In situ structures of RNA-dependent RNA polymerase inside bluetongue virus before and after uncoating.

Bluetongue virus (BTV), a major threat to livestock, is a multilayered, nonturreted member of the Reoviridae, a family of segmented dsRNA viruses characterized by endogenous RNA transcription through an RNA-dependent RNA polymerase (RdRp). To date, the structure of BTV RdRp has been unknown, limiting our mechanistic understanding of BTV transcription and hindering rational drug design effort targeting this essential enzyme. Here, we report the in situ structures of BTV RdRp VP1 in both the triple-layered virion and double-layered core, as determined by cryo-electron microscopy (cryoEM) and subparticle reconstruction. BTV RdRp has 2 unique motifs not found in other viral RdRps: a fingernail, attached to the conserved fingers subdomain, and a bundle of 3 helices: 1 from the palm subdomain and 2 from the N-terminal domain. BTV RdRp VP1 is anchored to the inner surface of the capsid shell via 5 asymmetrically arranged N termini of the inner capsid shell protein VP3A around the 5-fold axis. The structural changes of RdRp VP1 and associated capsid shell proteins between BTV virions and cores suggest that the detachment of the outer capsid proteins VP2 and VP5 during viral entry induces both global movements of the inner capsid shell and local conformational changes of the N-terminal latch helix (residues 34 to 51) of 1 inner capsid shell protein VP3A, priming RdRp VP1 within the capsid for transcription. Understanding this mechanism in BTV also provides general insights into RdRp activation and regulation during viral entry of other multilayered, nonturreted dsRNA viruses.

Bluetongue virus VP1 polymerase activity in vitro: template dependency, dinucleotide priming and cap dependency.

BACKGROUND: Bluetongue virus (BTV) protein, VP1, is known to possess an intrinsic polymerase function, unlike rotavirus VP1, which requires the capsid protein VP2 for its catalytic activity. However, compared with the polymerases of other members of the Reoviridae family, BTV VP1 has not been characterized in detail. METHODS AND FINDINGS: Using an in vitro polymerase assay system, we demonstrated that BTV VP1 could synthesize the ten dsRNAs simultaneously from BTV core-derived ssRNA templates in a single in vitro reaction as well as genomic dsRNA segments from rotavirus core-derived ssRNA templates that possess no sequence similarity with BTV. In contrast, dsRNAs were not synthesized from non-viral ssRNA templates by VP1, unless they were fused with specific BTV sequences. Further, we showed that synthesis of dsRNAs from capped ssRNA templates was significantly higher than that from uncapped ssRNA templates and the addition of dinucleotides enhanced activity as long as the last base of the dinucleotide complemented the 3' -terminal nucleotide of the ssRNA template. CONCLUSIONS: We showed that the polymerase activity was stimulated by two different factors: cap structure, likely due to allosteric effect, and dinucleotides due to priming. Our results also suggested the possible presence of cis-acting elements shared by ssRNAs in the members of family Reoviridae.

Reconstitution of bluetongue virus polymerase activity from isolated domains based on a three-dimensional structural model.

Bluetongue virus (BTV) is a double-stranded RNA virus of the Reoviridae family. The VP1 protein of BTV is the viral RNA-dependent RNA polymerase (RdRp), which is responsible for the replication of the viral genome. Currently there is no structural information available for VP1. By manual alignment of BTV, Reovirus and other viral RdRps we have generated a model for the structure of VP1, the RdRp of BTV. The structure can be divided into three domains: an N-terminal domain, a C-terminal domain, and a central polymerase domain. Mutation of the putative catalytic site in the central polymerase domain by site-directed mutagenesis abrogated in vitro replicase activity. Each of the domains was expressed individually and subsequently partially purified to obtain direct evidence for the location of polymerase activity and the nucleoside triphosphate binding site. The nucleoside triphosphate binding site was located by showing that CTP only bound to the full-length protein or to the polymerase domain and not to either of the other two domains. None of the domains had catalytic activity when tested individually or in tandem but when all three domains were mixed together the RdRp activity was reconstituted. This is the first report of the reconstitution of a functional viral RdRp in vitro from individual domains.

Purified recombinant bluetongue virus VP1 exhibits RNA replicase activity.

