Antigenic analysis of African measles virus field isolates: identification and localisation of one conserved and two variable epitope sites on the NP protein

Interference with the production of infectious viral particles and bimodal inhibition of replication are broadly conserved antiviral properties of IFITMs

IFITMs are broad antiviral factors that block incoming virions in endosomal vesicles, protecting target cells from infection. In the case of HIV-1, we and others reported the existence of an additional antiviral mechanism through which IFITMs lead to the production of virions of reduced infectivity. However, whether this second mechanism of inhibition is unique to HIV or extends to other viruses is currently unknown. To address this question, we have analyzed the susceptibility of a broad spectrum of viruses to the negative imprinting of the virion particles infectivity by IFITMs. The results we have gathered indicate that this second antiviral property of IFITMs extends well beyond HIV and we were able to identify viruses susceptible to the three IFITMs altogether (HIV-1, SIV, MLV, MPMV, VSV, MeV, EBOV, WNV), as well as viruses that displayed a member-specific susceptibility (EBV, DUGV), or were resistant to all IFITMs (HCV, RVFV, MOPV, AAV). The swapping of genetic elements between resistant and susceptible viruses allowed us to point to specificities in the viral mode of assembly, rather than glycoproteins as dominant factors of susceptibility. However, we also show that, contrarily to X4-, R5-tropic HIV-1 envelopes confer resistance against IFITM3, suggesting that viral receptors add an additional layer of complexity in the IFITMs-HIV interplay. Lastly, we show that the overall antiviral effects ascribed to IFITMs during spreading infections, are the result of a bimodal inhibition in which IFITMs act both by protecting target cells from incoming viruses and in driving the production of virions of reduced infectivity. Overall, our study reports for the first time that the negative imprinting of the virion particles infectivity is a conserved antiviral property of IFITMs and establishes IFITMs as a paradigm of restriction factor capable of interfering with two distinct phases of a virus life cycle.

IFITMs are interferon-regulated proteins that inhibit a broad range of viruses. Until recently, IFITMs had been described to arrest incoming viral particles in target cells, by inducing their retention in endosomal vesicles. More recently in the case of HIV-1, ours and other laboratories have highlighted the existence of an additional antiviral mechanism with which IFITMs could act in virus-producing cells, leading to the production of virion particles of reduced infectivity. In the present study, we assessed whether the negative imprinting of the virion particles infectivity was a conserved antiviral property of IFITMs by examining a panel of fourteen different DNA or RNA viruses. Our results indicate that a wide spectrum of viruses is susceptible to this antiviral mechanism of inhibition, although some are able to resist it. Swapping of elements between susceptible and resistant viruses strongly suggests that specificities in the mode of virion assembly and not the viral glycoprotein are the dominant factor in the susceptibility of a given virus to this inhibition. However, we also show that HIV-1 strains that engage the CCR5 co-receptor display a notable resistance towards IFITM3, indicating that at least in the case of HIV-1, co-receptor usage is likely to add an additional layer of complexity in the relationship established between IFITMs and the virus, that may or may not extend to other viral families as well. In the context of spreading infections, the results of this study highlight that the overall antiviral effect of IFITMs is mechanistically caused by a previously unappreciated dual mode of action in which they act both in target cells and in virus-producing cells, by respectively forcing endosome trapping of incoming viruses and by commandeering the formation of new virion particles of reduced infectivity. Overall, the results presented here indicate that the negative imprinting of viral particles is a largely conserved antiviral feature of IFITMs and point to IFITMs as a novel paradigm of innate defense proteins capable of interfering with viral replication at two distinct steps of a virus life cycle.

HSP90 Chaperoning in Addition to Phosphoprotein Required for Folding but Not for Supporting Enzymatic Activities of Measles and Nipah Virus L Polymerases

Nonsegmented negative-stranded RNA viruses, or members of the order Mononegavirales, share a conserved gene order and the use of elaborate transcription and replication machinery made up of at least four molecular partners. These partners have coevolved with the acquisition of the permanent encapsidation of the entire genome by the nucleoprotein (N) and the use of this N-RNA complex as a template for the viral polymerase composed of the phosphoprotein (P) and the large enzymatic protein (L). Not only is P required for polymerase function, but it also stabilizes the L protein through an unknown underlying molecular mechanism. By using NVP-AUY922 and/or 17-dimethylaminoethylamino-17-demethoxygeldanamycin as specific inhibitors of cellular heat shock protein 90 (HSP90), we found that efficient chaperoning of L by HSP90 requires P in the measles, Nipah, and vesicular stomatitis viruses. While the production of P remains unchanged in the presence of HSP90 inhibitors, the production of soluble and functional L requires both P and HSP90 activity. Measles virus P can bind the N terminus of L in the absence of HSP90 activity. Both HSP90 and P are required for the folding of L, as evidenced by a luciferase reporter insert fused within measles virus L. HSP90 acts as a true chaperon; its activity is transient and dispensable for the activity of measles and Nipah virus polymerases of virion origin. That the cellular chaperoning of a viral polymerase into a soluble functional enzyme requires the assistance of another viral protein constitutes a new paradigm that seems to be conserved within the Mononegavirales order.

IMPORTANCE

Viruses are obligate intracellular parasites that require a cellular environment for their replication. Some viruses particularly depend on the cellular chaperoning apparatus. We report here that for measles virus, successful chaperoning of the viral L polymerase mediated by heat shock protein 90 (HSP90) requires the presence of the viral phosphoprotein (P). Indeed, while P protein binds to the N terminus of L independently of HSP90 activity, both HSP90 and P are required to produce stable, soluble, folded, and functional L proteins. Once formed, the mature P+L complex no longer requires HSP90 to exert its polymerase functions. Such a new paradigm for the maturation of a viral polymerase appears to be conserved in several members of the Mononegavirales order, including the Nipah and vesicular stomatitis viruses.

Nuclear reprogramming with a non-integrating human RNA virus

INTRODUCTION

Advances in the field of stem cells have led to novel avenues for generating induced pluripotent stem cells (iPSCs) from differentiated somatic cells. iPSCs are typically obtained by the introduction of four factors--OCT4, SOX2, KLF4, and cMYC--via integrating vectors. Here, we report the feasibility of a novel reprogramming process based on vectors derived from the non-integrating vaccine strain of measles virus (MV).

