection together can solve the error catastrophe paradox. There is a principal difference between prebiotic molecule self-replication and proto-cell self-replication stages in the origin of life.

Conclusions/Significance

We have applied methods of statistical physics to make an important breakthrough in the molecular theory of the origin of life. Our results will inspire further studies on the molecular theory of the origin of life and biological evolution.     

23 The phylogenomic roots of modern biochemistry,translation, and the genetic code

The origin and evolution of modern biochemistry is a complex problem that has puzzled scientists for almost a century. In my laboratory, we have dissected the emergence of the very early macromolecules that populated primordial cells using ideographic (historical, retrodictive) approaches. Deep evolutionary signals were retrieved from a census of molecular structures and functions in thousands of nucleic acids and millions of proteins using powerful phylogenomic methods. These clock-like signals revealed that modern biochemistry resulted from gradual coevolution and accretion of molecular parts and molecules. This was made evident in the study of aminoacyl-tRNA synthetase (aaRS) enzymes and the ribosomal ensemble. aaRSs coevolved with tRNAs, as catalytic aaRS domains and acceptor arm tRNAs accreted domains, and RNA substructures. Similarly, the ribosome originated in its central ratchet mechanism and expanded by coevolving rRNA–protein interactions (Figure 1). Remarkably, while the first biochemical functions were metabolic, the translation, the genetic code, and the ribosome appeared quite late as ‘exacting’ mechanisms that enhanced protein folding speed and flexibility, benefiting the search for new molecular functions. Our timelines reveal that translation unfolded only after the rise of viruses but prior to the appearance of diversified archaeal microbes. Remarkably, its debut coincided with the rise of nucleotide and amino acid biosynthetic pathways .     

Primitive Genetic Polymers

Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles—a situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?In contemporary life, nucleic acids provide the amino acid sequence information required for protein synthesis, while protein enzymes carry out the catalysis required for nucleic acid synthesis. This mutual dependence has been described as a “chicken-or-the-egg” dilemma concerning which came first. However, requiring that these biopolymers appeared strictly sequentially may be an overly restrictive preconception—nucleic acids and noncoded peptides may have arisen independently and only later become dependent on each other. Nevertheless, the requirements for the chemical emergence of life would appear simplified if one polymer was initially able to store and transfer information as well as perform selective chemical catalysis—two essential features of life.The discovery of catalytic RNA molecules in the early 1980s (Kruger et al. 1982; Guerrier-Takada et al. 1983) created widespread interest in an earlier proposal (Woese 1967; Crick 1968; Orgel 1968) that nucleic acids were the first biopolymers of life, as nucleic acids transmit genetic information and could have once been responsible for catalyzing a wide range of reactions. The ever-increasing list of processes that involve RNA in contemporary life continues to strengthen this view (Mandal and Breaker 2004; Gesteland and Atkins 2006). Furthermore, the rule-based one-to-one pairing of complementary bases in a Watson-Crick duplex (Fig. 1) provides a robust mechanism for information transfer during replication that could have been operative from the advent of oligonucleotides. In contrast, there is no obvious and general mechanism by which the amino acid sequence of a polypeptide can be transferred to a new polypeptide as part of a replication process.Open in a separate windowFigure 1.Two base-paired RNA dinucleotide steps with functional units discussed in the text annotated. In contemporary life, the nucleoside linker is phosphate, and the information unit is one of the canonical nucleobases (A, G, C, and U). The contemporary trifunctional moiety, ribose, is coupled via N,O-acetals to the informational unit and via phosphoesters to the nucleoside linker.If we accept that nucleic acids must have appeared without the aid of coded proteins, we are still faced with the question of how the first nucleic acid molecules came to be. Broadly defined, there are two schools of thought regarding the origin of the earliest nucleic acids. In one school, it is proposed that abiotic chemical processes initially gave rise to nucleotides (i.e., phosphorylated nucleosides), which were then coupled together to yield polymers identical in chemical structure to contemporary RNA. In support of this model, Sutherland presents in his article current progress toward discovering possible chemical pathways for the prebiotic synthesis of RNA mononucleotides, as well as methods for their protein-free polymerization (Sutherland 2010).A second school of thought, discussed in this article, considers RNA to be a product of evolution, and that a different RNA-like polymer (or proto-RNA) was used by the earliest forms of life. Just as the deoxyribose sugar of DNA was likely the product of Darwinian evolution (selected for the hydrolytic stability it provides this long-lived biopolymer), so, too, might the sugar, phosphate, and bases of RNA have been refined by evolution. In this scenario, a proto-RNA is more likely to have spontaneously formed than RNA, because a proto-RNA could have had more favorable chemical characteristics (e.g., greater availability of precursors and ease of assembly), but such a polymer was eventually replaced, through evolution, by RNA (potentially after several incremental changes), based on functional characteristics (e.g. nucleoside stability, versatility in forming catalytic structures). Thus, contemporary RNA may possess chemical traits that, although optimally suited for contemporary life, may have been ill-suited for the earliest biopolymers, with the converse being true for proto-RNA.     

3 Origins and evolution of the translation machinery

The protein synthesis machinery largely evolved prior to the last common ancestor and hence its study can provide insight to early events in the origin of life, including the transition from the hypothetical RNA world to living systems as we know them. By utilizing information from primary sequences, atomic resolution structures, and functional properties of the various components, it is possible to identify timing relationships (Hsiao et al., 2009; Fox, 2010). Taken together, these timing events are used to develop a preliminary time line for major evolutionary events leading to the modern protein synthesis machinery. It has been argued that a key initial event was the hybridization of two or more RNAs that created the peptidyl transferase center, (PTC), of the ribosome (Agmon et al. 2005). The PTC, left side of figure, contains a characteristic cavity/pore that serves as the entrance to the exit tunnel and is thought to be essential to the catalysis (Fox et al., 2012). This cavity is distinct from typical RNA pores (right side of figure) in that the nitrogenous bases face towards the lumen of the pore and thus are available for hydrogen bonding interactions. In typical RNA pores, the bases carefully avoid the lumen region. In support of Agmon et al. 2005), it is argued that this key difference reflects the fact the pore was created by an early hybridization event rather than normal RNA folding.