Aminoacyl esterase activity of the Tetrahymena ribozyme

Novel and variant ribozymes obtained through in vitro selection

Ribozymes are RNA molecules capable of catalyzing chemical reactions. Natural ribozymes generally accelerate the rate of cleavage and ligation of specific phosphodiester bonds. In vitro selection of RNA is now being used as a powerful technique to isolate novel and variant ribozymes that carry out catalysis at phosphodiester and carbon bonds. The range of reactions catalyzed by in vitro selected ribozymes is now well beyond the scope of known natural ribozymes.

RNA-RNA interactions between oligonucleotide substrates for aminoacylation

RNA stem-loop microhelices with helix sequences based on tRNA acceptor stems can be charged with specific amino acids. Experiments were designed to test the possibility that microhelices could laterally associate through complementary loop sequences and thereby bring their attached aminoacyl groups close enough together to form a peptide bond. Computer simulations suggested that formation of such complexes would be sensitive to the number of loop nucleotides needed to span the grooves of the quasi-continuous helix of the intermolecular pseudoknot so formed. These predictions were conformed experimentally by observation of complex formation sensitivity to loop size. Complexes with optimized loop sizes had apparent bimolecular dissociation constants of approximately 100 nM with only three complementary base pairs between the respective loops. Single nucleotide substitutions that disrupted the predicted intermolecular loop-loop base-pairing abolished detectable association. Similarly, placing a gap between the short helix formed by loop-loop pairing and the adjacent acceptor stems also diminished complex formation. These experiments establish an experimental basis for microhelix association for peptide synthesis.

The New World of ribozymes

The number of RNA molecules that have novel catalytic activities has dramatically increased during the past two years. This ribozymic boom is not due to the discovery of additional examples of natural ribozymes but rather to the development of artificial ribozymes isolated by in vitro selection and evolution techniques. The structural and functional complexities of these artificial ribozymes, however, do not match those of the larger natural ribozymes. The understanding of both RNA structure and catalysis performed by natural and artificial ribozymes paves the way for the creation of RNA molecules that are able to efficiently catalyze more complex reactions.

Role of the 5.8S rRNA in ribosome translocation

Studies on the inhibition of protein synthesis by specific anti 5.8S rRNA oligonucleotides have suggested that this RNA plays an important role in eukaryotic ribosome function. Mutations in the 5. 8S rRNA can inhibit cell growth and compromise protein synthesis in vitro . Polyribosomes from cells expressing these mutant 5.8S rRNAs are elevated in size and ribosome-associated tRNA. Cell free extracts from these cells also are more sensitive to antibiotics which act on the 60S ribosomal subunit by inhibiting elongation. The extracts are especially sensitive to cycloheximide and diphtheria toxin which act specifically to inhibit translocation. Studies of ribosomal proteins show no reproducible changes in the core proteins, but reveal reduced levels of elongation factors 1 and 2 only in ribosomes which contain large amounts of mutant 5.8S rRNA. Polyribosomes from cells which are severely inhibited, but contain little mutant 5.8S rRNA, do not show the same reductions in the elongation factors, an observation which underlines the specific nature of the change. Taken together the results demonstrate a defined and critical function for the 5.8S rRNA, suggesting that this RNA plays a role in ribosome translocation.

DNA polymerization catalysed by a group II intron RNA in vitro

The excised group II intron bI1 from Saccharomyces cerevisiae can act as a ribozyme catalysing various chemical reactions with different substrate RNAs in vitro . Recently, we have described an editing-like RNA polymerization reaction catalysed by the bI1 intron lariat that proceeds in the 3'-->5'direction. Here we show that the bI1 lariat RNA can also catalyse successive deoxyribonucleotide polymerization reactions on exogenous substrate molecules. The basic mechanism of the reaction involved interacting cycles between an alternative version of partial reverse splicing (lariat charging) and canonical forward splicing (lariat discharging by exon ligation). With an overall chain growth in the 3'-->5' direction, the 5' exon RNAs (IBS1dN) were elongated by successive insertion of deoxyribonucleotides derived from single deoxyribonucleotide substitutions (dA, dG, dC or dT). All four deoxyribonucleotides were used as substrates, although with different efficiencies. Our findings extend the catalytic repertoire of group II intron RNAs not only by a novel DNA polymerization activity, but also by a DNA-DNA ligation capacity, supporting the idea that ribozymes might have been part of the first primordial polymerization machinery for both RNA and DNA.

