Selection of class I MHC-restricted peptides with the strip-of-helix hydrophobicity algorithm

A strip-of-helix hydrophobicity algorithm to predict class II MHC-restricted peptides, on the basis of their structural similarity to an amphipathic, alpha-helix in Ii, also predicted peptides which were presented to cytotoxic T-cells by class I MHC molecules. This algorithm ranked peptides according to mean Kyte-Doolittle hydrophobicity values of amino acids at positions n, n + 4, n + 7, n + 11, n + 14 and n + 18 in a sequence which when coiled as a putative alpha-helix, had the indicated residues in an axial strip along one side of the helix. Sequences selected for highly scoring, hydrophobic strips were required to have at least 1 of the 4 adjacent strips scoring more negatively than -1 in the strip-of-helix hydrophobicity index and the entire sequence could contain no prolines. This algorithm predicted the class I MHC-restricted, T-cell-presented peptides in sequences of 4 proteins from which some class I MHC-restricted, T-cell-presented sequences had been experimentally determined. Since both class I and class II MHC-restricted peptides could be identified with this algorithm, one can propose that: (1) foreign peptide-binding sites (desetopes) of the class I and class II MHC molecules are structurally similar; and (2) any one T-cell-presented peptide can be presented by some specific allele of both a class I and a class II MHC antigen.

Enzyme-linked immunosorbent assay of core antigens for clinical diagnosis of influenza

A solid-phase enzyme-linked immunosorbent assay (ELISA) with monoclonal secondary antibodies was used to detect matrix protein and nucleoprotein of influenza A. The sensitivity of the ELISA for highly purified A/Brazil nucleoprotein and matrix protein was 0.05 and 1.0 ng, respectively. Nasal washes from 10 of 20 adult subjects with culture-proven, naturally acquired infection caused by A/Brazil/11/78-like influenza virus were positive in the test, and 2 of 13 subjects with rhinovirus infection were falsely positive. To determine if ELISA results could be improved, nasal washes were obtained from 21 adult volunteers who had been inoculated intranasally with wild-type A/Korea/1/82 (five subjects) or A/Korea recombinants with matrix protein or RNA-2 protein of A/Ann Arbor/6/60 (16 subjects), and the nasal washes were processed by a variety of methods. Prompt addition of sodium azide to the nasal washes to limit bacterial growth, avoidance of freezing, and the use of an antiproteolytic agent all failed to improve ELISA results noticeably. Under the best conditions, ELISA was positive in only 12 of the 21 experimentally infected subjects and in 1 of 15 uninfected controls. Positive ELISA results in experimentally infected subjects correlated significantly with the titer of live virus in the nasal washes (r = +0.506; P less than 0.001). Detection of gradient-purified whole influenza virus or isolated core antigen in ELISA was inhibited by prior incubation with nasal washes, and the inhibitory activity was only partly decreased by heat treatment of the secretions. At present, the use of ELISA for detection of influenza antigens in respiratory secretions is not sufficiently sensitive or specific for routine laboratory diagnosis of influenza.

Chemical crosslinking of bacteriophage phi 6 nucleocapsid proteins

phi 6 is a lipid-containing dsRNA bacteriophage of Pseudomonas syringae. Its nucleocapsid (NC) has common features with Reoviridae core particles. We report here the crosslinking of phi 6 NC proteins with cleavable 12-A span chemical crosslinker, dithiobis(succinimidyl propionate). The crosslinked complexes were analyzed in two-dimensional polyacrylamide gels or by using monoclonal antibodies to uncleaved protein complexes in one-dimensional protein gels. The NC surface protein (P8) forms a series of multimeric homopolymers. The phi 6 lytic enzyme, protein P5, is associated with P8 on the NC surface. The interior NC proteins P1 and P4, associated with the virus polymerase activity, are also in contact with the P8 shell. A P1 + P4 complex is also formed. Only one of the NC proteins (P7) did not easily form complexes with the other NC proteins. These results indicate a very closely packed P8 surface lattice with specific contacts to the internal NC proteins.