The polymerase protein of all known double-stranded RNA (dsRNA) viruses is located within a complex subviral core particle that is responsible for transcription of the viral genome. For members of the family Reoviridae, this particle allows messenger sense RNA synthesis while sequestering the viral genome away from cellular dsRNA surveillance systems during infection of eukaryotic cells. The core particle of bluetongue virus (BTV) consists of the major structural proteins VP3 and VP7 and the minor enzymatic proteins VP1 (polymerase), VP4 (capping enzyme), and VP6 (helicase). In this report we have characterized fully processive dsRNA synthesis by VP1 from a viral plus-strand RNA template in the absence of the other proteins of the BTV core. This replicase activity consists of de novo initiation of synthesis, followed by elongation of the minus strand. Purified VP1 exhibits little sequence specificity for BTV plus-strand template, suggesting that the choice of viral over nonviral RNA template comes from its association with other proteins within the viral core.

Multimers of the bluetongue virus nonstructural protein, NS2, possess nucleotidyl phosphatase activity: similarities between NS2 and rotavirus NSP2.

The nonstructural protein, NS2, of bluetongue virus is a nonspecific single- stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. NS2 shares these features with the nonstructural protein, NSP2, of rotavirus, which like BTV is a member of the family Reoviridae. Recently, NSP2 was shown to have an NTPase activity and an autokinase activity that catalyzed its phosphorylation in vitro. To examine NS2 for similar enzymatic activities, the protein was expressed in bacteria with a C-terminal His-tag and purified to homogeneity. Recombinant (r)NS2 possessed nonspecific RNA-binding activity and formed 8-10S homomultimers of the same approximate size as rNSP2 homomultimers. Notably, enzymatic assays performed with rNS2 showed that the protein hydrolyzed the alpha, beta, and gamma phosphodiester bonds of all four NTPs. Therefore, rNS2 possesses a nucleotidyl phosphatase activity instead of the NTPase activity of NSP2, which only hydrolyzes the gamma phosphodiester bonds of NTPs. NS2 did not exhibit any autokinase activity in vitro, unlike NSP2. However, both NS2 and NSP2 were phosphorylated in vitro by cellular kinases. Although the nature of the enzymatic activities differs significantly, the fact that both NS2 and NSP2 hydrolyze NTPs, undergo phosphorylation, bind RNA, and assemble into multimers consisting of 6 +/- 2 subunits suggests that they are functional homologs.

Guanylyltransferase and RNA 5'-triphosphatase activities of the purified expressed VP4 protein of bluetongue virus.

We have examined the RNA-capping enzyme activities of bluetongue virus (BTV) minor core protein, VP4. Recombinant BTV VP4 protein was purified to homogeneity from insect cell culture infected with a baculovirus VP4 of BTV serotype 10. We demonstrate that the purified protein, and VP4 encapsidated in core-like particles, react with GTP and covalently bind GMP via a phosphoamide linkage, a characteristic feature of guanylyltransferase enzyme. VP4 also catalyses a GTP-PPi exchange reaction indicating that the protein is the guanylyltransferase of the virus. In addition, VP4 possesses an RNA 5'-triphosphatase activity which catalyses the first step in the RNA-capping sequence. Further, an inorganic pyrophosphatase activity was identified which may aid the transcription activity within the virus by removing inorganic pyrophosphate which is an inhibitor of the polymerization reaction. Finally, the direct evidence of VP4 capping activity has been obtained by demonstrating in vitro transfer of GMP to the 5' end of in vitro synthesized BTV ssRNA transcripts to form a cap structure.

Bluetongue virus VP6 protein binds ATP and exhibits an RNA-dependent ATPase function and a helicase activity that catalyze the unwinding of double-stranded RNA substrates.

RNA-dependent ATPase and helicase activities have been identified associated with the purified VP6 protein of bluetongue virus, a member of the Orbivirus genus of double-stranded RNA (dsRNA; Reoviridae family) viruses. In addition, the protein has an ATP binding activity. RNA unwinding of duplexes occurred with both 3' and 5' overhang templates, as well as with blunt-ended dsRNA, an activity not previously identified in other viral helicases. Although little sequence similarity to other helicases was detected, certain similarities to motifs commonly attributed to such proteins were identified.