The Cbp2 protein stimulates the splicing of the omega intron of yeast mitochondria

The Cbp2 protein is encoded in the nucleus and is required for the splicing of the terminal intron of the mitochondrial COB gene in Saccharomyces cerevisiae . Using a yeast strain that lacks this intron but contains a related group I intron in the precursor of the large ribosomal RNA, we have determined that Cbp2 protein is also required for the normal accumulation of 21S ribosomal RNA in vivo . Such strains bearing a deletion of the CBP2 gene adapt slowly to growth in glycerol/ethanol media implying a defect in derepression. At physiologic concentrations of magnesium, Cbp2 stimulates the splicing of the ribosomal RNA intron in vitro . Nevertheless, Cbp2 is not essential for splicing of this intron in mitochondria nor is it required in vitro at magnesium concentrations >5 mM. A similar intron exists in the large ribosomal RNA (LSU) gene of Saccharomyces douglasii . This intron does need Cbp2 for catalytic activity in physiologic magnesium. Similarities between the LSU introns and COB intron 5 suggest that Cbp2 may recognize conserved elements of the these two introns, and protein-induced UV crosslinks occur in similar sites in the substrate and catalytic domains of the RNA precursors.

Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes

A classic approach in biology, both organismal and cellular, is to compare morphologies in order to glean structural and functional commonalities. The comparative approach has also proven valuable on a molecular level. For example, phylogenetic comparisons of RNA sequences have led to determination of conserved secondary and even tertiary structures, and comparisons of protein structures have led to classifications of families of protein folds. Here we take this approach in a mechanistic direction, comparing protein and RNA enzymes. The aim of comparing RNA and protein enzymes is to learn about fundamental physical and chemical principles of biological catalysis. The more recently discovered RNA enzymes, or ribozymes, provide a distinct perspective on long-standing questions of biological catalysis. The differences described in this review have taught us about the aspects of RNA and proteins that are distinct, whereas the common features have helped us to understand the aspects that are fundamental to biological catalysis. This has allowed the framework that was put forth by Jencks for protein catalysts over 20 years ago (1) to be extended to RNA enzymes, generalized, and strengthened.

Ribozymes: aiming at RNA replication and protein synthesis

The RNA world hypothesis is founded on the idea of an RNA replicase, or self-replicating RNA molecule, and presupposes the later emergence of ribozymes capable of catalyzing the synthesis of peptides. The recent demonstrations of ribozyme-catalyzed template-directed primer extension, and of ribozyme-catalyzed amide bond synthesis, confirm the plausibility of the RNA world, and highlight the steps that remain to be demonstrated in the laboratory.

Influence of substrate structure on cleavage by hammerhead ribozyme

We compared the cleavage by a hammerhead ribozyme of a wild-type precursor tRNA (pre-tRNA leu(3)) and a structurally altered mutant form. We also analyzed the cleavage reactions of these tRNAs catalyzed by a ribozyme variant that was designed to complement the mutant precursor tRNA. Kinetic analyses reveal that the kcat values are nearly the same for the wild-type and the mutant substrate RNAs. However, the Km values differ considerably, being higher for the wild-type substrate. Thus, the formation of the ribozyme-substrate complex, but not the chemical cleavage step, is affected by these changes. Time course studies were performed, at different temperatures, to estimate the efficiency of the cleavage reactions and the effect of temperature. The cleavage of mutant precursor tRNA is generally faster than the wild-type at all temperatures analyzed. These results suggest that substrate structures can limit ribozyme efficiency, presumably by hindering the hybridization step.