Localization of RNA polymerases on influenza viral ribonucleoproteins by immunogold labeling

Monospecific antisera for the influenza polymerase proteins and high resolution immunoelectron microscopy have been used to investigate the topographical distribution of the polymerase molecules on influenza ribonucleoproteins (RNPs). Antibodies to PB1, PB2, and PA identify a single polymerase binding site located at, or very close to, the end of each RNP. Double labeling experiments confirm that all three polymerases are at the same end of each RNP and that they are in close association.

Mapping of the tobacco vein mottling virus VPg cistron

The location of the cistron encoding the genome-linked protein (VPg) in the potyvirus tobacco vein mottling virus (TVMV) was investigated. Precipitation of 125I-labeled VPg with anti-tobacco etch virus 49K nuclear inclusion protein antiserum (which reacts with the NIa nuclear inclusion protein of TVMV) indicated that the TVMV VPg is immunologically related to NIa. Lysyl residues were found to be present at positions 2, 11, and 16 of the amino-terminal region of the VPg. A search of the TVMV polyprotein sequence for this distribution of lysyl residues revealed a unique location beginning at amino acid residue 1801, the proposed amino-terminus of the NIa protein.

Limiting dilution analysis of memory cytotoxic T lymphocytes specific for individual influenza virus gene products

The frequency of memory T cells specific for individual influenza virus gene products in the spleens of BALB/c mice primed with A/Puerto Rico/8/34/1(H1N1) (PR8) influenza A virus was determined by using limiting dilution protocols. The results confirm that the influenza virus nucleoprotein (NP) is the predominant protein recognized by BALB/c cytotoxic T lymphocyte (CTL). This was true whether the responder splenocytes were restimulated with homologous PR8 virus or heterologous A/Japan/305/57 (H2N2) (JAP). The frequency hierarchy for BALB/c splenocytes restimulated with PR8 was NP greater than PB2 greater than or equal to H1 greater than NS1 greater than H2. The frequency of CTL specific for all other influenza gene products was too low to calculate. The CTL hierarchy for BALB/c splenocytes restimulated with JAP was NP greater than NS1, with all others lower than 1 in 96,000.

Involvement of nucleoli and dense bodies in the intranuclear distribution of some capsid polypeptides in cells infected with herpes simplex virus type 1

The distribution of capsid proteins induced by herpes simplex virus type 1 infection was determined at the ultrastructural level. The antiserum A to total capsid proteins and the anti-NC1 and NC2 sera, all labeled with gold particles, decorated the entire thickness of both empty capsids and nucleocapsids filled with viral DNA. On the other hand, an antibody to NC3,4 protein produced a heavy labeling concentrated almost entirely along the internal surface of empty capsids, whereas full capsids were not labeled. DNase digestion of "full" capsids did not restore anti-NC3,4 protein binding at this site. Published biochemical data concerning viral protein distribution in capsids are conflicting, but if NC3,4 protein is present in full capsids, we suggest that new binding forces between capsid proteins occurred at the time of insertion of viral DNA which might conceal the relevant antigenic sites of NC3,4 proteins. Capsid proteins were abundantly present in the viral nucleoplasm and in most constituents of the infected cells particularly some nucleoli and some but not all dense bodies. However, whereas anti-NC1 serum labeled nucleoli but not dense bodies, both anti-NC2 and anti-NC3,4 sera stained only dense bodies but not nucleoli. Inhibition of replication of viral DNA which entered the cell during the infective period did not inhibit the production of capsid proteins. Inhibition of protein synthesis in late infected cells did not alter the distribution of capsid proteins.

