Loss of enzyme activity in a site-directed mutant of influenza neuraminidase compared to expressed wild-type protein

The application of pseudotypes to influenza pandemic preparedness

ABSTRACT 

Human and animal populations are constantly exposed to multiple influenza strains due to zoonotic spillover and rapid viral evolution driven by intrinsic error-prone replication and immunological pressure. In this context, antibody responses directed against the hemagglutinin protein on the surface of the virus are of importance since they have been shown to correlate with protective immunity. Serological techniques, detecting these responses, play a critical role in influenza pandemic preparedness in particular with regard to the measurement of vaccine immunogenicity. As the recent human pandemics (H1N1) and avian influenza outbreaks (H5 and H7) have demonstrated, there is an urgent need to be better prepared to assess the contribution of the antibody response to protection against newly emerged viruses and to evaluate the extent of pre-existing heterosubtypic immunity in populations. This review compares pseudotype-based assays with wild-type and virus-like particle virus assays and discusses their place in the pandemic preparedness against the influenza virus. It additionally addresses the state-of-the-art developments of pseudotype-based assays (chimeric hemagglutinins, multiplex and post-attachment) including the development and future deployment of assay kits and approaches toward standardization to both preclinical and clinical endpoints. Progress toward the development of an influenza pseudotype library for the purposes of pandemic preparedness is also outlined and discussed.

Importance of neuraminidase active-site residues to the neuraminidase inhibitor resistance of influenza viruses

Neuraminidase inhibitors (NAIs) are antivirals designed to target conserved residues at the neuraminidase (NA) enzyme active site in influenza A and B viruses. The conserved residues that interact with NAIs are under selective pressure, but only a few have been linked to resistance. In the A/Wuhan/359/95 (H3N2) recombinant virus background, we characterized seven charged, conserved NA residues (R118, R371, E227, R152, R224, E276, and D151) that directly interact with the NAIs but have not been reported to confer resistance to NAIs. These NA residues were replaced with amino acids that possess side chains having similar properties to maintain their original charge. The NA mutations we introduced significantly decreased NA activity compared to that of the A/Wuhan/359/95 recombinant wild-type and R292K (an NA mutation frequently reported to confer resistance) viruses, which were analyzed for comparison. However, the recombinant viruses differed in replication efficiency when we serially passaged them in vitro; the growth of the R118K and E227D viruses was most impaired. The R224K, E276D, and R371K mutations conferred resistance to both zanamivir and oseltamivir, while the D151E mutation reduced susceptibility to oseltamivir only (approximately 10-fold) and the R152K mutation did not alter susceptibility to either drug. Because the R224K mutation was genetically unstable and the emergence of the R371K mutation in the N2 subtype is statistically unlikely, our results suggest that only the E276D mutation is likely to emerge under selective pressure. The results of our study may help to optimize the design of NAIs.

Mutation of neuraminidase cysteine residues yields temperature-sensitive influenza viruses

The influenza virus neuraminidase (NA) is a tetrameric, virus surface glycoprotein possessing receptor-destroying activity. This enzyme facilitates viral release and is a target of anti-influenza virus drugs. The NA structure has been extensively studied, and the locations of disulfide bonds within the NA monomers have been identified. Because mutation of cysteine residues in other systems has resulted in temperature-sensitive (ts) proteins, we asked whether mutation of cysteine residues in the influenza virus NA would yield ts mutants. The ability to rationally design tight and stable ts mutations could facilitate the creation of efficient helper viruses for influenza virus reverse genetics experiments. We generated a series of cysteine-to-glycine mutants in the influenza A/WSN/33 virus NA. These were assayed for neuraminidase activity in a transient expression system, and active mutants were rescued into infectious virus by using established reverse genetics techniques. Mutation of two cysteines not involved in intrasubunit disulfide bonds, C49 and C146, had modest effects on enzymatic activity and on viral replication. Mutation of two cysteines, C303 and C320, which participate in a single disulfide bond located in the beta5L0,1 loop, produced ts enzymes. Additionally, the C303G and C320G transfectant viruses were found to be attenuated and ts. Because both the C303G and C320G viruses exhibited stable ts phenotypes, they were tested as helper viruses in reverse genetics experiments. Efficiently rescued were an N1 neuraminidase from an avian H5N1 virus, an N2 neuraminidase from a human H3N2 virus, and an N7 neuraminidase from an H7N7 equine virus. Thus, these cysteine-to-glycine NA mutants allow the rescue of a variety of wild-type and mutant NAs into influenza virus.

