Replication of viral RNA. XIV. Single-stranded minus strands as template for the synthesis of viral plus strands in vitro

Cell-free expression of RNA encoded genes using MS2 replicase

RNA replicases catalyse transcription and replication of viral RNA genomes. Of particular interest for in vitro studies are phage replicases due to their small number of host factors required for activity and their ability to initiate replication in the absence of any primers. However, the requirements for template recognition by most phage replicases are still only poorly understood. Here, we show that the active replicase of the archetypical RNA phage MS2 can be produced in a recombinant cell-free expression system. We find that the 3' terminal fusion of antisense RNAs with a domain derived from the reverse complement of the wild type MS2 genome generates efficient templates for transcription by the MS2 replicase. The new system enables DNA-independent gene expression both in batch reactions and in microcompartments. Finally, we demonstrate that MS2-based RNA-dependent transcription-translation reactions can be used to control DNA-dependent gene expression by encoding a viral DNA-dependent RNA polymerase on a MS2 RNA template. Our study sheds light on the template requirements of the MS2 replicase and paves the way for new in vitro applications including the design of genetic circuits combining both DNA- and RNA-encoded systems.

Protein-RNA Interactions in the Single-Stranded RNA Bacteriophages

Bacteriophages of the Leviviridae family are small viruses with short single-stranded RNA (ssRNA) genomes. Protein-RNA interactions play a key role throughout the phage life cycle, and all of the conserved phage proteins - the maturation protein, the coat protein and the replicase - are able to recognize specific structures in the RNA genome. The phage-coded replicase subunit associates with several host proteins to form a catalytically active complex. Recognition of the genomic RNA by the replicase complex is achieved in a remarkably complex manner that exploits the RNA-binding properties of host proteins and the particular three-dimensional structure of the phage genome. The coat protein recognizes a hairpin structure at the beginning of the replicase gene. The binding interaction serves to regulate the expression of the replicase gene and can be remarkably different in various ssRNA phages. The maturation protein is a minor structural component of the virion that binds to the genome, mediates attachment to the host and guides the genome into the cell. The maturation protein has two distinct RNA-binding surfaces that are in contact with different regions of the genome. The maturation and coat proteins also work together to ensure the encapsidation of the phage genome in new virus particles. In this chapter, the different ssRNA phage protein-RNA interactions, as well as some of their practical applications, are discussed in detail.

A design principle for a single-stranded RNA genome that replicates with less double-strand formation

Single-stranded RNA (ssRNA) is the simplest form of genetic molecule and constitutes the genome in some viruses and presumably in primitive life-forms. However, an innate and unsolved problem regarding the ssRNA genome is formation of inactive double-stranded RNA (dsRNA) during replication. Here, we addressed this problem by focusing on the secondary structure. We systematically designed RNAs with various structures and observed dsRNA formation during replication using an RNA replicase (Qβ replicase). From the results, we extracted a simple rule regarding ssRNA genome replication with less dsRNA formation (less GC number in loops) and then designed an artificial RNA that encodes a domain of the β-galactosidase gene based on this rule. We also obtained evidence that this rule governs the natural genomes of all bacterial and most fungal viruses presently known. This study revealed one of the structural design principles of an ssRNA genome that replicates continuously with less dsRNA formation.

Viral RNA-directed RNA polymerases use diverse mechanisms to promote recombination between RNA molecules

An earlier developed purified cell-free system was used to explore the potential of two RNA-directed RNA polymerases (RdRps), Qbeta phage replicase and the poliovirus 3Dpol protein, to promote RNA recombination through a primer extension mechanism. The substrates of recombination were fragments of complementary strands of a Qbeta phage-derived RNA, such that if aligned at complementary 3'-termini and extended using one another as a template, they would produce replicable molecules detectable as RNA colonies grown in a Qbeta replicase-containing agarose. The results show that while 3Dpol efficiently extends the aligned fragments to produce the expected homologous recombinant sequences, only nonhomologous recombinants are generated by Qbeta replicase at a much lower yield and through a mechanism not involving the extension of RNA primers. It follows that the mechanisms of RNA recombination by poliovirus and Qbeta RdRps are quite different. The data favor an RNA transesterification reaction catalyzed by a conformation acquired by Qbeta replicase during RNA synthesis and provide a likely explanation for the very low frequency of homologous recombination in Qbeta phage.