Enhanced recognition of a modified peptide antigen by cytotoxic T cells specific for influenza nucleoprotein

A previously identified Kd restricted epitope of influenza A virus nucleoprotein (147-161) was modified, resulting in recognition by Kd restricted cytotoxic T cells at significantly lower concentrations than the natural peptide sequence. This was achieved by first refining the epitope to the minimum determinant 147-158. Deletion of arginine 156 resulted in a peptide that was shown to be greatly superior in both dose response titrations and in its rate of association with cells to form targets. Analog peptides were tested to determine the important amino acid changes. These data suggest that T cell epitopes can be modified to result in improved immunological recognition.

Recognition by major histocompatibility complex class I-restricted cytolytic T lymphocytes of cells expressing vaccinia-encoded viral and class I proteins

Target cells expressing influenza virus hemagglutinin (HA) could be recognized by cytotoxic T lymphocytes (CTL) in conjunction with the murine major histocompatibility complex class I antigen, H-2Kd, when both antigens were encoded by recombinant vaccinia virus. This recognition occurred if HA and H-2Kd were encoded by separate vaccinia viruses following dual infection of target cells or if HA and H-2Kd were encoded by a single recombinant virus. In contrast, target cells expressing nucleoprotein (NP) were only recognized by H-2Kd-restricted CTL if both NP and H-2Kd were encoded by the same vaccinia virus. These results show that the requirements for association of H-2Kd with different viral antigens derived from HA or NP can vary. Possible factors contributing to this difference are discussed.

Mouse mammary tumor virus (MMTV) particles in extraorbital lacrymal and urethral glands of endogenous MMTV-carrying mice

Expression of mouse mammary tumor virus (MMTV) antigens was observed in a wide variety of exocrine glands in adult mice by an immunoperoxidase method using rabbit antisera against gp52 and p27 of MMTV. Both exogenous and endogenous MMTV-carrying SHN, GRS/A, C3H and DDD-Mtv-2 mice expressed both antigens in the mammary, extraorbital lacrymal, urethral, parotid and submandibular glands of both sexes and prostate, seminal vesicle and epididymis but not in the Harder's, Zymbal's sublingual and uterine glands. Endogenous MMTV-free but exogenous MMTV-carrying BALB/cfC3H mice showed antigen expressions only in the mammary gland. BALB/c mice free from either endogenous or exogenous MMTV did not express viral antigens in any tissues examined. Electronmicroscopically, MMTV A and B particles were detected in the above mentioned MMTV antigen positive non-mammary organs in endogenous MMTV-carrying mice. The results suggested that the endogenously expressing Mtv genes might produce mature MMTV in these non-mammary glandular systems.

Analysis of RNA synthesis of type 1 poliovirus by using an in vitro molecular genetic approach

Membranous crude replication complexes (CRC) were isolated from poliovirus-infected HeLa cells as recently described (N. Takeda, R.J. Kuhn, C.-F. Yang, T. Takegami, and E. Wimmer, J. Virol. 60:43-53, 1986). Viruses used to produce the CRC were poliovirus type 1 (Mahoney), [PV-1(M)], poliovirus type 1 (Sabin) [PV-1(S)], and four in vitro recombinants that were constructed from infectious cDNA clones. RNA synthesis in CRC was studied. No end-linked, full-length double-stranded poliovirus RNA was detected in CRC regardless of whether nonionic detergent (Nonidet P-40) was added prior to incubation. Synthesis of VPg-pU and VPg-pUpU, two nucleotidyl proteins presumed to be involved in the initiation of RNA synthesis, was slower at 30 degrees C in CRC induced by PV-1(S) than by PV-1(M). This observation was used to design a pulse-chase experiment whose result suggested that synthesis of VPg-pUpU occurred by uridylylation of VPg-pU. Synthesis of VPg-pU(pU) was thermosensitive in CRC induced by PV-1(S). With CRC of recombinant viruses, the thermosensitive block covaried to nucleotide substitutions in PV-1(S) that mapped to the virus-induced RNA polymerase 3Dpol. We conclude that plus-stranded RNA synthesis in CRC does not proceed via hairpin structures. The results of VPg-pU----VPg-pUpU synthesis are consistent with a model in which VPg-pU is the primer of RNA synthesis mediated by 3Dpol. The data suggest that uridylylation of VPg or a precursor thereof may be catalyzed by 3Dpol itself, a mechanism resembling events occurring in adenovirus DNA replication.

