Effects of viral protein, viral RNA, and some other polyelectrolytes on infection of tobacco protoplasts by TMV.
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Caseins↗
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Large language models improve annotation of prokaryotic viral proteins.
Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation approaches rely on alignment-based sequence homology methods, which are limited by the paucity of characterized viral proteins and divergence among viral sequences. Here we show that protein language models can capture prokaryotic viral protein function, enabling new portions of viral sequence space to be assigned biologically meaningful labels. When applied to global ocean virome data, our classifier expanded the annotated fraction of viral protein families by 29%. Among previously unannotated sequences, we highlight the identification of an integrase defining a mobile element in marine picocyanobacteria and a capsid protein that anchors globally widespread viral elements. Furthermore, improved high-level functional annotation provides a means to characterize similarities in genomic organization among diverse viral sequences. Protein language models thus enhance remote homology detection of viral proteins, serving as a useful complement to existing approaches.
Viral Proteins↗
[Iclusion proteins and viral proteins of the baculovirus of the dipteran Tipula paludosa (Meigen)].
Examination of the polyhedron protein by polyacrylamide gel electrophoresis shows only one polypeptide with a molecular weight of 25,500 +/- 500 daltons, while that of virion proteins reveals 13 polypeptides. No antigenic community could be demonstrated between the polyhedron protein of the Baculovirus of T. paludosa and the polyhedron protein of several other Baculoviruses.
Animals↗
The in vitro of Rous sarcoma virus RNA and function of the viral protein during the viral replication.
The gag gene and pol gene of the Rous sarcoma virus are translated in vitro from the 35S viral RNA. The env gene cannot be translated in vitro from the 35S RNA. For the in vitro translation of the src gene. 3' end fragments of the viral RNA are used. The gag protein p15 has a proteolytic activity and specifically processes its own protein precursor pr76. The gag protein p19 suppresses the in vitro translation of the pol gene.
Animals↗
Expression of viral proteins in mammalian cells transformed by avian sarcoma viruses.
The expression of viral proteins in nine lines of hamster and rat cells transformed by avian sarcoma viruses (ASV) was studied by indirect immunofluorescence with monospecific antisera to purified gp85 and p27 of AMV-B and a polyvalent antiserum to all the p proteins of this same virus. The lines of ASV-transformed cells were either low virus producers (VP) or inducible or non-inducible non producers (NP). Cytoplasmic expression of p proteins was observed in all the cell lines except the least inducible NP cell line, and cytoplasmic expression of gp85 in all the cell lines. The degree of expression varied widely with the lines and was not related to the class of permissiveness or inducibility. However, in the inducible NP class, the expression of p proteins and gp85 was higher in the most inducible cell lines. The data also suggest that the expression of the p proteins must be uncoordinate in at least some cell lines and must also be uncoordinate with the expression of gp85. In the VP cell lines and the most inducible NP lines, g85 and some p proteins other than p27 were also expressed on the cell membrane. The membrane expression of gp85 and the p proteins which were expressed appeared to be coordinate and to parallel the degree of cytoplasmic expression. In contrast, no, or a negligible expression of viral proteins was observed on the membrane of the least inducible and the non-inducible cell lines. These results suggest that there may exist translational and/or post-translational controls of the expression of viral proteins in the ASV-transformed mammalian cells and that the permissiveness and the inducibility of the cells may depend on the insertion of viral proteins in the cell membrane. The failure of p27 to insert in the cell membrane could account for the low permissiveness or the non-permissiveness of the cells.
Alpharetrovirus↗
Synthesis of viral proteins by the avian myeloblastosis viral core component.
Avian Myeloblastosis Viral (AMV) core component was isolated and shown to synthesize AMV proteins in vitro. This reaction was linearly dependent on viral core concentration, proceeded linearly with time, and was inhibited by puromycin and aurintricarboxylic acid. The proteins synthesized in vitro co-electrophoresed and co-chromatographed with known proteins, and were immunoprecipitated by total and monospecific antibodies to known AMV proteins.
Aurintricarboxylic Acid↗
Analysis of the defects of temperature-sensitive mutants of vesicular stomatitis virus: intracellular degradation of specific viral proteins.
