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Gottlieb P, Alimova A. Discovery and Classification of the φ6 Bacteriophage: An Historical Review. Viruses 2023; 15:1308. [PMID: 37376608 DOI: 10.3390/v15061308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/30/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
The year 2023 marks the fiftieth anniversary of the discovery of the bacteriophage φ6. The review provides a look back on the initial discovery and classification of the lipid-containing and segmented double-stranded RNA (dsRNA) genome-containing bacteriophage-the first identified cystovirus. The historical discussion describes, for the most part, the first 10 years of the research employing contemporary mutation techniques, biochemical, and structural analysis to describe the basic outline of the virus replication mechanisms and structure. The physical nature of φ6 was initially controversial as it was the first bacteriophage found that contained segmented dsRNA, resulting in a series of early publications that defined the unusual genomic quality. The technology and methods utilized in the initial research (crude by current standards) meant that the first studies were quite time-consuming, hence the lengthy period covered by this review. Yet when the data were accepted, the relationship to the reoviruses was apparent, launching great interest in cystoviruses, research that continues to this day.
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Affiliation(s)
- Paul Gottlieb
- Department of Molecular, Cellular and Biomedical Sciences, The City University of New York School of Medicine, New York, NY 10031, USA
| | - Aleksandra Alimova
- Department of Molecular, Cellular and Biomedical Sciences, The City University of New York School of Medicine, New York, NY 10031, USA
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2
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Liu H, Cheng L. Viral Capsid and Polymerase in Reoviridae. Subcell Biochem 2022; 99:525-552. [PMID: 36151388 DOI: 10.1007/978-3-031-00793-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The members of the family Reoviridae (reoviruses) consist of 9-12 discrete double-stranded RNA (dsRNA) segments enclosed by single, double, or triple capsid layers. The outer capsid proteins of reoviruses exhibit the highest diversity in both sequence and structural organization. By contrast, the conserved RNA-dependent RNA polymerase (RdRp) structure in the conserved innermost shell in all reoviruses suggests that they share common transcriptional regulatory mechanisms. After reoviruses are delivered into the cytoplasm of a host cell, their inner capsid particles (ICPs) remain intact and serve as a stable nanoscale machine for RNA transcription and capping performed using enzymes in ICPs. Advances in cryo-electron microscopy have enabled the reconstruction at near-atomic resolution of not only the icosahedral capsid, including capping enzymes, but also the nonicosahedrally distributed complexes of RdRps within the capsid at different transcriptional stages. These near-atomic resolution structures allow us to visualize highly coordinated structural changes in the related enzymes, genomic RNA, and capsid protein during reovirus transcription. In addition, reoviruses encode their own enzymes for nascent RNA capping before RNA releasing from their ICPs.
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Affiliation(s)
- Hongrong Liu
- Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China.
| | - Lingpeng Cheng
- Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China.
- School of Life Sciences, Tsinghua University, Beijing, China.
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3
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Affiliation(s)
- John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts 02111;
| | - Hung Fan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
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4
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Wang X, Son A. Effects of pretreatment on the denaturation and fragmentation of genomic DNA for DNA hybridization. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2013; 15:2204-12. [PMID: 24162665 DOI: 10.1039/c3em00457k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DNA hybridization is an important step for a number of bioassays such as fluorescence in situ hybridization, microarrays, as well as the NanoGene assay. Denaturation and fragmentation of genomic DNA are two critical pretreatments for DNA hybridization. However, no thorough and systematic characterization on denaturation and fragmentation has been carried out for the NanoGene assay so far. In this study, we investigated the denaturation and fragmentation of the bacterial gDNA with physical treatments (i.e., heating and sonication) and chemical treatments (i.e., dimethyl sulfoxide). First of all, a simple approach for indicating the denaturation fraction was developed based on the absorbance difference (i.e., hyperchromic effect) between the double-stranded DNA and single-stranded DNA fragments. Then the denaturation capabilities of the treatments to the gDNA were elucidated, followed by the examination of the possible renaturation over time. The fragmentation of the gDNA by each treatment was also investigated. Based on denaturation efficiency, minimum renaturation tendency, and fragmentation, the sonication method was found to be the best among the six methods. We further demonstrated that the sonication method produced the best result among the treatments examined for the DNA hybridization in the NanoGene assay.