The avian influenza virus nucleoprotein gene and a specific constellation of avian and human virus polymerase genes each specify attenuation of avian-human influenza A/Pintail/79 reassortant viruses for monkeys

Reassortant viruses which possessed the hemagglutinin and neuraminidase genes of wild-type human influenza A viruses and the remaining six RNA segments (internal genes) of the avian A/Pintail/Alberta/119/79 (H4N6) virus were previously found to be attenuated in humans. To study the genetic basis of this attenuation, we isolated influenza A/Pintail/79 X A/Washington/897/80 reassortant viruses which contained human influenza virus H3N2 surface glycoprotein genes and various combinations of avian or human influenza virus internal genes. Twenty-four reassortant viruses were isolated and first evaluated for infectivity in avian (primary chick kidney [PCK]) and mammalian (Madin-Darby canine kidney [MDCK]) tissue culture lines. Reassortant viruses with two specific constellations of viral polymerase genes exhibited a significant host range restriction of replication in mammalian (MDCK) tissue culture compared with that in avian (PCK) tissue culture. The viral polymerase genotype PB2-avian (A) virus, PB1-A virus, and PA-human (H) virus was associated with a 900-fold restriction, while the viral polymerase genotype PB2-H, PB1-A, and PA-H was associated with an 80,000-fold restriction of replication in MDCK compared with that in PCK. Fifteen reassortant viruses were subsequently evaluated for their level of replication in the respiratory tract of squirrel monkeys, and two genetic determinants of attenuation were identified. First, reassortant viruses which possessed the avian influenza virus nucleoprotein gene were as restricted in replication as a virus which possessed all six internal genes of the avian influenza A virus parent, indicating that the nucleoprotein gene is the major determinant of attenuation of avian-human A/Pintail/79 reassortant viruses for monkeys. Second, reassortant viruses which possessed the viral polymerase gene constellation of PB2-H, PB1-A, and PA-H, which was associated with the greater degree of host range restriction in vitro, were highly restricted in replication in monkeys. Since the avian-human influenza reassortant viruses which expressed either mode of attenuation in monkeys replicated to high titer in eggs and in PCK tissue culture, their failure to replicate efficiently in the respiratory epithelium of primates must be due to the failure of viral factors to interact with primate host cell factors. The implications of these findings for the development of live-virus vaccines and for the evolution of influenza A viruses in nature are discussed.

[Bacteriophage Mu transposase contains a fragment with primary structure similar to that of protein VPg covalently linked with poliovirus RNA]

A statistically valid similarity was found to exist between the amino acid sequences of poliovirus genome-linked protein VPg and a fragment of bacteriophage Mu transposase (Mu A protein). Based on this observation a hypothesis is proposed that the molecular mechanisms underlying the functions of the two proteins may be analogous. Both proteins are supposed to be site-specific endonucleases which form covalent linkage with the 5'-phosphate group of the nicked DNA or RNA strand. The amino acid residue participating in the formation of this linkage in MuA is tentatively identified as Tyr413.

Permanent cell lines established from ts-COS cells that regulate by temperature the amplification and expression of cloned genes

Temperature-sensitive COS cells have been transformed at restrictive temperature with SV40 replicons containing the neo or pac markers. Puromycin-resistant cell clones maintained at the restrictive temperature contain the pac gene integrated into the cell DNA. However, when the cells are shifted to the permissive temperature the pac gene is amplified in episomal forms up to 2-4 X 10(4) copies per cell. Concomitant with this, an induction of 35-300 fold in the levels of puromycin acetyl transferase activity is observed, leading to the accumulation of the enzyme up to 10-60 mU/mg of total cell protein. A band of apparent molecular weight 26,500 daltons is observed by polyacrylamide gel electrophoresis of induced culture extracts, that accounts for approximately 3% of the newly synthesized protein. The expression of non-selectable genes can also be regulated, as shown by the induction of influenza virus nucleoprotein synthesis in transformed cells. These results indicate that the ts-COS cells can be used as a highly efficient, regulable mammalian expression system.