METHODS

We produced a one-cycle MV vector by substituting the viral attachment protein gene with the green fluorescent protein (GFP) gene. This vector was further engineered to encode for OCT4 in an additional transcription unit.

RESULTS

After verification of OCT4 expression, we assessed the ability of iPSC reprogramming. The reprogramming vector cocktail with the OCT4-expressing MV vector and SOX2-, KLF4-, and cMYC-expressing lentiviral vectors efficiently transduced human skin fibroblasts and formed iPSC colonies. Reverse transcription-polymerase chain reaction and immunostaining confirmed induction of endogenous pluripotency-associated marker genes, such as SSEA-4, TRA-1-60, and Nanog. Pluripotency of derived clones was confirmed by spontaneous differentiation into three germ layers, teratoma formation, and guided differentiation into beating cardiomyocytes.

CONCLUSIONS

MV vectors can induce efficient nuclear reprogramming. Given the excellent safety record of MV vaccines and the translational capabilities recently developed to produce MV-based vectors now used for cancer clinical trials, our MV vector system provides an RNA-based, non-integrating gene transfer platform for nuclear reprogramming that is amenable for immediate clinical translation.

RIG-I self-oligomerization is either dispensable or very transient for signal transduction

Effective host defence against viruses depends on the rapid triggering of innate immunity through the induction of a type I interferon (IFN) response. To this end, microbe-associated molecular patterns are detected by dedicated receptors. Among them, the RIG-I-like receptors RIG-I and MDA5 activate IFN gene expression upon sensing viral RNA in the cytoplasm. While MDA5 forms long filaments in vitro upon activation, RIG-I is believed to oligomerize after RNA binding in order to transduce a signal. Here, we show that in vitro binding of synthetic RNA mimicking that of Mononegavirales (Ebola, rabies and measles viruses) leader sequences to purified RIG-I does not induce RIG-I oligomerization. Furthermore, in cells devoid of endogenous functional RIG-I-like receptors, after activation of exogenous Flag-RIG-I by a 62-mer-5'ppp-dsRNA or by polyinosinic:polycytidylic acid, a dsRNA analogue, or by measles virus infection, anti-Flag immunoprecipitation and specific elution with Flag peptide indicated a monomeric form of RIG-I. Accordingly, when using the Gaussia Luciferase-Based Protein Complementation Assay (PCA), a more sensitive in cellula assay, no RIG-I oligomerization could be detected upon RNA stimulation. Altogether our data indicate that the need for self-oligomerization of RIG-I for signal transduction is either dispensable or very transient.

Fatal measles virus infection prevented by brain-penetrant fusion inhibitors

Measles virus (MV) infection causes an acute childhood disease that can include infection of the central nervous system and can rarely progress to severe neurological disease for which there is no specific treatment. We generated potent antiviral peptide inhibitors of MV entry and spreading and MV-induced cell fusion. Dimers of MV-specific peptides derived from the C-terminal heptad repeat region of the MV fusion protein, conjugated to cholesterol, efficiently protect SLAM transgenic mice from fatal MV infection. Fusion inhibitors hold promise for the prophylaxis of MV infection in unvaccinated and immunocompromised people, as well as potential for the treatment of grave neurological complications of measles.

Biological feasibility of measles eradication

Because of the success of global measles control programs, the World Health Organization (WHO), along with its partner agencies, is once again considering the possibility of setting a target date for measles eradication. Measles would be the fourth viral agent to be eradicated joining the successful programs to eradicate smallpox and rinderpest virus, and the continuing effort to eradicate polio virus. A description of the recent progress toward measles eradication was recently published as a supplement in the Journal of Infectious Diseases (15 July, 2011, 204 (Suppl. 1)) and the reader is referred to this document for a detailed summary of the global status of measles control. This review will focus on the biologic and virologic aspects of measles eradication.

Molecular epidemiology of measles virus

Genetic characterization of wild-type measles viruses provides a means to study the transmission pathways of the virus and is an essential component of laboratory-based surveillance. Laboratory-based surveillance for measles and rubella, including genetic characterization of wild-type viruses, is performed throughout the world by the WHO Measles and Rubella Laboratory Network, which serves 166 countries in all WHO regions. In particular, the genetic data can help confirm the sources of virus or suggest a source for unknown-source cases as well as to establish links, or lack thereof, between various cases and outbreaks. Virologic surveillance has helped to document the interruption of transmission of endemic measles in some regions. Thus, molecular characterization of measles viruses has provided a valuable tool for measuring the effectiveness of measles control programs, and virologic surveillance needs to be expanded in all areas of the world and conducted during all phases of measles control.

Nucleocapsid structure and function

Measles virus belongs to the Paramyxoviridae family within the Mononegavirales order. Its nonsegmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (N) to form a helical nucleocapsid. This ribonucleoproteic complex is the substrate for both transcription and replication. The RNA-dependent RNA polymerase binds to the nucleocapsid template via its co-factor, the phosphoprotein (P). This chapter describes the main structural information available on the nucleoprotein, showing that it consists of a structured core (N(CORE)) and an intrinsically disordered C-terminal domain (N(TAIL)). We propose a model where the dynamic breaking and reforming of the interaction between N(TAIL) and P would allow the polymerase complex (L-P) to cartwheel on the nucleocapsid template. We also propose a model where the flexibility of the disordered N and P domains allows the formation of a tripartite complex (No-P-L) during replication, followed by the delivery of N monomers to the newly synthesized genomic RNA chain. Finally, the functional implications of structural disorder are also discussed in light of the ability of disordered regions to establish interactions with multiple partners, thus leading to multiple biological effects.

Study of measles virus recombinant proteins and their immunobiological properties

Recombinant proteins rN (nucleocapsid) and rH/Nh (hemagglutinin) of the measles virus strain NovO/96 of genotype A were obtained. The immunobiological properties of the proteins were studied in the reaction with a panel of positive and negative sera. BALB/c mice were immunized with recombinant proteins and native antigen of the measles virus strain NovO/96 in order to obtain hyperimmune serum and its analysis using ELISA (enzyme-linked immunosorbent assay) and PRN (plaque reduction neutralization). The hyperimmune sera against recombinant proteins and native antigen of the measles virus strain NovO/96 were found to be highly active in ELISA. The antibodies against the proteins rN and rH/Nh were found to be capable of neutralizing the virus in titer 1 : 13.5 and 1 : 22.9, respectively. The neutralization titer of the antibodies generated against native antigen of the measles virus strain NovO/96 was 1 : 25.7.

