A new method for the purification of Q RNA-dependent RNA polymerase

Facile production and rapid purification of functional recombinant Qβ replicase heterotetramer complex

We describe an improved method for the production of recombinant Qβ replicase heterotetramer. The successful expression of the soluble Qβ RNA polymerase complex depends on the EF-Ts and EF-Tu subunits being co-expressed prior to β-subunit expression. Efficient co-expression requires two different inducible operons to co-ordinate the expression of the heterotrimer. The complete heterotetramer enzyme complex is achieved by production of the recombinant S1-subunit of Qβ replicase in a separate host. This approach represents a facile way for producing and purifying large amounts of soluble and active recombinant Qβ replicase tetramer without the necessity of a His-tag for purification.

Identification of two forms of Q{beta} replicase with different thermal stabilities but identical RNA replication activity

The enzyme Qβ replicase is an RNA-dependent RNA polymerase, which plays a central role in infection by the simple single-stranded RNA virus bacteriophage Qβ. This enzyme has been used in a number of applications because of its unique activity in amplifying RNA from an RNA template. Determination of the thermal stability of Qβ replicase is important to gain an understanding of its function and potential applications, but data reported to date have been contradictory. Here, we provide evidence that these previous inconsistencies were due to the heterogeneous forms of the replicase with different stabilities. We purified two forms of replicase expressed in Escherichia coli, which differed in their thermal stability but showed identical RNA replication activity. Furthermore, we found that the replicase undergoes conversion between these forms due to oxidation, and the Cys-533 residue in the catalytic β subunit and Cys-82 residue in the EF-Tu subunit of the replicase are essential prerequisites for this conversion to occur. These results strongly suggest that the thermal stable replicase contains the intersubunit disulfide bond between these cysteines. The established strategies for isolating and purifying a thermally stable replicase should increase the usefulness of Qβ replicase in various applications, and the data regarding thermal stability obtained in this study may yield insight into the precise mechanism of infection by bacteriophage Qβ.

Functional Qbeta replicase genetically fusing essential subunits EF-Ts and EF-Tu with beta-subunit

Qbeta replicase, an RNA-dependent RNA polymerase of RNA coliphage Qbeta, is a heterotetramer composed of a phage-encoded beta-subunit and three host-encoded proteins: the ribosomal protein S1 (alpha-subunit), EF-Tu, and EF-Ts. Several purification methods for Qbeta replicase were described previously. However, in our efforts to improve the production of Qbeta replicase, a substantial amount of the beta-subunit overproduced in Escherichia coli cells was found as insoluble aggregates. In this paper, we describe two kinds of method of producing Qbeta replicase. In one kind, both EF-Tu and EF-Ts subunits were expressed with the beta-subunit, and in the other kind, the beta-subunit was genetically fused with EF-Tu and EF-Ts. The fused protein, a single-chain alpha-less Qbeta replicase, was mostly found in the soluble fraction and could be readily purified. These results pave the way for the large-scale production of the highly purified form of this enzyme.

Internal and 3' RNA initiation by Qbeta replicase directed by CCA boxes

RNA initiation by Qbeta replicase directed by the short-sequence CCA at the 3'-end of all RNAs amplified by this enzyme has been studied. Most CCA repeats in an RNA consisting of 12 CCAs serve as independent sites of de novo RNA initiation, with initiation occurring opposite the 3'-C residue of each CCA. Qbeta replicase is thus capable of internal initiation remote from the 3'-end, although predominant initiation occurs close to the 3'-end. The precise 3'-terminal sequence in (CCA)(n)-containing RNAs influences the number and position of active initiation sites near the 3'-terminus. C residues are required at the initiation site, whereas the position of purines (especially A residues) influences the selection of initiation sites. The template activity of (CCA)(n) RNAs is positively correlated with the number of CCA repeats. Three CCA repeats added to the 3'-end of a nontemplate 83-nt RNA are sufficient to activate transcription by Qbeta replicase. These experiments show that CCA boxes can act as strong initiation sites in the absence of specific cis-acting signals derived from Qbeta RNA, although the efficiency of initiation is modulated by surrounding sequence.