The influence of the isolation technique of influenza virus nucleoprotein on its antigenic properties

ELISA has been used to study the antigenic properties 1. of influenza virus nucleoprotein (NP-1) isolated from virions with the help of preparative polyacrylamide gel electrophoresis (PAGE); 2. of virion ribonucleoprotein (NP-2), and 3. of NP structures prepared by dissociation of ribonucleoprotein into RNA and protein in sucrose gradient containing NaCl (NP-3). The investigation of immunologic cross-reactivity has shown complete identity of NP-2 and NP-3 and their striking difference from NP-1. In contrast to NP-2, NP-3 was not contaminated by other virus antigens, it was a good immunogen and could be used for preparation of monospecific antisera of high titre. NP-1 did not induce a high antibody response,however, like NP-2 and NP-3, it retained its capacity to react with antisera to native virus. Owing to its simple production and high yield, this protein can be used in serodiagnosis for testing the antibody level against NP-protein in convalescent sera.

Class I MHC molecules rather than other mouse genes dictate influenza epitope recognition by cytotoxic T cells

Influenza nucleoprotein (NP) is an important target antigen for influenza A virus cross-reactive cytotoxic T cells (Tc). Here we examine the NP epitope recognized by cloned and polyclonal BALB/c Tc and the genetics of this recognition pattern. We can define NP residues 147-161 as the epitope seen in conjunction with Kd, the only H-2d class I responder allele for NP restriction. H-2d/H-2b F1 mice (C57BL X DBA/2) primed by influenza infection lyse only H-2d target cells treated with peptide 147-161 while H-2b targets are recognized only after treatment with NP residues 365-379 (previously found to be recognized by Db restricted Tc cells). Tc cell recognition of NP peptide 147-161 is entirely dictated by expression of Kd and not by other B10 or C3H background genes of congenic mice. Restriction of a unique NP sequence by each responder class I major histocompatibility complex (MHC) allele suggests that antigen and class I MHC interact for Tc recognition.

[Genome-linked proteins in DNA and RNA viruses]

General principles of the organization of viral nucleic acid--protein covalent complexes are formulated. Participation of the genome-linked proteins in the initiation of viral nucleic acid replication is discussed.

Searching for MHC-restricted anti-viral antibodies: antibodies recognizing the nucleoprotein of influenza virus dominate the serological response of C57BL/6 mice to syngeneic influenza-infected cells

An attempt has been made to generate monoclonal antibodies which recognize the same target structures on influenza-infected cells as those seen by cytotoxic T lymphocyte (CTL) receptors. Such antibodies, if they mimicked the T cell receptor specificity, would be expected to be both virus specific and restricted in their binding by the major histocompatibility complex (MHC) antigens. Approximately 200 hybridomas from C57BL/6 (H-2b) mice primed and boosted with influenza virus (X-31)-infected EL4 (a C57BL/6 T cell lymphoma) were screened for reactivity on infected and uninfected cells of different MHC haplotypes. Of the 10 hybridoma antibodies which were identified as being reactive with X-31-infected EL4, but not uninfected EL4, all reacted equally well with X-31-infected cells of H-2b, H-2d and H-2k haplotypes, indicating a lack of MHC restriction in their recognition of the infected cells. Unexpectedly, 7 of the 10 monoclonal antibodies were found to react specifically with the purified influenza virus nucleoprotein (NP), a predominant viral antigen in CTL recognition of infected cells. Fluorescence-activated flow cytometry confirmed that these antibodies were able to recognize NP serological determinants on the surface of viable, infected cells, but the anti-NP antibodies were unable to block the lytic activity of an NP-specific CTL clone.

