A Conserved Basic Patch and Central Kink in the Nipah Virus Phosphoprotein Multimerization Domain Are Essential for Polymerase Function.

Nipah virus is a highly lethal zoonotic pathogen found in Southeast Asia that has caused human encephalitis outbreaks with 40%-70% mortality. NiV encodes its own RNA-dependent RNA polymerase within the large protein, L. Efficient polymerase activity requires the phosphoprotein, P, which tethers L to its template, the viral nucleocapsid. P is a multifunctional protein with modular domains. The central P multimerization domain is composed of a long, tetrameric coiled coil. We investigated the importance of structural features found in this domain for polymerase function using a newly constructed NiV bicistronic minigenome assay. We identified a conserved basic patch and central kink in the coiled coil that are important for polymerase function, with R555 being absolutely essential. This basic patch and central kink are conserved in the related human pathogens measles and mumps viruses, suggesting that this mechanism may be conserved.

Mass spectrometry-based investigation of measles and mumps virus proteome.

BACKGROUND: Measles (MEV) and mumps virus (MUV) are enveloped, non-segmented, negative single stranded RNA viruses of the family Paramyxoviridae, and are the cause of measles and mumps, respectively, both preventable by vaccination. Aside from proteins coded by the viral genome, viruses are considered to contain host cell proteins (HCPs). The presence of extracellular vesicles (ECVs), which are often co-purified with viruses due to their similarity in size, density and composition, also contributes to HCPs detected in virus preparations, and this has often been neglected. The aim was to identify which virus-coded proteins are present in MEV and MUV virions, and to try to detect which HCPs, if any, are incorporated inside the virions or adsorbed on their outer surface, and which are more likely to be a contamination from co-purified ECVs. METHODS: MUV, MEV and ECVs were purified by ultracentrifugation, hydrophobic interaction chromatography and immunoaffinity chromatography, proteins in the samples were resolved by SDS-PAGE and subjected to identification by MALDI-TOF/TOF-MS. A comparative analysis of HCPs present in all samples was carried out. RESULTS: By proteomics approach, it was verified that almost all virus-coded proteins are present in MEV and MUV particles. Protein C in MEV which was until now considered to be non-structural viral protein, was found to be present inside the MeV virions. Results on the presence of HCPs in differently purified virus preparations imply that actin, annexins, cyclophilin A, moesin and integrin ß1 are part of the virions. CONCLUSIONS: All HCPs detected in the viruses are present in ECVs as well, indicating their possible function in vesicle formation, or that most of them are only present in ECVs. Only five HCPs were constantly present in purified virus preparations, regardless of the purification method used, implying they are likely the integral part of the virions. The approach described here is helpful for further investigation of HCPs in other virus preparations.

Investigation of the thermal shift assay and its power to predict protein and virus stabilizing conditions.

Protein thermal shift assay (TSA) has been extensively used in investigation of protein stabilization (for protein biopharmaceutics stabilization, protein crystallization studies or screening of recombinant proteins) and drug discovery (screening of ligands or inhibitors). This work aimed to analyze thermal shift assay results in comparison to protein polymerization (multimerization and aggregation) propensity and test the most stabilizing formulations for their stabilization effect on enveloped viruses. Influence of protein concentration, buffer pH and molarity was tested on three proteins (immunoglobulin G, ovalbumin, and albumin) and results showed that each of these factors has an impact on determined shift in protein melting point Tm, and the impact was similar for all three proteins. In case of ovalbumin, molecular dynamics simulations were performed with the goal to understanding molecular basis of protein's thermal stability dependence on pH. Effect of three denaturing agents in a wide concentration range on Tm showed nicely that chemical denaturation occurs only at the highest concentrations. Results showed similar effect on Tm for most formulations on different proteins. Most successful formulations were tested for enveloped virus stabilizing potential using cell culture infectivity assay (CCID50) and results showed lack of correlation with TSA results. Only weak correlation of Tm shift and protein polymerization measured by SEC-HPLC was obtained, meaning that polymerization cannot be predicted from Tm shifts.