The metabolism of viral RNA and proteins has been studied in cells infected with temperature-sensitive mutant strains of vesicular stomatitis virus. Certain viral proteins encoded by the mutant strains, usually the putative mutant protein for the assigned complementation group, were shown to be degraded more rapidly at the nonpermissive temperature than were the wild-type proteins. Group III mutants (tsG33, tsM301) encode M proteins which are degraded three- to fourfold faster than the wild-type protein. This defect cannot be fully rescued by coinfection with wild-type virus, and thus the defect appears to be in the M protein itself. Mutants tsM601 (VI) and tsG41(IV) encode N proteins which are degraded much faster than the wild-type protein and also share the property of being defective in replication of viral RNA, suggesting a correlation between these phenotypic properties. Furthermore, the L proteins of tsG11(I) and tsG13(I) are more labile than the wild-type protein at the nonpermissive temperature. The G protein of tsM501(V) did not undergo the change in electrophoretic mobility previously shown to be the result of sialylation, suggesting that it is defective in maturation or glycosylation at the nonpermissive temperature. Three of the mutants previously isolated in this laboratory, tsM502(V), tsM601(VI), and tsM602(VI), were shown to be defective in viral RNA synthesis at the nonpermissive temperature. Mutant tsM601(VI) was defective mainly in viral RNA replication, whereas tsM502(V) appeared to be totally defective for viral RNA transcription and replication at the nonpermissive temperature.
L Cells↗
Chromatographic separation and antigenic analysis of proteins of the oncornaviruses. V. Identification of a new murine viral protein, p15(E).
Profiling of murine leukemia virus (MuLV) proteins by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS-PAGE) has revealed a low-molecular-weight protein which does not appear in the corresponding region of viral protein profiles obtained by gel filtration in 6 M guanidine hydrochloride. This protein species, termed p15(E), is easily demonstrable in MuLV isolates for which the viral p15 and p12 proteins have almost identical electrophoretic mobilities; this leaves a protein slightly larger than these two in the PAGE system unaccounted for in the gel filtration system. However, antiserum against the void volume fraction of the gel filtration eluate precipitated the p15(E) component from solubilized, radiolabeled virions, as shown by SDS-PAGE analysis of such immunoprecipitates. Comparative radioprecipitation analyses of this type revealed that for various MuLV isolates p15(E) was distinguishable from p15 in terms of serological reactivities, relative mobilities in gel electrophoresis, and relative efficiencies of labeling with individual amino acids. Thus it appears that, as is the case for avian oncornaviruses, MuLVs contain seven major structural proteins.
Animals↗
Simple method for preparation of specific antisera against viral proteins: rabbit antisera against equine infectious anemia virus proteins p26 and p16.
A simple method for preparation of highly specific antisera against equine infectious anemia virus proteins p26 and p16 is described. Viral proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The motility of the viral proteins in the gel was compared with standards. Unstained portions of the slab gel were sliced into 5-mm bands, emulsified with Freund's complete adjuvant, and injected into rabbits to produce specific antisera.
Animals↗
Chromatographic separation and antigenic analysis of proteins of the oncornaviruses. III. Avian viral proteins with group-specific antigenicity.
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Alpharetrovirus↗
Metaproteomic profiling reveals viral proteins and associated host proteomic alterations in glioblastoma.
Glioblastoma (GB) is a WHO grade 4 brain cancer with dismal prognosis, yet its aetiology remains poorly defined. Although viral involvement has been proposed, findings across studies remain inconsistent, reflecting inherent limitations of individual technologies and cohort size. Here we applied metaproteomic profiling to a publicly available GB proteome dataset (12 control, 21 adjacent, 159 tumour) and an independent cohort of 81 samples (37 control, 44 tumour) to detect viral proteins in tumour and controls tissues. Across cohorts, we detected viral proteins from diverse species, with human herpesviruses (HHV-1, 2, and 8) more frequently detected in GB tumours compared with control tissues. Analysis of the host tumour proteome revealed differential abundance of proteins related to transcriptional regulation, RNA processing, protein translation, immune responses, and mitochondrial-associated metabolism. Correlation analysis identified associations between viral and human proteins, with several linked to biological processes previously implicated in DNA virus-host interactions. Further stratification of tumour by HHV-1 status showed consistent alterations in proteins associated with mitochondrial-associated metabolism, protein turnover, and cell adhesion/signalling.In summary, this study demonstrates the feasibility of metaproteomics for detecting viral components in archival GB tissues. Using this approach, we observed differences in viral protein landscape across cohorts and identified associations between viral presence and host proteomic features, providing a protein-level framework for future studies of virus-host interactions in GB.
