Substrate 2'-hydroxyl groups required for ribozyme-catalyzed polymerization

RNA Polymerase Ribozyme That Recognizes the Template-Primer Complex through Tertiary Interactions

RNA enzymes (ribozymes) often rely on specific base-pairing interactions to engage RNA substrates, which limits the substrate sequence generality of these enzymes. An RNA polymerase ribozyme that was previously optimized by directed evolution to operate in a more efficient and sequence-general manner can now recognize the RNA template, RNA primer, and incoming nucleoside 5'-triphosphate (NTP) entirely through tertiary interactions. As with proteinaceous polymerases, these tertiary interactions are largely agnostic to the sequence of the template, which is an essential property for the unconstrained transmission of genetic information. The polymerase ribozyme exhibits Michaelis-Menten saturation kinetics, with a catalytic rate of 0.1-1 min^-1 and a K_m of 0.1-1 μM. Earlier forms of the polymerase did not exhibit a saturable substrate binding site, but this property emerged over the course of directed evolution as the ribozyme underwent a structural rearrangement of its catalytic center. The optimized polymerase makes tertiary contacts with both the template and primer, including a critical interaction at the C2' position of the template nucleotide that opposes the 3'-terminal nucleotide of the primer. UV cross-linking studies paint a picture of how several portions of the ribozyme, including regions that were remodeled by directed evolution, come together to position the template, primer, and NTP within the active site for RNA polymerization.

Abiogenesis through gradual evolution of autocatalysis into template-based replication

How life emerged from inanimate matter is one of the most intriguing questions posed to modern science. Central to this research are experimental attempts to build systems capable of Darwinian evolution. RNA catalysts (ribozymes) are a promising avenue, in line with the RNA world hypothesis whereby RNA pre-dated DNA and proteins. Since evolution in living organisms relies on template-based replication, the identification of a ribozyme capable of replicating itself (an RNA self-replicase) has been a major objective. However, no self-replicase has been identified to date. Alternatively, autocatalytic systems involving multiple RNA species capable of ligation and recombination may enable self-reproduction. However, it remains unclear how evolution could emerge in autocatalytic systems. In this review, we examine how experimentally feasible RNA reactions catalysed by ribozymes could implement the evolutionary properties of variation, heredity and reproduction, and ultimately allow for Darwinian evolution. We propose a gradual path for the emergence of evolution, initially supported by autocatalytic systems leading to the later appearance of RNA replicases.

The NTP binding site of the polymerase ribozyme

A previously developed RNA polymerase ribozyme uses nucleoside triphosphates (NTPs) to extend a primer 3′-terminus, templated by an RNA template with good fidelity, forming 3′-5′-phosphordiester bonds. Indirect evidence has suggested that the ribozyme's accessory domain binds the NTP with a highly conserved purine-rich loop. To determine the NTP binding site more precisely we evolved the ribozyme for efficient use of 6-thio guanosine triphosphate (6sGTP). 6sGTP never appeared in the evolutionary history of the ribozyme, therefore it was expected that mutations would appear at the NTP binding site, adapting to more efficient binding of 6sGTP. Indeed, the evolution identified three mutations that mediate 200-fold improved incorporation kinetics for 6sGTP. A >50-fold effect resulted from mutation A156U in the purine-rich loop, identifying the NTP binding site. This mutation acted weakly cooperative with two other beneficial mutations, C113U in the P2 stem near the catalytic site, and C79U on the surface of the catalytic domain. The preference pattern of the ribozyme for different NTPs changed when position 156 was mutated, confirming a direct contact between position 156 and the NTP. The results suggest that A156 stabilizes the NTP in the active site by a hydrogen bond to the Hoogsteen face of the NTP.

RNA-Catalyzed Polymerization of Deoxyribose, Threose, and Arabinose Nucleic Acids

An RNA-dependent RNA polymerase ribozyme that was highly optimized through in vitro evolution for the ability to copy a broad range of template sequences exhibits promiscuity toward other nucleic acids and nucleic acid analogues, including DNA, threose nucleic acid (TNA), and arabinose nucleic acid (ANA). By operating on various RNA templates, the ribozyme catalyzes multiple successive additions of DNA, TNA, or ANA monomers, although with reduced efficiency compared to RNA monomers. The ribozyme can also copy DNA or TNA templates to complementary RNAs, and to a lesser extent it can operate when both the template and product strands are composed of DNA, TNA, or ANA. These results suggest that polymerase ribozymes, which are thought to have replicated RNA genomes during the early history of life, could have transferred RNA-based genetic information to and from DNA, enabling the emergence of DNA genomes prior to the emergence of proteins. In addition, genetic systems based on nucleic acid-like molecules, which have been proposed as precursors or contemporaries of RNA-based life, could have been operated upon by a promiscuous polymerase ribozyme, thus enabling the evolutionary transition between early genetic systems.

