Flexibility of NS5 Methyltransferase-Polymerase Linker Region Is Essential for Dengue Virus Replication

We examined the function of the conserved Val/Ile residue within the dengue virus NS5 interdomain linker (residues 263 to 272) by site-directed mutagenesis. Gly substitution or Gly/Pro insertion after the conserved residue increased the linker flexibility and created slightly attenuated viruses. In contrast, Pro substitution abolished virus replication by imposing rigidity in the linker and restricting NS5''s conformational plasticity. Our biochemical and reverse genetics experiments demonstrate that NS5 utilizes conformational regulation to achieve optimum viral replication.     

Hepatitis C Virus NS5B and Host Cyclophilin A Share a Common Binding Site on NS5A

Nonstructural protein 5B (NS5B) is essential for hepatitis C virus (HCV) replication as it carries the viral RNA-dependent RNA polymerase enzymatic activity. HCV replication occurs in a membrane-associated multiprotein complex in which HCV NS5A and host cyclophilin A (CypA) have been shown to be present together with the viral polymerase. We used NMR spectroscopy to perform a per residue level characterization of the molecular interactions between the unfolded domains 2 and 3 of NS5A (NS5A-D2 and NS5A-D3), CypA, and NS5B_Δ21. We show that three regions of NS5A-D2 (residues 250–262 (region A), 274–287 (region B), and 306–333 (region C)) interact with NS5B_Δ21, whereas NS5A-D3 does not. We show that both NS5B_Δ21 and CypA share a common binding site on NS5A that contains residues Pro-306 to Glu-323. No direct molecular interaction has been detected by NMR spectroscopy between HCV NS5B_Δ21 and host CypA. We show that cyclosporine A added to a sample containing NS5B_Δ21, NS5A-D2, and CypA specifically inhibits the interaction between CypA and NS5A-D2 without altering the one between NS5A-D2 and NS5B_Δ21. A high quality heteronuclear NMR spectrum of HCV NS5B_Δ21 has been obtained and was used to characterize the binding site on the polymerase of NS5A-D2. Moreover these data highlight the potential of using NMR of NS5B_Δ21 as a powerful tool to characterize in solution the interactions of the HCV polymerase with all kinds of molecules (proteins, inhibitors, RNA). This work brings new insights into the comprehension of the molecular interplay between NS5B, NS5A, and CypA, three essentials proteins for HCV replication.     

Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface

Flavivirus nonstructural protein 5 (NS5) consists of methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, which catalyze 5’-RNA capping/methylation and RNA synthesis, respectively, during viral genome replication. Although the crystal structure of flavivirus NS5 is known, no data about the quaternary organization of the functional enzyme are available. We report the crystal structure of dengue virus full-length NS5, where eight molecules of NS5 are arranged as four independent dimers in the crystallographic asymmetric unit. The relative orientation of each monomer within the dimer, as well as the orientations of the MTase and RdRp domains within each monomer, is conserved, suggesting that these structural arrangements represent the biologically relevant conformation and assembly of this multi-functional enzyme. Essential interactions between MTase and RdRp domains are maintained in the NS5 dimer via inter-molecular interactions, providing evidence that flavivirus NS5 can adopt multiple conformations while preserving necessary interactions between the MTase and RdRp domains. Furthermore, many NS5 residues that reduce viral replication are located at either the inter-domain interface within a monomer or at the inter-molecular interface within the dimer. Hence the X-ray structure of NS5 presented here suggests that MTase and RdRp activities could be coordinated as a dimer during viral genome replication.     

A Crystal Structure of the Dengue Virus NS5 Protein Reveals a Novel Inter-domain Interface Essential for Protein Flexibility and Virus Replication

