Further isolation and characterization of temperature-sensitive mutants of influenza virus

[Dynamics of the influenza virus genome regulated by cellular host factors]

For efficient replication of the influenza virus genome and its post-replicational processes, not only viral factors but also host-derived cellular factors (host factors) are required. The influenza virus genome exists as viral ribonucleoprotein (vRNP) complexes with viral RNA-dependent RNA polymerases and nucleoprotein (NP). Using biochemical and proteomics approaches, we have identified host factors which are required for the vRNP replication and the progeny vRNP transport. We found that MCM complex, a cellular DNA replication licensing factor, is required for successful viral genome replication. In concert with the replication reaction, the nascent RNA chains are encapsidated with NP by cellular splicing factor UAP56. Further, after nuclear export of vRNP, we revealed that vRNP is transported to the plasma membrane using cholesterol-enriched recycling endosomes through cell cycle-independent activation of the centrosome by YB-1, which is a mitotic centrosomal protein. Depletion of YB-1 shows that the cholesterol-enriched endosomes are important for clustering of viral structural proteins at lipid rafts to assemble the virus particles concomitantly with the arrival of vRNP beneath the plasma membrane.

Inhibition of Influenza Virus A/WSN Replication by Serine Protease Inhibitors and anti-Protease Antibodies

The serine protease inhibitors, aprotinin and 6-amidino-2-naphthyl-p-guanidinobenzoate (Futhan), showed striking antiviral activity in the plaque assay of the canine kidney (MDCK) cell-WSN strain system. Anti-cathepsin B IgG antibody/showed the greatest inhibitory effect on plaque formation, followed by anti-factor X antibody and then anti-plasminogen antibody. Anti-cathepsin B antibody inhibited the proteolytic cleavage of haemagglutinin (HA). These results suggest that a serine protease-like enzyme and the other protein that binds to anti-cathepsin B antibody may be involved in the process of WSN HA cleavage on the membrane surface of MDCK cells.

Oseltamivir expands quasispecies of influenza virus through cell-to-cell transmission

The population of influenza virus consists of a huge variety of variants, called quasispecies, due to error-prone replication. Previously, we reported that progeny virions of influenza virus become infected to adjacent cells via cell-to-cell transmission pathway in the presence of oseltamivir. During cell-to-cell transmission, viruses become infected to adjacent cells at high multiplicity since progeny virions are enriched on plasma membrane between infected cells and their adjacent cells. Co-infection with viral variants may rescue recessive mutations with each other. Thus, it is assumed that the cell-to-cell transmission causes expansion of virus quasispecies. Here, we have demonstrated that temperature-sensitive mutations remain in progeny viruses even at non-permissive temperature by co-infection in the presence of oseltamivir. This is possibly due to a multiplex infection through the cell-to-cell transmission by the addition of oseltamivir. Further, by the addition of oseltamivir, the number of missense mutation introduced by error-prone replication in segment 8 encoding NS1 was increased in a passage-dependent manner. The number of missense mutation in segment 5 encoding NP was not changed significantly, whereas silent mutation was increased. Taken together, we propose that oseltamivir expands influenza virus quasispecies via cell-to-cell transmission, and may facilitate the viral evolution and adaptation.

Tamiflu-resistant but HA-mediated cell-to-cell transmission through apical membranes of cell-associated influenza viruses

The infection of viruses to a neighboring cell is considered to be beneficial in terms of evasion from host anti-virus defense systems. There are two pathways for viral infection to “right next door”: one is the virus transmission through cell-cell fusion by forming syncytium without production of progeny virions, and the other is mediated by virions without virus diffusion, generally designated cell-to-cell transmission. Influenza viruses are believed to be transmitted as cell-free virus from infected cells to uninfected cells. Here, we demonstrated that influenza virus can utilize cell-to-cell transmission pathway through apical membranes, by handover of virions on the surface of an infected cell to adjacent host cells. Live cell imaging techniques showed that a recombinant influenza virus, in which the neuraminidase gene was replaced with the green fluorescence protein gene, spreads from an infected cell to adjacent cells forming infected cell clusters. This type of virus spreading requires HA activation by protease treatment. The cell-to-cell transmission was also blocked by amantadine, which inhibits the acidification of endosomes required for uncoating of influenza virus particles in endosomes, indicating that functional hemagglutinin and endosome acidification by M2 ion channel were essential for the cell-to-cell influenza virus transmission. Furthermore, in the cell-to-cell transmission of influenza virus, progeny virions could remain associated with the surface of infected cell even after budding, for the progeny virions to be passed on to adjacent uninfected cells. The evidence that cell-to-cell transmission occurs in influenza virus lead to the caution that local infection proceeds even when treated with neuraminidase inhibitors.

