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Synthesis and Characterization of a Full-Length Infectious cDNA Clone of Tomato Mottle Mosaic Virus. Viruses 2021; 13:v13061050. [PMID: 34206030 PMCID: PMC8229035 DOI: 10.3390/v13061050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Tomato mottle mosaic virus (ToMMV) is a noteworthy virus which belongs to the Virgaviridae family and causes serious economic losses in tomato. Here, we isolated and cloned the full-length genome of a ToMMV Chinese isolate (ToMMV-LN) from a naturally infected tomato (Solanum lycopersicum L.). Sequence analysis showed that ToMMV-LN contains 6399 nucleotides (nts) and is most closely related to a ToMMV Mexican isolate with a sequence identity of 99.48%. Next, an infectious cDNA clone of ToMMV was constructed by a homologous recombination approach. Both the model host N. benthamiana and the natural hosts tomato and pepper developed severe symptoms upon agroinfiltration with pToMMV, which had a strong infectivity. Electron micrographs indicated that a large number of rigid rod-shaped ToMMV virions were observed from the agroinfiltrated N. benthamiana leaves. Finally, our results also confirmed that tomato plants inoculated with pToMMV led to a high infection rate of 100% in 4–5 weeks post-infiltration (wpi), while pepper plants inoculated with pToMMV led to an infection rate of 40–47% in 4–5 wpi. This is the first report of the development of a full-length infectious cDNA clone of ToMMV. We believe that this infectious clone will enable further studies of ToMMV genes function, pathogenicity and virus–host interaction.
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Wege C, Koch C. From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1591. [PMID: 31631528 DOI: 10.1002/wnan.1591] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/04/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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Zhang Z, Liu L, Wu H, Liu L, Kang B, Peng B, Gu Q. The 96th Amino Acid of the Coat Protein of Cucumber Green Mottle Mosaic Virus Affects Virus Infectivity. Viruses 2017; 10:E6. [PMID: 29295571 PMCID: PMC5795419 DOI: 10.3390/v10010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 12/16/2017] [Accepted: 12/22/2017] [Indexed: 11/17/2022] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) is one of the most devastating viruses infecting members of the family Cucurbitaceae. The assembly initiation site of CGMMV is located in the coding region of the coat protein, which is not only involved in virion assembly but is also a key factor determining the long-distance movement of the virus. To understand the effect of assembly initiation site and the adjacent region on CGMMV infectivity, we created a GTT deletion mutation in the GAGGTTG assembly initiation site of the infectious clone of CGMMV, which we termed V97 (deletion mutation at residue 97 of coat protein), followed by the construction of the V94A and T104A mutants. We observed that these three mutations caused mosaic after Agrobacterium-mediated transformation in Nicotiana benthamiana, albeit with a significant delay compared to the wild type clone. The mutants also had a common spontaneous E96K mutation in the coat protein. These results indicated that the initial assembly site and the sequence of the adjacent region affected the infectivity of the virus and that E96 might play an essential role in this process. We constructed two single point mutants-E96A and E96K-and three double mutants-V94A-E96K, V97-E96K and T104A-E96K-to further understand the role of E96 in CGMMV pathogenesis. After inoculation in N. benthamiana, E96A showed delayed systemic symptoms, but the E96K and three double mutants exhibited typical symptoms of mosaic at seven days post-infection. Then, sap from CGMMV-infected N. benthamiana leaves was mechanically inoculated on watermelon plants. We confirmed that E96 affected CGMMV infection using double antibody sandwich-enzyme-linked immunosorbent assay (DAS-ELISA), reverse transcription-polymerase chain reaction (RT-PCR), and sequencing, which further confirmed the successful infection of the related mutants, and that E96K can compensate the effect of the V94, V97, and T104 mutations on virus infectivity. In addition, Northern blotting showed that the accumulation of viral RNA corroborated the severity of the symptoms.
