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Abstract
The discovery of a new class of pathogen, viruses, in the late 19th century, ushered in a period of study of the biochemical and structural properties of these entities in which plant viruses played a prominent role. This was, in large part, due to the relative ease with which sufficient quantities of material could be produced for such analyses. As analytical techniques became increasingly sensitive, similar studies could be performed on the viruses from other organisms. However, plant viruses continued to play an important role in the development of molecular biology, including the demonstration that RNA can be infectious, the determination of the genetic code, the mechanism by which viral RNAs are translated, and some of the early studies on gene silencing. Thus, the study of plant viruses should not be considered a "niche" subject but rather part of the mainstream of virology and molecular biology.
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Li Y, Wang Y, Hu J, Xiao L, Tan G, Lan P, Liu Y, Li F. The complete genome sequence, occurrence and host range of Tomato mottle mosaic virus Chinese isolate. Virol J 2017; 14:15. [PMID: 28137291 PMCID: PMC5282660 DOI: 10.1186/s12985-016-0676-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/26/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Tomato mottle mosaic virus (ToMMV) is a recently identified species in the genus Tobamovirus and was first reported from a greenhouse tomato sample collected in Mexico in 2013. In August 2013, ToMMV was detected on peppers (Capsicum spp.) in China. However, little is known about the molecular and biological characteristics of ToMMV. METHODS Reverse transcription-polymerase chain reaction (RT-PCR) and rapid identification of cDNA ends (RACE) were carried out to obtain the complete genomic sequences of ToMMV. Sap transmission was used to test the host range and pathogenicity of ToMMV. RESULTS The full-length genomes of two ToMMV isolates infecting peppers in Yunnan Province and Tibet Autonomous Region of China were determined and analyzed. The complete genomic sequences of both ToMMV isolates consisted of 6399 nucleotides and contained four open reading frames (ORFs) encoding 126, 183, 30 and 18 kDa proteins from the 5' to 3' end, respectively. Overall similarities of the ToMMV genome sequence to those of the other tobamoviruses available in GenBank ranged from 49.6% to 84.3%. Phylogenetic analyses of the sequences of full-genome nucleotide and the amino acids of its four proteins confirmed that ToMMV was most closely related to Tomato mosaic virus (ToMV). According to the genetic structure, host of origin and phylogenetic relationships, the available 32 tobamoviruses could be divided into at least eight subgroups based on the host plant family they infect: Solanaceae-, Brassicaceae-, Cactaceae-, Apocynaceae-, Cucurbitaceae-, Malvaceae-, Leguminosae-, and Passifloraceae-infecting subgroups. The detection of ToMMV on some solanaceous, cucurbitaceous, brassicaceous and leguminous plants in Yunnan Province and other few parts of China revealed ToMMV only occurred on peppers so far. However, the host range test results showed ToMMV could infect most of the tested solanaceous and cruciferous plants, and had a high affinity for the solanaceous plants. CONCLUSIONS The complete nucleotide sequences of two Chinese ToMMV isolates from naturally infected peppers were verified. The tobamoviruses were divided into at least eight subgroups, with ToMMV belonging to the subgroup that infected plants in the Solanaceae. In China, ToMMV only occurred on peppers in the fields till now. ToMMV could infect the plants in family Solanaceae and Cucurbitaceae by sap transmission.
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Affiliation(s)
- Yueyue Li
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yang Wang
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - John Hu
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822, USA
| | - Long Xiao
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanlin Tan
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
- Modern Education Technology Center, Yunnan Agricultural University, Kunming, 650201, China
| | - Pingxiu Lan
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yong Liu
- Hunan Academy of Agricultural Sciences, Plant Protection Institute, Changsha, 410125, China.
| | - Fan Li
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, 650201, China.
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Briand JP, Keith G, Guilley H. Nucleotide sequence at the 5' extremity of turnip yellow mosaic virus genome RNA. Proc Natl Acad Sci U S A 2010; 75:3168-72. [PMID: 16592542 PMCID: PMC392735 DOI: 10.1073/pnas.75.7.3168] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The sequence of the first 110 nucleotides at the 5' extremity of turnip yellow mosaic virus genome RNA has been determined. The sequence is blocked at its 5' terminus with the group pppm(7)G and contains two AUG triplets. The determined sequence bears a strong resemblance to the 5' noncoding region of rabbit beta-globin mRNA. Region 95-103 of the sequence can base-pair with part of the 3' extremity of either the genome RNA or the coat protein mRNA.
