Beta Replicase Research Articles

Importance of Metastable RNA Folding in Template-Replicase Interactions

We consider the autocatalytic synthesis of MDV-1 RNA by Q beta replicase, which proceeds by template-instructed replication. We predict the effect of a particular point mutation in the sequence on the overall doubling time and conjecture its role on the recognition step. The mutation considered destabilizes the folding of the internal recognition site. The theoretical analysis is based on the calculation of nonequilibrium re-folding events which occur in the RNA chains as they are being synthesized. Free-energy minima are irrelevant. In order to test the theoretical findings, we incubate both the natural template and the mutant simultaneously, in the presence of the replicase. The experiment reveals that the mutation facilitates the enzyme-template interaction, thus enhancing recognition. However, examining the exponential phase of the replication kinetics, where the enzyme is in large excess with respect to the RNA species, we can conclude that the mutant presents a larger overall doubling time, in good agreement with our theoretical findings.

Quantitative assays based on the use of replicatable hybridization probes.

Amplifiable hybridization probes--molecules with a probe sequence embedded within the sequence of a replicatable RNA--will promote the development of sensitive clinical assays. To demonstrate their utility, we prepared a recombinant RNA that contained a 30-nucleotide-long probe complementary to a conserved region of the pol gene in human immunodeficiency virus type 1 (HIV-1) mRNA. Test samples were prepared, each containing a different number of HIV-1 transcripts that served as simulated HIV-1 mRNA targets. Hybridizations were carried out in a solution containing the chaotropic salt, guanidine thiocyanate. Probe-target hybrids were isolated by reversible target capture on paramagnetic particles. The probes were then released from their targets and amplified by incubation with the RNA-directed RNA polymerase, Q beta replicase (EC 2.7.7.48). The replicase copied the probes in an exponential manner: after each round of copying, the number of RNA molecules doubled. The amount of RNA synthesized in each reaction (approximately 50 ng) was sufficient to measure without using radioisotopes. Kinetic analysis of the reactions demonstrated that the number of HIV-1 targets originally present in each sample could be determined by measuring the time it took to synthesize a particular amount of RNA (the longer the synthesis took, the fewer the number of targets originally present). The results suggest that clinical assays involving replicatable hybridization probes will be simple, accurate, sensitive, and automatable.

Correlation of pause sites in MDV-1 RNA replication with kinetic refolding of the growing chain. A Monte Carlo simulation of the Markov process.

We consider a template-instructed MDV-1 RNA replication catalyzed by Q beta replicase. The relaxation of the effective binding of the growing chain to the enzyme is simulated, considering a Markov process where refolding events in the chain are concomitant with chain elongation events. When realistic transition probabilities are considered, it becomes evident that the pause sites in replication are due to relaxation of the binding by folding of the growing chain.

An in vivo recombinant RNA capable of autocatalytic synthesis by Qβ replicase

A variety of small RNAs ranging from tens to hundreds of nucleotides in length grow autocatalytically in a Q beta replicase (Q beta phage RNA-dependent RNA polymerase) reaction in the absence of added template, and similar RNAs are found in Q beta phage-infected Escherichia coli cells. Three such RNAs have been sequenced. One of them that is 221 nucleotides (nt) long ('MDV-1' RNA) has been found to be partially homologous to Q beta phage RNA 8, which might be considered as an indication of its origination from by-products of the Q beta RNA replication. To gain further insight into the origin and function of these RNAs, we have sequenced a new RNA, 120 nt long, isolated from the products of spontaneous synthesis by the nominally RNA-free Q beta replicase preparation. The minus strand of this RNA appeared to be a recombinant RNA, composed of the internal fragment of Q beta RNA (approximately 80 nt long) and the 33-nt-long 3'-terminal fragment of E. coli tRNA(1Asp). This seems to be the first strong indication of RNA recombination in bacterial cells. The various implications of this finding are discussed.

Replication and evolution of short-chained RNA species replicated by Q beta replicase.