The expressed VP4 protein of bluetongue virus binds GTP and is the candidate guanylyl transferase of the virus.

A minor core protein, VP4, of bluetongue virus serotype 10 (BTV-10) has been synthesized in insect cells infected with a genetically manipulated recombinant baculovirus. When insect cells were coinfected by this recombinant virus and a recombinant baculovirus expressing the two major core proteins (VP3 and VP7) of the virus, core-like particles (CLPs) consisting of all three proteins were formed. Purified CLPs reacted with [32P]GTP which was covalently bound to VP4 only. Similarly reconstituted CLPs with VP1 or VP6 did not form covalent complexes with [32P]GTP. The virion-derived VP4 was also shown to have GTP-binding activity. The covalent binding of GTP indicates that expressed VP4 not only is biologically active but also is the candidate guanylyl transferase of the virus. The optimum reaction conditions for GTP binding by VP4 have been investigated.

Evidence for genetic relationship between RNA and DNA viruses from the sequence homology of a putative polymerase gene of bluetongue virus with that of vaccinia virus: conservation of RNA polymerase genes from diverse species.

The nucleotide sequence of segment 1 of the double stranded RNA genome of bluetongue virus serotype 10 (BTV-10), encoding the largest viral core protein, VP1, has been determined. Linear sequence analysis of the predicted amino acid sequence of the 149-K Da protein, a putative component of the viral RNA-directed RNA polymerase, revealed extensive homology with the vaccinia virus 147K Da DNA-directed RNA polymerase subunit. Similar homologies were detected between the VP1 polypeptide and the beta chain subunit of Escherichia coli and common tobacco chloroplast RNA polymerases, yeast RNA polymerase II and III and fruit fly polymerase II.

The identification of factors capable of reversing the core-mediated inhibition of the bluetongue virus transcriptase.

The in vitro transcription reaction of bluetongue virus (BTV) is characterized by a core-mediated, temperature-dependent inhibition at high core concentrations and temperatures (Van Dijk & Huismans, 1980; Huismans, Van Dijk & Els, 1987a). It has been found that this inhibition is reversible and that an inactivated transcriptase reaction mixture can be reactivated by lowering the temperature of the reaction from 37 degrees C to 28 degrees C. In the same way it is possible to inactivate a reaction by increasing the incubation temperature from 28 degrees C to 37 degrees C. It was also found that the inhibition is counteracted by the addition of sucrose or glycerol. At relatively low core concentrations and in the presence of sucrose it is possible to obtain conditions under which transcription at 37 degrees C is more efficient than at 28 degrees C. The latter conditions probably reflect much better the in vivo temperature optimum for the BTV transcriptase than the in vitro conditions at very high core concentrations.

The effect of temperature on the in vitro transcriptase reaction of bluetongue virus, epizootic haemorrhagic disease virus and African horsesickness virus.

Virions of bluetongue virus (BTV), epizootic haemorrhagic disease virus (EHDV) and African horsesickness virus (AHSV) can be converted to core particles by treatment with chymotrypsin and magnesium. The conversion is characterized by the removal of the 2 outer capsid polypeptides of the virion. The loss of these 2 proteins results in an increase in density from 1,36 g/ml to 1,40 g/ml on CsCl gradients. The BTV, EHDV and AHSV core particles have an associated double-stranded RNA dependent RNA transcriptase that appears to transcribe mRNA optimally at 28 degrees C. It was found, at least in the case of BTV, that this low temperature preference is not an intrinsic characteristic of the transcriptase, but is due to a temperature-dependent inhibition of transcription at high core concentrations.

Ribonucleic acid polymerase activity associated with purified calf rotavirus.

The presence of an RNA-dependent RNA polymerase is demonstrated in purified rotavirus particles. Optimum polymerase activity was found between 45 to 50 degrees C, at pH 8, and in the presence of 10 mM-magnesium ions. The polymerase product was highly sensitive to pancreatic RNase (97%) in low or high salt concentration. The enzyme was activated by EDTA treatment of intact particles or heat shock. The similarities between reovirus, blue-tongue virus and rotavirus polymerases are discussed.