Kinetics at a multifunctional RNA active site

Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution

The ability of enzymes, including ribozymes, to catalyze side reactions is believed to be essential to the evolution of novel biochemical activities. It has been speculated that the earliest ribozymes, whose emergence marked the origin of life, were low in activity but high in promiscuity, and that these early ribozymes gave rise to specialized descendants with higher activity and specificity. Here, we review the concepts related to promiscuity and examine several cases of highly promiscuous ribozymes. We consider the evidence bearing on the question of whether de novo ribozymes would be quantitatively more promiscuous than later evolved ribozymes or protein enzymes. We suggest that while de novo ribozymes appear to be promiscuous in general, they are not obviously more promiscuous than more highly evolved or active sequences. Promiscuity is a trait whose value would depend on selective pressures, even during prebiotic evolution.

RNA aminoacylation mediated by sequential action of two ribozymes and a nonactivated amino acid

In the transition from the RNA world to the modern DNA/protein world, RNA-catalyzed aminoacylation might have been a key step towards early translation. A number of ribozymes capable of aminoacylating their own 3' termini have been developed by in vitro selection. However, all of those catalysts require a previously activated amino acid-typically an aminoacyl-AMP-as substrate. Here we present two ribozymes connected by intermolecular base pairing and carrying out the two steps of aminoacylation: ribozyme 1 loads nonactivated phenylalanine onto its phosphorylated 5' terminus, thereby forming a high-energy mixed anhydride. Thereafter, a complex of ribozymes 1 and 2 is formed by intermolecular base pairing, and the "activated" phenylalanine is transferred from the 5' terminus of ribozyme 1 to the 3' terminus of ribozyme 2. This kind of simple RNA aminoacylase complex was engineered from previously selected ribozymes possessing the two required activities. RNA aminoacylation with a nonactivated amino acid as described here is advantageous to RNA world scenarios because initial amino acid activation by an additional reagent (in most cases, ATP) and an additional ribozyme would not be necessary.

A general RNA-capping ribozyme retains stereochemistry during cap exchange

Numerous natural and artificial ribozymes have been shown to facilitate reactions that invert stereochemistry. Here, we demonstrate that an RNA-capping ribozyme retains stereochemistry at a phosphorus reaction center. The ribozyme synthesizes a broad range of 5'-5' RNA caps by exchanging phosphate groups around the alpha-phosphate found at the 5' terminus of the ribozyme. A ribozyme prepared with an Rp adenosine(5')alpha-thiotetraphosphate cap was found to exchange this cap for an Rp 4-thiouridine(5')alpha-thiotetraphosphate cap when incubated with 4-thiouridine triphosphate. The same Rp capped construct, when incubated with [gamma-(32)P]-ATP, exchanged the unlabeled ATP for a radiolabeled one while maintaining the same stereoconfiguration. In contrast, ribozymes prepared with an Sp cap failed to react even in the presence of thiophilic metal ions such as manganese. The kinetics of capping was also unusual as compared to inverting ribozymes. When the ribozyme was prepared with a triphosphate, capping was found to follow Michaelis-Menten-type kinetics even though the rate of pyrophosphate release was completely independent of nucleotide substrate concentration. Interestingly, the rate of capping and hydrolysis, when summed, was found to be indistinguishable from the rate of pyrophosphate release, indicating that an early rate-limiting step precedes both capping and hydrolysis. Together the retention of stereochemistry and kinetics imply that capping utilizes two inverting chemical steps that are separated by the transient formation of a rate-limiting covalent intermediate. As all protein enzymes that mediate similar capping reactions utilize a covalent intermediate, chemical necessity may have strongly guided the evolution of both protein and RNA-capping catalysts.

Two independently selected capping ribozymes share similar substrate requirements

We report the isolation and characterization of a second capping ribozyme, called 6.17. This ribozyme has substrate requirements that are very similar to a previously isolated capping ribozyme called Iso6. Both ribozymes promote capping and cap exchange reactions with a broad range of nucleotide substrates. The ribozymes mediate a reaction where the terminal phosphate of the nucleotide substrate attacks the alpha-phosphate found at the ribozyme's 5' terminus. This reaction involves the release of pyrophosphate during capping or a nucleotide during cap exchange. The second-order rate constants for 6.17 and Iso6 depend strongly on the length of the phosphate group found on the nucleotide substrate. Nucleoside diphosphates or triphosphates are efficiently utilized, while monophosphates are used approximately 20-fold less efficiently by both ribozymes. These ribozymes also have rates that increase as pH is decreased. Despite these similarities, the ribozymes are not identical and 6.17 performs optimally when incubated with divalent magnesium ions, while Iso6 displays a preference for calcium ions. Further, the ribozymes have globally different secondary structures; 6.17 has a complicated pseudoknot structure consisting of five helical elements, while Iso6 likely consists of four helical elements. We hypothesize that capping proceeds via an invariant phosphate dependent mechanism that imposes a nearly identical "catalytic fingerprint" on these two distinct ribozymes.