RNA genomes are quite common for viruses, but extremely rare in cellular organisms—RNA plasmids (Wickner 1986) may be regarded as inherited relics of viral infections—and thus RNA replication does not occur in the normal processing of cellular genetic information. The best-understood copying mechanism of viral RNA is the RNA-dependent RNA replication system of RNA coliphages (lentiviridae). It utilizes a single enzyme, called a replicase, and differs fundamentally in several respects from DNA replication:

Enzymatic synthesis and some properties of a model primitive tRNA.

A model primitive tRNA with the nucleotide sequence GGCCAAAAAAAGGCCp was synthesized using T4 RNA ligase. The nucleotide sequence of this newly synthesized oligonucleotide was confirmed by ladder analysis of several enzymatic digestion products. The secondary structure of the oligonucleotide was examined by comparison of the products of its digestion by single- and double-strand-specific nucleases with those of the digestion of the intermediate oligonucleotide GGCCAAAAAAAOH. The results indicated that the two GGCC segments of the 5' and 3' ends of the model tRNA may form base pairs in solution. The same conclusion was derived from the result of affinity-column chromatography of the model oligonucleotide. When 32pGGCCAAAAAAAGGCCOH was passed through a poly(U)-agarose column, about 70% of the applied sample bound to the poly(U)-agarose. In contrast, when the model oligonucleotide was passed through a poly(C)-agarose column, only 15% of the sample bound to the poly(C)-agarose. These results indicate that the newly synthesized oligonucleotide adopts a hairpin structure in solution. Two aspects of a potential biological activity of the synthetic model tRNA were examined. It was found that the oligonucleotide can bind to poly(U)-programmed 30S ribosomes and is recognized by Q beta replicase as a template for RNA synthesis.

Template-free RNA synthesis by Qβ replicase

In the absence of extraneously added template, standard preparations of Q beta replicase spontaneously synthesize RNA in vitro, possibly as a result of RNA contamination. Using special enzyme purifications, Sumper and Luce presented evidence that self-replicating RNA not present ab initio can grow out of 'template-free' incorporation mixtures. In contrast to DNA polymerase I and RNA polymerase, which also show de novo synthesis, the products synthesized 'de novo' by Q beta replicase are RNA species containing nonrepetitive sequences of defined lengths which differ between experiments, even when synthesized under identical conditions, in fingerprints, chain lengths and kinetic parameters. Kinetic analysis of the de novo processes distinguished it from template-instructed synthesis and excluded an assumption of self-replicating RNA contamination. These conclusions were questioned recently by Hill and Blumenthal, who claimed to show that highly purified Q beta replicase preparations cannot produce RNA de novo. We now present evidence that, under the conditions required for de novo synthesis, Q beta replicase prepared according to their method is also capable of de novo synthesis. Furthermore, we show that Q beta replicase condenses nucleoside triphosphates to more or less random oligonucleotides.

Secondary structure as primary determinant of the efficiency of ribosomal binding sites in Escherichia coli.

Using a previously described vector (pKL203) we fused several heterologous ribosomal binding sites (RBSs) to the lacZ gene of E. coli and then studied the variation in expression of the fusions. The RBSs originated from bacteriophage Q beta and MS2 genes and the E. coli genes for elongation factor EF-Tu A and B and ribosomal protein L11 (rplK). The synthesis of the lacZ fusion proteins was measured by an immuno precipitation method and found to vary at least 100-fold. Lac-specific mRNA synthesis follows the variation in protein production. It appears that there is a correlation between the efficiency of an RBS to function in the expression of the fused gene and the lack of secondary structure, involving the Shine and Dalgarno nucleotides (SDnts) and/or the initiation codon. This efficiency is context dependent. The sequence of the SD nts and the length and sequence of the spacer region up to the initiation codon alone are not able to explain our results. Deletion mutations, created in the phage Q beta replicase RBS, reveal a complex pattern of control of expression, probably involving the use of a "false" initiation site.