Sorting of influenza A virus RNA genome segments after nuclear export

The genome of the influenza A virus consists of eight different segments. These eight segments are thought to be sorted selectively in infected cells. However, the cellular compartment where segments are sorted is not known. We examined using temperature sensitive (ts) mutant viruses and cell fusion where segments are sorted in infected cells. Different cells were infected with different ts mutant viruses, and these cells were fused. In fused cells, genome segments are mixed only in the cytoplasm, because M1 prevents their re-import into the nucleus. We made a marker ts53 virus, which has silent mutations in given segments and determined the reassortment frequency on all segments using ts1 and marker ts53. In both co-infected and fused cells, all of marker ts53 segments and ts1 segments were incorporated into progeny virions in a random fashion. These results suggest that influenza virus genome segments are sorted after nuclear export.

Crystal structure of the polymerase PA(C)-PB1(N) complex from an avian influenza H5N1 virus

The recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer has crucial roles in viral RNA replication and transcription. It contains three proteins: PA, PB1 and PB2. PB1 harbours polymerase and endonuclease activities and PB2 is responsible for cap binding; PA is implicated in RNA replication and proteolytic activity, although its function is less clearly defined. Here we report the 2.9 ångström structure of avian H5N1 influenza A virus PA (PA(C), residues 257-716) in complex with the PA-binding region of PB1 (PB1(N), residues 1-25). PA(C) has a fold resembling a dragon's head with PB1(N) clamped into its open 'jaws'. PB1(N) is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1(N) to PA(C) at the atomic level, demonstrating a potential target for novel anti-influenza therapeutics. We also discuss a potential nucleotide binding site and the roles of some known residues involved in polymerase activity. Furthermore, to explore the role of PA in viral replication and transcription, we propose a model for the influenza RdRp heterotrimer by comparing PA(C) with the lambda3 reovirus polymerase structure, and docking the PA(C) structure into an available low resolution electron microscopy map.

De novo replication of the influenza virus RNA genome is regulated by DNA replicative helicase, MCM

By dissecting and reconstituting a cell-free influenza virus genome replication system, we have purified and identified the minichromosome maintenance (MCM) complex, which is thought to be a DNA replicative helicase, as one of the host factors that regulate the virus genome replication. MCM interacted with the PA subunit of the viral RNA-dependent RNA polymerase that is found to be involved in the replication genetically. The virus genome replication was decreased in MCM2 knockdown cells. The viral polymerase appeared to be a nonproductive complex, that is, it was capable of initiating replication but produced only abortive short RNA chains. MCM stimulated de novo-initiated replication reaction by stabilizing a replication complex during its transition from initiation to elongation. Based on the findings, including the result that the MCM-mediated RNA replication reaction was competed with exogenously added RNA, we propose that MCM functions as a scaffold between the nascent RNA chains and the viral polymerase.

Involvement of influenza virus PA subunit in assembly of functional RNA polymerase complexes

The RNA-dependent RNA polymerase of influenza virus consists of three subunits, PB1, PB2, and PA, and synthesizes three kinds of viral RNAs, vRNA, cRNA, and mRNA. PB1 is a catalytic subunit; PB2 recognizes the cap structure for generation of the primer for transcription; and PA is thought to be involved in viral RNA replication. However, the process of polymerase complex assembly and the exact nature of polymerase complexes involved in synthesis of the three different RNA species are not yet clear. ts53 virus is a temperature-sensitive (ts) mutant derived from A/WSN/33 (A. Sugiura, M. Ueda, K. Tobita, and C. Enomoto, Virology 65:363-373, 1975). We confirmed that the mRNA synthesis level of ts53 remains unaffected at the nonpermissive temperature, whereas vRNA synthesis is largely reduced. Sequencing of the gene encoding ts53 PA and recombinant virus rescue experiments revealed that an amino acid change from Leu to Pro at amino acid position 226 is causative of temperature sensitivity. By glycerol density gradient analyses of nuclear extracts prepared from wild-type virus-infected cells, we found that polymerase proteins sediment in three fractions: one (H fraction) consists of RNP complexes, another (M fraction) contains active polymerases but not viral RNA, and the other (L fraction) contains inactive forms of polymerases. Pulse-chase experiments showed that polymerases in the L fraction are converted to those in the M fraction. In ts53-infected cells, polymerases accumulated in the L fraction. These results strongly suggest that PA is involved in the assembly of functional viral RNA polymerase complexes from their inactive intermediates.

Model suggesting that replication of influenza virus is regulated by stabilization of replicative intermediates

The RNA-dependent RNA polymerase of influenza A virus is responsible for both transcription and replication of negative-sense viral RNA. It is thought that a "switching" mechanism regulates the transition between these activities. We demonstrate that, in the presence of preexisting viral RNA polymerase and nucleoprotein (NP), influenza A virus synthesizes both mRNA (transcription) and cRNA (replication) early in infection. We suggest that there may be no switch regulating the initiation of RNA synthesis and present a model suggesting that nascent cRNA is degraded by host cell nucleases unless it is stabilized by newly synthesized viral RNA polymerase and NP.