Chance and necessity in the selection of nucleic acid catalysts

In Tom Stoppard's famous play [Rosencrantz and Guildenstern are Dead], the ill-fated heroes toss a coin 101 times. The first 100 times they do so the coin lands heads up. The chance of this happening is approximately 1 in 10(30), a sequence of events so rare that one might argue that it could only happen in such a delightful fiction. Similarly rare events, however, may underlie the origins of biological catalysis. What is the probability that an RNA, DNA, or protein molecule of a given random sequence will display a particular catalytic activity? The answer to this question determines whether a collection of such sequences, such as might result from prebiotic chemistry on the early earth, is extremely likely or unlikely to contain catalytically active molecules, and hence whether the origin of life itself is a virtually inevitable consequence of chemical laws or merely a bizarre fluke. The fact that a priori estimates of this probability, given by otherwise informed chemists and biologists, ranged from 10(-5) to 10(-50), inspired us to begin to address the question experimentally. As it turns out, the chance that a given random sequence RNA molecule will be able to catalyze an RNA polymerase-like phosphoryl transfer reaction is close to 1 in 10(13), rare enough, to be sure, but nevertheless in a range that is comfortably accessible by experiment. It is the purpose of this Account to describe the recent advances in combinatorial biochemistry that have made it possible for us to explore the abundance and diversity of catalysts existing in nucleic acid sequence space.

The search for missing links between self-replicating nucleic acids and the RNA world

The notion that modern metabolism was derived from a complex 'RNA world' in which most reactions were catalyzed by ribozymes has received wide acceptance. However, the evolutionary links between the first self-replicating systems and ribozymes as complex as, say, the Group I self-splicing intron or the HDV ribozyme, have remained elusive. While prebiotic chemists have succeeded in synthesizing short oligonucleotides, it is not immediately obvious how these could have replicated and evolved to the point where they could assume complex shapes and catalytic functions. Nonetheless, recent experiments from a variety of disciplines suggest a plausible pathway from prebiotic chemistry to complex metabolism, and this review is intended as a hypothetical roadmap for the origin and subsequent evolution of life.

Enzymatic synthesis of polymers containing nicotinamide mononucleotide

Nicotinamide mononucleoside 5'-diphosphate in its reduced form is an excellent substrate for polynucleotide phosphorylase from Micrococcus luteus both in de novo polymerization reactions and in primer extension reactions. The oxidized form of the diphosphate is a much less efficient substrate; it can be used to extend primers but does not oligomerize in the absence of a primer. The cyanide adduct of the oxidized substrate, like the reduced substrate, polymerizes efficiently. Loss of cyanide yields high molecular weight polymers of the oxidized form. Terminal transferase from calf thymus accepts nicotinamide mononucleoside 5'-triphosphate as a substrate and efficiently adds one residue to the 3'-end of an oligodeoxynucleotide. T4 polynucleotide kinase accepts oligomers of nicotinamide mononucleotide as substrates. However, RNA polymerases do not incorporate nicotinamide mononucleoside 5'-triphosphate into products on any of the templates that we used.

Re-creating the RNA world

Results from in vitro selection experiments can be used to construct and test models for the evolution of the RNA world. Surprisingly, the success of selected RNAs at binding ligands and catalyzing reactions may make it difficult to determine precisely the lineage of molecular fossils, molecules that are believed to have survived from the RNA world to the present.