Kinetics of RNA replication: competition and selection among self-replicating RNA species

The process of Darwinian selection in the self-replication of single-stranded RNA by Q beta replicase was investigated by analytical and computer-simulation methods. For this system, the relative population change of the competing species was found to be a useful definition of selection value, calculable from measurable kinetic parameters and concentrations of each species. Critical differences in the criteria for selection were shown to pertain for replicase/RNA ratios greater than or less than 1, for the case that formation of double-stranded RNA occurs and when comparisons are made of closed with open systems. At a large excess of enzyme, RNA species grow exponentially without interfering with each other, and selection depends only on the fecundity of the species, i.e., their overall replication rates. For RNA concentrations greater than the replicase concentration, the selection of species is governed by their abilities to compete for enzyme. Under conditions where formation of double strands occurs, competition leads to a coexistence of the species; the selection values vanish, and the concentration ratios depend only on the template binding and double-strand formation rates. The approach to coexistence is rapid, because when its competitors are in a steady state, a species present in trace amount is amplified exponentially. When formation of hybrid double strands occurs at a substantial rate, coexistence of hybridizing species is essentially limited to cases where the formation rate of heterologous double strands is smaller than the geometric mean of the formation rates of the homologous double strands. At limiting cases, e.g. in the steady states, simple analytical expressions for the main aspects of the selection process were found. Experimental data support the analytical expressions and the simulations.

Transcription from bacteriophage T7 and SP6 RNA polymerase promoters in the presence of 3'-deoxyribonucleoside 5'-triphosphate chain terminators.

RNA synthesis by T7 RNA polymerase or SP6 RNA polymerase is 100-1000 times more sensitive to the presence of the 3'-deoxyribonucleoside 5'-triphosphate chain terminators than is RNA synthesis by Escherichia coli RNA polymerase or Q beta replicase. These ribonucleotide analogues do not alter the specificity of each polymerase for its own promoters nor do they alter the site at which synthesis is initiated. Transcription by T7 RNA polymerase or SP6 RNA polymerase in the presence of relatively low concentrations of these chain terminators offers a useful route for determining the nucleotide sequence of any DNA segment that is inserted immediately downstream from a homologous bacteriophage promoter. This sequencing procedure was used to explore the effects that different dinucleotides have on the specificity of initiation at two different T7 RNA polymerase promoters.

The activity of discrete fragments of ribosomal protein S1 in Q beta replicase function.

As a subunit of bacteriophage Q beta replicase, ribosomal protein S1 is required for tight binding of the enzyme to Q beta RNA and for the initiation of Q beta RNA transcription. To compare these properties of S1 with its functions in protein synthesis, we have reconstituted altered replicase enzymes by adding discrete fragments of S1 to Q beta replicase lacking S1 (R(-S1]. We show that the NH2-terminal region of S1 is required for S1 subunit interactions in replicase since a trypsin-resistant fragment (denoted S1-F1) lacking the NH2-terminal 31% of S1 is functionally inactive and does not seem to bind to R(-S1). Previous studies with S1-F1 indicated that this NH2-terminal region is required for S1 to bind to the ribosome. Our results also show that the COOH-terminal region of S1 is dispensable for S1's function in replicase because a mutant of S1 (m1-S1) lacking 21% of the COOH-terminal portion of the chain is as active as wild type S1 in replicase and binds to R(-S1) with comparable affinity. In protein synthesis, the mutant m1-S1 is known to substitute for S1 but is only about 75% as efficient as wild type S1.

Kinetics of ribonucleic acid replication

The reaction kinetics of single-stranded RNA replication were investigated by means of analytical and computer simulation methods. A model reaction mechanism is proposed that is in accord with the extensive experimental data available for the replication of various templates by the enzyme Q beta replicase. Despite the complexity of this mechanism, conventional concepts of steady-state and dynamic enzyme catalysis and plausible values of the rate and stability constants for the elementary reactions suffice to provide detailed understanding of RNA replication kinetics. The main features can be described with simple formulas that are analogous to traditional descriptions of enzyme kinetics.