3'-End labeling of nucleic acids by a polymerase ribozyme

A polymerase ribozyme can be used to label the 3' end of RNA or DNA molecules by incorporating a variety of functionalized nucleotide analogs. Guided by a complementary template, the ribozyme adds a single nucleotide that may contain a fluorophore, biotin, azide or alkyne moiety, thus enabling the detection and/or capture of selectively labeled materials. Employing a variety of commercially available nucleotide analogs, efficient labeling was demonstrated for model RNAs and DNAs, human microRNAs and natural tRNA.

Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3' end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life.

RNA synthesis by in vitro selected ribozymes for recreating an RNA world

The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms. This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms. These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates. The strengths and weaknesses regarding each ribozyme’s possible function in a self-replicating RNA network are described, together with the obstacles that need to be overcome before an RNA world organism can be generated in the laboratory.

In-ice evolution of RNA polymerase ribozyme activity

Mechanisms of molecular self-replication have the potential to shed light on the origins of life. In particular, self-replication through RNA-catalysed templated RNA synthesis is thought to have supported a primordial 'RNA world'. However, existing polymerase ribozymes lack the capacity to synthesize RNAs approaching their own size. Here, we report the in vitro evolution of such catalysts directly in the RNA-stabilizing medium of water ice, which yielded RNA polymerase ribozymes specifically adapted to sub-zero temperatures and able to synthesize RNA in ices at temperatures as low as -19 °C. The combination of cold-adaptive mutations with a previously described 5' extension operating at ambient temperatures enabled the design of a first polymerase ribozyme capable of catalysing the accurate synthesis of an RNA sequence longer than itself (adding up to 206 nucleotides), an important stepping stone towards RNA self-replication.

Propensities for loop structures of RNA & DNA backbones

RNA oligonucleotides exhibit a large tendency to bend and form a loop conformation which is a major motif contributing to their complex three-dimensional structure. This is in contrast to DNA molecules that predominantly form the double-helix structure. In this paper we investigate by molecular dynamics simulation, as well as, by its combination with the replica-exchange method, the propensity of RNA chains containing the GCUAA pentaloop to form spontaneously a hairpin conformation. The results were then compared with those of analogous hybrid oligonucleotides in which the ribose groups in the loop-region were substituted by deoxyriboses. We find that the RNA oligomers exhibit a marginal excess stability to form loop structures. The equilibrium constant for opening the loop to an extended conformation is twice as large in the hybrid than it is in the RNA chain. Analyses of the hydrogen bonds indicate that the excess stability for forming a hairpin is a result of hydrogen bonds the 2'-hydroxyls in the loop region form with other groups in the loop. Of these hydrogen bonds, the most important is the hydrogen bond donated from the 2'-OH at the first position of the loop to N7 of adenine at the forth position. RNA and DNA backbones are characterized by different backbone dihedral angles and sugar puckering that can potentially facilitate or hamper the hydrogen bonds involving the 2'-OH. Nevertheless, the sugar puckerings of all the pentaloop nucleotides were not significantly different between the two chains displaying the C3'-endo conformation characteristic to the A-form double helix. All of the other backbone dihedrals also did not show any considerable difference in the loop-region except of the δ-dihedral. In this case, the RNA loop exhibited bimodal distributions corresponding to, both, the RNA and DNA backbones, whereas the loop of the hybrid chain behaved mostly as that of a DNA backbone. Thus, it is possible that the behavior of the δ-dihedrals in the loop-region of the RNA adopts conformations that facilitate the intra-nucleotide hydrogen bondings of the 2'-hydroxyls, and consequently renders loop structures in RNA more stable.