Mutations affecting the sensitivity of the influenza virus neuraminidase to 4-guanidino-2,4-dideoxy-2,3-dehydro-N-acetylneuraminic acid

4-Guanidino-2,4-dideoxy-2,3-dehydro-N-acetylneuraminic acid (4-guanidino-Neu5Ac2en) specifically inhibits the influenza virus neuraminidase (NA) through interaction of the guanidino group with conserved Glu 119 and Glu 227 residues in the substrate binding pocket of the enzyme. To understand the mechanism by which influenza viruses become resistant to 4-guanidino-Neu5Ac2en, we investigated mutations at amino acid residues 119 and 227 in the influenza virus NA for their effects on this compound and on NA activity. The NA gene was cloned from the NWS-G70c virus, and mutations were introduced at the codon for amino acid residue 119 or 227. All of the 13 mutants containing a change at residue 119 were transported to the cell surface, although their expression levels ranged from 68.2 to 91.3% of wild type. Mutant NAs that retained at least 20% of the wild-type enzymatic activity were tested for their sensitivity to 4-guanidino-Neu5Ac2en and found to be sevenfold less sensitive to this compound than was the wild-type NA. By contrast, only 6 of 13 mutants defined by modifications at residue 227 were transported to the cell surface, and those NAs lacked substantial enzymatic activity (9% of wild type, at most). These results suggest that only a limited number of resistant viruses arise through mutations at Glu 119 and Glu 227 under selective pressure from 4-guanidino-Neu5Ac2en and that the development of compounds which interact with 227 Glu more strongly than does 4-guanidino-Neu5Ac2en may reduce the likelihood of drug-resistant viruses still further.

Identification of critical contact residues in the NC41 epitope of a subtype N9 influenza virus neuraminidase

We have examined amino acids on influenza virus neuraminidase (NA) subtype N9 (A/tern/Australia/G70c/75) which are in contact with monoclonal antibody NC41 to analyze individual interactions important for antibody recognition. The crystal structure of NA complexed with NC41 Fab1 shows antibody contacts at 19 amino acid residues on the NA surface which are localized on five polypeptide loops surrounding the enzyme active site. Fifteen mutant NA genes were constructed to encode a protein which contained a single amino acid substitution and these were tested for effects of the replacement on NC41 binding. Our data revealed that NAs with changes at 368, 400, and 434 completely lost NC41 recognition. NAs with side chains replaced at residues 346 and 373 exhibited binding reduced to less than 50% of wild-type binding. Changes in seven other contacting residues, including substituted side chains which differed considerably from wild-type NA in size and charge, had no significant effect on NC41 binding. These results indicate that only a few of the many residues which make up an epitope are crucial for interaction and provide the critical contacts required for antibody recognition. This implies that antibody escape mutants are selected only if they contain changes at these crucial sites, or changes which introduce bulky side chains that sterically prevent antibody attachment.

Transfer of the hemagglutinin activity of influenza virus neuraminidase subtype N9 into an N2 neuraminidase background

It has previously been shown that influenza virus neuraminidase (NA) of the N9 subtype is unusual in that it possesses hemagglutinin activity as well as NA activity. Loss of red cell binding in certain escape mutants suggested that the hemagglutinating site is separate from the NA active site and involves at least two of the polypeptide loops found on the surface of the molecule (Webster et al., 1987. J. Virol. 61, 2910-2916). We have used site-directed mutagenesis to transfer the amino acids in these loops at positions 368-370 and 399-403 of N9 NA (A/tern/Australia/G70c/75), separately and together, into subtype N2 NA (A/Tokyo/3/67). The three mutant proteins were expressed from an SV40 transient expression system (Fuerst et al., 1986. Proc. Natl. Acad. Sci. USA. 83, 8122-8126). The mutant which contained both loops of N9 NA had acquired the hemagglutinin activity of N9. The agglutinated red cells are released by the enzyme activity of N9 NA, indicating that the agglutination involves binding to sialic acid in the same configuration as does the parental N9 NA, and an inhibitor of NA did not affect hemagglutination, indicating that this site is separate from the NA site as in parental N9.

