Melinda J. Pryor

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.

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.

Glycosylation Mutants of Dengue Virus NS1 Protein

The non-structural glycoprotein NS1 of dengue virus type 2 contains sites for N-linked glycosylation at Asn-130 and Asn-207. NS1 synthesized in infected cells is glycosylated at both locations. We have now examined the dimerization and secretion of NS1 lacking one or both of these sites by transient expression of mutagenized cDNA inserted into a simian virus 40-based vector. Immunoblotting and radioimmunoprecipitation were used to detect NS1 associated with transfected cells and in the extracellular medium. Elimination of one or both glycosylation sites did not abolish dimerization and secretion of NS1. However, NS1 lacking Asn-207 showed reduced dimer stability and secretion. Treatment of secreted NS1 with endoglycosidase H demonstrated that complex glycans were attached at Asn-130 and high-mannose glycans at Asn-207.

Growth restriction of dengue virus type 2 by site-specific mutagenesis of virus-encoded glycoproteins

The three flavivirus glycoproteins prM, E and NS1 are formed by post-translational cleavage and are glycosylated by the addition of N-linked glycans. NS1 may form homodimers, whereas E may form homodimers, homotrimers or heterodimers (prM-E). Modification of these processes by mutagenesis of the proteins has the potential to generate viruses that are restricted in growth and are possible vaccine candidates. Using an SV40-based expression system, we previously analysed dimerization and secretion of the NS1 protein of dengue virus type 2 (DEN-2) with mutations in the conserved Cys residues, or within hydrophilic or hydrophobic regions, or at glycosylation sites. In this study, mutations which reduce cleavage at the DEN-2 prM/E signalase cleavage site are described. On the basis of earlier and current results with transient expression, six mutations which reduced NS1 dimerization and two mutations which inhibited prM/E cleavage were analysed individually for their effects on virus growth using a genomic length cDNA clone. Two viruses were obtained that showed reduced growth in cell culture and attenuation of neurovirulence when inoculated into 3-day-old mice. One of these viruses encoded NS1 that lacked the second glycosylation site, the other encoded a Ser --> Ile change at the -3 position of the prM/E cleavage site. A third virus encoding a mutation in NS1 within a hydrophilic region grew as well as the parental virus. No virus was detected for the remaining five mutations.

Mutagenesis of the dengue virus type 2 NS3 proteinase and the production of growth-restricted virus.

The N-terminal one-third of the NS3 protein of Dengue virus type 2 (DEN-2) complexes with co-factor NS2B to form an active serine proteinase which cleaves the viral polyprotein. To identify sites within NS3 that may interact with NS2B, seven regions within the NS3 proteinase outside the conserved flavivirus enzyme motifs were mutated by alanine replacement. Five sites contained clusters of charged residues and were hydrophilic. Two sites were hydrophobic and highly conserved among flaviviruses. The effects of five mutations on NS2B/3 processing were examined using a COS cell expression system. Four retained significant proteinase activity. Three of these mutations and two more were introduced into genomic-length cDNA and tested for their effects on virus replication. The five mutant viruses showed reduced plaque size and two of the five showed significantly reduced titres. All seven mutations were mapped on the X-ray crystal structure of the DEN-2 NS3 proteinase: three were located at the N terminus and two at the C terminus of the NS2B-binding cleft. Two mutations were at the C terminus of the proteinase domain and one was solvent-exposed. The study demonstrated that charged-to-alanine mutagenesis in the viral proteinase can be used to produce growth-restricted flaviviruses that may be useful in the production of attenuated vaccine strains.

The Biarsenical Dye Lumio™ Exhibits a Reduced Ability to Specifically Detect Tetracysteine-Containing Proteins Within Live Cells

Investigating the localisation of proteins within live cells via fluorescence microscopy typically involves the fusion of the protein of interest to a large fluorescent protein such as green fluorescent protein (GFP). Alternate fluorescent labelling technologies such as the fluorescent biarsenical dye molecules (e.g. FlAsH, ReAsH) are preferable to the use of large fusion proteins in many respects and allow greater flexibility in terms of the location of the labelling site. We assessed the ability of the FlAsH-derived biarsenical dye molecule Lumio™ to label a range of tetracysteine containing proteins within live cells and report that although in some circumstances Lumio is capable of positively detecting such proteins, the sensitivity and specificity of labelling is significantly reduced, making the Lumio-labelling system unsuitable for the detection of a wide range of protein within live cells.

Dengue virus RNA polymerase NS5: a potential therapeutic target?

Dengue fever (DF)/dengue haemorrhagic fever (DHF) is the most common arthropod-borne viral infection, where it is now estimated that 2.5-3 billion people world-wide are at risk of infection. Currently there is no available treatment, in the form of vaccine or drug, making eradication of the mosquito vector the only viable control measure, which has proved costly and of limited success. There are a number of different vaccines undergoing testing, but whilst a dengue vaccine is clearly desirable, there are several issues which make live-attenuated vaccines problematic. These include the phenomenon of antibody-dependent enhancement (ADE) and the possibility of recombination of attenuated vaccine strains with wild-type flavivirus members reverting vaccines to a virulent form. Until we gain a better understanding of these issues and their associated risks, the safety of any live dengue vaccine cannot be assured. It therefore may be safer and more feasible for therapeutic-based approaches to be developed as an alternative to live vaccines. As our understanding of dengue molecular biology expands, new potential targets for drugs are emerging. One of the most promising is the dengue non-structural protein 5 (NS5), the largest and most highly conserved of the dengue proteins. This review examines the unique properties of NS5, including its functions, interactions, subcellular localisation and regulation, and looks at ways in which some of these may be exploited in our quest for effective drugs.