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Affiliation(s)
- Xiaofang Wang
- Department of Civil Engineering, Auburn University, Auburn, AL 36849, USA
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5
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Kalmakoff J, Lewandowski LJ, Black DR. Comparison of the ribonucleic Acid subunits of reovirus, cytoplasmic polyhedrosis virus, and wound tumor virus. J Virol 2010; 4:851-6. [PMID: 16789117 PMCID: PMC375948 DOI: 10.1128/jvi.4.6.851-856.1969] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Double-stranded ribonucleic acid (RNA) from intact cytoplasmic polynedrosis virus (CPV) and wound tumor virus (WTV) was analyzed by polyacrylamide gel electrophoresis. Using RNA from type 3 reovirus as a standard, it was calculated that CPV-RNA consisted of 9 subunits corresponding to a molecular weight of 12.7 x 10(6) and WTV-RNA consisted of 12 subunits corresponding to a molecular weight of 15.5 x 10(6).
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Affiliation(s)
- J Kalmakoff
- Department of Molecular Biology and Virus Laboratory, University of California, Berkeley, California 94720
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6
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Lewandowski LJ, Kalmakoff J, Tanada Y. Characterization of a Ribonucleic Acid Polymerase Activity Associated with Purified Cytoplasmic Polyhedrosis Virus of the Silkworm Bombyx mori. J Virol 2010; 4:857-65. [PMID: 16789118 PMCID: PMC375949 DOI: 10.1128/jvi.4.6.857-865.1969] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purified cytoplasmic-polyhedrosis virus has been found to have associated with it a polymerase activity capable of catalyzing the synthesis of virus-specific, single-stranded ribonucleic acid (RNA) from the double-stranded RNA genome.
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Affiliation(s)
- L J Lewandowski
- Department of Molecular Biology and Virus Laboratory, and Division of Entomology, University of California, Berkeley, California 94720
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7
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Smith RE, Furuichi Y. Gene mapping of cytoplasmic polyhedrosis virus of silkworm by the full-length mRNA prepared under optimized conditions of transcription in vitro. Virology 2008; 103:279-90. [PMID: 18631652 DOI: 10.1016/0042-6822(80)90187-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/1980] [Indexed: 11/29/2022]
Abstract
Viral mRNA synthesis by the RNA polymerase associated with purified cytoplasmic polyhedrosis virus (CPV) was studied. The formation of full-length mRNA products was facilitated by including in the reaction mixture 100 mM sodium acetate, high concentrations of ribonucleoside triphosphates, and proteinase K. The 10 different species of CPV mRNAS were resolved into 9 discrete RNA bands by agarose gel electrophoresis at pH 3.5 in buffer containing 7 M urea. Each purified viral mRNA hybridized specifically to one of the viral genome segments which were separated by polyacrylamide gel electrophoresis into the 10 species of dsRNA. The relationship between the genome segments and their cognate mRNAs synthesized in vitro is thus established. Under optimal conditions of mRNA synthesis each of the genome segments was transcribed at a similar rate as determined from the yield of individual separated mRNA species. A recycling model of genome-associated RNA polymerase for viral transcription is discussed.
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Affiliation(s)
- R E Smith
- Roche Institute of Molecular Biology, Nutley, New Jersey 07110, USA
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8
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Broering TJ, Kim J, Miller CL, Piggott CDS, Dinoso JB, Nibert ML, Parker JSL. Reovirus nonstructural protein mu NS recruits viral core surface proteins and entering core particles to factory-like inclusions. J Virol 2004; 78:1882-92. [PMID: 14747553 PMCID: PMC369481 DOI: 10.1128/jvi.78.4.1882-1892.2004] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Accepted: 10/28/2003] [Indexed: 11/20/2022] Open
Abstract
Mammalian reoviruses are thought to assemble and replicate within cytoplasmic, nonmembranous structures called viral factories. The viral nonstructural protein mu NS forms factory-like globular inclusions when expressed in the absence of other viral proteins and binds to the surfaces of the viral core particles in vitro. Given these previous observations, we hypothesized that one or more of the core surface proteins may be recruited to viral factories through specific associations with mu NS. We found that all three of these proteins--lambda 1, lambda 2, and sigma 2--localized to factories in infected cells but were diffusely distributed through the cytoplasm and nucleus when each was separately expressed in the absence of other viral proteins. When separately coexpressed with mu NS, on the other hand, each core surface protein colocalized with mu NS in globular inclusions, supporting the initial hypothesis. We also found that lambda 1, lambda 2, and sigma 2 each localized to filamentous inclusions formed upon the coexpression of mu NS and mu 2, a structurally minor core protein that associates with microtubules. The first 40 residues of mu NS, which are required for association with mu 2 and the RNA-binding nonstructural protein sigma NS, were not required for association with any of the three core surface proteins. When coexpressed with mu 2 in the absence of mu NS, each of the core surface proteins was diffusely distributed and displayed only sporadic, weak associations with mu 2 on filaments. Many of the core particles that entered the cytoplasm of cycloheximide-treated cells following entry and partial uncoating were recruited to inclusions of mu NS that had been preformed in those cells, providing evidence that mu NS can bind to the surfaces of cores in vivo. These findings expand a model for how viral and cellular components are recruited to the viral factories in infected cells and provide further evidence for the central but distinct roles of viral proteins mu NS and mu 2 in this process.
