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Moradi Z, Maghdoori H, Nazifi E, Mehrvar M. Complete Genomic Characterization of Two Beet Soil-Borne Virus Isolates from Turkey: Implications of Comparative Analysis of Genome Sequences. THE PLANT PATHOLOGY JOURNAL 2021; 37:152-161. [PMID: 33866757 PMCID: PMC8053846 DOI: 10.5423/ppj.oa.12.2020.0223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Sugar beet (Beta vulgaris L.) is known as a key product for agriculture in several countries across the world. Beet soil-borne virus (BSBV) triggers substantial economic damages to sugar beet by reducing the quantity of the yield and quality of the beet sugars. We conducted the present study to report the complete genome sequences of two BSBV isolates in Turkey for the first time. The genome organization was identical to those previously established BSBV isolates. The tripartite genome of BSBV-TR1 and -TR3 comprised a 5,835-nucleotide (nt) RNA1, a 3,454-nt RNA2, and a 3,005-nt RNA3 segment. According to sequence identity analyses, Turkish isolates were most closely related to the BSBV isolate reported from Iran (97.83-98.77% nt identity). The BSBV isolates worldwide (n = 9) were phylogenetically classified into five (RNA-coat protein read through gene [CPRT], TGB1, and TGB2 segments), four (RNA-rep), or three (TGB3) lineages. In genetic analysis, the TGB3 revealed more genetic variability (Pi = 0.034) compared with other regions. Population selection analysis revealed that most of the codons were generally under negative selection or neutral evolution in the BSBV isolates studied. However, positive selection was detected at codon 135 in the TGB1, which could be an adaptation in order to facilitate the movement and overcome the host plant resistance genes. We expect that the information on genome properties and genetic variability of BSBV, particularly in TGB3, TGB1, and CPRT genes, assist in developing effective control measures in order to prevent severe losses and make amendments in management strategies.
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Affiliation(s)
- Zohreh Moradi
- Department of Plant Pathology, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University, P.O. Box 578, Sari,
Iran
| | - Hossein Maghdoori
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, P.O. Box 91779-1163, Mashhad,
Iran
| | - Ehsan Nazifi
- Department of Biology, Faculty of Basic Sciences, University of Mazandaran, P.O. Box 47416-95447, Babolsar,
Iran
| | - Mohsen Mehrvar
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, P.O. Box 91779-1163, Mashhad,
Iran
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Bernet GP, Elena SF. Distribution of mutational fitness effects and of epistasis in the 5' untranslated region of a plant RNA virus. BMC Evol Biol 2015; 15:274. [PMID: 26643527 PMCID: PMC4672503 DOI: 10.1186/s12862-015-0555-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the causes and consequences of phenotypic variability is a central topic of evolutionary biology. Mutations within non-coding cis-regulatory regions are thought to be of major effect since they affect the expression of downstream genes. To address the evolutionary potential of mutations affecting such regions in RNA viruses, we explored the fitness properties of mutations affecting the 5'-untranslated region (UTR) of a prototypical member of the picorna-like superfamily, Tobacco etch virus (TEV). This 5' UTR acts as an internal ribosomal entry site (IRES) and is essential for expression of all viral genes. RESULTS We determined in vitro the folding of 5' UTR using the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) technique. Then, we created a collection of single-nucleotide substitutions on this region and evaluated the statistical properties of their fitness effects in vivo. We found that, compared to random mutations affecting coding sequences, mutations at the 5' UTR were of weaker effect. We also created double mutants by combining pairs of these single mutations and found variation in the magnitude and sign of epistatic interactions, with an enrichment of cases of positive epistasis. A correlation exists between the magnitude of fitness effects and the size of the perturbation made in the RNA folding structure, suggesting that the larger the departure from the predicted fold, the more negative impact in viral fitness. CONCLUSIONS Evidence that mutational fitness effects on the short 5' UTR regulatory sequence of TEV are weaker than those affecting its coding sequences have been found. Epistasis among pairs of mutations on the 5' UTR ranged between the extreme cases of synthetic lethal and compensatory. A plausible hypothesis to explain all these observations is that the interaction between the 5' UTR and the host translational machinery was shaped by natural selection to be robust to mutations, thus ensuring the homeostatic expression of viral genes even at high mutation rates.
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Affiliation(s)
- Guillermo P Bernet
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain.
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain.