Ribose 2'-Hydroxyl Groups Stabilize RNA Hairpin Structures Containing GCUAA Pentaloop

The chemical structure of RNA and DNA is very similar; however, the three-dimensional conformation of these two nucleic acids is very different. Whereas the DNA adopts a repetitive structure of a double-stranded helix, RNA is primarily single stranded with a complex three-dimensional structure in which the hairpin is the most common secondary structure. Apart from the difference between uracil and thymine, the difference in the chemical structure between RNA and DNA is the presence of a hydroxyl group at position 2' of the sugar (ribose) instead of a hydrogen (deoxyribose). In this paper, we present molecular dynamics simulations addressing the contribution of 2'-hydroxyls to the stability of a GCUAA pentaloop motif. The results indicate that the 2'-hydroxyls stabilize the hairpin conformation of the GCUAA pentaloop relative to an analogous oligonucleotide in which the ribose sugars in the loop region were substituted with deoxyriboses. The magnitude of the stabilization was found to be 23.8 ± 4.1 kJ/mol using an alchemical mutations free energy method and 4.2 ± 6.5 kJ/mol using potential of mean force calculations. The latter indicates that in addition to its larger thermodynamic stability the RNA hairpin is also kinetically more stable. We find that the excess stability is a result of intrahairpin hydrogen bonds in the loop region between the 2'-hydroxyls and sugars, bases, and phosphates. The hydrogen bonds with the sugars and phosphates involve predominantly interactions with adjacent nucleotides. However, the hydrogen bonds with the bases involve also interactions between groups on opposite sides of the loop or with the middle base of the loop and are therefore likely to contribute significantly to the stability of the loop. Of these hydrogen bonds, the most frequent is observed between the 2'-hydroxyl at the first position of the pentaloop with N6/N7 of adenine at the forth position, as well as between the 2'-hydroxyl at position -1 with N6 of adenine at the fifth position. Our results contribute to the notion that one of the important roles of the ribose sugars in RNA is to facilitate hairpin formation.

Arginine cofactors on the polymerase ribozyme

The RNA world hypothesis states that the early evolution of life went through a stage in which RNA served both as genome and as catalyst. The central catalyst in an RNA world organism would have been a ribozyme that catalyzed RNA polymerization to facilitate self-replication. An RNA polymerase ribozyme was developed previously in the lab but it is not efficient enough for self-replication. The factor that limits its polymerization efficiency is its weak sequence-independent binding of the primer/template substrate. Here we tested whether RNA polymerization could be improved by a cationic arginine cofactor, to improve the interaction with the substrate. In an RNA world, amino acid-nucleic acid conjugates could have facilitated the emergence of the translation apparatus and the transition to an RNP world. We chose the amino acid arginine for our study because this is the amino acid most adept to interact with RNA. An arginine cofactor was positioned at ten different sites on the ribozyme, using conjugates of arginine with short DNA or RNA oligonucleotides. However, polymerization efficiency was not increased in any of the ten positions. In five of the ten positions the arginine reduced or modulated polymerization efficiency, which gives insight into the substrate-binding site on the ribozyme. These results suggest that the existing polymerase ribozyme is not well suited to using an arginine cofactor.

Polymerase ribozyme efficiency increased by G/T-rich DNA oligonucleotides

The RNA world hypothesis states that the early evolution of life went through a stage where RNA served as genome and as catalyst. The replication of RNA world organisms would have been facilitated by ribozymes that catalyze RNA polymerization. To recapitulate an RNA world in the laboratory, a series of RNA polymerase ribozymes was developed previously. However, these ribozymes have a polymerization efficiency that is too low for self-replication, and the most efficient ribozymes prefer one specific template sequence. The limiting factor for polymerization efficiency is the weak sequence-independent binding to its primer/template substrate. Most of the known polymerase ribozymes bind an RNA heptanucleotide to form the P2 duplex on the ribozyme. By modifying this heptanucleotide, we were able to significantly increase polymerization efficiency. Truncations at the 3'-terminus of this heptanucleotide increased full-length primer extension by 10-fold, on a specific template sequence. In contrast, polymerization on several different template sequences was improved dramatically by replacing the RNA heptanucleotide with DNA oligomers containing randomized sequences of 15 nt. The presence of G and T in the random sequences was sufficient for this effect, with an optimal composition of 60% G and 40% T. Our results indicate that these DNA sequences function by establishing many weak and nonspecific base-pairing interactions to the single-stranded portion of the template. Such low-specificity interactions could have had important functions in an RNA world.