Genetics of influenza viruses

Influenza A viruses contain genomes composed of eight separate segments of negative-sense RNA. Circulating human strains are notorious for their tendency to accumulate mutations from one year to the next and cause recurrent epidemics. However, the segmented nature of the genome also allows for the exchange of entire genes between different viral strains. The ability to manipulate influenza gene segments in various combinations in the laboratory has contributed to its being one of the best characterized viruses, and studies on influenza have provided key contributions toward the understanding of various aspects of virology in general. However, the genetic plasticity of influenza viruses also has serious potential implications regarding vaccine design, pathogenicity, and the capacity for novel viruses to emerge from natural reservoirs and cause global pandemics.

A fatal relationship--influenza virus interactions with the host cell

Influenza A viruses are important worldwide pathogens for humans and different animal species. The infectious agent is the prototype of the orthomyxoviridae which are characterized by a segmented negative strand RNA genome that is replicated in the nucleus of the infected cell. The genome has a combined coding capacity of about 13 kb and contains the genetic information for ten viral proteins. Despite this relatively small coding capacity--large DNA viruses like herpes or poxviruses express about 150-200 gene products--influenza A viruses are able to successfully infect and multiply in a wide range of mammalian and avian species. It is therefore not surprising that influenza A viruses extensively use and manipulate host cell functions. This includes multiple interactions of viral proteins with cellular proteins. In recent years an increasing amount of information about the identity of the cellular factors that are involved in viral transcription and replication, intracellular trafficking of viral components and assembly of the virus particle has accumulated. This article aims to review recent developments in this field with a focus on cellular factors and processes which are activated by the virus to either support viral replication or to counteract host-cell defense mechanisms.

Histones as a target for influenza virus matrix protein M1

Matrix protein M1 purified from influenza A and B viruses has been analyzed for its ability to specifically interact with cellular proteins by immune coprecipitation and by an in vitro binding assay on nitrocellulose on PVDF membranes. When M1 was mixed with lysates of uninfected cells there was selective binding of histones H2A, H2B, H3, and H4. Week binding of H1 was also observed. The binding specificity of M1 was confirmed by using purified histones. The M1-histone complexes were dependent on pH and ionic strength, indicating electrostatic interactions. Chemical cleavage of M1 by formic acid into an N-terminal 9-kDa fragment and a C-terminal 18-kDa fragment did not abolish interaction with histones. However, after treatment with 1 M sodium chloride cleaved M1 no longer bound to histones, whereas uncleaved M1 showed an increased binding activity after salt treatment. These findings suggest that both N- and C-terminal domains of M1 are involved in histone binding and that conformation of M is an important factor in this interaction. The data support the notion that there is specific interaction of M1 with nucleosomes during the nuclear phase of influenza virus replication.

Influenza virus hemagglutinin and neuraminidase glycoproteins stimulate the membrane association of the matrix protein

We have analyzed the mechanism by which the matrix (M1) protein associates with cellular membranes during influenza A virus assembly. Interaction of the M1 protein with the viral hemagglutinin (HA) or neuraminidase (NA) glycoprotein was extensively analyzed by using wild-type and transfectant influenza viruses as well as recombinant vaccinia viruses expressing the M1 protein, HA, or NA. Membrane binding of the M1 protein was significantly stimulated at the late stage of virus infection. Using recombinant vaccinia viruses, we found that a relatively small fraction (20 to 40%) of the cytoplasmic M1 protein associated with cellular membranes in the absence of other viral proteins, while coexpression of the HA and the NA stimulated membrane binding of the M1 protein. The stimulatory effect of the NA (>90%) was significant and higher than that of the HA (>60%). Introduction of mutations into the cytoplasmic tail of the NA interfered with its stimulatory effect. Meanwhile, the HA may complement the defective NA and facilitate virus assembly in cells infected with the NA/TAIL(-) transfectant. In conclusion, the highly conserved cytoplasmic tails of the HA and NA play an important role in virus assembly.

Nuclear trafficking of influenza virus ribonuleoproteins in heterokaryons

The influenza virus nucleoprotein (NP), matrix protein (M1), and ribonucleoproteins (vRNPs) undergo regulated nuclear import and export during infection. Their trafficking was analyzed by using interspecies heterokaryons containing nuclei from infected and uninfected cells. Under normal conditions, it was demonstrated that the vRNPs which were assembled in the nucleus and transported to the cytosol were prevented from reimport into the nucleus. To be import competent, they must first assemble into virions and enter by the endosomal entry pathway. In influenza virus mutant ts51, in which M1 is defective, direct reimport took place but was inhibited by heterologous expression of wild-type M1. These data confirm M1's role as the inhibitor of premature nuclear import and as the main regulator of nuclear transport of vRNPs. In addition to this vRNP shuttling, M1 also shuttled between the nucleus and the cytoplasm in ts51-infected cells. When NP was expressed in the absence of virus infection, it was also found to be a shuttling protein.