Sequence of the nucleocapsid gene and genome and antigenome promoters for an isolate of porpoise morbillivirus

We have determined the first complete sequence of the nucleocapsid (N) gene of the porpoise morbillivirus (PMV) as well as the genome leader and trailer sequences which encode the genome and antigenome promoters, respectively. The PMV N gene is 1686 nucleotides long with a single open reading frame (ORF) encoding a protein of 523 amino acids with a predicted molecular weight of 57.39kDa. The nucleotide sequence of the N gene shows the closest identity (89%) to that of another cetacean morbillivirus, dolphin morbillivirus (DMV). Lower degrees of identity were found with the other members of the morbilliviruses genus; 67% identity to PDV and RPV, 68% to PPRV, 69% to CDV and 70% to MV. The distance from the 3' end of the genome up to the start of the N ORF is 107 nucleotides, identical to that found in all other morbilliviruses, and encompasses the genome promoter (GP) sequence. This promoter shows the same regions of conservation as found in other morbilliviruses with repeated CXXXXX motifs at positions 79-84, 85-90, and 91-96, the same bi-partite promoter arrangement found in many paramyxoviruses. The antigenome promoter (AGP) shows a similar arrangement, indicating a high degree of conservation in these functionally important regions.

Mapping and structural analysis of B-cell epitopes on the morbillivirus nucleoprotein amino terminus

By analysing the antigenic structure of the morbillivirus nucleoprotein (N) using a competitive-binding assay of monoclonal antibodies (mAbs), six different antigenic sites were identified previously. By using Pepscan methodology complemented by analysis of truncated N proteins, a better characterization of five of these antigenic sites was provided: I, II, III, IV and VI. mAbs specific to Rinderpest virus, defining antigenic sites II, III and IV, and those common to four morbilliviruses, delineating sites I and VI, were analysed in the present study. It was found that all but one mapped to the same region, between aa 120 and 149 of N. However, the mAb 3-1 epitope was located in the carboxy-terminal region (aa 421-525). This result may indicate the high immunogenicity of the amino-terminal variable region, at least in the mouse. It was surprising that the epitope of mAb 33-4, antigenic site VI, which recognized all morbilliviruses so far tested, was located in one of the two non-conserved regions between morbillivirus N proteins. It is shown that the conserved amino acid motif (126)EAD(128)----(131)F-------(148)EN(149) is critical for epitope constitution and recognition.

A practical overview of protein disorder prediction methods

In the past few years there has been a growing awareness that a large number of proteins contain long disordered (unstructured) regions that often play a functional role. However, these disordered regions are still poorly detected. Recognition of disordered regions in a protein is important for two main reasons: reducing bias in sequence similarity analysis by avoiding alignment of disordered regions against ordered ones, and helping to delineate boundaries of protein domains to guide structural and functional studies. As none of the available method for disorder prediction can be taken as fully reliable on its own, we present an overview of the methods currently employed highlighting their advantages and drawbacks. We show a few practical examples of how they can be combined to avoid pitfalls and to achieve more reliable predictions.

High pathogenicity of wild-type measles virus infection in CD150 (SLAM) transgenic mice

Measles virus (MV) infection causes an acute childhood disease, associated in certain cases with infection of the central nervous system and development of a severe neurological disease. We have generated transgenic mice ubiquitously expressing the human protein SLAM (signaling lymphocytic activation molecule), or CD150, recently identified as an MV receptor. In contrast to all other MV receptor transgenic models described so far, in these mice infection with wild-type MV strains is highly pathogenic. Intranasal infection of SLAM transgenic suckling mice leads to MV spread to different organs and the development of an acute neurological syndrome, characterized by lethargy, seizures, ataxia, weight loss, and death within 3 weeks. In addition, in this model, vaccine and wild-type MV strains can be distinguished by virulence. Furthermore, intracranial MV infection of adult transgenic mice generates a subclinical infection associated with a high titer of MV-specific antibodies in the serum. Finally, to analyze new antimeasles therapeutic approaches, we created a recombinant soluble form of SLAM and demonstrated its important antiviral activity both in vitro and in vivo. Taken together, our results show the high susceptibility of SLAM transgenic mice to MV-induced neurological disease and open new perspectives for the analysis of the implication of SLAM in the neuropathogenicity of other morbilliviruses, which also use this molecule as a receptor. Moreover, this transgenic model, in allowing a simple readout of the efficacy of an antiviral treatment, provides unique experimental means to test novel anti-MV preventive and therapeutic strategies.

The intrinsically disordered C-terminal domain of the measles virus nucleoprotein interacts with the C-terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded

Measles virus is a negative-sense, single-stranded RNA virus within theMononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. Themeasles virus nucleoprotein consists of a structured N-terminal domain, and of an intrinsically disordered C-terminal domain, N_TAIL (aa 401–525), which undergoes induced folding in the presence of the C-terminal domain (XD, aa 459–507) of the viral phosphoprotein. With in N_TAIL, an α-helical molecular recognition element (α-MoRE, aa 488–499) involved in binding to P and in induced folding was identified and then observed in the crystal structure of XD. Using small-angle X-ray scattering, we have derived a low-resolution structural model of the complex between XD and N_TAIL, which shows that most of N_TAIL remains disordered in the complex despite P-induced folding within the α-MoRE. The model consists of an extended shape accommodating the multiple conformations adopted by the disordered N-terminal region of N_TAIL, and of a bulky globular region, corresponding to XD and to the C terminus of N_TAIL (aa 486–525). Using surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and heteronuclear magnetic resonance, we show that N_TAIL has an additional site (aa 517–525) involved in binding to XD but not in the unstructured-to-structured transition. This work provides evidence that intrinsically disordered domains can establish complex interactions with their partners, and can contact them through multiple sites that do not all necessarily gain regular secondary structure.