Molecular evolution of transfer RNA from two precursor hairpins: implications for the origin of protein synthesis

In this paper we are going to present a model for the coevolution of major components of the protein synthesis machinery in a primordial RNA world. We propose that the essential prerequisites for RNA-based protein synthesis, i.e., tRNA-like molecules, ribozymic charging catalysts, small-subunit(SSU) rRNA, and large-subunit(LSU) rRNA, evolved from the same ancestral RNA molecule. Several arguments are considered which suggest that tRNA-like molecules were derived by tandem joining of template-flanking hairpin structures involved in replication control. It is further argued that the ancestors of contemporary group I tRNA introns catalyzed such hairpin joining reactions, themselves also giving rise to the ribosomal RNAs. Our model includes a general stereochemical principle for the interaction between ribozymes and hairpin-derived recognition structures, which can be applied to such seemingly different processes as RNA polymerization, aminoacylation, tRNA decoding, and peptidyl transfer, implicating a common origin for these fundamental functions. These and other considerations suggest that generation and evolution of tRNA were coupled to the evolution of synthetases, ribosomal RNAs, and introns from the beginning and have been a consequence arising from the original function of tRNA precursor hairpins as replication and recombination control elements.

Self-incorporation of coenzymes by ribozymes

RNA molecules that are assembled from the four standard nucleotides contain a limited number of chemical functional groups, a characteristic that is generally thought to restrict the potential for catalysis by ribozymes. Although polypeptides carry a wider range of functional groups, many contemporary protein-based enzymes employ coenzymes to augment their capabilities. The coenzymes possess additional chemical moieties that can participate directly in catalysis and thereby enhance catalytic function. In this work, we demonstrate a mechanism by which ribozymes can supplement their limited repertoire of functional groups through RNA-catalyzed incorporation of various coenzymes and coenzyme analogues. The group I ribozyme of Tetrahymena thermophila normally mediates a phosphoester transfer reaction that results in the covalent attachment of guanosine to the ribozyme. Here, a shortened version of the ribozyme is shown to catalyze the self-incorporation of coenzymes and coenzyme analogues, such as NAD+ and dephosphorylated CoA-SH. Similar ribozyme activities may have played an important role in the "RNA world," when RNA enzymes are thought to have maintained a complex metabolism in the absence of proteins and would have benefited from the inclusion of additional functional groups.

Evolution of the aminoacyl-tRNA synthetases and the origin of the genetic code

The aminoacyl-tRNA synthetases exist as two enzyme families which were apparently generated by divergent evolution from two primordial synthetases. The two classes of enzymes exhibit intriguing familial relationships, in that they are distributed nonrandomly within the codon-amino acid matrix of the genetic code. For example, all XCX codons code for amino acids handled by class II synthetases, and all but one of the XUX codons code for amino acids handled by class I synthetases. One interpretation of these patterns is that the synthetases coevolved with the genetic code. The more likely explanation, however, is that the synthetases evolved in the context of an already-established genetic code--a code which developed earlier in an RNA world. The rules which governed the development of the genetic code, and led to certain patterns in the coding catalog between codons and amino acids, would also have governed the subsequent evolution of the synthetases in the context of a fixed code, leading to patterns in synthetase distribution such as those observed. These rules are (1) conservative evolution of amino acid and adapter binding sites and (2) minimization of the disruptive effects on protein structure caused by codon meaning changes.

On the levels of enzymatic substrate specificity: implications for the early evolution of metabolic pathways

The most frequently invoked explanation for the origin of metabolic pathways is the retrograde evolution hypothesis. In contrast, according to the so-called "patchwork" theory, metabolism evolved by the recruitment of relatively inefficient small enzymes of broad specificity that could react with a wide range of chemically related substrates. In this paper it is argued that both sequence comparisons and experimental results on enzyme substrate specificity support the patchwork assembly theory. The available evidence supports previous suggestions that gene duplication events followed by a gradual neoDarwinian accumulation of mutations and other minute genetic changes lead to the narrowing and modification of enzyme function in at least some primordial metabolic pathways.