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Affiliation(s)
- Zhenwei Zhang
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Liming Liu
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Huijie Wu
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Lifeng Liu
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Baoshan Kang
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Bin Peng
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Qinsheng Gu
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
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Eber FJ, Eiben S, Jeske H, Wege C. RNA-controlled assembly of tobacco mosaic virus-derived complex structures: from nanoboomerangs to tetrapods. NANOSCALE 2015; 7:344-55. [PMID: 25407780 DOI: 10.1039/c4nr05434b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The in vitro assembly of artificial nanotubular nucleoprotein shapes based on tobacco mosaic virus-(TMV-)-derived building blocks yielded different spatial organizations of viral coat protein subunits on genetically engineered RNA molecules, containing two or multiple TMV origins of assembly (OAs). The growth of kinked nanoboomerangs as well as of branched multipods was determined by the encapsidated RNAs. A largely simultaneous initiation at two origins and subsequent bidirectional tube elongation could be visualized by transmission electron microscopy of intermediates and final products. Collision of the nascent tubes' ends produced angular particles with well-defined arm lengths. RNAs with three to five OAs generated branched multipods with a maximum of four arms. The potential of such an RNA-directed self-assembly of uncommon nanotubular architectures for the fabrication of complex multivalent nanotemplates used in functional hybrid materials is discussed.
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Affiliation(s)
- Fabian J Eber
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany.
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Ma D, Xie Y, Zhang J, Ouyang D, Yi L, Xi Z. Self-assembled controllable virus-like nanorods as templates for construction of one-dimensional organic–inorganic nanocomposites. Chem Commun (Camb) 2014; 50:15581-4. [DOI: 10.1039/c4cc07057g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Geiger FC, Eber FJ, Eiben S, Mueller A, Jeske H, Spatz JP, Wege C. TMV nanorods with programmed longitudinal domains of differently addressable coat proteins. NANOSCALE 2013; 5:3808-16. [PMID: 23519401 DOI: 10.1039/c3nr33724c] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The spacing of functional nanoscopic elements may play a fundamental role in nanotechnological and biomedical applications, but is so far rarely achieved on this scale. In this study we show that tobacco mosaic virus (TMV) and the RNA-guided self-assembly process of its coat protein (CP) can be used to establish new nanorod scaffolds that can be loaded not only with homogeneously distributed functionalities, but with distinct molecule species grouped and ordered along the longitudinal axis. The arrangement of the resulting domains and final carrier rod length both were governed by RNA-templated two-step in vitro assembly. Two selectively addressable TMV CP mutants carrying either thiol (TMVCys) or amino (TMVLys) groups on the exposed surface were engineered and shown to retain reactivity towards maleimides or NHS esters, respectively, after acetic acid-based purification and re-assembly to novel carrier rod types. Stepwise combination of CP(Cys) and CP(Lys) with RNA allowed fabrication of TMV-like nanorods with a controlled total length of 300 or 330 nm, respectively, consisting of adjacent longitudinal 100-to-200 nm domains of differently addressable CP species. This technology paves the way towards rod-shaped scaffolds with pre-defined, selectively reactive barcode patterns on the nanometer scale.
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Affiliation(s)
- Fania C Geiger
- Department of New Materials and Biosystems, Max-Planck-Institute for Intelligent Systems, University of Heidelberg, Heisenbergstrasse 3, 70569 Stuttgart, Germany
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Kraft DJ, Kegel WK, van der Schoot P. A kinetic Zipper model and the assembly of tobacco mosaic virus. Biophys J 2012; 102:2845-55. [PMID: 22735535 DOI: 10.1016/j.bpj.2012.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 05/01/2012] [Accepted: 05/03/2012] [Indexed: 11/29/2022] Open
Abstract
We put forward a modified Zipper model inspired by the statics and dynamics of the spontaneous reconstitution of rodlike tobacco mosaic virus particles in solutions containing the coat protein and the single-stranded RNA of the virus. An important ingredient of our model is an allosteric switch associated with the binding of the first protein unit to the origin-of-assembly domain of the viral RNA. The subsequent addition and conformational switching of coat proteins to the growing capsid we believe is catalyzed by the presence of the helical arrangement of bound proteins to the RNA. The model explains why the formation of complete viruses is favored over incomplete ones, even though the process is quasi-one-dimensional in character. We numerically solve the relevant kinetic equations and show that time evolution is different for the assembly and disassembly of the virus, the former exhibiting a time lag even if all forward rate constants are equal. We find the late-stage assembly kinetics in the presence of excess protein to be governed by a single-exponential relaxation, which agrees with available experimental data on TMV reconstruction.
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Affiliation(s)
- Daniela J Kraft
- Van 't Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute for NanoMaterials Science, Utrecht University, Utrecht, The Netherlands.