Conversion of a class II integral membrane protein into a soluble and efficiently secreted protein: multiple intracellular and extracellular oligomeric and conformational forms

The NH2 terminus of the F1 subunit of the paramyxovirus SV5 fusion protein (fusion related external domain; FRED) is a hydrophobic domain that is implicated as being involved in mediating membrane fusion. We have examined the ability of the FRED to function as a combined signal/anchor domain by substituting it for the natural NH2-terminal signal/anchor domain of a model type II integral membrane protein: the hybrid protein (NAF) was expressed in eukaryotic cells. The FRED was shown to act as a signal sequence, targeting NAF to the lumen of the ER, by the fact that NAF acquired N-linked carbohydrate chains. Alkali fractionation of microsomes indicated that NAF is a soluble protein in the lumen of the ER, and the results of NH2-terminal sequence analysis showed that the FRED is cleaved at a site predicted to be recognized by signal peptidase. NAF was found to be efficiently secreted (t1/2 approximately 90 min) from the cell. By using a combination of sedimentation velocity centrifugation and immunoprecipitation assays using polyclonal and conformation-specific monoclonal antibodies it was found that extracellular NAF consisted of a mixture of monomers, disulfide-linked dimers, and tetramers. The majority of the extracellular NAF molecules were not reactive with the conformation-specific monoclonal antibodies, suggesting they were not folded in a native form and that only the NAF tetramers had matured to a native conformation such that they exhibited NA activity. The available data indicate that NAF is transported intracellularly in multiple oligomeric and conformational forms.

Sialic acid is cleaved from glycoconjugates at the cell surface when influenza virus neuraminidases are expressed from recombinant vaccinia viruses

Three different influenza virus neuraminidase (NA) genes have been subcloned into the vector pSC11 and expressed from the recombinant vaccinia viruses. These genes are from influenza viruses A/Tokyo/3/67 (N2); A/tern/Australia/G70c/75 (N9); and B/Hong Kong (HG)(NA of B/Lee/40). Cells infected with recombinants containing the NA gene express enzymatically active NA on the cell surface. The expressed protein results in the infected cells beings stripped of sialic acid, the receptor for influenza virus. This is not due to cleavage by NA from detached cells since at low multiplicity of infection only cells present at plaques are devoid of sialic acid. Thus NA is able to cleave sialic acid from neighboring glycoconjugates on the same membrane.

The scanning model for translation: an update

The small (40S) subunit of eukaryotic ribosomes is believed to bind initially at the capped 5'-end of messenger RNA and then migrate, stopping at the first AUG codon in a favorable context for initiating translation. The first-AUG rule is not absolute, but there are rules for breaking the rule. Some anomalous observations that seemed to contradict the scanning mechanism now appear to be artifacts. A few genuine anomalies remain unexplained.

Oligomeric structure of a prototype retrovirus glycoprotein

The structure of the Rous sarcoma virus envelope glycoprotein complex was studied by sedimentation gradient centrifugation analyses of detergent-solubilized wild-type and mutant envelope (env) gene products. These studies show that the envelope glycoprotein forms an oligomer during biosynthesis, which is most likely a trimer, and that this is the form of the complex found in virions. Our results are consistent with oligomer formation and transport out of the endoplasmic reticulum being closely linked. From analyses of mutant envelope proteins we conclude that the extracellular domain of the glycoprotein is sufficient for oligomer formation but that the transmembrane domain is required to stabilize this complex. Additional experiments suggest that interactions between external domains of the membrane-spanning, gp37 polypeptides are those most important for the formation of trimers. The significance of these observations to retroviral replication and implications for antiviral drug development are discussed.