Aminoacyl-RNA synthesis catalyzed by an RNA

An RNA has been selected that rapidly aminoacylates its 2'(3') terminus when provided with phenylalanyl-adenosine monophosphate. That is, the RNA accelerates the same aminoacyl group transfer catalyzed by protein aminoacyl-transfer RNA synthetases. The best characterized RNA reaction requires both Mg2+ and Ca2+. These results confirm a necessary prediction of the RNA world hypothesis and represent efficient RNA reaction (> or = 10(5) times accelerated) at a carbonyl carbon, exemplifying a little explored type of RNA catalysis.

Ribozymes, recognition and evolution

Precision in the recognition and orientation of substrate is important in the selectivity of catalysis by natural enzymes. Several new ribozyme species have been evolved using in vitro selection/mutagenesis which make use of precise substrate recognition to catalyze a variety of reactions.

Cleavage of an amide bond by a ribozyme

A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, kcat, is 0.1 x 10(-5) min-1 to 1 x 10(-5) min-1 for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10(3) as compared with the uncatalyzed reaction.

Pseudouridine and O2'-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins

Pseudouridine (5-ribosyluracil, psi) was the first of a host of modified nucleoside constituents detected in cellular RNA and it remains the most abundant, being broadly distributed in the RNA of archaebacteria, eubacteria and eukaryotes. Like some other modifications, psi is particularly abundant in more complex organisms, reaching 2-3% of the total nucleoside constituents in tRNA, snRNA and rRNA of multicellular plants and animals. Like all other modified nucleosides, psi arises by site-specific, enzymically catalyzed modification of a nucleoside residue in an RNA molecule. Unlike all other modified nucleosides, psi arises by isomerisation (not substitution) of a classical nucleoside, uridine (1-ribosyluracil). There have been suggestions that key processes such as ribosome assembly and peptidyl transfer may rely, more than is generally appreciated, on RNA modifications such as O2'-methylation and pseudouridylation, respectively. However, a persuasive case for the view that secondary modifications are of primary importance in ribosome function has not been convincingly made. Accordingly, we think it is timely to broaden what is generally meant by the 'catalytic properties of rRNA', and to ask, to what extent do modifications contribute to in vivo rates of ribosome assembly and ribosomal peptide-bond synthesis? The first part of this article sets forth the evidence that there is a conspicuous association between modified nucleosides and cellular RNAs that participate in group-transfer reactions. The second part reviews evidence in support of the view that the functions of psi and other modified nucleosides are likely of central importance for understanding the dynamics and stereostructural modeling at functionally significant sites in the ribosome.

Enrichment for RNA molecules that bind a Diels-Alder transition state analog

RNA molecules that bind a transition state analog for a Diels-Alder reaction (Kd = 0.35 +/- 0.05 mM) were isolated from a starting pool of approximately 10(14) sequences by affinity chromatography. After the initial rise and plateau of the amount of RNA that eluted with soluble analog, a step gradient elution was used to further enrich the pool for sequences with higher affinities for the target. To our knowledge, the isolation of RNA molecules that bind either a nonplanar or a hydrophobic ligand has not been reported previously. A conserved nucleotide sequence and secondary structure present in many of the RNA molecules are necessary but not sufficient for binding the analog. No catalysts of the targeted Diels-Alder reaction were found among the binders. The absence of catalysis contrasts with previous successful experiments with antibodies and suggests that other strategies may be needed to identify oligonucleotides with diverse catalytic activities.