Humans↗
Epitope Tagging and Coimmunoprecipitation to Identify Viral Protein Interactors.
Affinity purification-mass spectrometry (AP-MS) is a powerful proteomic approach for dissecting the interaction network between virus and host. Traditional AP-MS employs overexpression of viral proteins as baits to enrich host interactors. However, overexpressed viral proteins may mislocalize to inappropriate cellular compartments and trigger endoplasmic reticulum stress by overwhelming the protein-folding machinery, which leads to false identification of host factors. To overcome these limitations, we introduce an AP-MS strategy based on direct infection with an epitope-tagged chikungunya virus (CHIKV/myc-E2), which we used to successfully uncover two new antiviral factors in CHIKV cellular reservoirs-macrophages. In this protocol, we will describe this technique step by step: (1) design and construction of myc-tagged virus by advanced multi-fragment assembly, (2) in vitro transcription and preparation of infectious myc-tagged virus stocks, and (3) immunoprecipitation of myc-tagged viral protein and its interactome for mass spectrometry analysis. This strategy enables accurate identification of viral interactors in a physiologically relevant context, providing a framework for future proteomic studies using tagged viruses.
Chikungunya virus↗
Viral protein synthesis in Friend erythroleukemia cell lines.
Viral protein synthesis was studied in two Friend virus-induced erythroleukemia cell lines (Ostertag cell lines FSD1-F4 and B8) by the technique of immuno-precipitation with monospecific antisera to the major envelope glycoprotein gp70 and major core protein p30. One of the cell lines (F4) releases active Friend virus complex to the growth medium, where release of virus from the other cell line (B8) is barely or nondetectable. It was found that in the nonproducer cell line B8, a large-molecular-weight protein of about 65,000 containing p30 antigenic determinants is synthesized, yet no p30 is produced upon prolonged incubation and chase, suggesting that this might be the actual lesion that prevents mature virus production by these cells. In both cell lines, the predominant protein species that is immunoprecipitated with monospecific anti-gp70 serum is a protein of 55,000 to 60,000 daltons that is labeled with glucosamine to a much lesser extent that gp70 and appears to become heterogeneous with time. Large amounts of gp70 can be detected in the cell-free medium, but none of the unstable species of 55,00 to 60,000 molecular weight.
Cell Line↗
Lifetimes of mRNA molecules directing the synthesis of viral proteins in herpes simplex virus-infected cells.
Possible variations in the functional lifetimes of herpes simplex virus type 1 mRNA molecules in infected HeLa cells were studied. As shown by the rate of decrease of radioactive amino acid incorporation into viral proteins after the addition of actinomycin, the average lifetime of early viral mRNA's are shorter than those for the late messenger species. In addition, when the viral proteins made after the addition of actinomycin were further analyzed by gel electrophoresis, it was found that messengers for individual viral proteins translated within the early or late time period also had some differences in their functional lifetimes. These results indicate that the synthesis of herpes simplex virus type 1 proteins during the replicative cycle is regulated in part by mechanisms controlling the functional lifetimes of viral mRNA's.
Cycloheximide↗
Detection of adenovirus type 2-induced early polypeptides using cycloheximide pretreatment to enhance viral protein synthesis.