[SH and HN Protein Genetic Characterization Analysis of Mumps Virus Isolated in Liaoning Province from 2008 to 2014].

To analyze the genetic characterization of epidemic mumps virus strains in Liaoning Province and provide the basis for mumps control. A total of 32 mumps viruses strains were isolated during 2008-2104. The fragment of SH genes and HN genes were amplified by RT-PCR, the PCR products were sequenced and analyzed. Basing on the 316 nucleotides of SH gene, The phylogenetic analyses were processed with the data of WHO mumps reference strains downloaded from GenBank and 32 mumps viruses strains. It showed that the 31 mumps virus strains belong to F genotype except MuVi/Liaoning. CHN/16.11 which was G genotype . Comparing to the A reference strains (Jeryl-Lynn and S-79), F genotype MuV were mutated on 12 amino acids sites and 27 amino acids siteson on HN gene. F genotype MuV added one N-glycosylation site in 464th-466th amino acids. The antigenic sites on HN were mutated on 121th, 123th, 279th, 287th, 336th, 356th and 442th. Maybe, it will influence the MuV antigenic.

Stability, biophysical properties and effect of ultracentrifugation and diafiltration on measles virus and mumps virus.

Measles virus and mumps virus (MeV and MuV) are enveloped RNA viruses used for production of live attenuated vaccines for prophylaxis of measles and mumps disease, respectively. For biotechnological production of and basic research on these viruses, the preparation of highly purified and infectious viruses is a prerequisite, and to meet that aim, knowledge of their stability and biophysical properties is crucial. Our goal was to carry out a detailed investigation of the stability of MeV and MuV under various pH, temperature, shear stress, filtration and storage conditions, as well as to evaluate two commonly used purification techniques, ultracentrifugation and diafiltration, with regard to their efficiency and effect on virus properties. Virus titers were estimated by CCID50 assay, particle size and concentration were measured by Nanoparticle tracking analysis (NTA) measurements, and the host cell protein content was determined by ELISA. The results demonstrated the stability of MuV and MeV at pH <9 and above pH 4 and 5, respectively, and aggregation was observed at pH >9. Storage without stabilizer did not result in structural changes, but the reduction in infectivity after 24 hours was significant at +37 °C. Vortexing of the viruses resulted in significant particle degradation, leading to lower virus titers, whereas pipetting had much less impact on virus viability. Diafiltration resulted in higher recovery of both total and infectious virus particles than ultracentrifugation. These results provide important data for research on all upstream and downstream processes on these two viruses regarding biotechnological production and basic research.

Identification of mumps virus protein and lipid composition by mass spectrometry.

BACKGROUND: Mumps virus is a negative-sense, single stranded RNA virus consisting of a ribonucleocapsid core enveloped by a lipid membrane derived from host cell, which causes mumps disease preventable by vaccination. Since virus lipid envelope and glycosylation pattern are not encoded by the virus but dependent on the host cell at least to some extent, the aim of this work was to analyse L-Zagreb (L-Zg) mumps virus lipids and proteins derived from two cell types; Vero and chicken embryo fibroblasts (CEF). Jeryl Lynn 5 (JL5) mumps strain lipids were also analysed. METHODS: Virus lipids were isolated by organic phase extraction and subjected to 2D-high performance thin layer chromatography followed by lipid extraction and identification by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Virus samples were also subjected to gel electrophoresis under denaturating conditions and protein bands were excised, in-gel trypsinized and identified by MS as well as tandem MS. RESULTS: Results showed that lipids of both mumps virus strains derived from Vero cells contained complex glycolipids with up to five monosaccharide units whereas the lipid pattern of mumps virus derived from CEF was less complex. Mumps virus was found to contain expected structural proteins with exception of fusion (F) protein which was not detected but on the other hand, V protein was detected. Most interesting finding related to the mumps proteins is the detection of several forms of nucleoprotein (NP), some of which appear to be C-terminally truncated. CONCLUSIONS: Differences found in lipid and protein content of mumps virus demonstrated the importance of detailed biochemical characterization of mumps virus and the methodology described here could provide a means for a more comprehensive quality control in vaccine production.