Recognition of bacteriophage Qbeta plus strand RNA as a template by Qbeta replicase: role of RNA interactions mediated by ribosomal proteins S1 and host factor

RNA-protein interactions between bacteriophage Qbeta plus strand RNA and the components of the Qbeta replicase system were studied by deletion analysis. Internal, 5'-terminal and 3'-terminal deletions were assayed for template activity with replicase in vitro. Of the two internal binding sites previously described for replicase, we found that the S-site (map position 1247 to 1346) could be deleted without any significant effect on template activity, whereas deletion of the M-site (map position 2545 to 2867) resulted in a strong inactivation and a high salt sensitivity of the residual activity. Binding complexes of the deletion mutant RNAs with the different proteins involved in Qbeta RNA replication were analysed by electron microscopy. The formation of looped complex structures, previously reported and explained as simultaneous interactions with replicase at the S and the M-site, was abolished by deleting the S-site but, surprisingly, not by deleting the M-site. The same types of complexes observed with replicase were also formed with purified protein S1 (the alpha subunit of replicase), suggesting that these internal interactions with Qbeta RNA are mediated by the S1 protein. The Qbeta host factor, a protein required for the template activity of the Qbeta plus strand, was reported earlier to form similar complexes by binding to the S and M-sites (or adjacent sites) and in addition to the 3'-end, resulting in double-looped structures. The patterns of looped complexes observed with the deletion mutant RNAs suggest that the binding of host factor might not involve the S and M-sites themselves but adjacent downstream sites. An additional internal host factor interaction near map position 2300 was detected with several mutant RNAs. Qbeta RNA molecules with 3'-truncations formed 3'-terminal loops with similar efficiency as wild-type RNA, indicating that recognition of the 3'-end by host factor is not dependent on a specific 3'-terminal base sequence.

RNA sequencing using fluorescent-labeled dideoxynucleotides and automated fluorescence detection

Although dideoxy terminated sequencing of RNA, using reverse transcriptase and oligodeoxynucleotide primers, is now a well established method, the accuracy is limited by sequence ambiguities due to unspecific chain termination events. A protocol is described which circumvents these ambiguities by using fluorescence labels tagged to dideoxynucleotides. Only chain terminations caused by dideoxynucleotides were detected while premature terminated cDNA's remain undetectable. In addition, the remaining multiple signals at nucleotide positions can be assigned to sequence heterogeneities within the RNA sequence to be determined.

Transcription of a bacteriophage lambda DNA site blocks growth of Escherichia coli

The rap mutation in Escherichia coli prevents the growth of bacteriophage lambda. Phage mutations that overcome rap inhibition (bar) have been mapped to loci in the pL operon. We cloned and sequenced three mutations in two of these loci: barIa to the left arm of the lambda attachment site (attP) and barII in the ssb (ea10) gene. The mutations represent single base-pair changes within nearly identical 16-base-pair DNA segments. Each mutation disrupts a sequence of dyad symmetry within the segment. Plasmids carrying a bar+ sequence downstream to an active promoter are lethal to rap, but not rap+, bacteria. The bar sequences isolated from the lambda bar mutants are not lethal. We synthesized a minimal lambda barIa+ sequence, 5'-TATATTGATATTTATATCATT, and cloned it downstream to an inducible promoter. When transcribed, this sequence is sufficient to kill a rap strain.

Traveling waves of in vitro evolving RNA

Populations of short self-replicating RNA variants have been confined to one side of a reaction-diffusion traveling wave front propagating along thin capillary tubes containing the Q beta viral enzyme. The propagation speed is accurately measurable with a magnitude of about 1 micron/sec, and the wave persists for hundreds of generations (of duration less than 1 min). Evolution of RNA occurs in the wavefront, as established by front velocity changes and gel electrophoresis of samples drawn from along the capillary. The high population numbers (approximately equal to 10(11], their well-characterized biochemistry, their short generation time, and the constant conditions make the system ideal for evolution experiments. Growth is monitored continuously by excitation of an added RNA-sensitive fluorescent dye, ethidium bromide. An analytic expression for the front velocity is derived for the multicomponent kinetic scheme that reduces, for a high RNA-enzyme binding constant, to the Fisher form v = 2 square root of kappa D, where D is the diffusion constant of the complex and kappa is the low-concentration overall replication rate coefficient. The latter is confirmed as the selective value-determining parameter by numerical solution of a two-species system.

Template-dependent RNA polymerase from black beetle virus-infected Drosophila melanogaster cells

Infection of cultured cells of Drosophila melanogaster with black beetle virus (BBV) induces an RNA polymerase that is bound to cellular particulate material in a complex with a template RNA. We have solubilized the polymerase by treatment of the relevant particulates with detergents such as dodecyl-beta-D-maltoside. The polymerase activity was made dependent upon exogenous RNA by destruction of the endogenous template RNA with micrococcal nuclease. Addition of BBV RNA1 or RNA2 induced synthesis of full-length negative-strand RNA isolated as a double-stranded complex with the added RNA. Newly synthesized plus strands were also detected in the RNA2 complexes. Certain other viral RNAs also induced synthesis of their negative strands.

Towards an experimental analysis of molecular self-organization and precellular Darwinian evolution

An experimental system is described, which opens up a novel pathway towards a molecular understanding of the origin of life. The systemic conditions for the evolution of biological macromolecules are investigated in detail.