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Fukuda M, Meshi T, Okada Y, Otsuki Y, Takebe I. Correlation between particle multiplicity and location on virion RNA of the assembly initiation site for viruses of the tobacco mosaic virus group. Proc Natl Acad Sci U S A 2010; 78:4231-5. [PMID: 16593057 PMCID: PMC319763 DOI: 10.1073/pnas.78.7.4231] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The initiation site for reconstitution on genome RNA was determined by electron microscopic serology for a watermelon strain of cucumber green mottle mosaic virus (CGMMV-W), which is chemically and serologically related to tobacco mosaic virus (TMV). The initiation site was located at the same position as that of the cowpea strain, a virus that produces short rods of encapsidated subgenomic messenger RNA for the coat protein (a two-component TMV), being about 320 nucleotides away from the 3' terminus, and hence within the coat protein cistron. Although CGMMV-W was until now believed to be a single-component TMV, the location of the initiation site indicated the presence of short rods containing coat protein messenger RNA in CGMMV-W-infected tissue, as in the case for the cowpea strain. We found such short rods in CGMMV-W-infected tissue. The results confirmed our previous hypothesis that the site of the initiation region for reconstitution determines the rod multiplicity of TMV. The finding of the second two-component TMV, CGMMV, indicates that the cowpea strain of TMV is not unique in being a two-component virus and that the location of the assembly initiation site on the genome RNA can be a criterion for grouping of viruses.
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Affiliation(s)
- M Fukuda
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Tokyo 113, Japan
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Shire SJ, Stegkert JJ, Schuster TM. Mechanism of tobacco mosaic virus assembly: Incorporation of 4S and 20S protein at pH 7.0 and 20 degrees C. Proc Natl Acad Sci U S A 2010; 78:256-60. [PMID: 16592945 PMCID: PMC319031 DOI: 10.1073/pnas.78.1.256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanism of assembly of tobacco mosaic virus (TMV) has been investigated at pH 7.0 and 20 degrees C by analytical ultracentrifugation. Under these conditions the overall rates of interconversion of 4S and 20S TMV coat protein are sufficiently slow to make possible measurements of the concentrations of remaining 4S and 20S TMV coat protein after addition of homologous RNA to solutions containing, initially, various mass ratios of 20S protein to 4S protein. It has been possible to measure, by schlieren boundary analysis, the relative rates of incorporation of 4S and 20S TMV protein into the growing nucleoprotein rod over the range of initial 20S:4S protein mass ratios from 93:7 to 18:82. The results show that the amount of incorporation of 20S TMV protein depends on the initial 20S:4S mass ratio between approximately 100% and 60% 20S protein but that reconstitution can proceed with approximately 100% 20S TMV protein to form full virus-size rods. However, when the initial protein solutions have less than 60% 20S protein, approximately 80% of the reconstituted nucleoprotein is preferentially formed from 4S coat protein. The remaining approximately 20% appears to require preformed 20S coat protein. These results suggest that a larger region of RNA than previously estimated is involved in the rate-limiting nucleation step in assembly and may explain previously conflicting results concerning the elongation phase of assembly when starting with partially assembled rods.
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Affiliation(s)
- S J Shire
- Biochemistry and Biophysics Section, Biological Sciences Group, University of Connecticut, Storrs, Connecticut 06268
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Meshi T, Ishikawa M, Motoyoshi F, Semba K, Okada Y. In vitro transcription of infectious RNAs from full-length cDNAs of tobacco mosaic virus. Proc Natl Acad Sci U S A 2010; 83:5043-7. [PMID: 16593727 PMCID: PMC323886 DOI: 10.1073/pnas.83.14.5043] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We have cloned full-length double-stranded cDNAs of tobacco mosaic virus (TMV) (tomato strain L) RNA into a transcription vector, pPM1, which facilitates the correct transcription initiation from the first nucleotide of the inserted double-stranded cDNA, corresponding to the 5' end of TMV RNA. When plasmid DNA is linearized at a unique restriction site (Mlu I) introduced just downstream of the double-stranded cDNA insert and used as a template for in vitro transcription by Escherichia coli RNA polymerase in the presence of m(7)GpppG, the transcribed RNAs are infectious for tobacco plants. A simple reconstitution procedure increases the infectivity >100 times. Unexpectedly, both the uncapped transcript and the transcript from the uncut plasmid DNA are also infectious, although their infectivities are very low. The progeny viruses multiplying in tobacco plants accurately reflect the cloned sequence. By the same method, we succeeded in the in vitro transcription of infectious RNA of attenuated strain L(11)A, which is phenotypically distinguishable from wild-type TMV on both tobacco and tomato plants.