Possible role of aminoacyl-RNA complexes in noncoded peptide synthesis and origin of coded synthesis

Images

Landscapes: complex optimization problems and biopolymer structures

The evolution of RNA molecules in replication assays, viroids and RNA viruses can be viewed as an adaptation process on a 'fitness' landscape. The dynamics of evolution is hence tightly linked to the structure of the underlying landscape. Global features of landscapes can be described by statistical measures like number of optima, lengths of walks and correlation functions. The evolution of a quasispecies on such landscapes exhibits three dynamical regimes depending on the replication fidelity: Above the "localization threshold" the population is centered around a (local) optimum. Between localization and "dispersion threshold" the population is still centered around a consensus sequence, which, however, changes in time. For very large mutation rates the population spreads in sequence space like a gas. The critical mutation rates separating the three domains depend strongly on characteristics properties of the fitness landscapes. Statistical characteristics of RNA landscapes are accessible by mathematical analysis and computer calculations on the level of secondary structures: these RNA landscapes belong to the same class as well known optimization problems and simple spin glass models. The notion of a landscape is extended to combinatory maps, thereby allowing for a direct statistical investigation of the sequence structure relationships of RNA at the level of secondary structures. Frequencies of structures are highly non-uniform: we find relatively few common and many rare ones, as expressed by a generalized form of Zipf's law. Using an algorithm for inverse folding we show that sequences sharing the same structure are distributed randomly over sequence space. Together with calculations of structure correlations and a survey of neutral mutations this provides convincing evidence that RNA landscapes are as simple as they could possibly be for evolutionary adaptation: Any desired secondary structure can be found close to an arbitrary initial sequence and at the same time almost all bases can be substituted sequentially without ever changing the shape of the molecule. Consequences of these results for evolutionary optimization, the early stages of life, and molecular biotechnology are discussed.

Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation

We propose a phylogeny for the evolution of tRNA that is based on the ubiquity and conservation of tRNA-like structures in the replication of contemporary genomes. This phylogeny is unique in suggesting that the function of tRNA in replication dates back to the very beginnings of life on earth, before the advent of templated protein synthesis. The origin we propose for tRNA has distinct implications for the order in which other components of the modern translational apparatus evolved. We further suggest that the "top half" of modern tRNA-a coaxial stack of the acceptor stem on the T psi C arm--is the ancient structural and functional domain and that the "bottom half" of tRNA--a coaxial stack of the dihydrouracil arm on the anticodon arm--arose later to provide additional specificity.

Inventing and improving ribozyme function: rational design versus iterative selection methods

Two major strategies for generating novel biological catalysts exist. One relies on our knowledge of biopolymer structure and function to aid in the 'rational design' of new enzymes. The other, often called 'irrational design', aims to generate new catalysts, in the absence of detailed physicochemical knowledge, by using selection methods to search a library of molecules for functional variants. Both strategies have been applied, with considerable success, to the remodeling of existing ribozymes and the development of ribozymes with novel catalytic function. The two strategies are by no means mutually exclusive, and are best applied in a complementary fashion to obtain ribozymes with the desired catalytic properties.

Expanding the scope of RNA catalysis

The basic notions of transition state theory have been exploited in the past to generate highly selective catalysts from the vast library of antibody molecules in the immune system. These same ideas were used to isolate an RNA molecule, from a large library of RNAs, that catalyzes the isomerization of a bridged biphenyl. The RNA-catalyzed reaction displays Michaelis-Menten kinetics with a catalytic rate constant (kcat) of 2.8 x 10(-5) per minute and a Michaelis constant (Km) of 542 microM; the reaction is competitively inhibited by the planar transition state analog with an inhibition constant (Ki) value of approximately 7 microM. This approach may provide a general strategy for expanding the scope of RNA catalysis beyond those reactions in which the substrates are nucleic acids or nucleic acid derivatives.

Retroviral insertions in the murine His-1 locus activate the expression of a novel RNA that lacks an extensive open reading frame

The His-1 locus is a common site of viral insertion in murine myeloid leukemias induced by the wild mouse ecotropic retrovirus, CasBrM. In this report, we describe the cloning of a novel gene at the His-1 locus and show that His-1 expression is associated with the transformed phenotype. Northern (RNA) blot analysis identified His-1 transcripts in four transformed myeloid cell lines but in no normal tissues examined. Two of these cell lines were derived from retrovirus-induced myeloid leukemias that harbor integrated proviruses which drive His-1 gene expression by promoter insertion. The two other cell lines expressed a discrete 3-kb His-1 RNA that is derived from a novel gene consisting of three exons that span 6 kb on mouse chromosome 2. The His-1 gene is conserved as a single-copy sequence in multiple vertebrate species and is expressed as a spliced and polyadenylated RNA. A protein-coding region is not evident from analysis of the His-1 sequence because of the presence of multiple small open reading frames, none of which are greater than 219 bp. This lack of an extensive open reading frame is an unusual feature that is shared by other RNA molecules believed to function in the absence of translation.