Structural studies on the authentic mumps virus nucleocapsid showing uncoiling by the phosphoprotein.

Mumps virus (MuV) is a highly contagious pathogen, and despite extensive vaccination campaigns, outbreaks continue to occur worldwide. The virus has a negative-sense, single-stranded RNA genome that is encapsidated by the nucleocapsid protein (N) to form the nucleocapsid (NC). NC serves as the template for both transcription and replication. In this paper we solved an 18-Å-resolution structure of the authentic MuV NC using cryo-electron microscopy. We also observed the effects of phosphoprotein (P) binding on the MuV NC structure. The N-terminal domain of P (PNTD) has been shown to bind NC and appeared to induce uncoiling of the helical NC. Additionally, we solved a 25-Å-resolution structure of the authentic MuV NC bound with the C-terminal domain of P (PCTD). The location of the encapsidated viral genomic RNA was defined by modeling crystal structures of homologous negative strand RNA virus Ns in NC. Both the N-terminal and C-terminal domains of MuV P bind NC to participate in access to the genomic RNA by the viral RNA-dependent-RNA polymerase. These results provide critical insights on the structure-function of the MuV NC and the structural alterations that occur through its interactions with P.

Roles of serine and threonine residues of mumps virus P protein in viral transcription and replication.

UNLABELLED: Mumps virus (MuV), a paramyxovirus containing a negative-sense nonsegmented RNA genome, is a human pathogen that causes an acute infection with symptoms ranging from parotitis to mild meningitis and severe encephalitis. Vaccination against mumps virus has been effective in reducing mumps cases. However, recently large outbreaks have occurred in vaccinated populations. There is no anti-MuV drug. Understanding replication of MuV may lead to novel antiviral strategies. MuV RNA-dependent RNA polymerase minimally consists of the phosphoprotein (P) and the large protein (L). The P protein is heavily phosphorylated. To investigate the roles of serine (S) and threonine (T) residues of P in viral RNA transcription and replication, P was subjected to mass spectrometry and mutational analysis. P, a 392-amino acid residue protein, has 64 S and T residues. We have found that mutating nine S/T residues significantly reduced and mutating residue T at 101 to A (T101A) significantly enhanced activity in a minigenome system. A recombinant virus containing the P-T101A mutation (rMuV-P-T101A) was recovered and analyzed. rMuV-P-T101A grew to higher titers and had increased protein expression at early time points. Together, these results suggest that phosphorylation of MuV-P-T101 plays a negative role in viral RNA synthesis. This is the first time that the P protein of a paramyxovirus has been systematically analyzed for S/T residues that are critical for viral RNA synthesis. IMPORTANCE: Mumps virus (MuV) is a reemerging paramyxovirus that caused large outbreaks in the United States, where vaccination coverage is very high. There is no anti-MuV drug. In this work, we have systematically analyzed roles of Ser/Thr residues of MuV P in viral RNA synthesis. We have identified S/T residues of P critical for MuV RNA synthesis and phosphorylation sites that are important for viral RNA synthesis. This work leads to a better understanding of viral RNA synthesis as well as to potential novel strategies to control mumps.

Mumps postexposure prophylaxis with a third dose of measles-mumps-rubella vaccine, Orange County, New York, USA.

Although the measles-mumps-rubella (MMR) vaccine is not recommended for mumps postexposure prophylaxis (PEP), data on its effectiveness are limited. During the 2009-2010 mumps outbreak in the northeastern United States, we assessed effectiveness of PEP with a third dose of MMR vaccine among contacts in Orthodox Jewish households who were given a third dose within 5 days of mumps onset in the household's index patient. We compared mumps attack rates between persons who received a third MMR dose during the first incubation period after onset in the index patient and 2-dose vaccinated persons who had not. Twenty-eight (11.7%) of 239 eligible household members received a third MMR dose as PEP. Mumps attack rates were 0% among third-dose recipients versus 5.2% among 2-dose recipients without PEP (p=0.57). Although a third MMR dose administered as PEP did not have a significant effect, it may offer some benefits in specific outbreak contexts.