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Affiliation(s)
- T Meshi
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Tokyo 113, Japan
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11
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Fukuda M, Okada Y. Elongation in the major direction of tobacco mosaic virus assembly. Proc Natl Acad Sci U S A 2010; 82:3631-4. [PMID: 16593565 PMCID: PMC397839 DOI: 10.1073/pnas.82.11.3631] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Butler and Lomonossoff [Butler, P. J. G. & Lomonossoff, G. P. (1978) J. Mol. Biol. 126, 877-882] claim that the elongation in the major direction (3'-->5') proceeds by incorporation of disk protein in tobacco mosaic virus (TMV) assembly. The strongest argument they have for this theory is the periodicity of 50 or 100 nucleotides that they observed in the banding pattern of the protected RNAs during the first few minutes of the assembly reaction. We repeated their experiment using TMV-OM (a common Japanese strain) disk protein and TMV-OM RNA. We observed a banding pattern similar to theirs, but we found the long protected RNA at 6 min to be from the 260-nm intermediate particle rather than from the full-length TMV RNA. We also carried out the assembly reaction between TMV-OM disk protein, as well as cucumber green mottle mosaic virus (CGMMV) protein, and three strains of TMV RNAs. During the course of each assembly reaction, we examined the banding patterns. We demonstrated that the banding pattern of the protected RNA differs depending on what kind of RNA is used, rather than on what kind of aggregational state the protein is in. Specifically, the similar banding pattern observed for CGMMV subunit protein was also observed for TMV disk protein in the assembly reaction with TMV (OM) RNA. We showed previously that the assembly reaction between CGMMV protein and TMV RNA proceeds by incorporation of CGMMV subunit protein. This strongly indicates that the banding pattern of the protected RNA does not arise from the stepwise addition of the 20S disk protein.
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Affiliation(s)
- M Fukuda
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Tokyo 113, Japan
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12
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Klug A. From Virus Structure to Chromatin: X-ray Diffraction to Three-Dimensional Electron Microscopy. Annu Rev Biochem 2010; 79:1-35. [DOI: 10.1146/annurev.biochem.79.091407.093947] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron Klug
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
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Sano Y, Inoue H, Hiragi Y. Differences of reconstitution process between tobacco mosaic virus and cucumber green mottle mosaic virus by synchrotron small angle X-ray scattering using low-temperature quenching. JOURNAL OF PROTEIN CHEMISTRY 1999; 18:801-5. [PMID: 10691191 DOI: 10.1023/a:1020689720082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The differences of the reconstitution process of tobacco mosaic virus (TMV) and its mutant, cucumber green mottle mosaic virus (CGMMV) were investigated by the solution X-ray scattering measurements with the synchrotron radiation source using low-temperature quenching. The reconstitution in an aqueous solution is completely stopped below 5 degrees C. The TMV and CGMMV assembly was traced by the small-angle X-ray scattering (SAXS) measurements at 5 degrees C on a series of solutions prepared by low-temperature quenching after incubation at 20 degrees C for an appropriate interval between 0 and 60 min. The SAXS results were analyzed by the Guinier plot, the Kratky plot and the distance distribution function. The incubation of RNA and protein of CGMMV did not reconstitute at the initial reaction stages below 5 min and then began to reconstitute gradually. After 60 min, the radius of gyration for CGMMV reconstitution process reached almost the value for the initial stage of TMV reconstitution process. This is due to the fact the formation of double-layered disk in CGMMV protein is much slower than in TMV protein.
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Affiliation(s)
- Y Sano
- National Food Research Institute, Tsukuba City, Ibaraki, Japan.