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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Elbeaino T, Digiaro M, Martelli GP. Complete sequence of Fig fleck-associated virus, a novel member of the family Tymoviridae. Virus Res 2011; 161:198-202. [PMID: 21840352 DOI: 10.1016/j.virusres.2011.07.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/19/2022]
Abstract
The complete nucleotide sequence and the genome organization were determined of a novel virus, tentatively named Fig fleck-associated virus (FFkaV). The viral genome is a positive-sense, single-stranded RNA 7046 nucleotides in size excluding the 3'-terminal poly(A) tract, and comprising two open reading frames. ORF1 encodes a polypeptide of 2161 amino acids (p240), which contains the signatures of replication-associated proteins and the coat protein cistron (p24) at its 3' end. ORF2 codes for a 461 amino acid protein (p50) identified as a putative movement proteins (MP). In phylogenetic trees constructed with sequences of the putative polymerase and CP proteins FFkaV consistently groups with members of the genus Maculavirus, family Tymoviridae. However, the genome organization diverges from that of the two completely sequenced maculaviruses, Grapevine fleck virus (GFkV) and Bombix mori Macula-like virus (BmMLV), as it exhibits a structure resembling that of Maize rayado fino virus (MRFV), the type species of the genus Marafivirus and of Olive latent virus 3 (OLV-3), an unclassified virus in the family Tymoviridae. FFkaV was found in field-grown figs from six Mediterranean countries with an incidence ranging from 15% to 25%.
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Affiliation(s)
- Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Via Ceglie 9, 70010 Valenzano, Bari, Italy
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4
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Loew R, Heinz N, Hampf M, Bujard H, Gossen M. Improved Tet-responsive promoters with minimized background expression. BMC Biotechnol 2010; 10:81. [PMID: 21106052 PMCID: PMC3002914 DOI: 10.1186/1472-6750-10-81] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 11/24/2010] [Indexed: 11/10/2022] Open
Abstract
Background The performance of the tetracycline controlled transcriptional activation system (Tet system) depends critically on the choice of minimal promoters. They are indispensable to warrant low expression levels with the system turned "off". On the other hand, they must support high level of gene expression in the "on"-state. Results In this study, we systematically modified the widely used Cytomegalovirus (CMV) minimal promoter to further minimize background expression, resulting in an improved dynamic expression range. Using both plasmid-based and retroviral gene delivery, our analysis revealed that especially background expression levels could be significantly reduced when compared to previously established "standard" promoter designs. Our results also demonstrate the possibility to fine-tune expression levels in non-clonal cell populations. They also imply differences regarding the requirements for tight regulation and high level induction between transient and stable gene transfer systems. Conclusions Until now, our understanding of mammalian transcriptional regulation including promoter architecture is limited. Nevertheless, the partly empirical modification of cis-elements as shown in this study can lead to the specific improvement of the performance of minimal promoters. The novel composite Ptet promoters introduced here will further expand the utility of the Tet system.
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Oh DH, Dassanayake M, Haas JS, Kropornika A, Wright C, d'Urzo MP, Hong H, Ali S, Hernandez A, Lambert GM, Inan G, Galbraith DW, Bressan RA, Yun DJ, Zhu JK, Cheeseman JM, Bohnert HJ. Genome structures and halophyte-specific gene expression of the extremophile Thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis. PLANT PHYSIOLOGY 2010; 154:1040-52. [PMID: 20833729 PMCID: PMC2971586 DOI: 10.1104/pp.110.163923] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The genome of Thellungiella parvula, a halophytic relative of Arabidopsis (Arabidopsis thaliana), is being assembled using Roche-454 sequencing. Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. T. parvula genome structure and DNA sequences were compared with orthologous regions from Arabidopsis and publicly available bacterial artificial chromosome sequences from Thellungiella salsuginea (previously Thellungiella halophila). The three-way comparison of sequences, from one abiotic stress-sensitive species and two tolerant species, revealed extensive sequence conservation and microcolinearity, but grouping Thellungiella species separately from Arabidopsis. However, the T. parvula segments are distinguished from their T. salsuginea counterparts by a pronounced paucity of repeat sequences, resulting in a 30% shorter DNA segment with essentially the same gene content in T. parvula. Among the genes is SALT OVERLY SENSITIVE1 (SOS1), a sodium/proton antiporter, which represents an essential component of plant salinity stress tolerance. Although the SOS1 coding region is highly conserved among all three species, the promoter regions show conservation only between the two Thellungiella species. Comparative transcript analyses revealed higher levels of basal as well as salt-induced SOS1 expression in both Thellungiella species as compared with Arabidopsis. The Thellungiella species and other halophytes share conserved pyrimidine-rich 5' untranslated region proximal regions of SOS1 that are missing in Arabidopsis. Completion of the genome structure of T. parvula is expected to highlight distinctive genetic elements underlying the extremophile lifestyle of this species.