[SH protein genetic characterization analysis of wild-type mumps virus isolated in Liaoning province from 2008 to 2011].

A total of 13 mumps virus strains were isolated using Vero/Slam cell line from the patients' throat swabs and urines during mumps outbreaks and sporadics in liaoning Province from 2008 to 2011. Fragments of 316 nucleotides containing SH genes from 13 mumps virus isolates were amplified by RT-PCR, the PCR products were sequenced and analyzed. Based on the 316 nucleotides of SH gene, the phylogenetic trees were constructed with WHO mumps reference strains downloaded from GenBank and 13 mumps virus strains. It showed that the 12 mumps virus strains in 2008-2011 belonged to F genotype, nucleotide acids and amino acids similarities were 94.9%-100.0% and 83.3%-100.0%. Compared to the F reference strains, nucleotide acids and amino acids similarities were 92.4%-97.2% and 96.5% 84.2%, indicating that liaoning mumps strains had large genotype variation. Furthermore, compared to other genotype mumps strains, 6 nucleotides mutations (C(Nt65), C(Nt105), G(Nt137), C(Nt192), C(Nt239), G(NT262)) in SH gene were shared in all of liaoning F genotype mumps viruses. However these mutations were not found in other genotypes of mumps viruses. Conserved amino acids in SH protein of some liaoning mumps strains had changed (S to P at position 2 P to L at position 6 T to N at positon 23 L to P/R at position 48). The genotype specific triplet IML (at position 28-30) was changed to TMP in strain 2008-001-007 2011-015 s, nucleotide acids and amino acids similarities of strain 2008-001-07 were 87.5% and 79.8%, compared to F reference strains respectively, and 96.8% and 97.4% respectively compared to the G reference strains, in dicating strain 2008-001-07 belonged to G genotype,which was first found in mainland China.

[Study of interaction of polystirolsulphonate with polymerization degree of 8 and polyallylamin with bilayer lipids membranes].

Interaction of polystirolsulphonate with polymerization degree of 8 (PSS-8) and polyallylamin PAA (molecular mass 60 kilodaltons) with viruses from bloodline of paramixo- and orthomixoviruses by the example of measles virus, parotitis and flu leads to the decreasing of infective activity. The possible mechanism of viral inhibitive action of these chemical compounds is damaging of interfacial antigenic proteins of paramixo- and orthomixoviruses. In this study it was detected the change of surface tension of bilayer lipid membrane in the presence of PSS-8 and PAA. The change of surface tension leads to disorder in viral proteins adsorption in bilayer lipid membrane. This process could lead to disorder of juncture and self-assembly of virions.

[Genetic characterization of wild-type mumps virus isolated in Liaoning Province].

Three mumps virus strains were isolated using Vero/Slam cell line from the patients' throat swabs and urines during mumps outbreaks and sporadic period in Liaoning province from 2008. Fragments of 1028 nucleotides including SH genes from 3 mumps virus isolates were amplified by RT-PCR, the PCR products were ligated into pMD19-T vector and cloned to JM109 cell. By blue-white selection, the positive white clones were sequenced and analyzed. Based on the 316 nucleotides of SH gene, the phylogenetic analyses were processed with WHO mumps reference strains downloaded from GenBank and 3 mumps viruses strains. It wan shown that the 3 mumps virus strains isolated in 2008 belonged to F genotype, 3 strains (LN-2008-001-06, LN-2008-001-07 and LN-2008-001-10) showed a nucleotide and amino acid similarity of 98.7%-100% and 94.7%-100% respectively. Two strains (LN-2008-001-06 and LN-2008-001-10) had the same sequence completely. Comparing to the F reference strains, the 3 mumps virus strains' nucleotide and amino acid similarity of 92.4%-96.2% and 84.2%-94.7% respectively. Due to the limited strain numbers, whether the F genotype was the predominant circulating genotype can not be determined. The surveillance on the mumps virus in Liaoning should be therefore strengthened.