High-level transient expression of influenza virus proteins from a series of SV40 late and early replacement vectors

We have constructed a collection of simian virus 40 (SV40) plasmid vectors useful for transient or constitutive expression of cDNA or genomic DNA in animal cells. Most vectors contain several unique restriction sites downstream from the SV40 late or early promoter, and are available with or without the virus-specific splicing signals. The use of these vectors for transient expression in monkey cells of X47 (H3N2) influenza hemagglutinin (HA) and matrix protein (M1) was demonstrated. Membrane-bound (HAm) as well as secreted forms of the HA glycoprotein lacking the sequence of the C-terminal anchor (HA-) have been obtained. Depending on the insert, the type of vector and the amount of transfected DNA, HA levels in COS cells [Gething and Sambrook, Nature 293 (1981) 620-625] transfected with late replacement SV40 vectors vary from 10(9) (HAm) to 10(8) (HA-) molecules per transfected cell. The maximum expression levels with early replacement vectors in COS cells are at least 50 times lower. In addition to the optimalization and the characterization of the expression of each vector-coded influenza protein, cotransfections, including vectors expressing HAm, neuraminidase (NA) and M1, were undertaken. The latter experiments did not result in a measureable amount of HAm or NA in the cell culture medium, suggesting that expression of these three structural viral proteins does not result in budding of (empty) influenza particles from the cell surface.

Site-directed mutation of the active site of influenza neuraminidase and implications for the catalytic mechanism

Different isolates of influenza virus show a high degree of amino acid sequence variation in their surface glycoproteins. Conserved residues located in the substrate-binding pocket of the influenza virus neuraminidase are therefore likely to be involved in substrate binding or enzyme catalysis. In order to study the structure and function of the active site of this protein, a full-length cDNA clone of the neuraminidase gene from influenza A/Tokyo/3/67 was subcloned into aN M13 vector and amino acid substitutions were made in selected residues by using the oligonucleotide mismatch technique. The mutant neuraminidase genes were expressed from a recombinant SV40 vector, and the proteins were analyzed for synthesis, transport to the cell surface, and proper three-dimensional folding by internal and surface immunofluorescence. The mutant neuraminidase proteins were then assayed to determine the effect of the amino acid substitution on enzyme activity. Twelve of the 14 mutant proteins were correctly folded and were transported to the cell surface in a manner identical with that of the wild type. Two of these have full enzyme activity, but seven mutants, despite correct three-dimensional structure, have completely lost neuraminidase activity. Two mutants were active at low pH. The properties of the mutant enzymes suggest a possible mechanism of neuraminidase action.

Determination of the epitope 264 on the hemagglutinin molecule of influenza H1N1 virus by site-specific mutagenesis

Full-length cDNA of HA gene derived from B-1-23 virus, a variant of A/USSR/90/77 (A/USSR/77) (H1N1) which had been selected with monoclonal antibody (mAb) 264 and contained an amino acid change at position 190 of the HA1 region, was cloned into the SV40 expression vector. Hemabsorbing or fusion activities of the HA protein expressed on CV-1 cells infected with the recombinant virus were indistinguishable from those of the authentic HA protein on B-1-23 virus infected cells. The antigenicity of the expressed HA protein was examined with five monoclonal antibodies to the HA of A/USSR/77 virus. The HA protein reacted with all mAbs except for mAb 264. To define the area of epitope 264, we prepared seven HA cDNAs modified by site-specific mutagenesis and cloned them into the SV40 expression vector (SVHA). The single base change from G to A at position 642 of B-1-23 HA cDNA replaced Asn at position 190 of the HA protein with Asp. The resulting HA protein, the amino acid sequence of which was the same as that in A/USSR/77, regained the binding activity with mAb 264. F. L. Raymond et al. (1984, In "Segmented Negative Strand Viruses" (R. W. Compans and D. H. L. Bishop, Eds.), pp. 253-258, Academic Press, Orlando; 1986, Virology 148, 275-287) and A. P. Kendal et al. (1984, In "Modern Approaches to Vaccines," pp. 151-157, Harvard Univ. Press, Cambridge) showed that changed amino acid residues 219(Lys) and 227(Glu) in A/Brazil/11/78 and 189(Lys) and 225(Asp) in A/Lackland/3/78 were presumably included in the area of epitope 264 by the nucleotide sequence analysis. Of those amino acids, our results show it is the residues 190 and 219 and possibly residue 189 that are involved in the epitope 264, but neither residue 225 nor 227.