Electroporation of influenza virus ribonucleoprotein complexes for rescue of the nucleoprotein and matrix genes

Reverse genetics has been successfully used for the generation of recombinant influenza virus with altered biological properties. The standard method is based on DEAE-dextran transfection of in vitro reconstituted influenza virus ribonucleoprotein complex (RNP) into helper virus infected cells with subsequent selection of the recombinant viruses. Here we report the utilization of electroporation for reverse genetics of influenza virus as an improvement over the standard method. In a neuraminidase (NA) gene rescue system, we were able to demonstrate that electroporation of in vitro reconstituted NA RNP of influenza A/WSN/33 (H1N1) virus into WSN/HK virus infected cells allows the rescue of the transfectant WSN virus. The titer of transfectant virus obtained using electroporation is comparable to that generated using the DEAE-dextran transfection method. More significantly, the ratio of transfectant virus to helper virus is as much as 20-fold greater than that achieved using the DEAE-dextran system. We have also used electroporation to generate recombinant influenza virus carrying cDNA-derived matrix (M) gene or nucleoprotein (NP) gene of the WSN virus by using the temperature-sensitive (ts) mutants ts51 and ts56 as helper viruses. In the case of electroporation of M gene RNP, 88% of the viruses isolated after selection at 39 degrees C were transfectants. In contrast, the majority of viruses obtained using the DEAE-dextran transfection method were revertants of the helper virus. The NP-gene transfectant was only generated by the electroporation method. Our results suggest that electroporation of influenza virus RNP may be a useful method for generation of recombinant influenza viruses, especially in a system in which a ts mutant is used as helper virus.

Hyperphosphorylation of mutant influenza virus matrix protein, M1, causes its retention in the nucleus

The matrix (M1) protein of influenza virus is a major structural component, involved in regulation of viral ribonucleoprotein transport into and out of the nucleus. Early in infection, M1 is distributed in the nucleus, whereas later, it is localized predominantly in the cytoplasm. Using immunofluorescence microscopy and the influenza virus mutant ts51, we found that at the nonpermissive temperature M1 was retained in the nucleus, even at late times after infection. In contrast, the viral nucleoprotein (NP), after a temporary retention in the nucleus, was distributed in the cytoplasm. Therefore, mutant M1 supported the release of the viral ribonucleoproteins from the nucleus, but not the formation of infectious virions. The point mutation in the ts51 M1 gene was predicted to encode an additional phosphorylation site. We observed a substantial increase in the incorporation of 32Pi into M1 at the nonpermissive temperature. The critical role of this phosphorylation site was demonstrated by using H89, a protein kinase inhibitor; it inhibited the expression of the mutant phenotype, as judged by M1 distribution in the cell. Immunofluorescence analysis of ts51-infected cells after treatment with H89 showed a wild-type phenotype. In summary, the data indicated that the ts51 M1 protein was hyperphosphorylated at the nonpermissive temperature and that this phosphorylation was responsible for its aberrant nuclear retention.

Growth control of influenza A virus by M1 protein: analysis of transfectant viruses carrying the chimeric M gene

Analysis of fast-growing reassortants (AWM viruses) of influenza A virus produced by mixed infection with a fast-growing WSN strain and a slowly growing Aichi strain indicated that the M gene plays a role in the regulation of virus growth rate at an early step of infection (J. Yasuda, T. Toyoda, M. Nakayama, and A. Ishihama, Arch. Virol. 133:283-294, 1993). To determine which of the two M gene products, M1 or M2, is responsible for the growth rate control, one recombinant WSN virus (CWA) clone possessing a chimeric M gene (WSN M1-Aichi M2) was generated by using an improved reverse genetics and transfection system. The recombinant CWA virus retained the phenotype of both large plaque formation and early onset of virus growth. This indicates that the WSN M1 protein is responsible for rapid virus growth.

Isolation and classification of temperature-sensitive mutants of influenza B virus

We isolated 25 temperature-sensitive mutants of B/Kanagawa/73 strain generated by mutagenesis with 5-fluorouracil and classified them into seven recombination groups by pair-wise crosses. All mutants showed a ratio of plaquing efficiency at the nonpermissive temperature (37.5 C) to the permissive temperature (32 C) of 10(-4) or less. At 37.5 C most of group I, II, and III mutants did not produce appreciable amounts of protein, but all other group mutants were protein synthesis-positive. A group VII mutant produced active hemagglutinin (HA) and neuraminidase (NA) at the nonpermissive temperature, but Group V mutants produced only active NA and were defective in the HA molecule. The other group mutants, including group IV mutants with mutation only in the NA gene (8, 10), lacked both activities at the nonpermissive temperature. One of nine influenza B virus isolates in 1989 had EOP 37.5/32 of 1/3 x 10(-2) and belonged to recombination group VII.

Nuclear retention of M1 protein in a temperature-sensitive mutant of influenza (A/WSN/33) virus does not affect nuclear export of viral ribonucleoproteins

We investigated the properties of ts51, an influenza virus (A/WSN/33) temperature-sensitive RNA segment 7 mutant. Nucleotide sequence analysis revealed that ts51 possesses a single nucleotide mutation, T-261----C, in RNA segment 7, resulting in a single amino acid change. Phenylalanine (position 79) in the wild-type M1 protein was substituted by serine in ts51. This mutation was phenotypically characterized by dramatic nuclear accumulation of the M1 protein and interfered with some steps at the late stage of virus replication, possibly affecting the assembly and/or budding of viral particles. However, although M1 protein was retained within the nucleus, export of the newly synthesized viral ribonucleoprotein containing the minus-strand RNA into the cytoplasm was essentially the same at both permissive and nonpermissive temperatures. The roles of M1 in the export of viral ribonucleoproteins from the nucleus into the cytoplasm and in the virus particle assembly process are discussed.

