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Unravelling the Stability and Capsid Dynamics of the Three Virions of Brome Mosaic Virus Assembled Autonomously In Vivo. J Virol 2020; 94:JVI.01794-19. [PMID: 31996436 DOI: 10.1128/jvi.01794-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022] Open
Abstract
Viral capsids are dynamic assemblies that undergo controlled conformational transitions to perform various biological functions. The replication-derived four-molecule RNA progeny of Brome mosaic virus (BMV) is packaged by a single capsid protein (CP) into three types of morphologically indistinguishable icosahedral virions with T=3 quasisymmetry. Type 1 (B1V) and type 2 (B2V) virions package genomic RNA1 and RNA2, respectively, while type 3 (B3+4V) virions copackage genomic RNA3 (B3) and its subgenomic RNA4 (sgB4). In this study, the application of a robust Agrobacterium-mediated transient expression system allowed us to assemble each virion type separately in planta Experimental approaches analyzing the morphology, size, and electrophoretic mobility failed to distinguish between the virion types. Thermal denaturation analysis and protease-based peptide mass mapping experiments were used to analyze stability and the conformational dynamics of the individual virions, respectively. The crystallographic structure of the BMV capsid shows four trypsin cleavage sites (K65, R103, K111, and K165 on the CP subunits) exposed on the exterior of the capsid. Irrespective of the digestion time, while retaining their capsid structural integrity, B1V and B2V released a single peptide encompassing amino acids 2 to 8 of the N-proximal arginine-rich RNA binding motif. In contrast, B3+4V capsids were unstable with trypsin, releasing several peptides in addition to the peptides encompassing four predicted sites exposed on the capsid exterior. These results, demonstrating qualitatively different dynamics for the three types of BMV virions, suggest that the different RNA genes they contain may have different translational timing and efficiency and may even impart different structures to their capsids.IMPORTANCE The majority of viruses contain RNA genomes protected by a shell of capsid proteins. Although crystallographic studies show that viral capsids are static structures, accumulating evidence suggests that, in solution, virions are highly dynamic assemblies. The three genomic RNAs (RNA1, -2, and -3) and a single subgenomic RNA (RNA4) of Brome mosaic virus (BMV), an RNA virus pathogenic to plants, are distributed among three physically homogeneous virions. This study examines the thermal stability by differential scanning fluorimetry (DSF) and capsid dynamics by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses following trypsin digestion of the three virions assembled separately in vivo using the Agrobacterium-mediated transient expression approach. The results provide compelling evidence that virions packaging genomic RNA1 and -2 are distinct from those copackaging RNA3 and -4 in their stability and dynamics, suggesting that RNA-dependent capsid dynamics play an important biological role in the viral life cycle.
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Swanson MM, Ansel-McKinney P, Houser-Scott F, Yusibov V, Loesch-Fries LS, Gehrke L. Viral coat protein peptides with limited sequence homology bind similar domains of alfalfa mosaic virus and tobacco streak virus RNAs. J Virol 1998; 72:3227-34. [PMID: 9525649 PMCID: PMC109790 DOI: 10.1128/jvi.72.4.3227-3234.1998] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/1997] [Accepted: 12/12/1997] [Indexed: 02/06/2023] Open
Abstract
An unusual and distinguishing feature of alfalfa mosaic virus (AMV) and ilarviruses such as tobacco streak virus (TSV) is that the viral coat protein is required to activate the early stages of viral RNA replication, a phenomenon known as genome activation. AMV-TSV coat protein homology is limited; however, they are functionally interchangeable in activating virus replication. For example, TSV coat protein will activate AMV RNA replication and vice versa. Although AMV and TSV coat proteins have little obvious amino acid homology, we recently reported that they share an N-terminal RNA binding consensus sequence (Ansel-McKinney et al., EMBO J. 15:5077-5084, 1996). Here, we biochemically compare the binding of chemically synthesized peptides that include the consensus RNA binding sequence and lysine-rich (AMV) or arginine-rich (TSV) environment to 3'-terminal TSV and AMV RNA fragments. The arginine-rich TSV coat protein peptide binds viral RNA with lower affinity than the lysine-rich AMV coat protein peptides; however, the ribose moieties protected from hydroxyl radical attack by the two different peptides are localized in the same area of the predicted RNA structures. When included in an infectious inoculum, both AMV and TSV 3'-terminal RNA fragments inhibited AMV RNA replication, while variant RNAs unable to bind coat protein did not affect replication significantly. The data suggest that RNA binding and genome activation functions may reside in the consensus RNA binding sequence that is apparently unique to AMV and ilarvirus coat proteins.