An extended cellular space method for simulating autocatalytic oligonucleotides

Self-replicating nucleotides and other self-replicating molecules are an active area of study today by organic chemists. Such studies are important for improving our understanding of the origins of life. Computational studies of self-replicating molecules could increase our insight into their properties, but existing computational techniques have been limited in their usefulness for such reactions (numerical simulation of differential equations requires reaction rate constants that are difficult to obtain, cellular automata models are too restrictive for modeling molecular movements and bindings, etc.). We have thus developed an efficient modified cellular automata method that supports the study of self-replicating oligonucleotides. We explain this method and illustrate its use with a specific self-replicating (autocatalytic) deoxyribohexanucleotide.

Retroviral insertions in the murine His-1 locus activate the expression of a novel RNA that lacks an extensive open reading frame

The His-1 locus is a common site of viral insertion in murine myeloid leukemias induced by the wild mouse ecotropic retrovirus, CasBrM. In this report, we describe the cloning of a novel gene at the His-1 locus and show that His-1 expression is associated with the transformed phenotype. Northern (RNA) blot analysis identified His-1 transcripts in four transformed myeloid cell lines but in no normal tissues examined. Two of these cell lines were derived from retrovirus-induced myeloid leukemias that harbor integrated proviruses which drive His-1 gene expression by promoter insertion. The two other cell lines expressed a discrete 3-kb His-1 RNA that is derived from a novel gene consisting of three exons that span 6 kb on mouse chromosome 2. The His-1 gene is conserved as a single-copy sequence in multiple vertebrate species and is expressed as a spliced and polyadenylated RNA. A protein-coding region is not evident from analysis of the His-1 sequence because of the presence of multiple small open reading frames, none of which are greater than 219 bp. This lack of an extensive open reading frame is an unusual feature that is shared by other RNA molecules believed to function in the absence of translation.

Inhibition of protein synthesis by an efficiently expressed mutation in the yeast 5.8S ribosomal RNA

Recent studies on the inhibition of protein synthesis by specific anti 5.8S rRNA oligonucleotides strongly suggested that this RNA plays an important role in eukaryotic ribosome function. To evaluate this possibility further, a ribosomal DNA transcription unit from Schizosaccharomyces pombe was cloned into yeast shuttle vectors with copy numbers ranging from 2 to approximately 90 per cell; to allow direct detection of expressed RNA and to disrupt the function of the 5.8S rRNA molecule, a five base insertion was made in a universally conserved GAAC sequence. The altered mobility of the mutant RNA was readily detected by gel electrophoresis and analyses indicated that mutant RNA transcription reflected the ratio of plasmid to endogenous rDNA. The highest copy number plasmid resulted in about 40-50% mutant RNA. This mutant RNA was readily integrated into the ribosome structure resulting in an in vivo ribosome population which was also about 40-50% mutant; the rates of growth and protein synthesis were equally reduced by approximately 40%. A comparable level of inhibition in protein synthesis was demonstrated in vitro and polyribosomal profiles revealed a consistent increase in size. Subsequent RNA analyses indicated a normal distribution of mutant RNA in both monoribosomes and polyribosomes, but elevated tRNA levels in mutant polyribosomes. Additional mutations in alternate GAAC sequences revealed similar but cumulative effects on both protein synthesis and polyribosome profiles. Taken together, these results suggest little or no effect on initiation but provide in vivo evidence of a functional role for the 5.8S rRNA in protein elongation.