Localization of the Q Replicase Recognition Site in MDV-1 RNA

Fragments of MDV-1 RNA (a small, naturally occurring template for Q beta replicase) that were missing nucleotides at either their 5' end or their 3' end were still able to form a complex with Q beta replicase. By assaying the binding ability of fragments of different length, it was established that the binding site for Q beta replicase is determined by nucleotide sequences that are located near the middle of MDV-1 RNA. Fragments missing nucleotides at their 5' end were able to serve as templates for the synthesis of complementary strands, but fragments missing nucleotides at their 3' end were inactive, indicating that the 3'-terminal region of the template is required for the initiation of RNA synthesis. The nucleotide sequences of both the 3' terminus and the central binding region of MDV-1 (+) RNA are almost identical to sequences at the 3' terminus and at an internal region of Q beta (-) RNA.

Terminal adenylation in the synthesis of RNA by Q beta replicase.

We investigated the apparent requirement that Q beta replicase must add a nontemplated adenosine to the 3' end of newly synthesized RNA strands. We used abbreviated MDV-1 (+)-RNA templates that lacked either 62 or 63 nucleotides at their 5' end in Q beta replicase reactions. The MDV-1 (-)-RNA strands synthesized from these abbreviated (+)-strand templates were released from the replication complex, yet they did not possess a nontemplated 3'-terminal adenosine. These results imply that, despite observations that all naturally occurring RNAs synthesized by Q beta replicase possess a nontemplated 3'-adenosine, the addition of an extra adenosine is not an obligate step for the release of completed strands. Since the abbreviated templates lacked a normal 5' end, it is probable that a particular sequence at the 5' end of the template is required for terminal adenylation to occur.

Q beta replicase containing a Bacillus stearothermophilus elongation factor.

We purified Q beta replicase containing EF-Ts from Bacillus stearothermophilus in place of the homologous polypeptide from Escherichia coli. The hybrid enzyme was fully active in the transcription of a variety of templates. It was found to be qualitatively similar to native Q beta replicase with respect to a variety of parameters which measure the efficiency of initiation of RNA synthesis. The results demonstrated that Q beta replicase can tolerate substantial alterations in the EF-Tu X Ts component of the enzyme. These alterations resulted in only minor perturbations of catalytic properties.

Does Q beta replicase synthesize RNA in the absence of template?

Q beta replicase, in the absence of added template, will synthesize RNA autocatalytically. A variety of small RNa species, termed '6S RNAs' are generated. As this reaction purportedly occurs in the absence of template, it has been termed 'de novo' RNA synthesis. The question of whether Q beta replicase can polymerize replicatable RNA molecules, without instruction from a template, has important evolutionary implications. The finding that Q beta replicase was able to synthesize RNA de novo was based on (1) failure to find contaminating RNA in Q beta replicase preparations; (2) differences in the sizes of products of apparently identical reactions; and (3) kinetic differences between template-instructed and de novo reactions. Here wer describe a procedure for production of Q beta replicase lacking one of its subunits, ribosomal protein S1, involving column chromatography in the presence of a low concentration of urea. We show that the resulting highly purified enzyme will not synthesize detectable RNA in the absence of added template. We show also that the ability to perform a reaction kinetically indistinguishable from the de novo synthesis reaction can be restored to the highly purified enzyme by adding a heat-stable, alkali-labile component of Q beta replicase preparations. Thus our findings suggest that, in the novo reaction, Q beta replicase is replicating previously undetected contaminating RNA molecules.

Q beta replicase containing altered forms of ribosomal protein S1.