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Affiliation(s)
- Teresa J Broering
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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9
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Mochow-Grundy M, Dermody TS. The reovirus S4 gene 3' nontranslated region contains a translational operator sequence. J Virol 2001; 75:6517-26. [PMID: 11413319 PMCID: PMC114375 DOI: 10.1128/jvi.75.14.6517-6526.2001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reovirus mRNAs are efficiently translated within host cells despite the absence of 3' polyadenylated tails. The 3' nontranslated regions (3'NTRs) of reovirus mRNAs contain sequences that exhibit a high degree of gene-segment-specific conservation. To determine whether the 3'NTRs of reovirus mRNAs serve to facilitate efficient translation of viral transcripts, we used T7 RNA polymerase to express constructs engineered with full-length S4 gene cDNA or truncation mutants lacking sequences in the 3'NTR. Full-length and truncated s4 mRNAs were translated using rabbit reticulocyte lysates, and translation product sigma3 was quantitated by phosphorimager analysis. In comparison to full-length s4 mRNA, translation of the s4 mRNA lacking the 3'NTR resulted in a 20 to 50% decrease in sigma3 produced. Addition to translation reactions of an RNA oligonucleotide corresponding to the S4 3'NTR significantly enhanced translation of full-length s4 mRNA but had no effect on s4 mRNA lacking 3'NTR sequences. Translation of s4 mRNAs with smaller deletions within the 3'NTR identified a discrete region capable of translational enhancement and a second region capable of translational repression. Differences in translational efficiency of full-length and deletion-mutant mRNAs were independent of RNA stability. Protein complexes in reticulocyte lysates that specifically interact with the S4 3'NTR were identified by RNA mobility shift assays. RNA oligonucleotides lacking either enhancer or repressor sequences did not efficiently compete the binding of these complexes to full-length 3'NTR. These results indicate that the reovirus S4 gene 3'NTR contains a translational operator sequence that serves to regulate translational efficiency of the s4 mRNA. Moreover, these findings suggest that cellular proteins interact with reovirus 3'NTR sequences to regulate translation of the nonpolyadenylated reovirus mRNAs.
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Affiliation(s)
- M Mochow-Grundy
- Department of Microbiology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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10
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Farsetta DL, Chandran K, Nibert ML. Transcriptional activities of reovirus RNA polymerase in recoated cores. Initiation and elongation are regulated by separate mechanisms. J Biol Chem 2000; 275:39693-701. [PMID: 11007773 DOI: 10.1074/jbc.m004562200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The particle-associated reovirus polymerase synthesizes mRNA within only certain viral particle types. Reovirus cores, subviral particles lacking outer capsid proteins mu1, sigma3, and sigma1, produce mRNA and abortive transcripts. Reovirus virions, which contain complete outer capsids, cannot produce mRNA and produce few abortive transcripts. Recoated cores are virion-like particles generated by the addition of recombinant outer capsid proteins to cores. We used recoated cores to analyze transcriptional regulation by reovirus outer capsid proteins. Partially recoated particles, containing less than virion amounts of mu1 and sigma3, synthesized mRNA at levels inversely proportional to outer capsid protein levels. Fully recoated cores exhibited undetectable mRNA synthesis levels, as did virions. However, recoated cores produced high levels of abortive transcripts. Recoated core abortive transcripts remained particle-associated and appeared to inhibit further abortive transcript production. Proteolysis of recoated cores removing mu1 and sigma3 released accumulated abortive transcripts and relieved inhibition of mRNA and abortive transcript synthesis. These results suggest transcriptional elongation, but not initiation, is blocked by virion-like amounts of mu1 and sigma3. Particle-associated abortive transcripts may down-regulate transcriptional initiation. Minor outer capsid protein sigma1 had no demonstrable effect on transcriptional activities. Transcriptional regulation may ensure progeny virions do not compete with transcribing particles for ribonucleoside triphosphates.