High-efficiency formation of influenza virus transfectants

cDNA-derived RNAs were introduced into the genomes of influenza viruses by using an improved ribonucleoprotein (RNP) transfection protocol. Up to 10(5) viral transfectants with a novel neuraminidase gene could be obtained by using a 35-mm dish (10(6) cells) for RNP transfection. In addition to genes coding for surface proteins (hemagglutinin and neuraminidase), we also exchanged a gene coding for nonsurface proteins. The cDNA-derived influenza A/PR/8/34 virus NS gene was introduced into a temperature-sensitive mutant with a defect in this gene. We suggest that the term influenza virus transfectant be used for those viruses which are made by RNP transfection with cDNA-derived RNA.

Studies on the regulation of influenza virus RNA replication: a differential inhibition of the synthesis of vRNA segments in shift-up experiments with ts mutants

The regulation of influenza virus vRNA synthesis in the course of the reproduction cycle was studied with the use of a series of ts mutants in shift-up experiments. The synthesis of vRNA segments was registered by means of polyacrylamide gel electrophoresis of nucleocapsid-associated RNA isolated from the infected cells labelled with [3H]uridine after the shift-up to a semi-permissive temperature. Each mutant exhibited a specific differential pattern of vRNA synthesis inhibition after the shift-up. The most affected segments were either vRNA 4, vRNAs 4 and 7, or vRNAs 4, 6, and 7 in cells infected, respectively, with ts mutants C15 (ts lesion in PB1 gene), C45 (ts lesion in PA gene) and CmN3 (ts lesion in NS gene). The synthesis of vRNAs 1, 2, and 3 was relatively resistant to the shift-up in the cells infected with C15 or C45 and more sensitive in the cells infected with C44 (ts lesion in PB2 gene) or CmN3. The replication of the "early" genes (vRNAs 5 and 8) was generally least affected by the shift-up. The results are discussed in connection with the "early-late" transition of vRNA synthesis pattern in the course of infection.

Complementation and analysis of an NP mutant of influenza virus

Cell lines were constructed so as to express the influenza A virus nucleoprotein (NP) at levels approximating 5% of the total NP made throughout virus infection. Two types of cell lines were analyzed. One cell line (NP-5) expresses only the NP while another cell line was constructed which expresses the three viral polymerase proteins in addition to the NP (3PNP-4). Both cell lines were able to complement the growth of an NP mutant, ts56, at the non-permissive temperature. The 3PNP-4 cell line, constructed by transfecting a cell line already expressing the three polymerase proteins, continued to be able to complement viral PB2 mutants. In addition, sequence analysis was performed on the NP gene segment of A/WSN/33 and ts56 viruses. This analysis revealed that the mutant phenotype exhibited by ts56 at non-permissive temperature is due to a single serine to asparagine change (at codon 332) within the protein.

Influenza virus RNA replication in vitro: synthesis of viral template RNAs and virion RNAs in the absence of an added primer

The two steps in influenza virus RNA replication are (i) the synthesis of template RNAs, i.e., full-length copies of the virion RNAs, and (ii) the copying of these template RNAs into new virion RNAs. We prepared nuclear extracts from infected HeLa cells that catalyzed both template RNA and virion RNA synthesis in vitro in the absence of an added primer. Antibody depletion experiments implicated nucleocapsid protein molecules not associated with nucleocapsids in template RNA synthesis for antitermination at the polyadenylation site used during viral mRNA synthesis. Experiments with the WSN influenza virus temperature-sensitive mutant ts56 containing a defect in the nucleocapsid protein proved that the nucleocapsid protein was indeed required for template RNA synthesis both in vivo and in vitro. Nuclear extracts prepared from mutant virus-infected cells synthesized template RNA at the permissive temperature but not at the nonpermissive temperature, whereas the synthesis of mRNA-size transcripts was not decreased at the nonpermissive temperature. Antibody depletion experiments showed that nucleocapsid protein molecules not associated with nucleocapsids were also required for the copying of template RNA into virion RNA. In contrast to the situation with the synthesis of transcripts complementary to virion RNA, no discrete termination product(s) were made during virion RNA synthesis in vitro in the absence of nucleocapsid protein molecules.

Viral RNA polymerases

Recent progress in molecular biological techniques revealed that genomes of animal viruses are complex in structure, for example, with respect to the chemical nature (DNA or RNA), strandedness (double or single), genetic sense (positive or negative), circularity (circle or linear), and so on. In agreement with this complexity in the genome structure, the modes of transcription and replication are various among virus families. The purpose of this article is to review and bring up to date the literature on viral RNA polymerases involved in transcription of animal DNA viruses and in both transcription and replication of RNA viruses. This review shows that the viral RNA polymerases are complex in both structure and function, being composed of multiple subunits and carrying multiple functions. The functions exposed seem to be controlled through structural interconversion.