Inhibition of ubiquitination and stabilization of human ubiquitin E3 ligase PIRH2 by measles virus phosphoprotein

Using a C-terminal domain (PCT) of the measles virus (MV) phosphoprotein (P protein) as bait in a yeast two-hybrid screen, a cDNA identical to the recently described human p53-induced-RING-H2 (hPIRH2) cDNA was isolated. A glutathione S-transferase-hPIRH2 fusion protein expressed in bacteria was able to pull down P protein when mixed with an extract from P-expressing HeLa cells in vitro, and myc-tagged hPIRH2 could be reciprocally co-immunoprecipitated with MV P protein from human cells. Additionally, immunoprecipitation experiments demonstrated that hPIRH2-myc, MV P, and nucleocapsid (N) proteins form a ternary complex. The hPIRH2 binding site was mapped to the C-terminal X domain region of the P protein by using a yeast two-hybrid assay. The PCT binding site was mapped on hPIRH2 by using a novel yeast two-hybrid tagged PCR approach and by co-immunoprecipitation of hPIRH2 cysteine mutants and mouse/human PIRH2 chimeras. The hPIRH2 C terminus could mediate the interaction with MV P which was favored by the RING-H2 motif. When coexpressed with an enhanced green fluorescent protein-tagged hPIRH2 protein, MV P alone or in a complex with MV N was able to redistribute hPIRH2 to outside the nucleus, within intracellular aggregates. Finally, MV P efficiently stabilized hPIRH2-myc expression and prevented its ubiquitination in vivo but had no effect on the stability or ubiquitination of an alternative ubiquitin E3 ligase, Mdm2. Thus, MV P protein is the first protein from a pathogen that is able to specifically interact with and stabilize the ubiquitin E3 ligase hPIRH2 by preventing its ubiquitination.

Identification of measles virus genotypes from recent outbreaks in countries from the Eastern Mediterranean Region

BACKGROUND

Molecular characterization of measles viruses (MV) helps to identify transmission pathways of the virus and to document persistence or interruption of endemic virus circulation. In the Eastern Mediterranean Region, measles genotypes from only few countries have been documented.

OBJECTIVES

This study reports the genetic characteristics of virus strains from recent measles outbreaks in Tunisia, Libya, Syria and Iran in 2002-2003.

STUDY DESIGN

Virus sequences in the nucleoprotein gene were obtained by PCR amplification of virus isolates or serum samples. The sequences were compared to the reference ones for genotype identification and to other published sequences within the same genotype.

RESULTS AND CONCLUSIONS

The Tunisian and Libyan epidemic strains belonged to genotype B3, they were closely related to each other and to isolates from Western Africa. The Syrian and Iranian viruses belonged to genotype D4, and differed from each other and from the other published sequences within this genotype. Our results provide valuable baseline and new tools for improved virological measles surveillance in the future, at country, regional and global levels.

Measles virus nucleoprotein induces cell-proliferation arrest and apoptosis through NTAIL-NR and NCORE-FcgammaRIIB1 interactions, respectively

Measles virus (MV) nucleoprotein (N) is a cytosolic protein that is released into the extracellular compartment after apoptosis and/or secondary necrosis of MV-infected cells in vitro. Thus, MV-N becomes accessible to inhibitory cell-surface receptors: FcgammaRIIB and an uncharacterized nucleoprotein receptor (NR). MV-N is composed of two domains: NCORE (aa 1-400) and NTAIL (aa 401-525). To assess the contribution of MV-N domains and of these two receptors in suppression of cell proliferation, a human melanoma HT144 cell line expressing (HT144IIB1) or lacking FcgammaRIIB1 was used as a model. Specific and exclusive NCORE-FcgammaRIIB1 and NTAIL-NR interactions were shown. Moreover, NTAIL binding to human NR predominantly led to suppression of cell proliferation by arresting cells in the G0/G1 phases of the cell cycle, rather than to apoptosis. NCORE binding to HT144IIB1 cells primarily triggered caspase-3 activation, in contrast to HT144IIB1/IC- cells lacking the FcgammaRIIB1 intra-cytoplasmic tail, thus demonstrating the specific inhibitory effect of the NCORE-FcgammaRIIB1 interaction. MV-N- and NCORE-mediated apoptosis through FcgammaRIIB1 was inhibited by the pan-caspase inhibitor zVAD-FMK, indicating that apoptosis was dependent on caspase activation. By using NTAIL deletion proteins, it was also shown that the region of NTAIL responsible for binding to human NR and for cell growth arrest maps to one of the three conserved boxes (Box1, aa 401-420) found in N of Morbilliviruses. This work unveils novel mechanisms by which distinct domains of MV-N may display different immunosuppressive activities, thus contributing to our comprehension of the immunosuppressive state associated with MV infection. Finally, MV-N domains may be good tools to target tumour cell proliferation and/or apoptosis.

Measles virus phosphoprotein gene products: conformational flexibility of the P/V protein amino-terminal domain and C protein infectivity factor function

The measles virus (MV) P gene codes for three proteins: P, an essential polymerase cofactor, and V and C, which have multiple functions but are not strictly required for viral propagation in cultured cells. V shares the amino-terminal domain with P but has a zinc-binding carboxyl-terminal domain, whereas C is translated from an overlapping reading frame. During replication, the P protein binds incoming monomeric nucleocapsid (N) proteins with its amino-terminal domain and positions them for assembly into the nascent ribonucleocapsid. The P protein amino-terminal domain is natively unfolded; to probe its conformational flexibility, we fused it to the green fluorescent protein (GFP), thereby also silencing C protein expression. A recombinant virus (MV-GFP/P) expressing hybrid GFP/P and GFP/V proteins in place of standard P and V proteins and not expressing the C protein was rescued and produced normal ratios of mono-, bi-, and tricistronic RNAs, but its replication was slower than that of the parental virus. Thus, the P protein retained nearly intact polymerase cofactor function, even with a large domain added to its amino terminus. Having noted that titers of cell-associated and especially released MV-GFP/P were reduced and knowing that the C protein of the related Sendai virus has particle assembly and infectivity factor functions, we produced an MV-GFP/P derivative expressing C. Intracellular titers of this virus were almost completely restored, and those of released virus were partially restored. Thus, the MV C protein is an infectivity factor.