Structure of the nucleocapsid-binding domain from the mumps virus polymerase; an example of protein folding induced by crystallization.

The human pathogen mumps virus, like all paramyxoviruses, encodes a polymerase responsible for virally directed RNA synthesis. The template for the polymerase is the nucleocapsid, a filamentous protein-RNA complex harboring the viral genome. Interaction of the polymerase and the nucleocapsid is mediated by a small domain tethered to the end of the phosphoprotein (P), one of the polymerase subunits. We report the X-ray crystal structure of this region of mumps virus P (the nucleocapsid-binding domain, or NBD, amino acids 343-391). The mumps P NBD forms a compact bundle of three alpha-helices within the crystal, a fold apparently conserved across the Paramyxovirinae. In solution, however, the domain exists in the molten globule state. This is demonstrated through application of differential scanning calorimetry, circular dichroism spectroscopy, NMR spectroscopy, and dynamic light scattering. While the mumps P NBD is compact and has persistent secondary structure, it lacks a well-defined tertiary structure under normal solution conditions. It can, however, be induced to fold by addition of a stabilizing methylamine cosolute. The domain provides a rare example of a molten globule that can be crystallized. The structure that is stabilized in the crystal represents the fully folded state of the domain, which must be transiently realized during binding to the viral nucleocapsid. While the intermolecular forces that govern the polymerase-nucleocapsid interaction appear to be different in measles, mumps, and Sendai viruses, for each of these viruses, polymerase translocation involves the coupled binding and folding of protein domains. In all cases, we suggest that this will result in a weak-affinity protein complex with a short lifetime, which allows the polymerase to take rapid steps forward.

Structural characterization of mumps virus fusion protein core.

The fusion proteins of enveloped viruses mediating the fusion between the viral and cellular membranes comprise two discontinuous heptad repeat (HR) domains located at the ectodomain of the enveloped glycoproteins. The crystal structure of the fusion protein core of Mumps virus (MuV) was determined at 2.2 A resolution. The complex is a six-helix bundle in which three HR1 peptides form a central highly hydrophobic coiled-coil and three HR2 peptides pack against the hydrophobic grooves on the surface of central coiled-coil in an oblique antiparallel manner. Fusion core of MuV, like those of simian virus 5 and human respiratory syncytium virus, forms typical 3-4-4-4-3 spacing. The similar characterization in HR1 regions, as well as the existence of O-X-O motif in extended regions of HR2 helix, suggests a basic rule for the formation of the fusion core of viral fusion proteins.

Characterization of mumps virus strains with varying neurovirulence.

Mumps virus strains isolated during an epidemic in Lithuania in 1998 - 2000 were studied. Viruses of the neurovirulent C1 and non-neurovirulent C2 small hydrophobic (SH) genotype variant were sequenced for the haemagglutinin-neuraminidase (HN) and fusion (F) protein genes. Amino acid differences between C1 and C2 strains were found for both proteins. Two amino acid differences were of potential importance for the non-neurovirulent phenotype of the C2 virus. Four of 5 C2 strains exhibited the amino acid arginine instead of lysine at position 335 of the HN protein, and the amino acid phenylalanine was found instead of serine at amino acid position 195 of the F protein. Amino acid differences at these positions have previously been reported to associate with a change in neurovirulence and fusion activity. In addition, the HN gene of the neurovirulent Kilham strain of genotype A was sequenced. The deduced amino acid sequence showed different amino acids compared to both genotypes A and C on some positions. Notably, amino acid differences located in previously identified neutralizing epitopes were found at positions 266, 354 and 356 of the HN protein compared to other genotype A strains. The amino acid differences between Kilham virus strain and other genotype A strains and the similarity of the Kilham HN protein (7 positions) to neurovirulent genotype C strains on some amino acid positions may indicate a possible role for this protein in mumps virus neurovirulence.