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Butler PJ. Self-assembly of tobacco mosaic virus: the role of an intermediate aggregate in generating both specificity and speed. Philos Trans R Soc Lond B Biol Sci 1999; 354:537-50. [PMID: 10212933 PMCID: PMC1692540 DOI: 10.1098/rstb.1999.0405] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The tobacco mosaic virus (TMV) particle was the first macromolecular structure to be shown to self-assemble in vitro, allowing detailed studies of the mechanism. Nucleation of TMV self-assembly is by the binding of a specific stem-loop of the single-stranded viral RNA into the central hole of a two-ring sub-assembly of the coat protein, known as the 'disk'. Binding of the loop onto its specific binding site, between the two rings of the disk, leads to melting of the stem so more RNA is available to bind. The interaction of the RNA with the protein subunits in the disk cause this to dislocate into a proto-helix, rearranging the protein subunits in such a way that the axial gap between the rings at inner radii closes, entrapping the RNA. Assembly starts at an internal site on TMV RNA, about 1 kb from its 3'-terminus, and the elongation in the two directions is different. Elongation of the nucleated rods towards the 5'-terminus occurs on a 'travelling loop' of the RNA and, predominantly, still uses the disk sub-assembly of protein subunits, consequently incorporating approximately 100 further nucleotides as each disk is added, while elongation towards the 3'-terminus uses smaller protein aggregates and does not show this 'quantized' incorporation.
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Affiliation(s)
- P J Butler
- MRC Laboratory of Molecular Biology, Cambridge, UK
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Fukuda M, Okada Y. Bidirectional assembly of tobacco mosaic virus in vitro. Proc Natl Acad Sci U S A 1987; 84:4035-8. [PMID: 16593848 PMCID: PMC305016 DOI: 10.1073/pnas.84.12.4035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
THE TIMING OF THE BIDIRECTIONAL GROWTH IN THE ASSEMBLY REACTION OF TOBACCO MOSAIC VIRUS HAS BEEN THE SUBJECT OF CONTROVERSY: Does elongation actually occur simultaneously to 5' and 3' ends or sequentially, first to the 5' end and then to the 3' end? To determine the timing of elongation toward the 3' end directly, using the S1 nuclease mapping method on a cloned cDNA with micrococcal nuclease-digested tobacco mosaic virus RNA, we analyzed encapsidation of the RNA region that was located downstream from the assembly origin. The results clearly showed that elongation toward the 3' end did not occur for at least the first 4 min. Actually it was first observed at 8 min. It is concluded that, in the first 5-7 min, a rapid elongation of the nucleation complex occurs only toward the 5' end of the RNA and that this gives rise to an intermediate particle 260 nm long. Furthermore, the lengths of the RNA that were protected against S1 nuclease digestion showed a clear banding pattern that had a spacing of approximately 100 nucleotides. This supports the hypothesis that the 20S aggregate is kinetically favored as the protein source for elongation to the 3' end.
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Affiliation(s)
- M Fukuda
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Tokyo 113, Japan
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Ishikawa M, Meshi T, Motoyoshi F, Takamatsu N, Okada Y. In vitro mutagenesis of the putative replicase genes of tobacco mosaic virus. Nucleic Acids Res 1986; 14:8291-305. [PMID: 3786131 PMCID: PMC311860 DOI: 10.1093/nar/14.21.8291] [Citation(s) in RCA: 125] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have established an in vitro transcription system to produce infectious tobacco mosaic virus (TMV) RNA from a cloned cDNA copy. Using this system, several TMV mutants were transcribed in vitro from cDNA clones mutagenized at or near the leaky amber termination codon of the 130K protein gene, and their infectivity was assayed on tobacco plants. Three (two frame-shift and one non-sense) mutants with an intact 130K but a defective 180K protein gene were not infectious, while two mutants with a one-amino-acid insertion in the 180K protein gene were infectious. When the amber codon of the 130K protein gene was deleted, infectivity was lost. However, when the amber termination codon was replaced with ochre or tyrosine codon, infectivity was retained. Sequence analyses revealed that introduced mutations were retained in progeny viral sequences except in the progeny of the amber-to-tyrosine mutant, which was a mixture of the parental mutagenized virus and a pseudo-revertant with ochre codon.