Flavivirus RNA replication occurs within a replication complex (RC) that assembles on ER membranes and comprises both non-structural (NS) viral proteins and host cofactors. As the largest protein component within the flavivirus RC, NS5 plays key enzymatic roles through its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent-RNA polymerase (RdRp) domains, and constitutes a major target for antivirals. We determined a crystal structure of the full-length NS5 protein from Dengue virus serotype 3 (DENV3) at a resolution of 2.3 Å in the presence of bound SAH and GTP. Although the overall molecular shape of NS5 from DENV3 resembles that of NS5 from Japanese Encephalitis Virus (JEV), the relative orientation between the MTase and RdRp domains differs between the two structures, providing direct evidence for the existence of a set of discrete stable molecular conformations that may be required for its function. While the inter-domain region is mostly disordered in NS5 from JEV, the NS5 structure from DENV3 reveals a well-ordered linker region comprising a short 3₁₀ helix that may act as a swivel. Solution Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) analysis reveals an increased mobility of the thumb subdomain of RdRp in the context of the full length NS5 protein which correlates well with the analysis of the crystallographic temperature factors. Site-directed mutagenesis targeting the mostly polar interface between the MTase and RdRp domains identified several evolutionarily conserved residues that are important for viral replication, suggesting that inter-domain cross-talk in NS5 regulates virus replication. Collectively, a picture for the molecular origin of NS5 flexibility is emerging with profound implications for flavivirus replication and for the development of therapeutics targeting NS5.     

登革2型病毒非结构蛋白NS4B的原核表达、纯化及多克隆抗体制备

目的：原核表达、纯化登革2型病毒非结构蛋白NS4B,并制备其多克隆抗体,以研究其结构与功能。方法：扩增编码登革2型病毒NS4B的24-238位氨基酸残基的基因序列,并将其克隆到原核表达载体pGEX-4T-1,转化大肠杆菌BL21（DE3）,IPTG诱导表达;采用蛋白浸提方法从SDS-PAGE胶中回收融合蛋白;用纯化后的融合蛋白免疫BALB／c鼠制备多克隆抗体,采用间接免疫荧光法检测抗体效价。结果：原核表达了NS4B-GST融合蛋白,并获得了其多克隆抗体,抗体效价为1：800。结论：登革2型病毒NS4B的24-238位氨基酸残基可诱导小鼠产生具有较高效价和特异性的多克隆抗体,这为研究NS4B的结构与功能奠定了基础。     

Analysis of Flavivirus NS5 Methyltransferase Cap Binding

The flavivirus 2′-O-nucleoside N-terminal RNA methyltransferase (MTase) enzyme is responsible for methylating the viral RNA cap structure. To increase our understanding of the mechanism of viral RNA cap binding we performed a detailed structural and biochemical characterization of the guanosine cap-binding pocket of the dengue (DEN) and yellow fever (YF) virus MTase enzymes. We solved an improved 2.1 Å resolution crystal structure of DEN2 Mtase, new 1.5 Å resolution crystal structures of the YF virus MTase domain in apo form, and a new 1.45 Å structure in complex with guanosine triphosphate and RNA cap analog. Our structures clarify the previously reported DEN MTase structure, suggest novel protein-cap interactions, and provide a detailed view of guanine specificity. Furthermore, the structures of the DEN and YF proteins are essentially identical, indicating a large degree of structural conservation amongst the flavivirus MTases. Guanosine triphosphate analog competition assays and mutagenesis analysis, performed to analyze the biochemical characteristics of cap binding, determined that the major interaction points are (i) guanine ring via π−π stacking with Phe24, N1 hydrogen interaction with the Leu19 backbone carbonyl via a water bridge, and C2 amine interaction with Leu16 and Leu19 backbone carbonyls; (ii) ribose 2′ hydroxyl interaction with Lys13 and Asn17; and (iii) α-phosphate interactions with Lys28 and Ser215. Based on our mutational and analog studies, the guanine ring and α-phosphate interactions provide most of the energy for cap binding, while the combination of the water bridge between the guanine N1 and Leu19 carbonyl and the hydrogen bonds between the C2 amine and Leu16/Leu19 carbonyl groups provide for specific guanine recognition. A detailed model of how the flavivirus MTase protein binds RNA cap structures is presented.     

Evaluation of a Dengue NS1 Antigen Detection Assay Sensitivity and Specificity for the Diagnosis of Acute Dengue Virus Infection

Background

Currently, no dengue NS1 detection kit has regulatory approval for the diagnosis of acute dengue fever. Here we report the sensitivity and specificity of the InBios DEN Detect NS1 ELISA using a panel of well characterized human acute fever serum specimens.