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Affiliation(s)
- J P Briand
- Laboratoire de Virologie, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Université Louis Pasteur, 15, rue Descartes, 67084 Strasbourg, France
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Lu B, Stubbs G, Culver JN. Coat protein interactions involved in tobacco mosaic tobamovirus cross-protection. Virology 1998; 248:188-98. [PMID: 9721228 DOI: 10.1006/viro.1998.9280] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate the molecular role of the tobacco mosaic tobamovirus (TMV) coat protein (CP) in conferring cross-protection, a potato X potexvirus (PVX) vector (S. Chapman, Plant J. 2, 549-557, 1992) was used to systemically express a set of TMV mutant CPs in Nicotiana benthamiana prior to challenge inoculation with TMV. PVX-expressed wild-type TMV CP delayed TMV accumulation for up to 2 weeks compared to unprotected plants or plants preinfected with the unmodified PVX vector. Similar delays in TMV accumulation were obtained using TMV CPs that were deficient in virion formation but competent to assemble into helical aggregates. In contrast, TMV CPs that were incapable of helical aggregation or unable to bind viral RNA did not delay the accumulation of TMV. Furthermore, TMV CPs with enhanced intersubunit interactions that favor helical aggregation produced significantly greater delays in the accumulation of challenge TMV than obtained from the wild-type CP. Thus the capabilities of TMV CP to interact with viral RNA and self-associate in a helical fashion appear to be essential to its ability to confer protection. Taken together, these findings support a model for CP-mediated resistance in which the protecting CP recoats the challenge virus RNA as it disassembles.
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Affiliation(s)
- B Lu
- Department of Plant Biology, University of Maryland, College Park, Maryland, 20742, USA
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Lu B, Taraporewala F, Stubbs G, Culver JN. Intersubunit interactions allowing a carboxylate mutant coat protein to inhibit tobamovirus disassembly. Virology 1998; 244:13-9. [PMID: 9581773 DOI: 10.1006/viro.1998.9099] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tobacco mosaic tobamovirus (TMV) coat protein (CP) mutant E50Q lacks a repulsive intersubunit carboxylate group and can effectively inhibit the disassembly of wild-type TMV (Culver et al, 1995, Virology 206,724). To investigate the ability of this mutant CP to block disassembly, a series of second-site amino acid substitutions were added to the E50Q CP. These second-site mutations were designed to disrupt specific intersubunit stabilizing interactions involving hydrophobic or polar residues, salt bridges, and CP-RNA contacts. Results showed substitutions disrupting intersubunit interactions that face the disassembling surface of the virion dramatically reduced the ability of CP E50Q to inhibit TMV disassembly. Substitutions that disrupted the CP inner loop, RNA binding capabilities, or intersubunit interactions that faced away from the disassembling surface did not dramatically interfere with CP E50Q's ability to inhibit disassembly. Taken together, these findings suggest that intersubunit interactions made by 5' terminal E50Q subunits, not associated with RNA, provide the stabilizing forces that prevent virion disassembly. The role of these stabilizing interactions in TMV disassembly and their potential use for creating disassembly inhibiting CPs are discussed.
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Affiliation(s)
- B Lu
- Department of Plant Biology, University of Maryland, College Park 20742-4450, USA
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Ryu KH, Park WM. The complete nucleotide sequence and genome organization of odontoglossum ringspot tobamovirus RNA. Arch Virol 1995; 140:1577-87. [PMID: 7487489 DOI: 10.1007/bf01322531] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The complete nucleotide sequence of the genomic RNA of odontoglossum ringspot tobamovirus (ORSV) was determined. The RNA genome of ORSV is 6618 nucleotides long and contains five open reading frames (ORFs 1 to 5) coding for proteins of M(r) 126 K, 181 K, 34 K, 18 K and 52 K, respectively. This is the longest RNA of the known viruses of the Tobamovirus genus. The sequences of the ORSV RNA encoded proteins exhibit high homology to the proteins of the members of the Tobamovirus genus. The genomic organization and sequence analysis showed that ORSV is more closely related to tobacco mild green mosaic virus (TMGMV), pepper mild mottle virus (PMMV), tomato mosaic virus (ToMV) and TMV than to cucumber green mottle mosaic virus (CGMMV) and sunn-hemp mosaic virus (SHMV).