Crystal structure of the catalytic core of an RNA-polymerase ribozyme

Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best approximating that needed for RNA replication contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate among the fastest of known ribozymes. Here we present the 3.0 angstrom crystal structure of this ligase. The architecture resembles a tripod, its three legs converging near the ligation junction. Interacting with this tripod scaffold through a series of 10 minor-groove interactions (including two A-minor triads) is the unpaired segment that contributes to and organizes the active site. A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases.

A class I ligase ribozyme with reduced Mg2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions

The class I ligase was among the first ribozymes to have been isolated from random sequences and represents the catalytic core of several RNA-directed RNA polymerase ribozymes. The ligase is also notable for its catalytic efficiency and structural complexity. Here, we report an improved version of this ribozyme, arising from selection that targeted the kinetics of the chemical step. Compared with the parent ribozyme, the improved ligase achieves a modest increase in rate enhancement under the selective conditions and shows a sharp reduction in [Mg(2+)] dependence. Analysis of the sequences and kinetics of successful clones suggests which mutations play the greatest part in these improvements. Moreover, backbone and nucleobase interference maps of the parent and improved ligase ribozymes complement the newly solved crystal structure of the improved ligase to identify the functionally significant interactions underlying the catalytic ability and structural complexity of the ligase ribozyme.

Darwinian chemistry: towards the synthesis of a simple cell

The total synthesis of a simple cell is in many ways the ultimate challenge in synthetic biology. Outlined eight years ago in a visionary article by Szostak et al. (J. W. Szostak, D. P. Bartel and P. L. Luisi, Nature, 2001, 409, 387), the chances of success seemed remote. However, recent progress in nucleic acid chemistry, directed evolution and membrane biophysics have brought the prospect of a simple synthetic cell with life-like properties such as growth, division, heredity and evolution within reach. Success in this area will not only revolutionize our understanding of abiogenesis but provide a fertile test-bed for models of prebiotic chemistry and early evolution. Last but not least, a robust "living" protocell may provide a versatile and safe chassis for embedding synthetic devices and systems.

Improved polymerase ribozyme efficiency on hydrophobic assemblies

During an early step in the evolution of life, RNA served both as genome and as catalyst, according to the RNA world hypothesis. For self-replication, the RNA organisms must have contained an RNA that catalyzes RNA polymerization. As a first step toward recapitulating an RNA world in the laboratory, a polymerase ribozyme was generated previously by in vitro evolution and design. However, the efficiency of this ribozyme is about 100-fold too low for self-replication because of a low affinity of the ribozyme to its primer/template substrate. To improve the substrate interactions by colocalizing ribozyme and substrate on micelles, we attached hydrophobic anchors to both RNAs. We show here that the hydrophobic anchors led to aggregates with the expected size of the corresponding micelles. The micelle formation increased the polymerization yield of full-length products by 3- to 20-fold, depending on substrates and reaction conditions. With the best-characterized substrate, the improvement in polymerization efficiency was primarily due to reduced sequence-specific stalling on partially extended substrates. We discuss how, during the origin of life, micellar ribozyme aggregates could have acted as precursors to membrane-encapsulated life forms.

On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization

BACKGROUND

The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code.

RESULTS

Our main guide in constructing the models is the Darwinian Continuity Principle whereby a scenario for the evolution of a complex system must consist of plausible elementary steps, each conferring a distinct advantage on the evolving ensemble of genetic elements. Evolution of the translation system is envisaged to occur in a compartmentalized ensemble of replicating, co-selected RNA segments, i.e., in a RNA World containing ribozymes with versatile activities. Since evolution has no foresight, the translation system could not evolve in the RNA World as the result of selection for protein synthesis and must have been a by-product of evolution drive by selection for another function, i.e., the translation system evolved via the exaptation route. It is proposed that the evolutionary process that eventually led to the emergence of translation started with the selection for ribozymes binding abiogenic amino acids that stimulated ribozyme-catalyzed reactions. The proposed scenario for the evolution of translation consists of the following steps: binding of amino acids to a ribozyme resulting in an enhancement of its catalytic activity; evolution of the amino-acid-stimulated ribozyme into a peptide ligase (predecessor of the large ribosomal subunit) yielding, initially, a unique peptide activating the original ribozyme and, possibly, other ribozymes in the ensemble; evolution of self-charging proto-tRNAs that were selected, initially, for accumulation of amino acids, and subsequently, for delivery of amino acids to the peptide ligase; joining of the peptide ligase with a distinct RNA molecule (predecessor of the small ribosomal subunit) carrying a built-in template for more efficient, complementary binding of charged proto-tRNAs; evolution of the ability of the peptide ligase to assemble peptides using exogenous RNAs as template for complementary binding of charged proteo-tRNAs, yielding peptides with the potential to activate different ribozymes; evolution of the translocation function of the protoribosome leading to the production of increasingly longer peptides (the first proteins), i.e., the origin of translation. The specifics of the recognition of amino acids by proto-tRNAs and the origin of the genetic code depend on whether or not there is a physical affinity between amino acids and their cognate codons or anticodons, a problem that remains unresolved.