Temperature-sensitive defect of influenza A/Ann Arbor/6/60 cold-adapted variant leads to a blockage of matrix polypeptide incorporation into the plasma membrane of the infected cells

A temperature-sensitive (ts) defect in growth of the A/Ann Arbor/6/60 (A/AA/60) cold-adapted (ca) and ts variant strain has been studied. At the restrictive temperature of 38.5 degrees C, the variant synthesized all the viral polypeptides in normal amounts within the infected cells, but the virions released into the culture fluid contained greatly reduced amounts of the matrix (M1) polypeptide and showed significantly low infectivity per unit hemagglutinin activity. Cell fractionation experiments revealed that incorporation of the M1 polypeptide into plasma membranes of the variant-infected cells was selectively reduced at 38.5 degrees C, whilst it occurred normally at 34 degrees C. The ts reassortants between the A/AA/60 variant and the A/AA/1/80 wild type (wt) strain (non-ts), which had the M gene derived from the wt parent, also showed similar patterns. These results suggest that the ts defect of the variant and its ts reassortants involves the process of incorporation of the M1 polypeptide into the plasma membranes of the infected cells and that this defect is not attributable to the M gene of the variant.

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

Two temperature-sensitive mutants of WSN influenza virus, ts-61S and ts-134, possess defects in the hemagglutinin (HA) gene. These defects are characterized as a defective intracellular transport of the HA at the nonpermissive temperature and a marked thermolability. The nucleic acid sequences of the HA gene of these two viruses, as well as a series of revertant viruses, were determined. The deduced amino acid sequences demonstrate that the HA of ts-61S varied from the wild type protein by three amino acids while that of ts-134 differed by two residues. For both mutants, analysis of revertant viruses indicated that the phenotype of transport inhibition at the nonpermissive temperature and heat lability were associated with a single amino acid change in the globular portion of the molecule. In the case of ts-61S, the critical change in the HA was the replacement of a serine residue at position 110 with that of a proline. The mutational defect in the HA of ts-134 was due to the substitution of a tyrosine residue at position 159 with that of a histidine residue. Four of five revertants of ts-134 were suppressor revertants, of which some of the compensatory changes did not restore thermostability to the HA.

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.

Expression of the three influenza virus polymerase proteins in a single cell allows growth complementation of viral mutants

Transformed cell lines derived from murine C127 cells were constructed that express the influenza virus RNA-dependent RNA polymerase proteins (PA, PB1, and PB2). Cell lines that express only one or all three of the proteins were tested for their ability to complement temperature-sensitive viral mutants incubated at the nonpermissive temperature. Two cell lines were isolated that express all three polymerase genes and complement the growth of PB2 temperature-sensitive mutants at the nonpermissive temperature. One of these lines also complemented PA temperature-sensitive mutants. The viral titers obtained in these two cell lines were 12-fold to 1000-fold higher than the viral titers obtained upon growth of the corresponding temperature-sensitive mutant in C127 cells at the nonpermissive temperature.

Biological characteristics of a cold-adapted influenza A virus mutation residing on a polymerase gene

The biological function of a cold-adapted (ca) mutation residing on the PB2 gene of an influenza A/Ann Arbor/6/60 (A/AA/6/60) ca variant virus in the viral replication cycle at 25 degrees C was studied. The viral polypeptide synthesis of A/AA/6/60 ca variant at 25 degrees C was evident approximately 6 hours earlier than the wild type (wt) virus and yielded twice as many products. The quantitative analysis of viral complementary RNA (cRNA), synthesized in the presence of cycloheximide, revealed that A/AA/6/60 ca variant and a single gene reassortant that contains only the PB2 gene of the ca variant with remaining genes of the wt virus produced equal amount of cRNA at 25 degrees and 33 degrees C, which was an amount approximately four fold greater than the wt virus' cRNA synthesized at 25 degrees C. These results strongly suggest that the ca mutation residing on the PB2 gene of A/AA/6/60 ca variant affects the messenger RNA synthesis at 25 degrees C in the primary transcription.

Transcription and replication of eight RNA segments of influenza virus

A novel quantitation system of both plus- and minus-strand RNAs for all eight genome segments of influenza virus was developed using single-strand cDNAs as the probes for hybridization, and employed for the measurement of various RNA species in influenza virus WSN-infected MDBK cells. The synthesis rate and accumulation level of plus-strand RNAs differed considerably among eight RNA segments and were under temporal control. In contrast, eight vRNA molecules of minus polarity were synthesized coordinately at similar rates. Newly synthesized plus-strand RNAs were rapidly transported into the cytoplasm, particularly during the early phase of virus infection, but vRNAs accumulated in the nuclei until the late infection phase. The present data supported the differential regulation of synthesis and the separate transport between plus- and minus-strand RNAs.