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Affiliation(s)
- M M Swanson
- Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom
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Houser-Scott F, Ansel-McKinney P, Cai JM, Gehrke L. In vitro genetic selection analysis of alfalfa mosaic virus coat protein binding to 3'-terminal AUGC repeats in the viral RNAs. J Virol 1997; 71:2310-9. [PMID: 9032367 PMCID: PMC191340 DOI: 10.1128/jvi.71.3.2310-2319.1997] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The coat proteins of alfalfa mosaic virus (AMV) and the related ilarviruses bind specifically to the 3' untranslated regions of the viral RNAs, which contain conserved repeats of the tetranucleotide sequence AUGC. The purpose of this study was to develop a more detailed understanding of RNA sequence and/or structural determinants required for coat protein binding by characterizing the role of the AUGC repeats. Starting with a complex pool of 39-nucleotide RNA molecules containing random substitutions in the AUGC repeats, in vitro genetic selection was used to identify RNAs that bound coat protein. After six iterative rounds of selection, amplification, and reselection, 25% of the RNAs selected from the randomized pool were wild type; that is, they contained all four AUGC sequences. Among the 31 clones analyzed, AUGC was clearly the preferred selected sequence at the four repeats, but some nucleotide sequence variability was observed at AUGC(865-868) if the other three AUGC repeats were present. Variant RNAs that bound coat protein with affinities equal to or greater than that of the wild-type molecule were not selected. To extend the in vitro selection results, RNAs containing specific nucleotide substitutions were transcribed in vitro and tested in coat protein and peptide binding assays. The data strongly suggest that the AUGC repeats provide sequence-specific determinants and contribute to a structural platform for specific coat protein binding. Coat protein may function in maintaining the 3' ends of the genomic RNAs during replication by stabilizing an RNA structure that defines the 3' terminus as the initiation site for minus-strand synthesis.
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Affiliation(s)
- F Houser-Scott
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
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Fukumoto F, Omura T, Kimura I. Effect of protectants in L-drying on the conformation and infectivity of rice dwarf phytoreovirus. Arch Virol 1996; 141:1579-85. [PMID: 8856035 DOI: 10.1007/bf01718256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Purified rice dwarf phytoreovirus preparations, after rehydration following drying without freezing (L-drying) and sucrose density gradient centrifugation, sedimented to the same position as untreated controls. Upon storage at 65 degrees C, virion conformation in L-dried preparations supplemented with 1% sucrose was maintained better than without additives. Moreover, during storage for 6 years at -70 degrees C, infectivity of L-dried preparations from crude extracts of infected rice plants containing 5% sucrose was higher than controls based on the number of count of infected foci on cell monolayers and transmission to rice seedlings by leafhopper of the vector Nephotettix cincticeps, which had been injected with such extracts.
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Affiliation(s)
- F Fukumoto
- National Research Institute of Vegetables, Ornamental Plants and Tea, Mie, Japan
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Reusken CB, Bol JF. Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs. Nucleic Acids Res 1996; 24:2660-5. [PMID: 8758992 PMCID: PMC145989 DOI: 10.1093/nar/24.14.2660] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The 3'-terminal of the three genomic RNAs of alfalfa mosaic virus (AIMV) and ilarviruses contain a number of AUGC-motifs separated by hairpin structures. Binding of coat protein (CP) to such elements in the RNAs is required to initiate infection of these viruses. Determinants for CP binding in the 3'-terminal 39 nucleotides (nt) of AIMV RNA 3 were analyzed by band-shift assays. From the 5'- to 3'-end this 39 nt sequence contains AUGC-motif 3, stem-loop structure 2 (STLP2), AUGC-motif 2, stem-loop structure 1 (STLP1) and AUGC-motif 1. A mutational analysis showed that all three AUGC-motifs were involved in CP binding. Mutation of the A- and U-residues of motifs 1 or 3 had no effect on CP binding but similar mutations in motif 2 abolished CP binding. A mutational analysis of the stem of STLP1 and STLP2 confirmed the importance of these hairpins for CP binding. Randomization of the sequence of the stems and loops of STLP1 and STLP2 had no effect on CP binding as long as the secondary structure was maintained. This indicates that the two hairpins are not involved in sequence-specific interactions with CP. They may function in a secondary structure-specific interaction with CP and/or in the assembly of the AUGC-motifs in a configuration required for CP binding.
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Affiliation(s)
- C B Reusken
- Institute of Molecular Plant Sciences, Goriaeus Laboratories, Leiden University, The Netherlands
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Coombs KM, Brown DT. Form-determining functions in Sindbis virus nucleocapsids: nucleosomelike organization of the nucleocapsid. J Virol 1989; 63:883-91. [PMID: 2911124 PMCID: PMC247762 DOI: 10.1128/jvi.63.2.883-891.1989] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Purified intact Sindbis virus nucleocapsids were treated at different pH values or with various concentrations of divalent cations, cation chelators, salt, or formamide. The resulting structures were examined by velocity sedimentation, electron microscopy, and protein-protein cross-linking. Changes in each of the test conditions led to alterations in the sedimentation profile of treated nucleocapsids. Appropriate concentrations of formamide or divalent cations generated beaded strandlike structures similar in morphology to those generated from adenovirus cores and nucleosomes. The capsid protein and RNA remained associated with each other at NaCl concentrations less than or equal to 1 M or after treatment of the structures with alkaline pH up to and including pH 10.7. Protein and RNA were dissociated by salt concentrations of greater than 1 M, suggesting that the arginine-rich, amino-terminal portion of the capsid protein is responsible for binding the RNA. Protein-protein cross-linking also indicated that the capsid proteins remained associated in small aggregates under some of the conditions that caused dissociation of the nucleocapsid and suggested the presence of more than one type of protein-protein interaction in the nucleocapsids. Collectively, these data suggest that, like histones and adenovirus core proteins, the Sindbis virus capsid protein serves to package segments of the genome into nucleoprotein beads which are capable of interacting with each other to form the nucleocapsid structure.