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Affiliation(s)
- Dong-Ha Oh
- Department of Plant Biology , University of Illinois, Urbana, Illinois 61801, USA.
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6
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Shin HI, Kim HY, Cho TJ. The Pro/Hel region is indispensable for packaging non-replicating turnip yellow mosaic virus RNA, but not replicating viral RNA. Mol Cells 2010; 29:463-9. [PMID: 20396967 DOI: 10.1007/s10059-010-0057-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022] Open
Abstract
Turnip yellow mosaic virus (TYMV) is a spherical plant virus that has a single 6.3 kb positive strand RNA. The genomic RNA has a tRNA-like structure (TLS) at the 3'-end. The 3'-TLS and hairpins in the 5'-untranslated region supposedly serve as packaging signals; however, recent studies have shown that they do not play a role in TYMV RNA packaging. In this study, we focused on packaging signals by examining a series of deletion mutants of TYMV. Analysis of encapsidated viral RNA after agroinfiltration of the deletion constructs into Nicotiana benthamiana showed that the mutant RNA lacking the protease (Pro)/helicase (Hel) region was not encapsidated by the coat proteins provided in trans, implicating that a packaging signal lies in the Pro/Hel region. Examination of two Pro(-)Hel(-) mutants showed that protein activity from the Pro/Hel domains was dispensable for the packaging of the non-replicating TYMV RNA. In contrast, the mutant TYMV RNA lacking the Pro/Hel region was efficiently encapsidated when the mutant TYMV was co-introduced with a wild-type TYMV, suggesting that packaging mechanisms might differ depending on whether the virus is replicating or not.
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Affiliation(s)
- Hyun-Il Shin
- Department of Biochemistry, Chungbuk National University, Cheongju, 361-763, Korea
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Genomic and biological characterization of chiltepín yellow mosaic virus, a new tymovirus infecting Capsicum annuum var. aviculare in Mexico. Arch Virol 2010; 155:675-84. [PMID: 20229325 DOI: 10.1007/s00705-010-0639-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2009] [Accepted: 02/24/2010] [Indexed: 01/20/2023]
Abstract
The characterization of viruses infecting wild plants is a key step towards understanding the ecology of plant viruses. In this work, the complete genomic nucleotide sequence of a new tymovirus species infecting chiltepin, the wild ancestor of Capsicum annuum pepper crops, in Mexico was determined, and its host range has been explored. The genome of 6,517 nucleotides has the three open reading frames described for tymoviruses, putatively encoding an RNA-dependent RNA polymerase, a movement protein and a coat protein. The 5' and 3' untranslated regions have structures with typical signatures of the tymoviruses. Phylogenetic analyses revealed that this new virus is closely related to the other tymoviruses isolated from solanaceous plants. Its host range is mainly limited to solanaceous species, which notably include cultivated Capsicum species. In the latter, infection resulted in a severe reduction of growth, indicating the potential of this virus to be a significant crop pathogen. The name of chiltepin yellow mosaic virus (ChiYMV) is proposed for this new tymovirus.
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Chen SC, Desprez A, Olsthoorn RCL. Structural homology between bamboo mosaic virus and its satellite RNAs in the 5'untranslated region. J Gen Virol 2009; 91:782-7. [PMID: 19906937 DOI: 10.1099/vir.0.015941-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A structural element was identified in the 5'-proximal sequence of the bamboo mosaic virus (BaMV) RNA. Mutational analysis of the hairpin showed that disruptions of the secondary structure or substitutions of the loop sequences resulted in reduced accumulation of BaMV genomic RNA. Phylogenetic analysis further suggested the presence of structural homologues of this hairpin in all other potexviruses. In addition, remarkable structural homology was discovered between the BaMV hairpin and a stem-loop in the 5'untranslated region of satellite RNAs responsible for attenuation of BaMV in co-infected plants. The role of this homology in the helper-satellite interaction is discussed.