Methodology/Principal Findings

The InBios DENV Detect NS1 ELISA was tested using a panel composed of 334 serum specimens collected from acute febrile patients seeking care in a Bangkok hospital in 2010 and 2011. Of these patients, 314 were found to have acute dengue by either RT-PCR and/or anti-dengue IgM/IgG ELISA. Alongside the InBios NS1 ELISA kit, we compared the performance characteristics of the BioRad Platelia NS1 antigen kit. The InBios NS1 ELISA Ag kit had a higher overall sensitivity (86% vs 72.8%) but equal specificity (100%) compared to the BioRad Platelia kit. The serological status of the patient significantly influenced the outcome. In primary infections, the InBios NS1 kit demonstrated a higher sensitivity (98.8%) than in secondary infections (83.5%). We found significant variation in the sensitivity of the InBios NS1 ELISA kit depending on the serotype of the dengue virus and also found decreasing sensitivity the longer after the onset of illness, showing 100% sensitivity early during illness, but dropping below 50% by Day 7.

Conclusion/Significance

The InBios NS1 ELISA kit demonstrated high accuracy when compared to the initial clinical diagnosis with greater than 85% agreement when patients were clinically diagnosed with dengue illness. Results presented here suggest the accurate detection of circulating dengue NS1 by the InBios DENV Detect NS1 ELISA can provide clinicians with a useful tool for diagnosis of early dengue infections.     

Dengue virus nonstructural protein NS5 induces interleukin-8 transcription and secretion

Elevated circulating levels of chemokines have been reported in patients with dengue fever and are proposed to contribute to the pathogenesis of dengue disease. To establish in vitro models for chemokine induction by dengue 2 virus (DEN2V), we studied a variety of human cell lines and primary cells. DEN2V infection of HepG2 and primary dendritic cells induced the production of interleukin-8 (IL-8), RANTES, MIP-1alpha, and MIP-1beta, whereas only IL-8 and RANTES were induced following dengue virus infection of HEK293 cells. Chemokine secretion was accompanied by an increase in steady-state mRNA levels. No chemokine induction was observed in HEK293 cells treated with poly(I:C) or alpha interferon, suggesting a direct effect of virus infection. To determine the mechanism(s) involved in the induction of chemokine production by DEN2V, individual dengue virus genes were cloned into plasmids and expressed in HEK293 cells. Transfection of a plasmid expressing NS5 or a dengue virus replicon induced IL-8 gene expression and secretion. RANTES expression was not induced under these conditions, however. Reporter assays showed that IL-8 induction by NS5 was principally through CAAT/enhancer binding protein, whereas DEN2V infection also induced NF-kappaB. These results indicate a role for the dengue virus NS5 protein in the induction of IL-8 by DEN2V infection. Recruitment and activation of potential target cells to sites of DEN2V replication by virus-induced chemokine production may contribute to viral replication as well as to the inflammatory components of dengue virus disease.     

All Three Domains of the Hepatitis C Virus Nonstructural NS5A Protein Contribute to RNA Binding