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Affiliation(s)
- D L Farsetta
- Department of Biochemistry, Institute for Molecular Virology, and Cell and Molecular Biology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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11
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Gillian AL, Schmechel SC, Livny J, Schiff LA, Nibert ML. Reovirus protein sigmaNS binds in multiple copies to single-stranded RNA and shares properties with single-stranded DNA binding proteins. J Virol 2000; 74:5939-48. [PMID: 10846075 PMCID: PMC112090 DOI: 10.1128/jvi.74.13.5939-5948.2000] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/1999] [Accepted: 04/05/2000] [Indexed: 11/20/2022] Open
Abstract
Reovirus nonstructural protein sigmaNS interacts with reovirus plus-strand RNAs in infected cells, but little is known about the nature of those interactions or their roles in viral replication. In this study, a recombinant form of sigmaNS was analyzed for in vitro binding to nucleic acids using gel mobility shift assays. Multiple units of sigmaNS bound to single-stranded RNA molecules with positive cooperativity and with each unit covering about 25 nucleotides at saturation. The sigmaNS protein did not bind preferentially to reovirus RNA over nonreovirus RNA in competition experiments but did bind preferentially to single-stranded over double-stranded nucleic acids and with a slight preference for RNA over DNA. In addition, sigmaNS bound to single-stranded RNA to which a 19-base DNA oligonucleotide was hybridized at either end or near the middle. When present in saturative amounts, sigmaNS displaced this oligonucleotide from the partial duplex. The strand displacement activity did not require ATP hydrolysis and was inhibited by MgCl(2), distinguishing it from a classical ATP-dependent helicase. These properties of sigmaNS are similar to those of single-stranded DNA binding proteins that are known to participate in genomic DNA replication, suggesting a related role for sigmaNS in replication of the reovirus RNA genome.
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Affiliation(s)
- A L Gillian
- Department of Biochemistry and Institute for Molecular Virology, The College of Agricultural and Life Sciences, University of Wisconsin-Madison, 53706, USA
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12
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Williamson JD. Poxvirus DNA-dependent RNA polymerase. Rev Med Virol 1998; 8:119-128. [PMID: 10398500 DOI: 10.1002/(sici)1099-1654(199807/09)8:3<119::aid-rmv219>3.0.co;2-i] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- JD Williamson
- Department of Medical Microbiology, Imperial College School of Medicine at St Mary's, Norfolk Place, London W2 1PG, UK
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13
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Yue Z, Shatkin AJ. Enzymatic and control functions of reovirus structural proteins. Curr Top Microbiol Immunol 1998; 233:31-56. [PMID: 9599920 DOI: 10.1007/978-3-642-72092-5_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Z Yue
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854-5638, USA
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14
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Schiff LA. Reovirus capsid proteins sigma 3 and mu 1: interactions that influence viral entry, assembly, and translational control. Curr Top Microbiol Immunol 1998; 233:167-83. [PMID: 9599926 DOI: 10.1007/978-3-642-72092-5_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- L A Schiff
- Department of Microbiology, University of Minnesota, Minneapolis 55455, USA
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16
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Affiliation(s)
- D Baltimore
- Massachusetts Institute of Technology, Cambridge 02139, USA
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17
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18
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Abstract
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.
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Affiliation(s)
- A Ishihama
- Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
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19
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Abstract
Reovirus guanylyltransferase, studied as a covalent enzyme-GMP intermediate, was used to guanylate appropriate acceptor molecules in vitro to produce authentic cap structures. Guanylyltransferase activity was associated with lambda 2, the 140-kilodalton product of the L2 gene segment of reovirus serotypes 1 and 3.
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20
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Maratos-Flier E, Goodman MJ, Murray AH, Kahn CR. Ammonium inhibits processing and cytotoxicity of reovirus, a nonenveloped virus. J Clin Invest 1986; 78:1003-7. [PMID: 3760180 PMCID: PMC423744 DOI: 10.1172/jci112653] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Successful viral infection involves a series of interactions between the virus and the host cell. The outcome of viral infection is, in fact, dependent on intact cellular function; it is required for viral binding, internalization, and uncoating. To determine the potential importance of lysosomal processing on the outcome of infection with a nonenveloped virus, we have studied the effects of NH4Cl on the course of reovirus infection on a beta-cell tumor in culture. Addition of 10 mM NH4C1 to the medium inhibited viral growth by greater than 80% and reduced toxic effects of the virus on cell viability, protein, and DNA synthesis by 30-45%. In addition, synthesis of viral proteins was markedly decreased. Uptake of virus prelabeled with [35S]methionine was not affected by the ammonium; however, cleavage of mu1C, an outer capsid protein of the virus whose cleavage appears to be required for viral replication, was delayed. These results suggest that intracellular processing of reovirus is dependent on a lysosomal pathway and that disruption of this pathway can alter the course of viral infection.
