Peter J. Wright

Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5

Viruses of the family Flaviviridae are important human and animal pathogens. Among them, the Flaviviruses dengue (DENV) and West Nile (WNV) cause regular outbreaks with fatal outcomes. The RNA-dependent RNA polymerase (RdRp) activity of the non-structural protein 5 (NS5) is a key activity for viral RNA replication. In this study, crystal structures of enzymatically active and inactive WNV RdRp domains were determined at 3.0- and 2.35-Å resolution, respectively. The determined structures were shown to be mostly similar to the RdRps of the Flaviviridae members hepatitis C and bovine viral diarrhea virus, although with unique elements characteristic for the WNV RdRp. Using a reverse genetic system, residues involved in putative interactions between the RNA-cap methyltransferase (MTase) and the RdRp domain of Flavivirus NS5 were identified. This allowed us to propose a model for the structure of the full-length WNV NS5 by in silico docking of the WNV MTase domain (modeled from our previously determined structure of the DENV MTase domain) onto the RdRp domain. The Flavivirus RdRp domain structure determined here should facilitate both the design of anti-Flavivirus drugs and structure-function studies of the Flavivirus replication complex in which the multifunctional NS5 protein plays a central role.

Mutagenesis of the Dengue Virus Type 2 NS3 Protein within and outside Helicase Motifs: Effects on Enzyme Activity and Virus Replication

ABSTRACT The protein NS3 of Dengue virus type 2 (DEN-2) is the second largest nonstructural protein specified by the virus and is known to possess multiple enzymatic activities, including a serine proteinase located in the N-terminal region and an NTPase-helicase in the remaining 70% of the protein. The latter region has seven conserved helicase motifs found in all members of the family Flaviviridae. DEN-2 NS3 lacking the proteinase region was synthesized as a fusion protein with glutathione S-transferase in Escherichia coli. The effects of 10 mutations on ATPase and RNA helicase activity were examined. Residues at four sites within enzyme motifs I, II, and VI were substituted, and six sites outside motifs were altered by clustered charged-to-alanine mutagenesis. The mutations were also tested for their effects on virus replication by incorporation into genomic-length cDNA. Two mutations, both in motif I (G198A and K199A) abolished both ATPase and helicase activity. Two further mutations, one in motif VI (R457A,R458A) and the other a clustered charged-to-alanine substitution at R376KNGK380, abolished helicase activity only. No virus was detected for any mutation which prevented helicase activity, demonstrating the requirement of this enzyme for virus replication. The remaining six mutations resulted in various levels of enzyme activities, and four permitted virus replication. For the two nonreplicating viruses encoding clustered changes at R184KR186 and D436GEE439, we propose that the substituted residues are surface located and that the viruses are defective through altered interaction of NS3 with other components of the viral replication complex. Two of the replicating viruses displayed a temperature-sensitive phenotype. One contained a clustered mutation at D334EE336 and grew too poorly for further characterization. However, virus with an M283F substitution in motif II was examined in a temperature shift experiment (33 to 37°C) and showed reduced RNA synthesis at the higher temperature.

Identification of a major determinant of mouse neurovirulence of dengue virus type 2 using stably cloned genomic-length cDNA

A genomic-length cDNA clone corresponding to the RNA of dengue virus type 2 (DEN-2) New Guinea C strain (NGC) was constructed in a low copy number vector. The cloned cDNA was stably propagated in Escherichia coil and designated pDVWS501. RNA transcripts produced in vitro from the cDNA using T7 RNA polymerase yielded infectious virus (MON501) upon electroporation into BHK-21 cells. When compared with parental NGC virus, MON501 replicated to similar levels in Aedes albopictus C6/36 cells and showed similar neurovirulence in suckling mice. In contrast, a second genomic-length cDNA clone (pDVWS310) used as an intermediate in the construction of pDVWS501 produced virus (MON310) that replicated well in C6/36 cells but was not neurovirulent in mice. MON310 contained the prM and E genes of the non-neurovirulent PUO-218 strain in an NGC background. There were seven amino acid differences between the prM and E proteins of MON310 and MON501. The differences were generally conservative, with the exception of E residue 126, which was Glu in MON310 and Lys in MON501. To examine the role of this residue in mouse neurovirulence, substitutions of Glu --> Lys and Lys --> Glu were made in MON310 and MON501, respectively. The properties of these mutants clearly demonstrated that Lys at E residue 126 is a major determinant of DEN-2 mouse neurovirulence.