Identification of the influenza virus transcriptase by affinity-labeling with pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (PLP), a reversible inhibitor of in vitro transcription by fowl plaque virus, has been used to identify the transcriptase. Kinetic analyses showed that PLP competitively inhibits the addition of each nucleoside triphosphate in ApG-primed reactions, suggesting that both initiation and elongation are affected. The irreversible inhibition by PLP following reduction with borohydride was prevented by preincubation with the first substrate: GTP in unprimed reactions or CTP in the presence of ApG. On reaction of FPV proteins with PLP and [3H]borohydride the core protein PB1 was preferentially labeled and the labeling was selectively blocked by GTP or ApG + CTP. These data suggest that PB1 has the nucleotide-binding site of the transcriptase, is responsible for both initiation and elongation, and is apparently associated with the 3' ends of template RNAs in virions.

Temperature-sensitive influenza A virus clones originated by a cross between A/Aichi/2/68 (H3N2) and B/Yamagata/1/73

A genetic cross was performed between influenza viruses B/Yamagata/1/73 and clone 6-10, an A type influenza virus derived from a cross between A/Aichi/2/68 (H3N2) and B/Yamagata. Efficiency of plating of B/Yamagata at 39.5 degrees C was less than 10(-3) in MDCK cells, while that of clone 6-10 or A/Aichi was higher than 10(-1). Four of the 15 clones selected for HA of Aichi serotype from the mixed yield, where type B virus was predominant over type A, were temperature-sensitive (ts), with efficiency of plating at 39.5 degrees C less than 10(-2), exceeding the frequency of spontaneous ts mutants among clone 6-10 progeny. Thus, co-existing type B virus not only interfered with the replication of type A, but also rendered it temperature-sensitive. Genetic analysis of the 4ts clones using a set of ts mutants of influenza virus A/WSN (H0N1) revealed that these clones, in contrast with the spontaneous ts mutant of clone 6-10, with ts defect only in NP gene, possessed ts lesions in multiple genes including a common ts defect in M. Polyacrylamide gel electrophoresis of viral RNA and proteins of these clones showed an identical gel pattern to that of clone 6-10, although the rate of synthesis of individual viral polypeptide was variable from clone to clone.

Functional defects of fowl plague virus temperature-sensitive mutant having mutation in the neuraminidase

A fowl plague virus (FPV) temperature-sensitive mutant ts 5 having mutation lesions in the gene coding for the neuraminidase has been obtained. The mutant induced synthesis of cRNA, vRNA and proteins in cells under non-permissive conditions, but formation of virions including non-infectious ones was defective. The neuraminidase and haemagglutinin synthesized under non-permissive conditions possessed functional activity and could migrate from the rough endoplasmic reticulum into plasma membranes; however, cleavage of the haemagglutinin was reduced. In ts 5-infected cells under non-permissive conditions the synthesis of segments 5 and 8 of cRNA and vRNA was predominant both early and late in the reproduction cycle, and the synthesis of P1, P2, P3, HA and M proteins was reduced after approximately 3 hours. The data obtained suggest that involvement of the neuraminidase in the formation of infectious virions may have no direct association with the enzymatic activity of this protein, and that the mutation in the neuraminidase may affect regulation of replication and transcription processes.

Influenza virus temperature-sensitive cap (m7GpppNm)-dependent endonuclease

The first step in influenza viral mRNA synthesis is the endonucleolytic cleavage of heterologous RNAs containing cap 1 (m(7)GpppNm) structures to generate capped primers that are 10 to 13 nucleotides long, which are then elongated to form the viral mRNA chains. We examined the temperature sensitivity of these steps in vitro by using two WSN virus temperature-sensitive mutants, ts1 and ts6, which have a defect in the genome RNA segment coding for the viral PB2 protein. For these experiments, it was necessary to employ purified viral cores rather than detergent-treated virions to catalyze transcription, as preparations of detergent-treated virions contain destabilizing or inhibitory activities which render even the transcription catalyzed by wild-type virus temperature sensitive. Using purified wild-type viral cores, we found that the rates of endonucleolytic cleavage of capped primers and of overall transcription were similar at 39.5 and 33 degrees C, the in vivo nonpermissive and permissive temperatures, respectively. In contrast, the activities of the cap-dependent endonucleases of ts1 and ts6 viral cores at 39.5 degrees C were only about 15% of those at 33 degrees C. The steps in transcription after endonucleolytic cleavage of the capped RNA primer were largely, if not totally, temperature insensitive, indicating that the mutations in the PB2 protein found in ts1 and ts6 virions affect only the endonuclease step. The temperature-sensitive defect is most likely in the recognition of the 5'-terminal cap 1 structure that occurs as a required first step in the endonuclease reaction: the cap-dependent binding of a specific capped primer fragment to ts1 viral cores was temperature sensitive under conditions in which binding to wild-type viral cores was not affected by increasing the temperature from 33 to 39.5 degrees C. Thus, our results establish that the viral PB2 protein functions in cap recognition during the endonuclease reaction.