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Ewing DD, Sargent MD, Borsa J. Switch-on of transcriptase function in reovirus: analysis of polypeptide changes using 2-D gels. Virology 1985; 144:448-56. [PMID: 4060593 DOI: 10.1016/0042-6822(85)90285-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two-dimensional gel electrophoresis (IEF and SDS-PAGE) was used to examine virion polypeptide changes associated with switch-on of transcriptase function in reovirus. Results reveal that switch-on is correlated with altered electrophoretic behavior of a specific minor polypeptide (delta 1) which is present in intermediate subviral particles. A second finding is that each of the molecular weight classes of viral polypeptides exists as a series of subspecies with different isoelectric points. This suggests that extensive posttranslational modification of progeny viral polypeptides occurs during particle morphogenesis. These findings have important theoretical and practical implications.
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Cenatiempo Y, Twardowski T, Shoeman R, Ernst H, Brot N, Weissbach H, Shatkin AJ. Two initiation sites detected in the small s1 species of reovirus mRNA by dipeptide synthesis in vitro. Proc Natl Acad Sci U S A 1984; 81:1084-8. [PMID: 6583697 PMCID: PMC344769 DOI: 10.1073/pnas.81.4.1084] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Reovirus mRNAs directed the synthesis of fMet dipeptides in a translation initiation system reconstituted from rabbit reticulocyte initiation and elongation factors, Artemia salina 80S ribosomes, yeast fMet-tRNAiMet and Escherichia coli3H-labeled aminoacyl tRNAs. As predicted from the GC(U,G) codon that follows the 5'-proximal AUG in half of the viral mRNA species, fMet-Ala was the predominant dipeptide product obtained in response to a mixture of mRNAs or to the separated size classes of medium (m) and small (s) mRNA. The four individual small mRNA species each directed the synthesis of an fMet dipeptide that was consistent with the utilization of the 5'-proximal AUG for initiation. In addition to fMet-Asp, the s1 mRNA also directed fMet-Glu synthesis indicative of initiation in a second reading frame at the 5'-penultimate AUG. The tripeptide fMet-Glu-Tyr was also synthesized from s1 mRNA, which further verified this second initiation site. mRNAs containing 5'-terminal GpppG were 10-15% as active as the corresponding m7G-capped templates. The dipeptide assay provides a rapid method for determining initiation sites in individual mRNAs or in mixtures of mRNAs.
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25
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Flores J, Myslinski J, Kalica AR, Greenberg HB, Wyatt RG, Kapikian AZ, Chanock RM. In vitro transcription of two human rotaviruses. J Virol 1982; 43:1032-7. [PMID: 6292446 PMCID: PMC256214 DOI: 10.1128/jvi.43.3.1032-1037.1982] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The RNA polymerase activities of a cultivatable (Wa) and a noncultivatable (DS-1) strain of human rotavirus were studied. Under optimal conditions, transcription of all of their RNA segments occurred, as evidenced by the hybridization of labeled transcripts to genomic RNA. Cross-hybridization between the two viruses showed that none of their 11 genes were completely homologous. The transcription products could be translated in vitro, yielding proteins with an electrophoretic pattern resembling that obtained with proteins labeled in vivo during infection with the Wa virus.
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26
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Yamakawa M, Furuichi Y, Shatkin AJ. Reovirus transcriptase and capping enzymes are active in intact virions. Virology 1982; 118:157-68. [PMID: 7080437 DOI: 10.1016/0042-6822(82)90329-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Abstract
We studied the ability of chymotrypsin to activate the transcriptases of the three serotypes of reovirus. When we used conditions that reproducibly caused the activation of type 3 transcriptase by chymotrypsin alone, type 2 transcriptase was sometimes activated, and type 1 transcriptase was never activated. Using intertypic recombinants containing various combinations of genome segments from reovirus types 3 and 1, we showed that the M2 segment determined this difference. Biochemical experiments indicated that the digestion of reovirus type 1 by chromotrypsin was blocked at an intermediate stage in uncoating. We found conditions which reproducibly activated the transcriptases of all three serotypes. This allowed us to compare the biochemical properties of the three transcriptases. Although the monovalent cation preferences, divalent cation preferences and optima, and temperature optima of type 1, 2, and 3 transcriptases were indistinguishable, the pH activity curves were reproducibly different. The largest difference was between type 2 and 3 transcriptases; the pH optimum of type 2 transcriptase was lower than the pH optimum of type 3 transcriptase. Using intertypic recombinants containing various combinations of genome segments from reovirus types 2 and 3, we demonstrated that the L1 segment specified this difference.