The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinsically disordered proteins that fold upon binding to their physiological partner

The nucleoprotein of measles virus consists of an N-terminal domain, N(CORE) (aa 1-400), resistant to proteolysis, and a C-terminal domain, N(TAIL) (aa 401-525), hypersensitive to proteolysis and not visible by electron microscopy. Using two complementary computational approaches, we predict that N(TAIL) belongs to the class of natively unfolded proteins. Using different biochemical and biophysical approaches, we show that N(TAIL) is indeed unstructured in solution. In particular, the spectroscopic and hydrodynamic properties of N(TAIL) indicate that this protein domain belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The isolated N(TAIL) domain was shown to be able to bind to its physiological partner, the phosphoprotein (P), and to undergo an induced folding upon binding to the C-terminal moiety of P [J. Biol. Chem. 278 (2003) 18638]. Using a computational analysis, we have identified within N(TAIL) a putative alpha-helical molecular recognition element (alpha-MoRE, aa 488-499), which could be involved in binding to P via induced folding. We report the bacterial expression and purification of a truncated form of N(TAIL) (N(TAIL2), aa 401-488) devoid of the alpha-MoRE. We show that N(TAIL2) has lost the ability to bind to P, thus supporting the hypothesis that the alpha-MoRE may play a role in binding to P. We have further analyzed the alpha-helical propensities of N(TAIL2) and N(TAIL) using circular dichroism in the presence of 2,2,2-trifluoroethanol. We show that N(TAIL2) has a lower alpha-helical potential compared to N(TAIL), thus suggesting that the alpha-MoRE may be indeed involved in the induced folding of N(TAIL).

Measles virus protein interactions in yeast: new findings and caveats

Complementary DNA clones of measles virus N, N (S228Q; L229D), Ncore (N1-400), Ntail (N401-525), P, PNT (P1-230), PCT (P231-507), L, MEL (L800-2183) and EL (L1300-2183) were fused in frame downstream of the Gal4 binding domain (BD) or activating domain (AD). All but BD-L, BD-MEL and BD-EL, were detected by western blot, with additional C- and/or N-terminal truncated products in the case of BD-N, and BD-P. BD-P and BD-PNT directly activated the reporter genes, indicating that the PNT domain displays transactivating properties. In yeast two-hybrid assays, PNT and PCT domains bind to Ncore and Ntail domains, respectively, indicating that N and P interact in a head to tail orientation via two independent binding sites. BD-N (S228Q; L229D) and AD-N displayed no or poor interaction with P proteins possibly because they may not be properly folded. L binding site on P lies within the PCT domain, and two PCT binding sites lie within the L1-799 and L800-1300 regions. Thus, N to P and P to L protein interactions in measles virus shared many features with other related Paramyxoviridae. From a human cDNA library, several candidate partners of N protein were identified which all reacted with BD-Ncore, and RNA was found to bridge the N protein with one partner.

Structural disorder and modular organization in Paramyxovirinae N and P

The existence and extent of disorder within the replicative complex (N, P and the polymerase, L) of Paramyxovirinae were investigated, drawing on the discovery that the N-terminal moiety of the phosphoprotein (P) and the C-terminal moiety of the nucleoprotein (N) of measles virus are intrinsically unstructured. We show that intrinsic disorder is a widespread property within Paramyxovirinae N and P, using a combination of different computational approaches relying on different physico-chemical concepts. Notably, experimental support that has often gone unnoticed for most of the predictions has been found in the literature. Identification of disordered regions allows the unveiling of a common organization in all Paramyxovirinae P, which are composed of six modules defined on the basis of structure or sequence conservation. The possible functional significance of intrinsic disorder is discussed in the light of experimental data, which show that unstructured regions of P and N are involved in numerous interactions with several protein and protein-RNA partners. This study provides a contribution to the rather poorly investigated field of intrinsically disordered proteins and helps in targeting protein domains for structural studies.

Measles virus (MV) nucleoprotein binds to a novel cell surface receptor distinct from FcgammaRII via its C-terminal domain: role in MV-induced immunosuppression

During acute measles virus (MV) infection, an efficient immune response occurs, followed by a transient but profound immunosuppression. MV nucleoprotein (MV-N) has been reported to induce both cellular and humoral immune responses and paradoxically to account for immunosuppression. Thus far, this latter activity has been attributed to MV-N binding to human and murine FcgammaRII. Here, we show that apoptosis of MV-infected human thymic epithelial cells (TEC) allows the release of MV-N in the extracellular compartment. This extracellular N is then able to bind either to MV-infected or uninfected TEC. We show that recombinant MV-N specifically binds to a membrane protein receptor, different from FcgammaRII, highly expressed on the cell surface of TEC. This new receptor is referred to as nucleoprotein receptor (NR). In addition, different Ns from other MV-related morbilliviruses can also bind to FcgammaRII and/or NR. We show that the region of MV-N responsible for binding to NR maps to the C-terminal fragment (N(TAIL)). Binding of MV-N to NR on TEC triggers sustained calcium influx and inhibits spontaneous cell proliferation by arresting cells in the G(0) and G(1) phases of the cell cycle. Finally, MV-N binds to both constitutively expressed NR on a large spectrum of cells from different species and to human activated T cells, leading to suppression of their proliferation. These results provide evidence that MV-N, after release in the extracellular compartment, binds to NR and thereby plays a role in MV-induced immunosuppression.

Use of surface plasmon resonance for the measurement of low affinity binding interactions between HSP72 and measles virus nucleocapsid protein

The 72 kDa heat shock protein (HSP72) is a molecular chaperone that binds native protein with low affinity. These interactions can alter function of the substrate, a property known as HSP-mediated activity control. In the present work, BIAcore instrumentation was used to monitor binding reactions between HSP72 and naturally occurring sequence variants of the measles virus (MV) nucleocapsid protein (N), a structural protein regulating transcription/replication of the viral genome. Binding reactions employed synthetic peptides mimicking a putative HSP72 binding motif of N. Sequences were identified that bound HSP72 with affinities comparable to well-characterized activity control reactions. These sequences, but not those binding with lesser affinity, supported HSP72 activity control of MV transcription/replication. BIAcore instrumentation thus provides an effective way to measure biologically relevant low affinity interactions with structural variants of viral proteins.