Nucleotide clusters in deoxyribonucleic acids: sequence analysis of DNA using pyrimidine oligonucleotides as primers in the DNA polymerase I repair reaction

Pyrimidine oligonucleotides have been shown to prime the E. coli DNA polymerase I repair reaction, specifically and reproducibly. DNA molecules up to 30 nucleotides long have been obtained from the extension of oligopyrimidine primers, 9 to 11 nucleotides long isolated from the complementary (minus) strand of bacteriophage S13 RFDNA using S13 viral DNA as the template molecule. The sequences of the extended primers were determined from mobility shift following separation of partially extended primers by ionophoresis and homochromatography, and by a modification of the "plus" system of Sanger and Coulson (1975). The 3' leads to 5' exonuclease activity of E. coli DNA polymerase was utilized for the "plus" system in the presence of single dNTPs and also with two dNTPs in the reaction, to give a nearest neighbor type of analysis for sequence confirmation. The ready availability of oligopyrimidine primers from any DNA and the simplification of the "plus" method broaden the range of applicability of the primed DNA polymerase I repair reaction for DNA sequence analysis.

Host factor for coliphage Q beta RNA replication: presence in procaryotes and association with the 30S ribosomal subunit in Escherichia coli

The Host Factor required for in vitro coliphage Q beta RNA replication, a heat-stable RNA binding protein present in uninfected Escherichia coli, has been detected by both immunological and functional tests in Acinetobacter calcoaceticus, Klebsiella pneumoniae, Pseudomonas aeruginosa and Pseudomonas putida. It was not detectable by these criteria in Bacillus stearothermophilus, Bacillus subtilis, Caulobacter crescentus, Micrococcus lysodeikticus, Rhodopseudomonas capsulata or Saccharomyces cerevisiae. In Escherichia coli the Host Factor protein has been shown to be associated with ribosomes. It is demonstrated here that this association is specific for the 30S ribosomal subunit.

In vitro replication of tobacco mosaic virus RNA in tobacco callus cultures: solubilization of membrane-bound replicase and partial purification

A fraction containing membrane-bound tobacco mosaic virus RNA replicase was isolated form tobacco mosaic virus-infected tobacco callus cultures. The replicase activity reached a maximum 60 h after inoculation and then declined. The enzyme activity was insensitive to actinomycin D and DNase. The corresponding fraction from healthy callus contained essentially no activity. The viral RNA synthesis in vitro proceeded linearly for 30 min and required the four nucleotide triphosphates and Mg2+ ions. Mn2+ was a poor substitute for Mg2+. During RNA synthesis the product was at least 70% resistant to RNase in 2X SSC (0.15 M NaCl plus 0.015 M sodium citrate), but completely digested by RNase in 0.1X SSC. Analysis of the product by polns) that appeared to be replicative form and a partially RNase-resistant structure similar to replicative intermediate form. Washing the membrane-bound replicase with Mg2+-deficient buffer solubilized enzyme. The solubulized enzyme was further purified by DEAE-Sephadex column chromatography. The DEAE-purified enzyme was nearly completely dependent upon tobacco mosaic virus RNA for activity. Analysis of the product on a sucrose gradient revealed a double-stranded RNA with sedimentation of 16S and smaller heterogeneous RNase-sensitive products.

Reconstitution of Qbeta RNA replicase from a covalently bonded elongation factor Tu-Ts complex

Escherichia coli phage Qbeta RNA replicase, an RNA-dependent RNA polymerase (RNA-dependent RNA nucleotidyltransferase), is a tetramer composed of one phage-coded polypeptide and three host-supplied polypeptides which are known to function in the biosynthesis of proteins in the uninfected host. Two of these polypeptides, protein synthesis elongation factors EF-Tu and EF-Ts, can be covalently crosslinked with dimethyl suberimidate to form a complex which lacks the ability to catalyze the known host functions catalyzed by the individual elongation factors. Using a previously developed reconstitution system we have examined the effects of crosslinking the EF-Tu-Ts complex on reconstituted replicase activity. Renaturation is significantly more efficient when exogenously added native EF-Tu-Ts is crosslinked than when it is not. Crosslinked EF-Tu-Ts can be purified from a crude crosslinked postribosomal supernatant by its ability to replace EF-Tu and EF-Ts in the renaturation of denatured Qbeta replicase. A sample of Qbeta replicase with crosslinked EF-Tu-Ts replacing the individual elongation factors was prepared. Although it lacked EF-Tu and EF-Ts activities, it could initiate transcription of both poly(C) and Qbeta RNA normally and had approximately the same specific activity as control enzyme. Denatured Qbeta replicase formed with crosslinked EF-Tu-Ts was found to renature much more rapidly than untreated enzyme and, in contrast to normal replicase, its renaturation was not inhibited by GDP. The results demonstrate that EF-Tu and EF-Ts function as complex in Qbeta replicase and do not perform their known protein biosynthetic function in the RNA synthetic reaction.