Complete sequence analyses show that two defective interfering influenza viral RNAs contain a single internal deletion of a polymerase gene

Defective interfering (DI) influenza viral RNAs arise by internal deletion of progenitor RNAs. By using recombinant DNA cloning and DNA sequence analysis techniques, we have deduced the complete sequence of two such RNAs (L2b and L3), both arising from the same polymerase (P1) gene of WSN influenza virus. We have also partially determined the sequence of the P1 polymerase gene, including the sequence at the point of deletion and the flanking regions. Our sequence study shows the following. (i) Both L2b and L3 arise by a simple deletion in the P1 gene. (ii) L2b and L3 are 683 and 441 nucleotides long, respectively. (iii) The first 413 and 244 nucleotides of the 5' ends of L2b and L3, respectively, are identical to those of the 5' end of the P1 gene. (iv) The last 270 nucleotides of L2b and 197 nucleotides of L3 are the same as those of the 3' end of the P1 gene. (v) The entire sequence of L3 is present in the sequence of L2b. (vi) Both the 5' and the 3' termini, including the transcription stop and poly(A) addition signals of the progenitor P1 gene, are present in both L2b and L3. (vii) The sequences at the deletion point and the flanking region of the P1 gene do not resemble the consensus splicing sequence of spliced mRNA suggesting that a replicational event rather than splicing is involved in the formation of influenza defective interfering RNAs.

Occurrence of temperature-sensitive influenza A viruses in nature

The origin and characteristics of the first naturally occurring temperature-sensitive (ts) strain of influenza A virus identified in 1973, Xia-ts, are described. Natural ts strains were found to occur in the early egg passage material of all influenza A subtypes examined, but the proportion of ts virus varied from 8.3% for old H1N1 virus (1949 to 1957) to 82.4% for recent H3N2 virus (1979 to 1980). A number of strains were found to be composed of a mixture of ts and wild-type (ts+) particles. Six natural ts strains with different shutoff temperatures and one ts+ strain of the H1N1 subtype were tested in antibody-free volunteers. Strains with a shutoff temperature of 38 degrees C or lower caused very mild symptoms, whereas those with a shutoff temperature of 39 degrees C and the ts+ strain were much more reactogenic. By complementation tests against a set of prototype WSN ts mutants with a defined genetic lesion, the ts lesion of two H3N2 viruses (HK/8/68 and Xia-ts) was located on the NP gene and that of two H1N1 viruses (Tianjin/78/77 and Beijing/1/79) was located on the M protein gene. The present study demonstrates the widespread occurrence in nature of influenza viruses of different degrees of temperature sensitivity and presumably of different degrees of virulence.

Monoclonal antibodies to the influenza A virus nucleoprotein affecting RNA transcription

Monoclonal antibodies were used to map the antigenic domains of the A/WSN/33 (HoN1) influenza virus nucleoprotein. Three nonoverlapping antigenic regions of the nucleoprotein were identified by using competitive-binding enzyme-linked immunosorbent assays. Monoclonal antibodies to two nucleoprotein domains inhibited in vitro transcription of viral RNA, suggesting that these specific regions of the nucleoprotein are topographically or functionally involved in RNA transcription.

Influenza virus-specific RNA and protein syntheses in cells infected with temperature-sensitive mutants defective in the genome segment encoding nonstructural proteins

Virus-specific protein and RNA syntheses have been analyzed in chicken embryo fibroblast cells infected with two group IV temperature-sensitive (ts) mutants of influenza A (fowl plague) virus in which the ts lesion maps in RNA segment 8 (J. W. Almond, D. McGeoch, and R. D. Barry, Virology 92:416-427, 1979), known to code to code for two nonstructural proteins, NS1 and NS2. Both mutants induced the synthesis of similar amounts of all the early virus-specific proteins (P1, P2, P3, NP, and NS1) at temperatures that were either permissive (34 degrees C) or nonpermissive (40.5 degrees C) for replication. However, the synthesis of M protein, which normally accumulates late in infection, was greatly reduced in ts mutant-infected cells at 40.5 degrees C compared to 34 degrees C. The NS2 protein was not detected at either temperature in cells infected with one mutant (mN3), and was detected only at the permissive temperature in cells infected with mutant ts47. There was no overall reduction in polyadenylated (A+) complementary RNA, which functions as mRNA, in cells infected with these mutants at 40.5 degrees C compared to 34 degrees C, nor was there any evidence of selective accumulation of this type of RNA within the nucleus at the nonpermissive temperature. No significant differences in ts mutant virion RNA transcriptase activity were detected by assays in vitro at 31 and 40.5 degrees C compared to wild-type virus. Virus-specific non-polyadenylated (A-) complementary RNA, which is believed to act as the template for new virion RNA production, accumulated normally in cells at both 34 and 40.5 degrees C, but at 40.5 degrees C accumulation of new virion RNA was reduced by greater than 90% when compared to accumulation at 34 degrees C.