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Affiliation(s)
- K H Ryu
- Department of Agricultural Biology, College of Natural Resources, Korea University, Seoul, Korea
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Solis I, Garcia-Arenal F. The complete nucleotide sequence of the genomic RNA of the tobamovirus tobacco mild green mosaic virus. Virology 1990; 177:553-8. [PMID: 2371769 DOI: 10.1016/0042-6822(90)90520-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complete nucleotide sequence of the genomic RNA of the tobamovirus tobacco mild green mosaic virus (TM-GMV) was determined. It shows 64.4% sequence homology with the genomic RNA of tobacco mosaic virus (TMV) and 66.0% with that of tomato mosaic virus (ToMV). Its genomic organization is similar to that of TMV and ToMV. The 5' proximal open reading frame (ORF) encodes a 126K polypeptide and a 183K readthrough product in which nucleotide-binding and polymerase-sequence motifs are found. The third ORF encodes a 28.5K protein homologous to TMV and ToMV movement proteins. A conserved core is found with four other tobamoviruses and two tobraviruses suggesting a common mechanism of cell-to-cell movement for tobamo- and tobraviruses. The fourth ORF encodes the 17.5K coat protein. Homology between the RNAs of TMGMV and its satellite virus STMV is limited to their 3' termini, and structural comparisons suggest that this region may determine the nature of the satellite/helper virus interaction.
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Affiliation(s)
- I Solis
- Departamento de Patología Vegetal, E.T.S.I. Agronómos, Madrid, Spain
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Guilley H, Carrington JC, Balàzs E, Jonard G, Richards K, Morris TJ. Nucleotide sequence and genome organization of carnation mottle virus RNA. Nucleic Acids Res 1985; 13:6663-77. [PMID: 3840587 PMCID: PMC321984 DOI: 10.1093/nar/13.18.6663] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The complete nucleotide sequence of carnation mottle genomic RNA (4003 nucleotides) is presented. The sequence was determined for cloned cDNA copies of viral RNA containing over 99% of the sequence and was completed by direct sequence analysis of RNA and cDNA transcripts. The sequence contains two long open reading frames which together can account for observed translation products. One translation product would arise by suppression of an amber termination codon and the sequence raises the possibility that a second suppression event could also occur. Sequence homology exists between a portion of the carnation mottle virus sequence and that of putative RNA polymerases from other RNA viruses.
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Wilson T. Cotranslational disassembly of tobacco mosaic virus in vitro. Virology 1984; 137:255-65. [DOI: 10.1016/0042-6822(84)90217-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/1984] [Accepted: 05/30/1984] [Indexed: 11/29/2022]
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Palukaitis P, García-Arenal F, Sulzinski MA, Zaitlin M. Replication of tobacco mosaic virus VII. Further characterization of single- and double-stranded virus-related RNAs from TMV-infected plants. Virology 1983; 131:533-45. [DOI: 10.1016/0042-6822(83)90518-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/1983] [Accepted: 09/13/1983] [Indexed: 11/29/2022]
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Wilson TM, Glover JF. The origin of multiple polypeptides of molecular weight below 110 000 encoded by tobacco mosaic virus RNA in the messenger-dependent rabbit reticulocyte lysate. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 739:35-41. [PMID: 6830802 DOI: 10.1016/0167-4781(83)90041-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Multiple polypeptides encoded by tobacco mosaic virus (TMV) RNA in the messenger-dependent rabbit reticulocyte lysate are not attributable to contaminating 3'-coterminal RNA fragments, multiple leaky termination codons or endonuclease activity opening-up legitimate or spurious internal initiation sites. Quantitative analysis of polypeptides encoded over a range of added RNA concentrations from 0.09 microgram X ml-1 to 180 micrograms X ml-1 compared with those synthesized in response to size-fractionated RNAs from a crude virus preparation, or with RNA extracted from the alkali-stable fraction of TMV suggest that apart from four legitimate virus-coded products of apparent Mr approx. 165 000, 110 000, 30 000 and 17 500 all other polypeptides arise from the overlapping 5'-proximal cistrons either by (i) site-selective endonucleolytic cleavage, (ii) sense codon misreading, or (iii) specific regions of secondary structure on TMV RNA which impede ribosome translocation.
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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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Abouhaidar MG, Bancroft J. The polarity of assembly of papaya mosaic virus and tobacco mosaic virus RNAs with PMV-protein under conditions of nonspecificity. Virology 1980; 107:202-7. [DOI: 10.1016/0042-6822(80)90285-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/1980] [Indexed: 10/26/2022]
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Kukla BA, Guilley HA, Jonard GX, Richards KE, Mundry KW. Characterization of long guanosine-free RNA sequences from the Dahlemense and U2 strains of tobacco mosaic virus. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 98:61-6. [PMID: 111935 DOI: 10.1111/j.1432-1033.1979.tb13160.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Four naturally occurring strains of tobacco mosaic virus, U2, Dahlemense, CV4, and the bean form of tobacco mosaic virus, were tested for the existence of long T1 RNAase oligonucleotides analogous to the oligonucleotide omega found in the common or U1 strain of tobacco mosaic virus and which makes up the 5' non-coding region of the RNA molecule. U2 and Dahlemense RNA were each found to contain this type of long T1 RNAase oligonucleotide with chain lengths of 54 and 74--77 residues, respectively. The sequence of the two oligonucleotides was determined mostly by using 5'-32P-labelled material in vitro and rapid polyacrylamide gel sequencing techniques.