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Affiliation(s)
- Shih-Cheng Chen
- Leiden Institute of Chemistry, Department of Molecular Genetics, 2300 RA Leiden, The Netherlands
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9
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Tzanetakis IE, Tsai CH, Martin RR, Dreher TW. A tymovirus with an atypical 3'-UTR illuminates the possibilities for 3'-UTR evolution. Virology 2009; 392:238-45. [PMID: 19664793 DOI: 10.1016/j.virol.2009.06.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 06/19/2009] [Accepted: 06/24/2009] [Indexed: 02/02/2023]
Abstract
We report the complete genome sequence of Dulcamara mottle virus (DuMV), confirming its membership within the Tymovirus genus, which was previously based on physical and pathology evidence. The 5'-untranslated region (UTR) and coding region of DuMV RNA have the typical characteristics of tymoviral RNAs. In contrast, the 3'-UTR is the longest and most unusual yet reported for a tymovirus, possessing an internal poly(A) tract, lacking a 3'-tRNA-like structure (TLS) and terminating at the 3'-end with -UUC instead of the typical -CC(A). An expressible cDNA clone was constructed and shown to be capable of producing infectious DuMV genomic RNAs with -UUC 3'-termini. A chimeric Turnip yellow mosaic virus (TYMV) genome bearing the DuMV 3'-UTR in place of the normal TLS was constructed in order to investigate the ability of the TYMV replication proteins to amplify RNAs with -UUC instead of -CC(A) 3'-termini. The chimeric genome was shown to be capable of replication and systemic spread in plants, although amplification was very limited. These experiments suggest the way in which DuMV may have evolved from a typical tymovirus, and illuminate the ways in which viral 3'-UTRs in general can evolve.
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Shin HI, Tzanetakis IE, Dreher TW, Cho TJ. The 5′-UTR of Turnip yellow mosaic virus does not include a critical encapsidation signal. Virology 2009; 387:427-35. [DOI: 10.1016/j.virol.2009.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 01/19/2009] [Accepted: 02/04/2009] [Indexed: 10/21/2022]
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11
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Mielke N, Muehlbach HP. A novel, multipartite, negative-strand RNA virus is associated with the ringspot disease of European mountain ash (Sorbus aucuparia L.). J Gen Virol 2007; 88:1337-1346. [PMID: 17374780 DOI: 10.1099/vir.0.82715-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Four RNAs from a new plant-pathogenic virus, which we have tentatively named European mountain ash ringspot-associated virus (EMARAV), were identified and sequenced completely. All four viral RNAs could be detected in previous double-stranded RNA preparations. RNA 1 (7040 nt) encodes a protein with similarity to the RNA-dependent RNA polymerase of different members of the Bunyaviridae, a family containing five genera with viruses infecting invertebrates, vertebrates and plants. RNA 2 (2335 nt) encodes a 75 kDa protein containing a conserved motif of the glycoprotein precursor of the genus Phlebovirus. Immunological detection indicated the presence of proteins with the expected size of the precursor and one of its processing products. The amino acid sequence of protein p3 (35 kDa) encoded by RNA 3 shows similarities to a putative nucleocapsid protein of two still unclassified plant viruses. The fourth viral RNA encodes a 27 kDa protein that has no significant homology to any known protein. As is typical for members of the family Bunyaviridae, the 5′ and 3′ ends of all viral RNAs are complementary, which allows the RNA to form a panhandle structure. Comparison of these sequences demonstrates a conserved terminal part of 13 nt, similar to that of the bunyaviral genus Orthobunyavirus. Despite the high agreement of the EMARAV genome with several characteristics of the family Bunyaviridae, there are a few features that make it difficult to allocate the virus to this group. It is therefore more likely that this plant pathogen belongs to a novel virus genus.