Effects of site-specific mutation on structure and activity of influenza virus B/Lee/40 neuraminidase

A cDNA copy of the neuraminidase (NA) gene of a high-growing reassortant influenza virus which has the hemagglutinin of B/Hong Kong/8/73 and the NA of B/Lee/40 was cloned into plasmid pUC 9 and subcloned into a late-replacement SV40 vector so that the NA gene could be expressed in eukaryotic cells. The expressed protein was antigenically and enzymatically active. To study structure-function relationships in the B/Lee NA, particularly in comparison to the known structure of influenza A (N2) NA, specific mutations were introduced using synthetic oligonucleotides. Mutation of an apparently unpaired cysteine residue to serine at position 251 had no effect on protein transport or folding as judged by cell-surface reactivity with monoclonal antibodies, and the NA retained enzyme activity, confirming that this Cys is not essential for correct folding of the polypeptide. Mutation of Trp 364 to Leu abolished detectable enzyme activity, while mutation of Thr 368 to Val reduced enzyme activity to less than 25% of wild-type levels. Neither mutation affected antigenic properties. Therefore it is likely that both these side chains extend into the NA active site pocket. The results of these experiments are in accord with similarities in the structure of the B/Lee NA compared with that of influenza A (N2) NA. Although there is about 70% amino acid sequence difference between influenza A and B NAs, residues in the active site are highly conserved. Our in vitro mutagenesis experiments help to confirm the tentative alignment of sequences and have identified conserved amino acid side chains involved in enzyme activity.

Domains of virus glycoproteins

This chapter reviews current information about the structure and function of virus glycoproteins. There are few virus glycoproteins that provide prototypes for illustrating important relationships between the functions and glycoprotein structure. The discussion presented in the chapter concentrates on those viral glycoproteins that (1) span the lipid bilayer once, (2) are oriented such that the carboxy terminus comprises the cytoplasmic domain, and (3) contain asparagine-linked oligosaccharides. There are also viral glycoproteins with extensive O-linked glycosylation, some of which are also presented in the discussion. The chapter also focuses on the studies involving directed mutagenesis and construction of chimeric proteins. The effects of altering specific amino acid sequences, of swapping domains, and of adding a new domain to a protein serve to define the functions of a domain and to show that a domain can be independently associated with a specific function. The experiments described have been carried out by inserting the genes of particular viral glycoproteins—such as cDNAs—into expression vectors and transcribing the cDNAs from the promoter provided by the expression vector. This approach established that localization and functions such as the fusogenic activity are properties of the viral glycoprotein per se and do not require other viral-coded components.

Identification of defects in the neuraminidase gene of four temperature-sensitive mutants of A/WSN/33 influenza virus

Four influenza (A/WSN/33) mutants, temperature sensitive (ts) for neuraminidase (NA) (Sugiura et al., 1972, 1975) were analyzed. All four ts mutants were found to be defective at the nonpermissive temperature (39.5 degrees) both in enzymatic activity and in transport to the cell surface. Upon shift down to the permissive temperature (33 degrees), enzymatic activity and transport to the cell surface were both restored suggesting that the mutational defect is reversible. Comparative sequence analysis of the NA gene from ts mutants, their revertants and wild type WSN viruses revealed that in each case single point mutations causing amino acid substitutions were associated with the ts defect. The positions of each point mutation when mapped in the three-dimensional structure of NA varied. However, all four amino acid substitutions were located in beta-sheet strands of the head region. Several other amino acid changes not essential for the ts phenotype were found in each mutant NA. The nonessential changes were localized either in the stalk region or in the loop structures of the head, but none in the beta-sheet strands. Because both enzymatic activity and transport of NA were affected in all four mutants, we propose that the mutational phenotype is caused by a change in overall conformation rather than a localized change in the sialic acid binding site.