Synergism in replication and translation of messenger RNA in a cell-free system

Combination of the Q beta replicase reaction with the Escherichia coli cell-free translation system markedly enhances replication of a recombinant RQ-DHFR RNA consisting of the dihydrofolate reductase (DHFR) mRNA sequence inserted into RQ135(-1) RNA, an efficient naturally occurring Q beta replicase template. The enhancement is associated with a replication asymmetry previously described for the replication of Q beta phage RNA in vivo; the sense (+)-strands are produced in large excess over the antisense (-)-strands. This, in turn, results in increased synthesis of the functionally active DHFR. These effects are not observed when DHFR mRNAs or RQ135(-1) RNAs are used as templates, if the translation system is not complete, or if it is inhibited by puromycin. The coupled replication-translation of nonviral mRNA recombinants can serve as a useful model for studying the fundamental aspects of virus amplification and can be implemented for large-scale protein synthesis in vitro.

Structure of the poly(G) polymerase component of the bacteriophage f2 replicase

A rifampicin-resistant poly(G) polymerase has been purified from f2 sus 11-infected cells. The poly(G) polymerase is believed to represent part of the f2 replicase on the basis of several criteria. It is present only in infected cells and shares the characteristic rifampicin resistance of crude f2 replicase activity. Partially purified poly(G) polymerase preparations exhibit replicase activity, synthesizing f2 "lus"strand RNA from denatured, partially double-stranded f2 RNA template. Highly purified poly(G) polymerase preparations, although lacking replicase activity, contain a protein which is electrophoretically identical to the protein product of the viral replicase cistron.

Asynchronous synthesis of the complementary strands of the reovirus genome

The mechanism of replication of the double-stranded RNA genome of reovirus has been analyzed by tracing the fate of the parental double-stranded RNA genome and by determining whether the complementary strands, which comprise the progeny double-stranded RNA, are synthesized simultaneously or sequentially. The results indicate that the parental double-stranded RNA is conserved as the original duplex molecule within a subviral particle throughout the viral replicative cycle. The complementary strands, which form the progeny double-stranded RNA, are produced asynchronously. Minus strands are synthesized on preformed plus-strand templates, whereas plus strands appear to be synthesized on double-stranded RNA templates.

The nucleotide sequence at the 5'-terminus of the Q RNA minus trand

The sequence of the first 52 nucleotides at the 5'-end of the Qbeta minus strand has been determined and found to be complementary in an antiparallel fashion to the 3'-terminal region of the Qbeta plus strand. There are few similarities between the corresponding sequences of Qbeta plus and minus strands; however, both have a hydrogen-bonded loop close to the 5'-end. The sequence of the 3'-terminal region of the plus strand was deduced: there are no termination signals within the last 32 nucleotides. A notable homology exists between the 3'-ends of Qbeta and R17 RNA.

In vitro synthesis of poliovirus ribonucleic acid: role of the replicative intermediate

Poliovirus ribonucleic acid (RNA) polymerase crude extracts could be stored frozen in liquid nitrogen without loss of activity or specificity. The major in vitro product of these extracts was viral single-stranded RNA. However, after short periods of incubation with radioactive nucleoside triphosphates, most of the incorporated label was found in replicative intermediate. When excess unlabeled nucleoside triphosphate was added, the label was displaced from the replicative intermediate and accumulated as viral RNA. It is concluded from this experiment that the replicative intermediate is the precursor to viral RNA. In addition, some of the label was chased into double-stranded RNA. The implications of this finding are discussed.