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Fairall L, Finch JT, Hui CF, Cantor CR, Butler PJ. Studies of tobacco mosaic virus reassembly with an RNA tail blocked by a hybridised and cross-linked probe. EUROPEAN JOURNAL OF BIOCHEMISTRY 1986; 156:459-65. [PMID: 3754513 DOI: 10.1111/j.1432-1033.1986.tb09604.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Segments of cloned cDNA to tobacco mosaic virus RNA, 150--300-bases long, have been hybridised and cross-linked to the RNA, which has then been used for reassembly experiments. This enables the elongation reaction, which does not encapsidate the double-stranded region generated, to be stopped at specific regions along the RNA and the resulting particles to be characterised, by measuring the lengths of the rods in the electron microscope. With hybridisation to the 3'-tail the entire RNA contiguous to the nucleation region is encapsidated, from the 5'-terminus up to the modified region. When the double-stranded region is on the 5'-side of the nucleation region, the mean length of the particles corresponds to a situation in which the double-stranded region is unable to enter the central hole of the growing rod, but the 3'-tail of the RNA is completely encapsidated. The longest particles hybridised on the 5'-tail (i.e. in a class longer than the mean length) show an effect complementary to those with a 3'-block, and have lengths which correspond to encapsidation from the modified region to the 3'-terminus, despite the continued presence of the 5'-tail up the rod. In all cases where there is a remaining 5'-tail the lengths observed can only be explained if elongation has occurred substantially, or probably completely, along the 3'-tail. Hence elongation must have occurred simultaneously along both the 5' and 3'-tails of the tobacco mosaic virus RNA after initiation on the internal nucleation region.
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Saffran WA, Hui CF, Edelson RL, Cantor CR. Delivery of photoreactive psoralen derivatives to specific biological targets. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf01025193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Klug A. From macromolecules to biological assemblies. Nobel Lecture, 8 December 1982. Biosci Rep 1983; 3:395-430. [PMID: 6349708 DOI: 10.1007/bf01121953] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Strauss EG, Strauss JH. Replication strategies of the single stranded RNA viruses of eukaryotes. Curr Top Microbiol Immunol 1983; 105:1-98. [PMID: 6354610 DOI: 10.1007/978-3-642-69159-1_1] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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22
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Fukuda M, Okada Y. Mechanism of tobacco mosaic virus assembly: role of subunit and larger aggregate protein. Proc Natl Acad Sci U S A 1982; 79:5833-6. [PMID: 6964390 PMCID: PMC347004 DOI: 10.1073/pnas.79.19.5833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Tobacco mosaic virus (TMV) was reconstituted from the RNA of a common strain (OM) and the protein of a watermelon strain of cucumber green mottle mosaic virus (CGMMV-W), which is a member of the tobamovirus group. In 0.25 M phosphate buffer at 25 degrees C, CGMMV-W protein existed mainly as 21S aggregates. When this protein was mixed with OM RNA, complexes of short rods were formed but further elongation did not occur. After the addition of subunits in 0.1 M phosphate buffer at 25 degrees C, elongation to the 5' end of the RNA proceeded as fast as in the case of reconstitution with the usual equilibrium "disk preparation" of OM protein, to give 260-nm intermediates in the first 5-7 min. The results proved that the rapid elongation we previously observed in the reconstitution of TMV-OM following the assembly initiation is the outcome of preferential incorporation of TMV subunit protein. Either preformed 21S aggregate or the subunit of CGMMV protein was added to the 260-nm intermediate. Elongation to the 3' end of the RNA was investigated in 0.1 M phosphate buffer at 25 degrees C by measuring the distribution of rod length and the RNase-resistant infectivity. The results showed that the 21S aggregate is kinetically favored as the protein source during the slow elongation process.
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Hirth L, Richards KE. Tobacco mosaic virus: model for structure and function of a simple virus. Adv Virus Res 1981; 26:145-99. [PMID: 7223542 DOI: 10.1016/s0065-3527(08)60423-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Abstract
Assembly of tobacco mosaic virus is initiated by the binding of a specific loop of the RNA into the central hole of the disk aggregate of protein subunits. Since the nucleation loop is located about five-sixths along the RNA molecule, subsequent elongation must be bidirectional. We have now measured the rates of elongation in the two directions by determining the lengths of RNA protected from nuclease digestion at different times and using either intact TMV rNA, or RNA with most of the longer tail removed. Comparison of the rates with the protein supplied as either a mixture of disks with A-protein (a mixture of less aggregated states) or just A-protein, shows that different mechanisms and protein aggregates are used for the most rapid growth. When disks are present, they add more rapidly along the longer RNA tail but do not appear to add directly on the shorter tail. In contrast, smaller aggregates (A-protein) can add at both ends of the rod, but do so more slowly. Mechanisms for these processes are discussed. Preliminary results on the binding of the specific hexanucleotide AAGAAG to the disk are given and compared with the known changes on binding nonspecific hexanucleotides or the trinucleotide AAG.