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29
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Smith RE, Morgan MA, Furuichi Y. Separation of the plus and minus strands of cytoplasmic polyhedrosis virus and human reovirus double-stranded genome RNAs by gel electrophoresis. Nucleic Acids Res 1981; 9:5269-86. [PMID: 7029468 PMCID: PMC327519 DOI: 10.1093/nar/9.20.5269] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The complementary strands of most of the genome double-stranded RNA segments of insect cytoplasmic polyhedrosis virus (CPV) and human reovirus are separated for the first time by agarose gel electrophoresis in in the presence of 7 M urea. CPV (+) strands and most reovirus (-) strands migrate faster than the corresponding strands of opposite polarity. Glyoxal treatment, which modifies guanine residues and prevents G-C basepairing, results in a loss of strand resolution and concomitantly a significant decrease in electrophoretic mobilities. Reovirus mRNAs synthesized in vitro with ITP substituted for GTP show similar decreased electrophoretic mobilities as the glyoxalated mRNAs. These results clearly indicate that the basis for (+) and (-) strand resolution is the presence of secondary structure formed mainly by G-C(U) base-pairs that are maintained during gel electrophoresis in the presence of 7 M urea. When the plus and minus strands of CPV genomes were separated and compared for protein synthesizing activity, it was found that only the plus strands were able to form stable 80S ribosome-RNA initiation complexes in wheat germ cell-free extracts.
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30
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Croxson MC, Bellamy AR. Extraction of rotavirus from human feces by treatment with lithium dodecyl sulfate. Appl Environ Microbiol 1981; 41:255-60. [PMID: 6261684 PMCID: PMC243673 DOI: 10.1128/aem.41.1.255-260.1981] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A procedure has been developed for the isolation of rotavirus from human fecal specimens based on the resistance of the virus to treatment with cold 1% lithium dodecyl sulfate at neutral pH. A single detergent treatment of fecal material followed by low- and high-speed centrifugations yielded a virus suspension of sufficient purity for viral ribonucleic acid to be analyzed directly by electrophoresis on polyacrylamide gels.
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31
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Levin KH, Samuel CE. Biosynthesis of reovirus-specified polypeptides. purification and characterization of the small-sized class mRNAs of reovirus type 3: coding assignments and translational efficiencies. Virology 1980; 106:1-13. [PMID: 7414955 DOI: 10.1016/0042-6822(80)90216-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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32
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Van Dijk AA, Huismans H. The in vitro activation and further characterization of the bluetongue virus-associated transcriptase. Virology 1980; 104:347-56. [PMID: 6249033 DOI: 10.1016/0042-6822(80)90339-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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33
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Welsh JD, Leibowitz MJ, Wickner RB. Virion DNA-independent RNA polymerase from Saccharomyces cerevisiae. Nucleic Acids Res 1980; 8:2349-63. [PMID: 7003533 PMCID: PMC324086 DOI: 10.1093/nar/8.11.2349] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The "killer" plasmid and a larger double-stranded RNA plasmid of yeast exist in intracellular virion particles. Purification of these particles from a diploid killer strain of yeast (grown into stationary growth on ethanol) resulted in co-purification of a DNA-independent RNA polymerase activity. This activity incorporates and requires all four ribonucleoside triphosphates and will not act on deoxyribonucleoside triphosphates. The reaction requires magnesium, is inhibited by sulfhydryl-oxidizing reagents and high concentrations of monovalent cation, but is insensitive to DNase, alpha-amanitin, and actinomycin D. Pyrophosphate inhibits the reaction as does ethidium bromide. Exogenous nucleic acids have no effect on the reaction. The product is mostly single-stranded RNA, some of which is released from the enzymatically active virions.
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34
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Abstract
We examined the enzyme activities associated with progeny subviral particles isolated from L-cells infected with reovirus at 12 h postinfection. Activities normally present in reovirus cores were also found to be present in the progeny subviral particles, with the exception of the capping enzymes. The methylase and guanyl transferase activities, which constitute the capping system, were present in a masked form that could be activated by chymotrypsin digestion. The appearance of these progeny subviral particles in infected cells coincided with the time when mRNA synthesis was maximal, suggesting that viral mRNA synthesized at later times is uncapped.