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Leung DW, Browning KS, Heckman JE, RajBhandary UL, Clark JM. Nucleotide sequence of the 5' terminus of satellite tobacco necrosis virus ribonucleic acid. Biochemistry 1979; 18:1361-6. [PMID: 427118 DOI: 10.1021/bi00574a036] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Treatment of the RNA of satellite tobacco necrosis virus (STNV) with phosphomonoesterase followed by heat denaturation and treatment with polynucleotide kinase in the presence of [gamma-32P]ATP yields a STNV [5'-32P]RNA containing a homogeneous 5' terminus. Analyses of this STNV [5'-32P]RNA yield the sequence of the first 42 nucleotides from the 5'terminus of STNV RNA. This nucleotide sequence contains the translation initiation AUG codon starting at position 30 from the 5' terminus as indicated by match of subsequent nucleotides with the genetic code assignments for the N-terminal amino acids of STNV coat protein in the 5'-terminal sequence ppAGUAAAGACAGGAAACUU-UACUGACUAACAUGGCAAAACAAC. An interesting feature of this sequence is its potential to form a hairpin loop structure involving perfect Watson-Crick base pairing between the first seven nucleotides and nucleotides at positions 16--22.
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Hidaka S, Shimotohno K, Miura K, Takanami Y, Kubo S. Nucleotide sequence near the 5'-terminal of cucumber mosaic virus RNA No. 5 segment. FEBS Lett 1979; 98:115-8. [PMID: 428526 DOI: 10.1016/0014-5793(79)80165-9] [Citation(s) in RCA: 6] [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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Intermediates in the disassembly of tobacco mosaic virus at alkaline pH Infectivity, self-assembly, and translational activities. Virology 1978; 89:475-83. [DOI: 10.1016/0042-6822(78)90189-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/1978] [Indexed: 11/22/2022]
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Richards K, Jonard G, Jacquemond M, Lot H. Nucleotide sequence of cucumber mosaic virus-associated RNA 5. Virology 1978; 89:395-408. [DOI: 10.1016/0042-6822(78)90182-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/1978] [Indexed: 10/26/2022]
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Jonard G, Richards K, Mohier E, Gerlinger P. Nucleotide sequence at the 5' extremity of tobacco-mosaic-virus RNA. 2. The coding region (nucleotides 69-236). EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 84:521-31. [PMID: 639801 DOI: 10.1111/j.1432-1033.1978.tb12195.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the preceding paper it was shown that the first A-U-G codon in tobacco mosaic virus RNA is separated from the 5' terminus by a sequence of 68 nucleotides devoid of internal guanosine residues. In this paper we present the sequence of 165 residues immediately following the first potential initiation codon. The characterized sequence contains four nonsense codons but none are in phase with the prospective initiation codon. Several lines of evidence, including direct characterization of the portion of the RNA molecule which binds to and is protected by the ribosome in the course of initiation, all support the idea that the A-U-G at position 69-71 is a functional initiation signal for viral protein synthesis.
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Richards K, Guilley H, Jonard G, Hirth L. Nucleotide sequence at the 5' extremity of tobacco-mosaic-virus RNA. 1. The noncoding region (nucleotides 1-68). EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 84:513-9. [PMID: 639800 DOI: 10.1111/j.1432-1033.1978.tb12194.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The sequence of the 5' noncoding region of tobacco mosaic virus RNA has been determined. The noncoding region is 68 nucleotides long and is unusual in that it contains no internal guanosine residues. The long T1 oligonucleotide containing the guanosine-free tract was isolated from a T1 ribonuclease digest of tobacco mosaic virus RNA and sequenced by labelling techniques in vitro using polynucleotide kinase. The guanosine-free tract is terminated by the first potential initiation codon in the RNA molecule and several lines of evidence suggest that this AUG triplet is operational in initiating viral protein synthesis (see following paper). The 5'-noncoding region cannot base-pair extensively with the 3'-terminal sequence of 18-S ribosomal RNA from rabbit reticulocytes.
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