Fine structure of cells infected with human cytomegalovirus after treatment with 9-(1,3-dihydroxy-2-propoxymethyl)guanine

Infection with human cytomegalovirus (CMV) is characterized by cytological changes which are readily visualized by electron microscopy using ultrathin sections of infected cells. Treatment of such cells with 9-(1,3-dihydroxy-2-propoxymethyl)guanine (DHPG), a potent inhibitor of CMV, is effective when initiated at early or late times after infection and the response to such treatment has been studied by fine structural analysis. Inhibition of viral DNA synthesis by DHPG treatment (50 microM) late in virus infection resulted in a cessation of virus growth accompanied by a lack of development and possible regression in skein-like intranuclear inclusions together with a depletion in cytoplasmic dense bodies. Such changes were accompanied by the appearance of nuclear dense bodies. These were also present when virus growth was reduced (5 microM-DHPG) rather than completely inhibited (50 microM-DHPG) by treatment initiated from the time of infection. The nuclear bodies were predominantly of a reticular type structure after the early treatment but mainly of a homogeneous form when virus growth was interrupted at late times. Their presence appeared to be connected with the ability of infected cells to initiate the synthesis of late proteins and their morphology may relate to the extent of such protein synthesis. Unlike cytoplasmic dense bodies, provisional findings on the characterization of the nuclear bodies suggested that the 69K matrix protein was not present in abundance.

Organization of the Sindbis virus nucleocapsid as revealed by bifunctional cross-linking agents

Purified Sindbis virus nucleocapsids were reacted with a variety of bifunctional protein-specific cross-linking agents. The products were analyzed in concentration-gradient polyacrylamide gels and amounts of various products determined. These studies indicated that available lysine residues within adjacent capsid proteins in purified intact nucleocapsids are separated by 6 A. The capsid proteins in intact nucleocapsids are cross-linked in a pattern predicted for discrete monomeric entities, rather than in dimeric or trimeric aggregates. Purified, soluble capsid protein exists in a conformation that differs from the arrangement of protein within nucleocapsids. These conformational differences suggest that topological changes may occur in the capsid protein during virus maturation. Cross-linked nucleocapsids that were treated with RNases resulted in the generation of RNA-free protein shells that retained hexagonal morphology, indicating that, together, the RNA and protein form the outer surface of the nucleocapsid. These data are used to produce a model of the Sindbis virus nucleocapsid in which the proteins are arranged quasi-equivalently in a T = 4 icosahedral shell.

A novel method for transfection and expression of reconstituted DNA-protein complexes in eukaryotic cells

Transfection of foreign DNA into eukaryotic cells has become an important tool in molecular biology. Based on the results of previous studies of the core structure of human adenoviruses, we have developed a novel transfection method. The procedure involves the in vitro reconstitution of foreign DNA-of viral or other origins-with the major core protein VII of adenovirus type 2 (Ad2) or protamine from salmon sperm. Both proteins are rich in basic amino acids and appear to share structural features. The DNA-protein complexes are added directly to the medium of eukaryotic cells. The in vitro formation of specific DNA-protein complexes can be assessed by gel electrophoretic analyses. Bovine serum albumin does not enter into specific complexes with DNA. Transfection of DNA-protein VII or DNA-protamine complexes results in their rapid transport into the cell nuclei. About 2-4 hr after transfection, up to 40% of the DNA added to cell cultures in complexes can be found in the nucleus, as compared with less than 10% of the DNA when other transfection methods are applied or when naked DNA is added to cell cultures. DNAs transfected by the new method into mammalian or insect cells retain their characteristic restriction patterns at least 48 hr after transfection and are expressed efficiently. Supercoiled circular plasmid DNAs are converted to open circular or linear DNA. Expression has been measured both for transiently expressed genes (chloramphenicol acetyltransferase gene, Ad2 DNA in human HeLa cells) and for genes that have been integrated into the host genome and are expressed permanently, such as the gene for neomycin phosphotransferase in hamster BHK21 cells.(ABSTRACT TRUNCATED AT 250 WORDS)