Synthesis of proteins and glycoproteins in dengue type 2 virus-infected vero and Aedes albopictus cells.

Fifteen proteins were detected in Vero cells infected by dengue type 2 (DEN-2) virus that were not observed in mock-infected cells, namely P98, p82, P67, GP60, gp54, GP46, p30, p28, gp22, GP20, p18, gp16, p15, p14 and gp13. With the exceptions of gp54 and gp13, polypeptides corresponding to those listed above were also observed in DEN-2 virus-infected Aedes albopictus C6/36 cells. Pulse-chase labelling experiments suggested a possible precursor-product relationship between p30 and p28, and between gp22 and GP20. Peptide mapping and immunoprecipitation experiments showed that the major glycoproteins GP60, GP46 and GP20 were unrelated. Immunoprecipitations of infected cells with antiserum prepared against the DEN-2 soluble complement-fixing (SCF) antigen demonstrated that this antigen is equivalent to the non-structural glycoprotein GP46. The envelope glycoprotein (E) from virus grown in C6/36 cells migrated faster through polyacrylamide gels containing SDS than E from virus grown in Vero cells. [3H]Mannose-labelled glycopeptides of GP60, GP46 and GP20 were separated by gel filtration and by electrophoresis in Tris-borate gels; in addition, the polypeptides synthesized in infected cells in the presence of tunicamycin were analysed. The results revealed heterogeneity among the glycan units of GP60 and GP46.

Use of recombinant fusion proteins and monoclonal antibodies to define linear and discontinuous antigenic sites on the dengue virus envelope glycoprotein.

Sixteen overlapping fragments of the dengue-2 virus envelope (E) protein, expressed as trpE-E fusion products in Escherichia coli, were used to map the epitopes defined by a panel of 20 monoclonal antibodies (MAbs) by immunoblotting. Using this technique, the amino acid sequence of six antigenic domains on the E protein was characterized. Nonneutralizing MAbs were found to define either linear-specific, subcomplex-specific (amino acids 22-58), and complex-specific (amino acids 304-332) epitopes or a subcomplex conformational-dependent epitope requiring the presence of two closely linked amino acid sequences from the E protein, 60-97 and 298-397. Neutralizing MAbs, however, defined either group-reactive epitopes present on two overlapping domains (amino acids 60-135; amino acids 60-205) or type-, subcomplex-, complex-, subgroup-, and group-specific determinants (amino acids 298-397). These neutralizing epitopes were all found to be dependent upon disulfide bridges. Our results suggest that the maintenance of a topographical arrangement of discontinuous antigenic domains in the flavivirus E-protein is necessary to induce neutralizing and protective antibodies.

Nuclear Localization of Dengue Virus Nonstructural Protein 5 Through Its Importin α/β–Recognized Nuclear Localization Sequences is Integral to Viral Infection

Dengue virus nonstructural protein 5 (NS5) is a large multifunctional protein with a central role in viral replication. We previously identified two nuclear localization sequences (NLSs) within the central region of dengue virus type‐2 (DENV‐2) NS5 (‘aNLS’ and ‘bNLS’) that are recognized by the importin α/β and importin β1 nuclear transporters, respectively. Here, we demonstrate the importance of the kinetics of NS5 nuclear localization to virus production for the first time and show that the aNLS is responsible. Site‐specific mutations in the bipartite‐type aNLS or bNLS region were introduced into a reporter plasmid encoding green fluorescent protein fused to the N‐terminus of DENV‐2 NS5, as well as into DENV‐2 genomic length complementary DNA. Mutation of basic residues in the highly conserved region of the bNLS did not affect nuclear import of NS5. In contrast, mutations in either basic cluster of the aNLS decreased NS5 nuclear accumulation and reduced virus production, with the greatest reduction observed for mutation of the second cluster (K387K388K389); mutagenesis of both clusters abolished NS5 nuclear import and DENV‐2 virus production completely. The latter appeared to relate to the impaired ability of virus lacking nuclear‐localizing NS5, as compared with wild‐type virus expressing nuclear‐localizing NS5, to reduce interleukin‐8 production as part of the antiviral response. The results overall indicate that NS5 nuclear localization through the aNLS is integral to viral infection, with significant implications for other flaviviruses of medical importance, such as yellow fever and West Nile viruses.