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Affiliation(s)
- Nicole Mielke
- University of Hamburg, Biocentre Klein Flottbek, Department of Molecular Phytopathology and Genetics, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Hans-Peter Muehlbach
- University of Hamburg, Biocentre Klein Flottbek, Department of Molecular Phytopathology and Genetics, Ohnhorststrasse 18, 22609 Hamburg, Germany
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Komatsu K, Kagiwada S, Takahashi S, Mori T, Yamaji Y, Hirata H, Ozeki J, Yoshida A, Suzuki M, Ugaki M, Namba S. Phylogenetic characteristics, genomic heterogeneity and symptomatic variation of five closely related Japanese strains of Potato virus X. Virus Genes 2005; 31:99-105. [PMID: 15965614 DOI: 10.1007/s11262-005-2205-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 12/28/2004] [Accepted: 02/17/2005] [Indexed: 11/24/2022]
Abstract
To elucidate the genomic determinants of Potato virus X (PVX) strains, which cause diverse responses in host plants, we determined the complete genomic RNA sequences of four Japanese PVX strains: PVX-BS, -BH, -OG, and -TO. These four strains, plus the previously sequenced PVX-OS strain, differ in their pathogenicity in wild potato (Solanum demissum) and tobacco (Nicotiana tabacum cv. Samsun NN). The genomic sequences of these five PVX strains were highly homologous (i.e., the nucleotide sequence identity ranged from 95.4 to 98.5%). Phylogenetic analysis indicated that the Japanese PVX strains originated from an ancestral PVX strain in the European group, and that the virulence of these strains in both S. demissum and tobacco is not correlated with their phylogenetic relationships, suggesting that the pathogenicity of each strain in these host plants is determined by a relatively small number of nucleotides and can easily be altered independent of phylogenetic relationships. Particularly, OS, BH, and BS, which respectively produce markedly contrasting ringspot, mosaic, and asymptomatic infections in tobacco leaves, were the most closely related, suggesting that these three strains are an attractive model for analyzing the genetic determinants causing these symptoms. A possible correlation between the genomic and biological differences of these strains is discussed.
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Affiliation(s)
- Ken Komatsu
- Laboratory of Bioresource Technology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba, Kashiwa, 277-8562, Japan
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Koenig R, Barends S, Gultyaev AP, Lesemann DE, Vetten HJ, Loss S, Pleij CWA. Nemesia ring necrosis virus: a new tymovirus with a genomic RNA having a histidylatable tobamovirus-like 3′ end. J Gen Virol 2005; 86:1827-1833. [PMID: 15914862 DOI: 10.1099/vir.0.80916-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete nucleotide sequence of the genomic RNA of the new virus Nemesia ring necrosis virus (NeRNV), which is widespread in various ornamental plant species belonging to the Scrophulariaceae and Verbenaceae, has been determined. Based on its gene content, the folding properties of its 5′-untranslated region and in vitro translation experiments, NeRNV RNA is a typical tymovirus RNA. Its 3′ end, however, differs greatly from those of the valine-specific tymoviral RNAs that have been analysed previously. It can be folded into an upstream pseudoknot domain and a histidine-specific tRNA-like structure, a combination that, so far, has been found only in tobamoviral RNAs. The identity elements found in NeRNV RNA for recognition by yeast histidyl-tRNA synthetase are more similar to those of yeast tRNAHis than the ones found in tobacco mosaic virus RNA. As a result NeRNV RNA can be charged with histidine even more efficiently than tobacco mosaic virus RNA.
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Affiliation(s)
- R Koenig
- Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und biologische Sicherheit, Messeweg 11, D-38104 Braunschweig, Germany
| | - S Barends
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - A P Gultyaev
- Leiden Institute of Biology, Leiden University, Kaiserstraat 63, 2311 GP Leiden, The Netherlands
| | - D-E Lesemann
- Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und biologische Sicherheit, Messeweg 11, D-38104 Braunschweig, Germany
| | - H J Vetten
- Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und biologische Sicherheit, Messeweg 11, D-38104 Braunschweig, Germany
| | - S Loss
- Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und biologische Sicherheit, Messeweg 11, D-38104 Braunschweig, Germany
| | - C W A Pleij
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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Koenig R, Pleij CWA, Lesemann DE, Loss S, Vetten HJ. Molecular characterization of isolates of anagyris vein yellowing virus, plantago mottle virus and scrophularia mottle virus – comparison of various approaches for tymovirus classification. Arch Virol 2005; 150:2325-38. [PMID: 15883655 DOI: 10.1007/s00705-005-0545-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Accepted: 03/08/2005] [Indexed: 11/30/2022]
Abstract
The complete nucleotide sequences were determined for the genomic RNAs of three tymoviruses, i.e. isolates of anagyris vein yellowing virus (AVYV), plantago mottle virus (PlMoV) and scrophularia mottle virus (SrMV) which are all serologically closely related to ononis yellow mosaic virus (ibid) and to Nemesia ring necrosis virus (NeRNV), a recently described recombinant virus which is widely spread in commercially grown ornamental plant species belonging to the Scrophulariaceae. Total nucleotide and coat protein amino acid sequence identities revealed similar groupings in the genus tymovirus as serological studies did. The latter, however, tended to suggest much closer relationships than the molecular data and may fail to recognise the distinctiveness of new tymovirus species. The usefulness of various species demarcation criteria for the classification of tymoviruses is discussed.