The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein

The nucleoprotein of measles virus consists of an N-terminal moiety, N(CORE), resistant to proteolysis and a C-terminal moiety, N(TAIL), hypersensitive to proteolysis and not visible as a distinct domain by electron microscopy. We report the bacterial expression, purification, and characterization of measles virus N(TAIL). Using nuclear magnetic resonance, circular dichroism, gel filtration, dynamic light scattering, and small angle x-ray scattering, we show that N(TAIL) is not structured in solution. Its sequence and spectroscopic and hydrodynamic properties indicate that N(TAIL) belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The same epitopes are exposed in N(TAIL) and within the nucleoprotein, which rules out dramatic conformational changes in the isolated N(TAIL) domain compared with the full-length nucleoprotein. Most unstructured proteins undergo some degree of folding upon binding to their partners, a process termed "induced folding." We show that N(TAIL) is able to bind its physiological partner, the phosphoprotein, and that it undergoes such an unstructured-to-structured transition upon binding to the C-terminal moiety of the phosphoprotein. The presence of flexible regions at the surface of the viral nucleocapsid would enable plastic interactions with several partners, whereas the gain of structure arising from induced folding would lead to modulation of these interactions. These results contribute to the study of the emerging field of natively unfolded proteins.

Update on the global distribution of genotypes of wild type measles viruses

Molecular characterization of measles viruses is an important component of measles surveillance because these studies enhance our ability to identify the source and transmission pathways of the virus. Molecular surveillance is most beneficial when it is possible to observe the change in virus genotypes over time in a particular region. Such information can help to document the interruption of transmission of measles virus and thus provide an important method for assessing the effectiveness of vaccination programs. It is recommended that virus surveillance be conducted during all phases of measles control and be expanded to give an accurate description of the global distribution of measles genotypes. This review provides updated information on the circulation patterns of measles genotypes and examples of the utility of virologic surveillance.

Substitution of two residues in the measles virus nucleoprotein results in an impaired self-association

The nucleoprotein (N) of measles virus encapsidates viral genomic RNA to form a helical nucleocapsid. Its strong self-association is a major hurdle in determining its high-resolution structure using X-ray crystallography. We report the bacterial expression, purification, and characterization of a variant N that has lost its ability to form nucleocapsid-like structures after substitution of two residues by polar residues. Using immunoprecipitation, circular dichroism, and limited proteolysis studies, we show that this nucleoprotein retains a folding similar to wild-type N. Furthermore, the variant N binds the phosphoprotein, indicating that it retains biochemical relevance. We also present evidence indicating that the N-terminus of N lies at the surface of the nucleocapsid. Beyond the identification of one region of N involved in self-association, our results should facilitate structural studies of N using X-ray crystallography.

Identification and characterization of a regulatory domain on the carboxyl terminus of the measles virus nucleocapsid protein

The paramyxovirus template for transcription and genome replication consists of the RNA genome encapsidated by the nucleocapsid protein (N protein). The activity of the complex, consisting of viral polymerase plus template, can be measured with minireplicons in which the genomic coding sequence is replaced by chloramphenical acetyltransferase (CAT) antisense RNA. Using this approach, we showed that the C-terminal 24 amino acids of the measles virus N protein are dispensable for transcription and replication, based upon the truncation of N proteins used to support minireplicon reporter gene expression. Truncation at the C-terminal or penultimate amino acid 524 resulted in no change in CAT expression, whereas larger truncations spanning residues 523 to 502 were accompanied by an approximately twofold increase in basal activity. Reporter gene expression was enhanced by supplementation with the major inducible 70-kDa heat shock protein (Hsp72) for minireplicons with the N protein or the N protein truncated at position 525 or 524 but not in systems with a truncation at position 523 or 522. Naturally occurring sequence variants of the N protein with variations at positions 522 and 523 were also shown to lack Hsp72 responsiveness independent of changes in basal activity. Since these residues lie within a linear sequence predicting a direct Hsp72 interaction, N protein-Hsp72 binding reactions were analyzed by using surface plasmon resonance technology. Truncation of the C-terminal portion of the N protein by protease digestion resulted in a reduced binding affinity between Hsp72 and the N protein. Furthermore, with synthetic peptides, we established a correlation between the functional responsiveness and the binding affinity for Hsp72 of C-terminal N protein sequences. Collectively, these results show that the C-terminal 24 amino acids of the N protein represent a regulatory domain containing a functional motif that mediates a direct interaction with Hsp72.

A CD46CD[55-46] chimeric receptor, eight short consensus repeats long, acts as an inhibitor of both CD46 (MCP)- and CD150 (SLAM)-mediated cell-cell fusion induced by CD46-using measles virus

According to their cellular receptor use, measles virus (MV) strains can be separated into two phenotypes, CD46-using and CD46-non-using. A long chimeric receptor, CD46CD[55-46], was generated from the CD46 backbone, encompassing the four short consensus repeat (SCR) domains of CD46 linked via a flexible glycine hinge to SCR1 and SCR2 of CD55, SCR3 and SCR4 of CD46 and the STP, transmembrane and cytoplasmic tail of CD46. This chimeric receptor was proficient for MV binding but deficient in mediating MV-induced cell-to-cell fusion and virus replication, possibly due to the extended distance between the MV haemagglutinin (H) binding site (CD46 SCR1-SCR2) and the cell membrane. When coexpressed with either wild-type CD46 or CD150, this fusion-incompetent receptor exerted a dominant negative effect and inhibited both cell-to-cell fusion and entry of MV with CD46-using, but not CD46-non-using, phenotype. A soluble octameric CD46-C4bpalpha exhibited similar CD46- and CD150-mediated fusion inhibition properties only against CD46-using MV. This suggests that the long CD46CD[55-46] receptor acts by sequestering incoming MV prior to its binding to the shorter functional CD46 or CD150 receptor.

Genotypic and antigenic characterization of hemagglutinin proteins of African measles virus isolates

A comprehensive phylogenetic study based on the hemagglutinin (H) protein of all known African measles virus (MV) isolates is presented. The study includes 64 new H gene sequences from Ghana. Nigeria and South Africa as well as viruses from Zambia and The Gambia for which only incomplete sequencing data were available and that have previously not been genotyped. The results provide further support to the tentative assignment of the Nigerian and Ghanaian viruses to a new genotype B3 within clade B. A distinct geographic distribution pattern emerged with clade B viruses circulating exclusively in African countries north of the equator. All MV strains from southern Africa grouped in clades A and D with the majority of viruses belonging to genotype D4. The viruses considerably differed by their sensitivity to neutralization by monoclonal antibodies (mAb), but three selected antibodies were sufficient to distinguish between African MVs representing four different genotypes.