Molecular identification of mumps virus genotypes from clinical samples: standardized method of analysis.

A sensitive nested reverse transcription-PCR assay, targeting a short fragment of the gene encoding the small hydrophobic protein (SH gene), was developed to allow rapid characterization of mumps virus in clinical samples. The sensitivity and specificity of the assay were established using representative genotypes A, B, C, D, E, and F. Mumps virus RNA was characterized directly from cerebrospinal fluid (CSF) samples and in extracts of mumps virus isolates from patients with various clinical syndromes. Direct sequencing of products and subsequent phylogenetic analysis enabled genetic classification. A simple web-based system of sequence analysis was established. The study also allowed characterization of mumps virus strains from Argentina as part of a new subgenotype. This PCR assay for characterization of mumps infections coupled to a web-based analytical program provides a rapid method for identification of known and novel strains.

Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein.

Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in the mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 A resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 A, beta = 98.4 degrees. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion.

Synthesis of mumps virus nucleocapsid protein in yeast Pichia pastoris.

The expression of mumps virus nucleocapsid protein in yeast Pichia pastoris was investigated. Viral nucleocapsid proteins usually elicit a strong long-term humoral immune response in patients and experimental animals. Therefore, the detection of antibodies specific to mumps virus nucleoprotein can play an important role in immunoassays for mumps diagnosis. For producing a high-level of recombinant mumps virus nucleoprotein the expression system of yeast P. pastoris was employed. The recombinant nucleocapsid protein was purified by cesium chloride ultracentrifugation of yeast lysates. Electron microscopy of the purified recombinant nucleocapsid protein revealed a herring-bone structure similar to the one discovered in mammalian cells infected with mumps virus. The yield of purified nucleocapsid-like particles from P. pastoris constituted 2.1 mg per 1 g of wet biomass and was considerably higher in comparison to the other expression systems.

Characterization of mumps virus isolated in saitama prefecture, Japan, by sequence analysis of the SH gene.

Mumps virus (MuV) strains isolated from cerebrospinal fluid and throat swabs from patients in Saitama Prefecture and Tokyo, Japan, from 1997 to 2000 were examined by analyzing the SH gene nucleotide sequence (316-nt). Eighteen of the 20 strains studied were divided into three genotypes, recognized as B, G, and H in previous reports. Two genotypes (G and H) are believed to be new in Japan. Two of the 20 strains belonged to none of the previously reported genotypes (A-I), but were closely related to two known strains, MP94-H and Loug1/UK97. We propose that the two strains identified in this study together with the previously reported strains, MP94-H and Loug1/UK97, form a new genotype, designated J, based on the divergence of the SH gene nucleotide sequences between these four strains and other strains reported (genotypes A-I). Our results also suggest that more than two genotypes circulated in Saitama Prefecture from 1997 to 1999, but only one, genotype G, was in evidence in 2000. Genotype B was earlier reported as the predominant strain in Japan, but it became undetectable by the year 2000. These results provide important epidemiological data on mumps in Japan.

[Differentiation of mumps virus strains by polymerase chain reaction and silver stained single-strand conformation polymorphism analysis].

The cDNA fragments amplified through nested RT-PCR from the small hydrophobic (SH) protein gene and its flanking region of the five wild mumps viruses and Enders strain were subjected to single-strand conformation polymorphism (SSCP) analysis by using silver staining. These five wild isolates could be divided into three SSCP patterns and they were differentiated from the Enders strain. Two wild strains which have 3.4% heterology of the nucleotide acid sequence could be distinguished by the method. The results were well correlated with sequence analysis of the SH gene segments, indicating high applicability of the silver staining SSCP analysis for differentiation of mumps virus strains. Furthermore, the method, which is not only quick, sensitive, safe and reliable, but also reproducible and inexpensive, can be used in the molecular epidemiology study of mumps viruses.