CONCLUSION

We describe a stepwise model for the origin of the translation system in the ancient RNA world such that each step confers a distinct advantage onto an ensemble of co-evolving genetic elements. Under this scenario, the primary cause for the emergence of translation was the ability of amino acids and peptides to stimulate reactions catalyzed by ribozymes. Thus, the translation system might have evolved as the result of selection for ribozymes capable of, initially, efficient amino acid binding, and subsequently, synthesis of increasingly versatile peptides. Several aspects of this scenario are amenable to experimental testing.

The origin of replicators and reproducers

Replicators are fundamental to the origin of life and evolvability. Their survival depends on the accuracy of replication and the efficiency of growth relative to spontaneous decay. Infrabiological systems are built of two coupled autocatalytic systems, in contrast to minimal living systems that must comprise at least a metabolic subsystem, a hereditary subsystem and a boundary, serving respective functions. Some scenarios prefer to unite all these functions into one primordial system, as illustrated in the lipid world scenario, which is considered as a didactic example in detail. Experimentally produced chemical replicators grow parabolically owing to product inhibition. A selection consequence is survival of everybody. The chromatographized replicator model predicts that such replicators spreading on surfaces can be selected for higher replication rate because double strands are washed away slower than single strands from the surface. Analysis of real ribozymes suggests that the error threshold of replication is less severe by about one order of magnitude than thought previously. Surface-bound dynamics is predicted to play a crucial role also for exponential replicators: unlinked genes belonging to the same genome do not displace each other by competition, and efficient and accurate replicases can spread. The most efficient form of such useful population structure is encapsulation by reproducing vesicles. The stochastic corrector model shows how such a bag of genes can survive, and what the role of chromosome formation and intragenic recombination could be. Prebiotic and early evolution cannot be understood without the models of dynamics.

Real ribozymes suggest a relaxed error threshold

The error threshold for replication, the critical copying fidelity below which the fittest genotype deterministically disappears, limits the length of the genome that can be maintained by selection. Primordial replication must have been error-prone, and so early replicators are thought to have been necessarily short. The error threshold also depends on the fitness landscape. In an RNA world, many neutral and compensatory mutations can raise the threshold, below which the functional phenotype, rather than a particular sequence, is still present. Here we show, on the basis of comparative analysis of two extensively mutagenized ribozymes, that with a copying fidelity of 0.999 per digit per replication the phenotypic error threshold rises well above 7,000 nucleotides, which permits the selective maintenance of a functionally rich riboorganism with a genome of more than 100 different genes, the size of a tRNA. This requires an order of magnitude of improvement in the accuracy of in vitro-generated polymerase ribozymes. Incidentally, this genome size coincides with that estimated for a minimal cell achieved by top-down analysis, omitting the genes dealing with translation.

New ligase-derived RNA polymerase ribozymes

The search is underway for a catalytic RNA molecule capable of self-replication. Finding such a ribozyme would lend crucial support to the RNA World hypothesis, which holds that very early life-forms relied on RNA for both replicating and storing genetic information. We previously reported an RNA polymerase isolated from a pool of variants of an existing RNA ligase ribozyme. Here we report eight additional ligase-derived polymerase ribozymes isolated from this pool. Because each of them is a new potential starting point for further in vitro evolution and engineering, together they substantially enrich the set of candidates from which an RNA replicase ribozyme might eventually emerge.