Host factor for coliphage Qbeta RNA replication is present in Pseudomonas putida

Host Factor (HF)1, is a 12000 molecular weight polypeptide that is found in uninfected Escherichia coli and is required as a hexamer along with Qbeta replicase for in vitro replication of Qbeta phage RNA. It has recently been found to be associated with ribosomes and to bind tightly to poly(A). We report here the identification and purification of HF from Pseudomonas putida. HF can be detected in crude extracts by both functional activity in the Qbeta RNA replication assay and by immunodiffusion with antibody made against E. coli HF. HF from E. coli and P. putida chromatograph similarly on DEAE-cellulose and phosphocellulose. They have similar but not identical molecular weights as judged by SES-polyacrylamide gel electrophoresis. Like E. coli HF, P. putida HF was found to be associated with ribosomes and to bind tightly to poly(A). Furthermore, the pure protein from P. putida has full funcitonal activity in the in vitro Qbeta RNA replication assay. The findings that HF has been conserved during evolution, is associated with ribosomes, and binds poly(A), suggest that HF may be an important translational element in uninfected cells and that its role involves an interaction with RNA.

Phage Qbeta replicase: cell-free synthesis of the phage-specific subunit and its assembly with host subunits to form active enzyme

Cell-free translation of Qbeta RNA and subsequent partial purification of the enzyme resulted in replicase activity. From 0.5 to 1.5% of all R chains synthesised were found in the 7-S replicase complex. The presence in the 7-S complex of the host subunits of authentic replicase, i (= S1) and EF-Ts, was shown by the effect of antisera directed against ribosomal protein S1 and EF-Ts, respectively. Furthermore, the presence of EF-Ts was demonstrated by thermal denaturation of in vitro replicase made by a cell extract from an Escherichia coli mutant with a thermolabile EF-Ts. In vitro replicase did not assemble spontaneously during protein synthesis but was formed upon subsequent purification. Assembly could be induced by ammonium sulphate precipitation (60% saturation) alone. It is concluded that the functional phage-coded subunit synthesised in vitro recognises i and the EF-Tu - EF-Ts complex among a mixture of host proteins.

Initiation specificity of the poly(cytidylic acid)-dependent Qbeta replicase activity

The initiation specificity of RNA synthesis catalysed by the poly(C)-dependent Qbeta replicase activity was investigated with various synthetic ribopolymers as template. It was found that the initiation efficiency of a series of oligo(C) with various chain lengths is proportional to the template size. Synthetic riboheteropolymers containing cytidylic acid were accepted as templates only if they contained at their 3' end a cytidylic acid sequence of more than 5 nucleotides. Such an oligocytidylate sequence served also as an initiator sequence for copying the non-cytidylic-acid-containing part of the heterotemplate. RNA synthesis always began with the incorporation of GTP, even if the 3'-terminating nucleotide of the template was not cytidylic acid.

Minimal requirements for template recognition by bacteriophage Qbeta replicase: approach to general RNA-dependent RNA synthesis

Any oligo- or polynucleotide able to offer a C-C-C-sequence at the 3'-terminus and a second C-C-C-sequence in a defined steric position to Qbeta replicase is an efficient template. Corresponding chemical modifications convert non-template RNAs to template RNAs.

Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qbeta replicase

Highly purified coliphage Qbeta replicase when incubated without added template synthesizes self-replicating RNA species in an autocatalytic reaction. In this paper we offer strong evidence that this RNA production is directed by templates generated de novo during the lag phase. Contamination of the enzyme by traces of RNA templates was ruled out by the following experimental results: (1) Additional purification steps do not eliminate this RNA production. (2) The lag phase is lengthened to several hours by lowering substrate or enzyme concentration. At a nucleoside triphosphate concentration of 0.15 mM no RNA is produced although the template-directed RNA synthesis works normally. (3) Different enzyme concentrations lead to RNA species of completely different primary structure. (4) Addition of oligonucleotides or preincubation with only three nucleoside triphosphates affects the final RNA sequence. (5) Manipulation of conditions during the lag phase results in the production of RNA structures that are adapted to the particular incubation conditions applied (e.g., RNA resistant to nuclease attack or resistant to inhibitors or even RNAs "addicted to the drug," in the sense that they only replicate in the presence of a drug like acridine orange). RNA species obtained in different experiments under optimal incubation conditions show very similar fingerprint patterns, suggesting the operation of an instruction mechanism. A possible mechanism is discussed.

Synthesis of complementary strands of heterologous RNAs with Qbeta replicase

Qbeta replicase, in the presence of Mn(++), can use various RNAs as templates for synthesis of full-length RNA products and can also use Qbeta plus-strand RNA as template in the absence of host factors.