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Schuster TM, Scheele RB, Adams ML, Shire SJ, Steckert JJ, Potschka M. Studies on the mechanism of assembly of tobacco mosaic virus. Biophys J 1980; 32:313-29. [PMID: 7248451 PMCID: PMC1327310 DOI: 10.1016/s0006-3495(80)84959-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Sedimentation and proton binding studies on the endothermic self-association of tobacco mosaic virus (TMV) protein indicate that the so-called "20S" sedimenting protein is an interaction system involving at least the 34-subunit two-turn yield cylindrical disk aggregate and the 49-subunit three-turn helical rod. The pH dependence of this overall equilibrium suggests that disk formation is proton-linked through the binding of protons to the two-turn helix which is not present as significant concentrations near pH 7. There is a temperature-induced intramolecular conformation change in the protein leading to a difference spectrum which is complete in 5 x 10(-6) s at pH 7 and 20 degrees C and is dominated at 300 nm by tryptophan residues. Kinetics measurements of protein polymerization, from 10(-6) to 10(3) s, reveal three relaxation processes at pH 7.0, 20 degrees C, 0.10 M ionic strength K (H) PO4. The fastest relaxation time is a few milliseconds and represents reactions within the 4S protein distribution. The second fastest relaxation is 50-100 x 10(-3) s and represents elementary polymerization steps involved in the formation of the approximately 20 S protein. Analysis of the slowest relaxation, approximately 5 x 10(4) s, suggests that this very slow formation of approximately 20 S protein may be dominated by some first order process in the overall dissociation of approximately 20S protein. Sedimentation measurements of the rate of TMV reconstitution, under the same conditions, show by direct measurements of 4S and approximately 20S incorporation at various 4S to approximately 20S weight ratios that the relative rate of approximately 20S incorporation decreases almost linearly, from 0 to 50% 4S. There appears to be one or more regions of TMV-RNA, approximately 1-1.5 kilobases long, which incorporates approximately 20S protein exclusively. Solutions of approximately 95-100% approximately 20S protein have been prepared for the first time and used for reconstitution with RNA. Such protein solutions yield full size TMV, but at a slower rate than if 4S protein is added. Thus the elongation reaction in TMV assembly, following nucleation with approximately 20S protein, is not exclusively dependent upon the presence of either 4S or approximately 20S protein aggregates. The initial, maximum, rate of reconstitution increases about threefold when the protein composition is changed from 5% to 30% 4S protein, at constant total protein concentration at pH 7.0, 20 degrees C in 0.10 M ionic strength K (H)PO4. The probable binding frame at the internal assembly nucleation site of TMV-RNA has been determined by measuring the association constants for the binding of various trinucleoside diphosphates to helical TMV protein rods. The -CAG-AAG-AAG-sequence at the nucleation site is capable of providing at least 10-14 kcal/mol of sites of binding free energy for the nucleation event in TMV self-assembly.
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Lomonossoff GP, Butler PJ. Location and encapsidation of the coat protein cistron of tobacco mosaic virus. A bidirectional elongation of the nucleoprotein rod. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 93:157-64. [PMID: 108098 DOI: 10.1111/j.1432-1033.1979.tb12806.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The coat protein cistron of tobacco mosaic virus has been located on the viral RNA starting between 975 and 1050 nucleotides from the 3'-hydroxyl end. This locates its 5' end close to the origin for virus assembly, where the first protein disk interacts with RNA. It also means that the coat protein mRNA must have a short 5'-untranslated tail and a long (over 500 nucleotides) 3' one. The recovery of characteristic oligonucleotides in nuclease-protected rods during the growth from RNA and a protein disk preparation shows that elongation of the nucleated rods proceeds independently in both directions though, on average, much more rapidly along the longer 5' tail than the shorter 3' tail. Protected RNA of length equal to that in the complete virion is first seen within 6 min, showing that the most rapidly elongated particles are substantially complete by this time.
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