Epitopes and nuclear localization analyses of canine distemper virus nucleocapsid protein by expression of its deletion mutants

A series of nucleocapsid protein (NP)-deleted genes of the Onderstepoort strain was constructed in order to locate antigenic regions of the NP of canine distemper virus. The expression of proteins from 5'-deleted NP genes was examined in COS-7 cells by indirect immunofluorescence assay using three monoclonal antibodies (MAbs), c-5, f-5 and h-6, and a rabbit serum against NP. These MAbs reacted with two regions of NP. Amino acid residues from 1 to 80, and 337-358, were necessary and sufficient for formation of the epitopes identified by MAbs f-5 and h-6, and c-5, respectively. The proteins translated from intact or 3'-deleted genes were found to be localized in the nuclei of COS-7 cells, whereas the proteins from the 5'-deleted genes were mainly detected in the cytoplasm. These results suggested that 80 amino acid residues at the N-terminus are required for transportation of NP into the nucleus.

Role of CD46 in measles virus infection in CD46 transgenic mice

The susceptibility of CD46 (human membrane cofactor protein) transgenic mice to measles virus (MV) infection was investigated. Cell cultures (lung and kidney) established from transgenic and control mice showed that although both could be infected only those from the CD46+ mice gave fusion. A complete round of replication with the release of infectious virus was detected exclusively in the transgenic cell cultures whose permissiveness to MV was markedly less than that of Vero cells. The ability of MV to replicate in vivo in mice was studied using both vaccine and laboratory-adapted wild-type strains of virus. After intraperitoneal and intranasal inoculations of transgenic mice, virus replication could not be detected. In contrast intracerebral inoculation induced infection in both transgenic and nontransgenic mice. Our results from in vitro infection studies support the hypothesis that CD46 is a major host cell factor involved in the MV-induced fusion process and MV entry. The studies further indicate that MV tropism is not governed solely by the expression of the CD46 gene and that the high efficiency of the replicative cycles characteristic of fully permissive host cells requires additional factors, which are lacking in both transgenic and nontransgenic mice.

Molecular analysis of the nucleocapsid protein of recent isolates of canine distemper virus in Japan

We analyzed the molecular properties of the nucleocapsid protein (NP) of canine distemper viruses (CDV), isolated between 1992 and 1995 in Japan. Four CDV field isolates (Yanaka, Ueno, Hamamatsu, and Adachi strains) obtained were antigenically identical. Sequence analysis of entire region of the NP gene of a field isolate, the Yanaka strain, revealed that the NP gene contained 1683 nucleotides and was 93.2% homologous with a laboratory strain, the Onderstepoort strain. The deduced amino acid sequence contained 523 amino acids and was 95.2 and 99% homologous with those of the Onderstepoort and a virulent strain, A75/17 strain, respectively. Since most of the diversities in amino acid sequence occurred in two domains, at the N'- and the C'- termini, we further sequenced 3'-terminal regions of the remaining three field isolates. Based on the sequences, the new CDV isolates had one cluster that distinguished them from the laboratory strain.

Molecular epidemiology and changing distribution of genotypes of measles virus field strains in Japan

Based on phylogenetic and restriction fragment length polymorphism analyses of the hemagglutinin and nucleoprotein gene sequences, measles virus strains obtained in western Japan were divided into two types. Type 1 isolates have largely replaced type 2 isolates during the last 10 years in the area surveyed.

Use of synthetic peptides to identify measles nucleoprotein T-cell epitopes in vaccinated and naturally infected humans

Recombinant measles nucleoprotein (N) and synthetic peptides spanning the length of the N-protein-coding region were used with a proliferation assay to identify human T-cell epitopes in vaccinated and naturally infected adults. A number of epitopes were mapped to specific regions of the measles virus N. The proliferative response of at least two donors was mediated by CD4(+) T cells in association with HLA DR antigens. Over 70% of all donors tested responded to peptides representing amino acids 271-290, 367-386, 400-420, and 483-502, suggesting that these peptides may be broadly recognized within an HLA diverse population. The most frequently recognized T-cell epitopes in both naturally infected and vaccinated donors were located in the genetically heterogeneous carboxy-terminal half of the N. Analysis of patterns of peptide reactivity among vaccinated and naturally infected subjects identified several regions of potential difference between these two groups. Peptides 221-240 and 237-256 were recognized among 100% of naturally infected donors but among only 37.5% of vaccinated donors and therefore may be of further interest in studies to investigate induction of lifelong versus transient immunity to measles. Use of chimeric molecules containing multiple well-characterized T- and B-cell epitopes or genetic alteration of attenuated vaccine virus to enhance critical T-cell responses may eventually lead to the development of a vaccine candidate that can more closely model the patterns of immune response elicited by wild-type virus.

Rapid identification of measles virus strains by the heteroduplex mobility assay

The continued endemic presence of measles virus (MV), and the large number of isolates which are made in South Africa each year, demanded the use of a rapid and reliable pre-screening technique to select isolates for molecular epidemiological studies by sequence analysis. The heteroduplex mobility assay (HMA) was used to genetically characterize 47 MV isolates collected from three different provinces in South Africa, made between 1986 and 1995. The carboxyl-terminal 590 nt of the nucleocapsid (N) gene--the most variable region of the genome--was amplified by polymerase chain reaction (PCR) and subsequently subjected to HMA analysis for initial genotyping. The results showed three different patterns of heteroduplex formation by gel electrophoresis, representing two distinct wild-type lineages and one group of vaccine-like viruses. Comparison of HMA results with phylogenetic analysis of sequence data for several of the South African MV strains showed a complete correlation of results. The HMA proved to be a useful tool for screening MV isolates for use in molecular epidemiological studies.

A rapid culture assay for examining measles virus infections from urine specimens

BACKGROUND

Large numbers of measles virus (MV) specimens are processed in our laboratory each year as part of a molecular epidemiological study of MV in South Africa. The development of a sensitive, rapid virus isolation system is needed to cope with the number of specimens processed.

OBJECTIVES

A comparison was made of centrifugation-enhanced shell vial culture and standard tissue culture using B95a cells for the isolation of MV from throat swabs and urine.

STUDY DESIGN

The rapid method was initially evaluated using Schwarz vaccine virus and then compared to standard culture using throat swab specimens.