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Affiliation(s)
- K M Coombs
- Cell Research Institute, University of Texas, Austin 78713-7640
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Hiruki C. The dianthoviruses: a distinct group of isometric plant viruses with bipartite genome. Adv Virus Res 1987; 33:257-300. [PMID: 3296695 DOI: 10.1016/s0065-3527(08)60320-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Wengler G, Boege U, Wengler G, Bischoff H, Wahn K. The core protein of the alphavirus Sindbis virus assembles into core-like nucleoproteins with the viral genome RNA and with other single-stranded nucleic acids in vitro. Virology 1982; 118:401-10. [PMID: 7090184 DOI: 10.1016/0042-6822(82)90359-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Boege U, Wengler G, Wengler G, Wittmann-Liebold B. Primary structures of the core proteins of the alphaviruses Semliki Forest virus and Sindbis virus. Virology 1981; 113:293-303. [PMID: 7269244 DOI: 10.1016/0042-6822(81)90156-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Oostergetel G, Krijgsman P, Mellema J, Cusack S, Miller A. Evidence for the absence of swelling of alfalfa mosaic virions. Virology 1981; 109:206-10. [DOI: 10.1016/0042-6822(81)90489-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/1980] [Indexed: 10/26/2022]
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Garoff H, Frischauf AM, Simons K, Lehrach H, Delius H. The capsid protein of Semliki Forest virus has clusters of basic amino acids and prolines in its amino-terminal region. Proc Natl Acad Sci U S A 1980; 77:6376-80. [PMID: 6935652 PMCID: PMC350287 DOI: 10.1073/pnas.77.11.6376] [Citation(s) in RCA: 104] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The amino acid sequence of the capsid (C) protein was deduced from the nucleotide sequence of the C gene. This part of the viral 42S RNA genome was transcribed into double-stranded cDNA. The cDNA was cloned in the Escherichia coli chi 1776-pBR322 host-vector system and then the base sequence was determined with the technique described by Maxam and Gilbert. The amino acid sequence of the C protein shows a clustering of basic amino acids and prolines within the first 110 amino acids.
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Ulmanen I, Söderlund H, Kääriäinen L. Role of protein synthesis in the assembly of Semliki forest virus nucleocapsid. Virology 1979; 99:265-76. [PMID: 516447 DOI: 10.1016/0042-6822(79)90006-0] [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: 12/15/2022]
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Hull R. The stabilization of the particles of turnip rosette virus and of other members of the southern bean mosaic virus group. Virology 1977; 79:58-66. [PMID: 17216 DOI: 10.1016/0042-6822(77)90334-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Bouley JP, Briand JP, Witz J. The stability of eggplant mosaic virus: action of urea and alkaline pH on top and bottom components. Virology 1977; 78:425-32. [PMID: 17214 DOI: 10.1016/0042-6822(77)90119-2] [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: 12/12/2022]
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Lot H, Kaper JM. Physical and chemical differentiation of three strains of cucumber mosaic virus and peanut stunt virus. Virology 1976; 74:209-22. [PMID: 982815 DOI: 10.1016/0042-6822(76)90142-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Kaper JM. Molecular organization and stabilizing forces of simple RNA viruses. V. The role of lysyl residues in the stabilization of cucumber mosaic virus strain S. Virology 1976; 71:185-98. [PMID: 5803 DOI: 10.1016/0042-6822(76)90104-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Lister RM, Saksena KN. Some properties of Tulare apple mosaic and ILAR viruses suggesting grouping with tobacco streak virus. Virology 1976; 70:440-50. [PMID: 1266046 DOI: 10.1016/0042-6822(76)90285-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Boatman S, Kaper JM. Molecular organization and stabilizing forces of simple RNA viruses. IV. Selective interference with protein-RNA interactions by use of sodium dodecyl sulfate. Virology 1976; 70:1-16. [PMID: 1258371 DOI: 10.1016/0042-6822(76)90231-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Hsu CH, Sehgal OP, Pickett EE. Stabilizing effect of divalent metal ions on virions of southern bean mosaic virus. Virology 1976; 69:587-95. [PMID: 3878 DOI: 10.1016/0042-6822(76)90487-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ganguli PK. A relationship between the protein content of ribonucleoproteins and the G + C content of their RNA. Virology 1975; 65:289-93. [PMID: 1146232 DOI: 10.1016/0042-6822(75)90033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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