(35S) methionine-labeled polypeptides synthesized by adenovirus type 2-infected cells have been analyzed by polyacrylamide gradient gel electrophoresis and autoradiography. Cycloheximide (CH) was added to infected cultures to accumulate early viral mRNA relative to host cell mRNA. This allowed viral proteins to be synthesized in increased amounts relative to host proteins after removal of CH and pulse-labeling with (35S)methionine. During the labeling period arabinosyl cytosine was added to prevent the synthesis of late viral proteins. This procedure facilitated the detection of six early viral-induced polypeptides, designated EP1 through EP6 (early protein), with apparent molecular weights of 75,000 (75K), 42K, 21K, 18K, 15K, and 11K. Supportive data were obtained by coelectrophoresis of (35S)- and (3H)methionine-labeled polypeptides from infected and uninfected cells, respectively. Three of these early polypeptides have not been previously reported. CH pretreatment enhanced the rates of synthesis of EP4 and EP6 20- to 30-fold and enhanced that of the others approximately twofold. The maximal rates of synthesis of the virus-induced proteins varied, in a different manner, with time postinfection and CH pretreatment. Since CH pretreatment appears to increase the levels of early viral proteins, it may be a useful procedure to assist their isolation and functional characterization.
Adenoviridae↗
Purification of viral proteins from avian sarcoma virus QV2.
A procedure was established whereby most of the major viral proteins were isolated to apparent homogeneity in biologically and immunologically active forms from a single batch of avian sarcoma virus QV2. For the initial step of purification, gently disrupted virions were fractionated by CsCl centrifugation into envelope proteins, RNA-dependent DNA polymerase, and viral core proteins. Further purification of envelope glycoproteins and DNA polymerase was performed by affinity chromatography on agarose columns cross-linked with plant lectins and poly(C), respectively. On the other hand, core proteins were fractionated by a combination of gel filtration and ion-exchange column chromatography into components p27, p19, and p15. The core protein p15 thus isolated retained proteolytic activity even after storage for 6 months. The present study also demonstrated that QV2 p19 is structurally altered from the corresponding protein of avian myeloblastosis virus (AMV), a reference avian leukosis-sarcoma virus having a well-characterized polypeptide composition.
DNA-Directed DNA Polymerase↗
Viral protein sythesis by tissues from avian leukosis virus-infected chickens. II. Effect of passive neutralizing antibody in normal and agammaglobulinaemic chickens.
Synthesis in vitro of avian leukosis virus (ALV) group (gs proteins, p27 and p12, by various tissues from chickens infected within a few days after hatching was studied by means of autoradiography of immunoelectrophoretic patterns. Viral protein was synthesized in all tissues of chicks examined between days 18 and 50 of age after which time liver, kidney, bursa, thymus, and spleen became negative. The lung and genital organs of the chicks, however, continued to synthesize viral protein up to 100 days of age, when the experiment was ended. Repeated injections of neutralizing chicken antibody to ALV (Ab) starting on day 26 or 37 caused gs protein to decrease in spleen, liver, and thymus within 5 days but not in bursa, lung, and genital organs. Agammaglobulinaemic (Agamma) chickens showed prolonged persistence of gs protein synthesis in the spleen and liver; this synthesis was abrogated by passive Ab. Liver from Agamma chickens, however, also became negative without Ab treatment. The relative roles of antibody and cellular immunity in influencing ALV replication during the initial phase of infection before lymphoma development are discussed.
Agammaglobulinemia↗
Maturation of viral proteins in cells infected with temperature-sensitive mutants of vesicular stomatitis virus.
Maturation of viral proteins in cells infected with mutants of vesicular stomatitis virus was studied by surface iodination and cell fractionation. The movement of G, M, and N proteins to the virion bud appeared to be interdependent. Mutations thought to be in G protein prevented its migration to the cell surface, allowed neither M nor N protein to become membrane bound, and blocked formation of viral particles. Mutant G protein appeared not to leave the endoplasmic reticulum at the nonpermissive temperature, but this defect was partially reversible. In cells infected with mutants that caused N protein to be degraded rapidly or prevented its assembly into nucleocapsids, M protein did not bind to membranes and G protein matured to the cell surface, but never entered structures with the density of virions. Mutations causing M protein to be degraded prevented virion formation, and G protein behaved as in cells infected by mutants in N protein. These results are consistent with a model of virion formation involving coalescence of soluble nucleocapsid and soluble M protein with G protein already in the plasma membrane.
Cell Fractionation↗