A small aptamer with strong and specific recognition of the triphosphate of ATP

We report the in vitro selection of an RNA-based ATP aptamer with the ability to discriminate between adenosine ligands based on their 5' phosphorylation state. Previous selection of ATP aptamers yielded molecules that do not significantly discriminate between ligands at the 5' position. By applying a selective pressure that demands recognition of the 5' triphosphate, we obtained an aptamer that binds to ATP with a Kd of approximately 5 muM, and to AMP with a Kd of approximately 5.5 mM, a difference of 1100-fold. This aptamer demonstrates the ability of small RNAs to interact with negatively charged moieties.

RNA-catalyzed amino acid activation

We have selected RNAs that perform a new reaction that chemically activates amino acids, paralleling mixed phosphate anhydride synthesis by protein aminoacyl-transfer RNA synthetases. Care with recovery of the unstable reaction product was apparently essential to this selection. The best characterized RNA, KK13, requires only Ca2+ for reaction and is optimally active at low pH with KM = 50 mM and kcat = 1.1 min(-1) for activation of leucine. In conjunction with previous RNA-catalyzed aminoacyl-RNA synthesis, peptide bond formation, and RNA-based coding, these amino acid-activating RNAs complete an experimental demonstration that the four fundamental reactions of protein biosynthesis can be RNA-mediated. The appearance of translation in an RNA world is therefore supported.

In vitro selection of kinase and ligase deoxyribozymes

Exploration of the limits of biocatalysis has led to the discovery that DNA has significant potential for enzymatic function. This makes possible the construction of DNA enzymes or "deoxyribozymes" for catalyzing various chemical reactions that could be used to address fundamental questions in biocatalysis or that could find unique applications in biotechnology. Of significant interest are self-modification reactions, given the fundamental role that DNA serves in modern living systems. Recently, in vitro selection strategies have been used to isolate prototypical ATP-dependent deoxyribozymes from random-sequence populations of DNA that catalyze DNA phosphorylation and others that catalyze DNA adenylation. In nature, protein enzymes such as T4 DNA kinase and T4 DNA ligase catalyze identical chemical reactions. These findings suggest that DNA constructs could be engineered to efficiently catalyze other self-modifying reactions, including ATP-dependent DNA ligation. This article provides a detailed overview of the methods used to isolate deoxyribozymes that promote ATP-dependent DNA ligation.

RNA-Catalyzed CoA, NAD, and FAD synthesis from phosphopantetheine, NMN, and FMN

A novel in vitro selection method was developed to isolate RNA sequences with coenzyme-synthesizing activities. We used size-heterogeneous libraries containing randomized ribonucleotide sequences of four different lengths (30N, 60N, 100N, and 140N), all with 5'-ATP initiation. Two RNAs, CoES7 (30N) and CoES21 (60N), are able to catalyze the synthesis of three common coenzymes, CoA, NAD, and FAD, from their precursors, 4'-phosphopantetheine, NMN, and FMN, respectively. Both ribozymes require divalent manganese for activities. The results support the availability of these coenzymes in an RNA world, and point to a chemical explanation for the complex bipartite structures of many coenzymes.

RNA enzymes with two small-molecule substrates

BACKGROUND

The 'RNA world' hypothesis posits ancient organisms employing versatile catalysis by RNAs. In particular, such a metabolism would have required RNA catalysts that join small molecules. Such anabolic reactions now occur very widely, for example in phospholipid, terpene, amino acid and nucleotide synthetic pathways in modern organisms. Present RNA systems, however, do not perform such reactions using substrates that do not base pair. Here we ask whether this lack is a methodological artifact due to the practice of selection-amplification, or a fundamental property of active sites reconstructed within RNA structures.

RESULTS

Three rationally modified RNA enzymes, Iso6-G, Iso6-2G and Iso63G, catalyze the formation of (5'-->5') polyphosphate-linked oligonucleotides in trans. One of these, Iso6-G RNA, has a specific substrate site for a guanosine triphosphate, GTP, dGTP or ddGTP, and one nonspecific substrate site for a terminal-phosphate-containing small molecule. This ribozyme catalyzes multiple turnovers, proceeding at a constant rate. Guanosine specificity is probably not attributable to Watson-Crick base pairing.

CONCLUSIONS

Ribozymes can readily bind multiple small-molecule substrates simultaneously and catalyze reactions that build up larger products, apparently independent of substrate-RNA Watson-Crick base pairing. RNA enzymes therefore parallel proteins, which often overcome the entropic difficulties of positioning multiple small substrates for catalysis of anabolic reactions. These results support the idea of a complex ancestral metabolism based on RNA catalysis.