Transcription of Q beta RNA replicase requires that the host-encoded Escherichia coli ribosomal protein S1 be present as a subunit of the replicase. To determine whether the activities of S1 in protein synthesis are operational in Q beta RNA transcription, we formed altered replicase enzymes by reconstituting replicase lacking S1 (R(-S1)) with modified S1 species whose properties in nucleic acid binding and protein synthesis had been previously established. S1 derivatized with N-ethylmaleimide reconstitutes a modified replicase that is 81% as active as replicase reconstituted with unmodified S1. S1 derivatized with N-ethylmaleimide and unmodified S1 bind with comparable affinity to R(-S1) (1 X 10(8) M-1). These results indicate that the helix-unwinding properties of S1, which are known to be inactivated by N-ethylmaleimide modification, are not required for Q beta RNA transcription and that the sulfhydryl-derivatized region of S1 is not utilized in replicase subunit contacts. In contrast with its established ability to replace E. coli S1 on the ribosome, Caulobacter crescentus S1 does not reconstitute Q beta RNA transcription activity when added to R(-S1). Our results suggest this inactivity may be due to poor binding to R(-S1).

Transfer RNA cross-linked to the elongation factor Tu subunit of Q beta replicase does not inhibit Q beta RNA replication.

One of the four subunits of bacteriophage Q beta RNA replicase is elongation factor Tu (EF-Tu), the host aminoacyl-tRNA (AA-tRNA) binding protein. To determine whether the RNA polymerase activity requires the tRNA binding site of EF-Tu, we reconstituted replicase with EF-Tu . GTP covalently bound to AA-tRNA. This cross-linked ternary complex (XLTC) was formed by the reaction of N epsilon-bromoacetyl-Lys-tRNA with EF-Tu-GTP. In an EF-Tu-dependent system for the reconstitution of replicase, XLTC restored polymerase activity at least as well as an equivalent amount of EF-Tu. Replicase reconstituted with XLTC was resolved from replicase containing EF-Tu by chromatography on phosphocellulose, a result which confirmed that the tRNA moiety was incorporated into the enzyme. Chromatographic analysis of reconstitution mixtures revealed that XLTC was incorporated into replicase as extensively as EF-Tu. From these results, it appears that the AA-tRNA binding site on EF-Tu is not required for the assembly or activity of Q beta RNA replicase. Furthermore, because the tRNA macromolecule is cross-linked to His-66 of the EF-Tu, the region surrounding His-66 must normally be exposed on the surface of the replicase.

In vitro replication of bacteriophage GA RNA. Involvement of host factor(s) in GA RNA replication.

A certain factor(s) derived from Escherichia coli was found to extensively stimulate RNA synthesis by the RNA replicase of phage GA. This factor(s), named GA-HF (host factor(s) for GA RNA replication), was partially purified from an uninfected cell extract and characterized. In the presence of GA-HF, GA replicase synthesized 50-100 times more RNA than was synthesized in its absence, and was capable of synthesizing both the viral strand as well as its complementary strand. This factor(s) could not be replaced by HFI, which is necessary for the replication of Q beta RNA by Q beta replicase. In the presence of GA-HF, the GA RNA replication system has a characteristic template specificity. Group I and II phage RNAs, but none of the Group III and IV phage RNAs, showed template activity.

Roles of the host polypeptides in Q beta RNA replication. Host factor and ribosomal protein S1 allow initiation at reduced GTP concentration.

Initiation of transcription of favored templates by Q beta replicase requires a much lower GTP concentration than does transcription of templates that are selected against. Although the enzyme requires a high GTP concentration to initiate transcription of Q beta RNA, the presence of the host factor substantially reduces the GTP concentration requirement. In addition, the Q beta replicase preparation must contain ribosomal protein S1 for initiation to occur at low GTP. Mn2+ ions, which can substitute for host factor in Q beta RNA replication in vitro, and which reduce the template specificity of Q beta replicase, also reduce the GTP requirement for initiation. But while Mn2+ ions produce this effect with all templates, host factor is specific for Q beta RNA. When both host factor and Mn2+ are present, transcription of Q beta RNA occurs at a much lower GTP concentration. Thus, host factor and Mn2+ appear to reduce the GTP concentration requirement by different mechanisms.