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35
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Kortsaris A, Georgatsos JG, Taylor-Papadimitriou J. A cytidine specific endonuclease activity associated with purified reovirus virions. Biochem Biophys Res Commun 1980; 93:57-65. [PMID: 6246901 DOI: 10.1016/s0006-291x(80)80245-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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36
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Darzynkiewicz E, Shatkin AJ. Assignment of reovirus mRNA ribosome binding sites to virion genome segments by nucleotide sequence analyses. Nucleic Acids Res 1980; 8:337-50. [PMID: 7422544 PMCID: PMC327270 DOI: 10.1093/nar/8.2.337] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
All ten reovirus genome RNA segments were radiolabeled at their 3'-termini by incubation with RNA ligase and 32pCp. The extent of radiolabeling was similar for each of the double-stranded RNAs in the genome segment mixture. Radioactivity was equally distributed between the separated plus and minus strands indicating that the 5'-cap in plus strands did not block 3'-end-labeling of minus strands. The 3'-termini of the four S and three M segments included the common sequences: ...U-A-G-C in minus strands and ...U-C-A-U-C in plus strands. By comparing the minus strand 3'-sequences with 5'-sequences of reovirus mRNAs, small-size genome segments S2, S3 and S4 were correlated with the previously sequenced initiation fragments s46, s45 and s54 derived from small class mRNAs. Medium-size genome segments M1, M2 and M3 similarly were correlated with fragments m30, m52 and m44, respectively. The N-terminal amino acid sequences deduced from the mRNA nucleotide sequences can now be assigned to the nascent chains of particular reovirus proteins.
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37
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38
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Carter CA. Activation of reovirion-associated poly(A) polymerase and oligomer methylase by cofactor-dependent cleavage of mu polypeptides. Virology 1979; 94:417-29. [PMID: 452422 DOI: 10.1016/0042-6822(79)90472-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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39
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40
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McCrae MA, Joklik WK. The nature of the polypeptide encoded by each of the 10 double-stranded RNA segments of reovirus type 3. Virology 1978; 89:578-93. [PMID: 716218 DOI: 10.1016/0042-6822(78)90199-x] [Citation(s) in RCA: 204] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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41
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42
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Hashiro G, Loh PC, Yau JT. The preferential cytotoxicity of reovirus for certain transformed cell lines. Arch Virol 1977; 54:307-15. [PMID: 562142 DOI: 10.1007/bf01314776] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The susceptibility of a variety of cell lines of different mammalian origin to cytotoxic (CT) induction by either ultraviolet light-irradiated reovirus type 2 (UVR2) or viable reovirus type 2 plus the protein synthesis inhibitor, cycloheximide, was examined. The following groups of cells were found to be susceptible to CT-induction: certain tumor cells and spontaneously transformed cell lines of human origin and certain virally and spontaneously transformed cell lines of murine origin. The following groups of cells were found to be resistant: normal human diploid cell lines, primary and continuous cell cultures of subhuman primates, primary mouse cells, normal rat kidney cells and baby hamster kidney cells. Susceptibility to CT-induction could not be related to the adsorption of virus to cells, nor to the capacity of the cell to support virus replication.
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43
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Gomatos PJ, Kuechenthal I. Reovirus-specific enzyme(s) associated with subviral particles responds in vitro to polyribocytidylate to yield double-stranded polyribocytidylate-polyriboguanylate. J Virol 1977; 23:80-90. [PMID: 886647 PMCID: PMC515802 DOI: 10.1128/jvi.23.1.80-90.1977] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In reovirus-infected cells, virus-specific particles accumulate that have associated with them a polyribocytidylate [poly(C)]-dependent polymerase. This enzyme copies in vitro poly(C) to yield the double-stranded poly(C).polyriboguanylate [poly(G)]. The particles with poly(C)-dependent polymerase were heterogeneous in size, with most sedimenting from 300S to 550S. Exponential increase in these particles began at 23 h, and maximal amounts were present by 31 h, the time of onset of exponential growth of virus at 30 degrees C. Maximal amounts of particles with active transcriptase and replicase were present at 15 and 18 h after infection. Thereafter, there was a marked decrease in particles with active transcriptase and replicase until base line levels were reached at 31 h. Thus, the increase in poly(C)-responding particles occurred coincident with the decrease in particles with active transcriptase and replicase. The requirement for poly(C) as template was specific because no RNA was synthesized in vitro in response to any other homopolymer, including 2'-O-methyl-poly(C). Synthesis was optimal in the presence of Mn(2+) as the divalent cation, and no primer was necessary for synthesis. In contrast, the dinucleotide GpG markedly stimulated synthesis in the presence of 8 mM Mg(2+). The size of the poly(C).poly(G) synthesized in vitro was dependent on the size of the poly(C) used as template. This suggested that the whole template was copied into a complementary strand of similar size. The T(m) of the product was between 100 and 130 degrees C. Hydrolysis of the product labeled in [(32)P]GMP with alkali or RNase T2 yielded GMP as the only labeled mononucleotide. This does indicate that the synthesis of the poly(G) strand in vitro did not proceed by end addition to the poly(C) template, but proceeded on a separate strand.