The hepatitis C virus (HCV) nonstructural protein NS5A is critical for viral genome replication and is thought to interact directly with both the RNA-dependent RNA polymerase, NS5B, and viral RNA. NS5A consists of three domains which have, as yet, undefined roles in viral replication and assembly. In order to define the regions that mediate the interaction with RNA, specifically the HCV 3′ untranslated region (UTR) positive-strand RNA, constructs of different domain combinations were cloned, bacterially expressed, and purified to homogeneity. Each of these purified proteins was probed for its ability to interact with the 3′ UTR RNA using filter binding and gel electrophoretic mobility shift assays, revealing differences in their RNA binding efficiencies and affinities. A specific interaction between domains I and II of NS5A and the 3′ UTR RNA was identified, suggesting that these are the RNA binding domains of NS5A. Domain III showed low in vitro RNA binding capacity. Filter binding and competition analyses identified differences between NS5A and NS5B in their specificities for defined regions of the 3′ UTR. The preference of NS5A, in contrast to NS5B, for the polypyrimidine tract highlights an aspect of 3′ UTR RNA recognition by NS5A which may play a role in the control or enhancement of HCV genome replication.Hepatitis C virus (HCV) is a human pathogen which chronically infects nearly 3% of the world''s population (36, 37). Persistent infection, in 80% of cases, leads to chronic hepatitis which can progress to liver cirrhosis and, in the worst cases, hepatocellular carcinoma (37). Current therapies lack specificity and efficacy due largely to an incomplete understanding of the complex molecular mechanisms of virus infectivity, RNA replication, and assembly (4, 36). HCV is a member of the Flaviviridae family of enveloped viruses (30), with a positive-sense RNA genome of ∼9.6 kb consisting of a single open reading frame (ORF) that encodes 10 structural and nonstructural viral proteins (3, 16, 25). Cap-independent translation of the ORF (29) yields a large polyprotein of approximately 3,000 amino acid residues that is cleaved co- and posttranslationally by host and viral proteases into 10 mature virus proteins; these cleavage products are ordered from the amino to the carboxy terminus as follows: core (C), envelope proteins 1 and 2 (E1 and E2), p7, nonstructural protein 2 (NS2), NS3, NS4A, NS4B, NS5A, and NS5B (3, 16, 25). At the flanking ends of the genome are two highly conserved untranslated regions (UTRs). The 5′ UTR is highly structured and consists of the internal ribosome entry site (IRES), which is important for the initiation of cap-independent translation of the polyprotein (29). The 3′ UTR consists of a short genotype-specific variable region, a tract of variable length comprising solely pyrimidine residues (predominantly U), and a conserved 98-nucleotide sequence, known as the X region, containing three stem-loops (13, 23) (Fig. ​(Fig.1A).1A). The 3′ UTR is the initiation site for the synthesis of the negative-strand RNA during viral replication (13) and is involved in translational regulation.Open in a separate windowFIG. 1.The HCV 3′ UTR RNA. (A) The positive-strand 3′ UTR consists of three distinct regions, i.e., a short genotype-specific variable region, a polypyrimidine tract [poly(U/UC)] of variable length, and a conserved 98-nucleotide sequence known as the X region containing three stable stem-loops. The predicted structure of the genotype 1b 3′ UTR is shown. (B) Left panel, the integrities of in vitro-transcribed radiolabeled full-length 3′ UTR RNAs of genotypes 1b (nucleotides 9375 to 9595) and 2a (nucleotides 9443 to 9678) and the poly(U/UC) (nucleotides 9406 to 9497) and X region (nucleotides 9498 to 9595) of genotype 1b are shown on denaturing polyacrylamide gels. Right panel, the integrities of in vitro-transcribed radiolabeled RNAs comprising the 3′-terminal NS5B-coding region plus the 3′ UTR RNAs of genotypes 1b (nucleotides 9136 to 9595) and 2a (nucleotides 9204 to 9678) (KL-3′ UTR) are shown on denaturing polyacrylamide gels.HCV RNA replication occurs on membranous structures derived from the endoplasmic reticulum (ER) in a complex that includes host cell factors as well as viral nonstructural proteins, including NS5B, the RNA-dependent RNA polymerase (RdRp) which replicates the viral genome in vivo and in vitro (2, 25, 30). Initiation of the synthesis of the negative-strand RNA is thought to occur upon recognition and specific binding of the NS5B polymerase to the 3′ UTR of the genomic RNA (2, 16, 26). This replication activity and template specificity of NS5B in vivo are dependent, however, on the presence of the other nonstructural proteins, such as the proteases NS2 and NS3, which are required for polyprotein processing and helicase activity, and the multifunctional protein NS5A (16).NS5A is a proline-rich phosphoprotein that is absolutely required for viral replication and is also involved in virus particle assembly (9, 10, 20, 22, 35). Its specific function in the latter process is, however, still unknown. NS5A is membrane associated due to the presence of an N-terminal amphipathic helix that serves as a membrane anchor allowing association with ER-derived membranes (Fig. ​(Fig.2)2) (24, 27). The cytoplasmic portion of NS5A is organized into three domains that are separated by low-complexity sequences (Fig. ​(Fig.2A)2A) (20). The X-ray crystal structure of domain I has revealed that it is a zinc binding domain which forms a homodimer with contacts at the N-terminal ends of the molecules; the resultant large, basic groove at the dimeric interface has been proposed to be involved in RNA binding during viral replication (17, 33). NS5A has also been shown to interact with uridylate and guanylate-rich RNA and to bind to the 3′ ends of the HCV positive- and negative-strand RNAs (8). These observations suggest that NS5A may specifically interact with the large U/G stretches in the IRES of the 5′ UTR, implying a role in HCV translation and genome multiplication, while its interactions with the polypyrimidine tract of the 3′ UTR suggest that NS5A may affect the efficiency of RNA synthesis by NS5B (8, 28, 32). The reported interactions with both flanking regions of the HCV genome imply that NS5A may play a role in the switch between translation and replication that must occur during the viral life cycle (8).Open in a separate windowFIG. 2.Domain structure and expression of HCV NS5A. (A) Schematic diagram of the functional domains of NS5A and design of the constructs used in the study (genotype 1b NS5A protein numbering). The N-terminal amphipathic helix of NS5A (black box) is responsible for the interaction of NS5A with membranes. NS5A is organized into three domains that are separated by low-complexity sequences, indicated by black boxes. The NS5A constructs used all lacked the N-terminal amphipathic helix and were designed to include an N-terminal Strep tag and a C-terminal hexahistidine tag. (B and C) SDS-PAGE and Western blot analysis of the NS5A(ΔAH) and NS5A domain constructs purified by nickel affinity and Streptactin tag affinity chromatography. Coomassie brilliant blue-stained gels and Western blots (WB) using anti-NS5A antibodies for NS5A proteins of genotype 1b strain J4 (B) and genotype 2a strain JFH-1 (C) are shown.Among HCV genotypes, domains II and III are less well conserved than domain I (34). By mutational analysis, domain II, along with domain I, has been attributed to the replicase activity of NS5A (12). Contrastingly, domain III has been shown to be dispensable for RNA replication, and large heterologous insertions and deletions in this region can be tolerated, maintaining RNA replication (34). It has been shown, however, that these insertions and deletions within domain III do have an impact on virus particle assembly, highlighting the critical role of domain III NS5A in the viral life cycle (1, 10). Recent nuclear magnetic resonance (NMR) studies of domains II and III of NS5A revealed that they both adopt a natively unfolded state (6, 14, 15). The high degree of disorder and flexibility observed in these domains may contribute to the promiscuity of NS5A, which has been shown to interact with a variety of biological partners essential for NS5A function and virus persistence (11, 18, 19, 21, 31). In addition, regions within domains I and II of NS5A interact with NS5B, stimulating the in vitro activity of the polymerase and supporting the hypothesis that NS5A has a role in the modulation of RNA replication (28, 32).In this study, we have investigated in detail the RNA binding properties of NS5A. We have mapped the RNA binding regions of NS5A using bacterially expressed deletion constructs of NS5A and have assayed their binding affinity for HCV positive-strand 3′ UTR RNA. In addition, we provide evidence that the RNA binding activity of NS5A is specific and that NS5A interacts preferentially with the polypyrimidine region of the 3′ UTR.     