CRM1-mediated nuclear export of dengue virus RNA polymerase NS5 modulates interleukin-8 induction and virus production

Although all established functions of dengue virus NS5 (nonstructural protein 5) occur in the cytoplasm, its nuclear localization, mediated by dual nuclear localization sequences, is essential for virus replication. Here, we have determined the mechanism by which NS5 can localize in the cytoplasm to perform its role in replication, establishing for the first time that it is able to be exported from the nucleus by the exportin CRM1 and hence can shuttle between the nucleus and cytoplasm. We define the nuclear export sequence responsible to be residues 327–343 and confirm interaction of NS5 and CRM1 by pulldown assay. Significantly, greater nuclear accumulation of NS5 during infection due to CRM1 inhibition coincided with altered kinetics of virus production and decreased induction of the antiviral chemokine interleukin-8. This is the first report of a nuclear export sequence within NS5 for any member of the Flavivirus genus; because of its high conservation within the genus, it may represent a target for the treatment of diseases caused by several medically important flaviviruses.

Synthesis of dengue virus RNA in vitro: initiation and the involvement of proteins NS3 and NS5

SummaryAn assay for flavivirus RNA-dependent RNA polymerase activity in vitro was established using extracts of Vero cells infected with dengue virus type 2 (DEN-2) or Kunjin virus (KUN). RNA synthesis was initiated on a template of viral replicative form (RF) and RF was converted to the replicative intermediate (RI). The RNA-dependent RNA polymerase complex of DEN-2 utilised either DEN-2 or KUN RF as template, and similarly the KUN polymerase complex utilised either DEN-2 or KUN RF template. In addition, antibodies against the nonstructural proteins NS3 and NS5 inhibited the conversion of RF to RI, indicating that NS3 and NS5 are involved in viral RNA replication.

Small round-structured (Norwalk-like) viruses and classical human caliciviruses in Southeastern Australia

A total of 6,226 fecal samples collected from 1980 to 1996 in the Australian states of Victoria, New South Wales, and Tasmania from individuals with gastroenteritis were tested for small round‐structured viruses (SRSVs) and classical human caliciviruses (ClHuCVs) by electron microscopy. There were 223 samples positive for SRSVs, and nine positive for ClHuCVs. SRSVs were detected in individuals of all ages and were commonly associated with gastroenteritis outbreaks in nursing homes and hospitals. SRSVs were detected throughout the year, but were more common in the period from late winter to early summer in Australia (August to December). There were peaks of virus activity in the early 1980s and more recently in 1995 and 1996. Analyses by RT‐PCR and sequencing of a segment of ORF1 encoding the putative RNA polymerase for SRSVs and ClHuCVs showed the presence of viruses belonging to several genogroups. Viruses of genogroup 1 (Norwalk/Southampton‐like) and genogroup 3 (ClHuCVs) were relatively rare. Viruses of genogroup 2 (Snow Mountain‐like) were common, and could be divided into two subgroups, one containing Toronto/Mexico‐like viruses, the other Lordsdale/Camberwell‐like viruses. The majority of viruses detected belonged to this latter subgroup. J. Med. Virol. 55:312–320, 1998.

Processing of the dengue virus type 2 proteins prM and C-prM

A glycoprotein C-prM of 35,000 M(r) was immuno-precipitated from lysates of Aedes albopictus cells infected with dengue virus type 2 (DEN-2) using antisera directed against the C protein or an amino-terminal fragment of the prM glycoprotein. C-prM was not detected in infected Vero cells. The prM glycoprotein synthesized in infected A. albopictus and Vero cells was cleaved to produce the membrane-associated virion protein (M) and the non-M fragment (pr) immediately preceding or occurring simultaneously with the release of viral particles from cells. The cleavage was less efficient in mosquito cells. The pr fragment was found only in the medium and was not rapidly degraded. To obtain pr-specific and M-specific antisera for these studies, proteins containing fragments of DEN-2 prM fused with staphylococcal Protein A were synthesized in Escherichia coli using the expression vector pRIT2T. The fusion proteins were stable and were used to raise antisera in rabbits for immunoprecipitation of radiolabelled cell extracts and culture medium. This is the first report of the detection of a C-prM protein in flavivirus-infected cells and the identification of the pr component of prM.