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44
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Levin KH, Samuel CE. Biosynthesis of reovirus-specified polypeptides. Effect of methylation on the efficiency of reovirus genome expression in vitro. Virology 1977; 77:245-59. [PMID: 841860 DOI: 10.1016/0042-6822(77)90422-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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45
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46
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Hastings KE, Millward S. 5' Terminal noncoding sequence heterogeneity in reovirus mRNA. Nucleic Acids Res 1977; 4:195-205. [PMID: 866175 PMCID: PMC342419 DOI: 10.1093/nar/4.1.195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The nucleotide sequences of the mRNAs of reovirus appear to diverge near the 5' termini. Ribonuclease T1 digestion of methylated mRNA synthesized in vitro yielded seven different 5' terminal fragments of the form m7G5'pp5' GmpCpUp(Np)nGp. Chain length analysis showed that the parameter "n" in this structural formula assumes the values 3, 4 and 5.
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47
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Borsa J, Sargent MD, Kay CM, Oikawa K. Circular dichroism of intermediate subviral particles of reovirus. Elucidation of the mechanism underlying the specific monovalent cation effects on uncoating. Biochim Biophys Acta Gen Subj 1976; 451:619-27. [PMID: 63290 DOI: 10.1016/0304-4165(76)90157-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
1. Circular dichroic (CD) spectra of purified intermediate subviral particles of reovirus were determined in the presence of different monovalent cations. 2. The CD spectra reveal that reo intermediate subviral particles can exist in two conformationally different forms. The two forms are readily distinguished by comparison of their ellipticities in the wavelength regions 210 nm and 220 nm, with a Na+-induced form exhibiting a reduced negative ellipticity relative to a Cs+-induced form. 3. The transition between the Na+- and Cs+-induced forms is reversible by manipulation of the species of monovalent cation present and appears to be temperature independent. 4. Temperature variation studies on dilute suspensions of particles indicate that the Na+-induced form is stable, whereas the Cs+-induced from undergoes a second transition, temperature dependent and irreversible, to become a viral core. 5. A model is presented relating these observations to the known properties of reovirus uncoating and transcriptase activation.
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48
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Samuel CE, Joklik WK. Biosynthesis of reovirus-specified polypeptides. Initiation of reovirus messenger RNA translation in vitro and identification of methionyl-x initiation peptides. Virology 1976; 74:403-13. [PMID: 982834 DOI: 10.1016/0042-6822(76)90346-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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49
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Spandidos DA, Graham AF. Nonpermissive infection of L cells by an avian reovirus: restricted transcription of the viral genome. J Virol 1976; 19:977-84. [PMID: 987253 PMCID: PMC354938 DOI: 10.1128/jvi.19.3.977-984.1976] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Avian reovirus multiples in chicken embryo fibroblasts. Although the avian virus adsorbs to L cells and is uncoated therein, it does not multiply. In the nonpermissive infection of L cells with the avian reovirus only four of the genomic segments of the viral genome are transcribed, L1, M3, S3, and S4, and these are the same segments that have been designated previously as early functions in the permissive infection of L cells with type 3 reovirus. When L cells are co-infected with avian reovirus and type 3 virus all ten segments of the avian viral genome are transcribed, although there is no synthesis of avian viral double-stranded RNA. Type 3 reovirus multiplies almost normally in this mixed infection. The most likely explanation is that a cellular repressor blocks transcription of the six late segments of the avian viral genome and that this repressor is removed by the co-infection with type 3 virus. A second block prevents replication of the viral genome.
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50
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Furuichi Y, Muthukrishnan S, Tomasz J, Shatkin AJ. Mechanism of formation of reovirus mRNA 5'-terminal blocked and methylated sequence, m7GpppGmpC. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33218-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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