RESULTS

The shell via assay proved to be ten times more sensitive than standard culture in the initial evaluation. Of 43 throat swab specimens, 37 (86%) were positive and 6 (14%) negative in standard culture using B95a cells. The specimens were removed after adsorption in standard culture, frozen and then used in the shell vial assay. It was found that 16/27 were positive in the shell vial assay (24 of these 27 being positive in standard culture,) and 8 negative and 8 specimens gave an indeterminate result. For the 45 urine specimens used in the shell vial assay, 71% were positive, 11% negative and 18% gave an indeterminate result, due to too few cells being present for antigen determination by indirect fluorescent antibody assay. Results were obtained in 4 days, as opposed to the average of 14 days for confirmed isolation in standard culture.

CONCLUSION

Rapid culture substantially reduced total test time, was less labour-intensive and was as sensitive as standard culture for the isolation of measles virus from clinical specimens.

Conformational maturation of measles virus nucleocapsid protein

We have obtained a polyclonal antiserum, N-BE, against the denatured, amino-terminal half of the measles virus (MV) nucleocapsid (N) protein and a monoclonal antibody (MAb), N46, which recognizes a conformation-dependent epitope in the same region. Amino acid residues 23 to 239 were required and sufficient for the formation of the conformational epitope. Using these antibodies, we show that the N protein of MV is synthesized as a relatively unfolded protein which first appears in the free-protein pool. This nascent N protein undergoes a conformational change into a more folded mature form. This change does not require the participation of other viral proteins or genomic RNA. The mature N protein does not accumulate in the free-protein pool but is quickly and selectively incorporated into the viral nucleocapsids. The mature N protein is a target for interaction with the phosphoprotein (P protein) of MV. This interaction interferes with the recognition of the N protein by the N46 MAb. This suggests that the association with the P protein may mask the binding site for the N46 MAb or that it induces a conformational change in the N protein.

Baculovirus expression of the nucleoprotein gene of measles virus and utility of the recombinant protein in diagnostic enzyme immunoassays

A recombinant baculovirus that expresses the nucleoprotein gene of measles virus (Edmonston vaccine strain) under the transcriptional control of the polyhedrin promoter was generated. The expressed protein (B-MVN) comigrated with the authentic viral nucleoprotein as observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and it was phosphorylated. The B-MVN protein proved to be reactive with monoclonal antibodies in radioimmunoprecipitations, and it was immunogenic, eliciting in mice antisera that recognized the native nucleoprotein. In addition, the B-MVN protein was evaluated as a replacement source of antigen for whole virus in enzyme immunoassays (EIAs) for detection of measles virus-specific immunoglobulin M (IgM) and IgG antibodies. A capture IgM EIA with the B-MVN protein as antigen detected specific IgM antibodies in 18 (72%) acute- and all convalescent-phase specimens from 25 clinical measles cases and exceeded 99% specificity with 120 control specimens. An indirect IgG EIA with the B-MVN protein detected specific IgG antibodies in 129 of 131 (98%) serum specimens with antibodies to measles virus, and results obtained from testing 268 additional serum specimens were better correlated with measles virus-neutralizing antibodies than those obtained with a commercial EIA.

The matrix proteins of neurovirulent subacute sclerosing panencephalitis virus and its acute measles virus progenitor are functionally different

Persistence of measles virus in the brains of patients with subacute sclerosing panencephalitis (SSPE) is accompanied by changes in the viral matrix (M) protein. To understand the significance of these changes, cell culture and cell-free assays were developed to compare the functions of the M proteins of an SSPE virus Biken strain and its acute measles virus progenitor Nagahata strain. The Nagahata viral M protein is associated with the intracellular viral nucleocapsids and the plasma membrane, whereas the Biken viral M protein is localized mainly in the cytosol. The lack of M protein in the Biken viral nucleocapsids is due to a failure of the Biken M protein to bind to the viral nucleocapsids. The Biken M protein also fails to bind to the Nagahata viral nucleocapsids. Conversely, the Nagahata M protein can bind to the Biken viral nucleocapsids, although this association is not as stable at physiological salt concentration. These results offer concrete evidence that the M protein of an SSPE virus is functionally different from that of its progenitor acute measles virus.

The immune response to measles virus in mice

The T-helper response to the measles virus nucleoprotein (NP) has been studied in mice. The T-cell proliferative response was measured in lymphocytes from mice immunized with either a vaccinia measles-NP recombinant virus or a mouse neuro-adapted measles virus. A T-cell response was obtained with lymphocytes from H2d or H2k mice when stimulated with either measles virus or the NP expressed in bacteria. The response was CD4+ specific. The T-helper epitopes were mapped using truncated NP peptides. The major epitopes in both H2d and H2k mice were determined to be between amino acids 67-98. A further T-cell epitope (between amino acids 457-525) was identified when H2d mice were immunized with measles virus. Studies to quantitate the precursor cells for these epitopes confirmed that the region 67-98 of NP was immunodominant in both haplotypes immunized with the vaccinia-NP recombinant virus, whereas an additional major epitope was observed in the measles virus-infected H2d mice. The primary structure of the epitopes determined here are compared to predicted T-cell epitope motifs.

Mutated and hypermutated genes of persistent measles viruses which caused lethal human brain diseases

Persistent measles viruses (MVs) causing lethal human brain diseases are defective, and the structure of several mutated matrix genes has been elucidated previously. The present study of four persistent MVs revealed a high number of differences from a consensus sequence also in other genes. Amino acid changes accumulated in the carboxyl terminus of the nucleocapsid protein and in the amino terminus of the phosphoprotein, but did not significantly alter these products, which are implicated in viral replication and transcription. The contrary is true for the envelope glycoproteins: In three of four cases, mutations caused partial deletion of the short intracellular domain of the fusion protein, most likely compromising efficient viral budding. Moreover, in the hemagglutinin gene of a strain showing strongly reduced hemadsorption, 20 clustered A to G mutations, resulting in 16 amino acid changes, were detected. This hypermutation might be due to unwinding modification of a part of the MV RNA genome accidentally present in a double-stranded form. Finally, we classified four lytic and seven persistent MV strains on the basis of their sequences. Surprisingly, the four lytic viruses considered belong to the same class. The persistent viruses form more loosely defined groups, which all differ from the vaccine strain Edmonston.