Dual hydrolytic role for Pb(II) ions

RNA phosphodiester bonds can be cleaved by metal ions, of which Pb2+ is one of the most effective. It can cleave both generally and site-specifically, depending on the substrate and the conditions. In addition, metal ions are also known to cleave ester bonds between amino acid and the 3'-end of transfer RNA. Here we report that in aminoacylated transfer RNA, Pb2+ ions cleave internucleotide bonds in the 3'-end of tRNA and also cleaves the bond between tRNA and its amino-acid, attached at the 3'-end via an ester bond to the terminal ribose in aminoacyl tRNA. The two reactions proceed at different rates. The rate of deacylation is significantly faster than the rate of cleavage of phosphodiester bonds, with a pH-optimum of 7. This dual hydrolytic role is not seen for other metal ions examined, namely Zn(II), Cd(II) and Mn(II). The rate of the two kinds of hydrolyses by Pb2+ ions is compared with that of other metal-ions. The mechanism of cleavage is investigated further by modification of the 3'-end of tRNA.

The efficiency and versatility of catalytic RNA: implications for an RNA world

Because RNA is chemically and structurally dissimilar from protein, the finding of catalytic activity in RNA was initially surprising. Quantitative measurements of reaction rates show that RNA can be as efficient a catalyst as protein. On the other hand, the potential versatility of RNA to catalyze diverse types of reactions has only begun to be explored. Understanding the efficiency and versatility of RNA as a catalyst helps us evaluate origin-of-life scenarios involving self-replicating RNA, and may explain why RNA catalysis remains important in contemporary cells.

Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme

The L-21 ScaI ribozyme catalyzes sequence-specific cleavage of an oligonucleotide substrate. Cleavage is preceded by base pairing of the substrate to the internal guide sequence (IGS) at the 5' end of the ribozyme to form a short RNA duplex (P1). Tertiary interactions between P1 and the catalytic core dock P1 into the active site of the ribozyme. These include interactions between the catalytic core and 2'-hydroxyls of the substrate at nucleotide positions -3u and perhaps -2c. In this study, 2'-hydroxyls of the IGS strand that contribute to P1 recognition by the ribozyme are identified. IGS 2'-hydroxyls (nucleotide positions 22-27) were individually modified to either 2'-deoxy or 2'-methoxynucleotides within full-length semisynthetic L-21 ScaI ribozymes generated using T4 DNA ligase. Thermodynamic and kinetic characterization of the resulting IGS variant ribozymes justify the following conclusions: (i) 2'-Hydroxyls at nucleotide positions G22 and G25 play a critical energetic role in docking P1 into the catalytic core, contributing 2.6 and 2.1 kcal.mol-1, respectively. (ii) The loss of binding energy is manifest primarily as an increase in the rate of dissociation. Because turnover for the wild-type ribozyme is limited by product dissociation, G22 and G25 deoxy variants display up to a 20-fold increase in the multiple-turnover rate at saturating substrate. (iii) IGS tertiary interactions are energetically coupled with the tertiary interactions made to the substrate, consistent with P1 becoming undocked from its binding site in J8/7 upon substitution of either the G22 or G25 2'-hydroxyl. (iv) The G22 deoxy variant loses energetic coupling between guanosine and substrate binding, suggesting that in this variant the P1 helix is also undocked from its binding site in J4/5, the proposed site of guanosine and substrate interaction. Therefore, in combinations with previous studies four P1 2'-hydroxyls are implicated as important for docking. The contributions of the 2'-hydroxyl tertiary interactions are not equivalent and follow the hierarchical order G22 > G25 >> -3u > -2c. Because the G22 2'-hydroxyl appears to mediate P1 docking into both J8/7 and J4/5, it may serve as the molecular linchpin for the recognition of P1 by the catalytic core.