Paired Charge-to-Alanine Mutagenesis of Dengue Virus Type 4 NS5 Generates Mutants with Temperature-Sensitive, Host Range, and Mouse Attenuation Phenotypes

Charge-to-alanine mutagenesis of dengue virus type 4 (DEN4) NS5 gene generated a collection of attenuating mutations for potential use in a recombinant live attenuated DEN vaccine. Codons for 80 contiguous pairs of charged amino acids in NS5 were individually mutagenized to create uncharged pairs of alanine residues, and 32 recombinant mutant viruses were recovered from the 80 full-length mutant DEN4 cDNA constructs. These mutant viruses were tested for temperature-sensitive (ts) replication in both Vero cells and HuH-7 human hepatoma cells. Of the 32 mutants, 13 were temperature sensitive (ts) in both cell lines, 11 were not ts in either cell line, and 8 exhibited a host range (tshr) phenotype. One tshr mutant was ts only in Vero cells, and seven were ts only in HuH-7 cells. Nineteen of the 32 mutants were 10-fold or more restricted in replication in the brains of suckling mice compared to that of wild-type DEN4, and three mutants were approximately 10,000-fold restricted in replication. The level of temperature sensitivity of replication in vitro did not correlate with attenuation in vivo. A virus bearing two pairs of charge-to-alanine mutations was constructed and demonstrated increased temperature sensitivity and attenuation relative to either parent virus. This large set of charge-to-alanine mutations specifying a wide range of attenuation for mouse brain should prove useful in fine-tuning recombinant live attenuated DEN vaccines.