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Affiliation(s)
- R Koenig
- Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und Biologische Sicherheit, Braunschweig, Germany.
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15
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Matsuda D, Bauer L, Tinnesand K, Dreher TW. Expression of the two nested overlapping reading frames of turnip yellow mosaic virus RNA is enhanced by a 5' cap and by 5' and 3' viral sequences. J Virol 2004; 78:9325-35. [PMID: 15308727 PMCID: PMC506944 DOI: 10.1128/jvi.78.17.9325-9335.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The translation efficiency of an mRNA molecule is typically determined by its 5'- and/or 3'-untranslated regions (UTRs). Previously, we have found that the 3'-UTR of Turnip yellow mosaic virus (TYMV) RNA enhances translation synergistically with a 5' cap. Here, we use a luciferase reporter system in cowpea protoplasts to show that the 5' 217 nucleotides from TYMV genomic RNA enhance expression relative to a vector-derived 17-nucleotide 5'-UTR. Maximum expression was observed from RNAs with a cap and both 5' and 3' TYMV sequences. In paired reporter constructs, the 5' 217 nucleotides harboring the UTR and the first 43 or 41 codons of the two overlapping TYMV open reading frames (ORFs), ORF-69 and ORF-206, respectively, were fused in frame with the luciferase gene. This allowed expression from the initiation codon of each ORF (AUG69 and AUG206) to be monitored separately but from the normal sequence environment. Expression from both AUG codons was heavily dependent on a 5' cap, with a threefold-higher expression occurring from AUG69 than from AUG206 in the presence of the genomic 3'-UTR. Changes that interrupted the cap/3'-UTR synergy (i.e., removal of the cap or TYMV 3'-UTR) resulted in a higher proportion of initiation from AUG206. Mutation of the 3'-UTR to prevent aminoacylation, as well as deletion of 75% of the 5'-UTR, likewise resulted in a lower ratio of expression from AUG69 relative to AUG206. Mutation of each AUG initiation codon increased initiation from the other. Taken together, these results do not fully conform to the expectations of standard leaky ribosomal scanning and leave open the precise mechanism of ribosome commitment to AUG69 and AUG206. However, our observations do not support a recent proposal based on in vitro studies in which the 3'-UTR is proposed to direct cap-independent initiation specifically at AUG206 and not at AUG69 (S. Barends et al., Cell 112:123-129, 2003).
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Affiliation(s)
- Daiki Matsuda
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
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Dreher TW. Turnip yellow mosaic virus: transfer RNA mimicry, chloroplasts and a C-rich genome. MOLECULAR PLANT PATHOLOGY 2004; 5:367-75. [PMID: 20565613 DOI: 10.1111/j.1364-3703.2004.00236.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
SUMMARY Taxonomy: Turnip yellow mosaic virus (TYMV) is the type species of the genus Tymovirus, family Tymoviridae. TYMV is a positive strand RNA virus of the alphavirus-like supergroup. Physical properties: Virions are non-enveloped 28-nm T = 3 icosahedrons composed of a single 20-kDa coat protein that is clustered in 20 hexameric and 12 pentameric subunits. Infectious particles and empty capsids coexist in infected tissue. The genomic RNA is 6.3 kb long, with a 5'(m7)GpppG cap and a 3' untranslated region ending in a tRNA-like structure to which valine can be covalently added. The genome has a distinctive skewed C-rich, G-poor composition (39% C, 17% G). Viral proteins: Two proteins, whose open reading frames extensively overlap, are translated from the genomic RNA. p206, which contains sequences indicative of RNA capping, NTPase/helicase and polymerase activities, is the only viral protein that is necessary for genome replication in single cells. It is produced as a polyprotein and self-cleaved to yield 141- and 66-kDa proteins. p69 is required for virus movement within the plant and is also a suppressor of gene silencing. The coat protein is expressed from the single subgenomic RNA. Hosts and symptoms: TYMV has a narrow host range almost completely restricted to the Cruciferae. Experimental host species are Brassica pekinensis (Chinese cabbage) or B. rapa (turnip), in which diffuse chlorotic local lesions and systemic yellow mosaic symptoms appear. Arabidopsis thaliana can also be used. Clumping of chloroplasts and the accumulation of vesicular invaginations of the chloroplast outer membranes are distinctive cytopathological symptoms. High yields of virus are produced in all leaf tissues, and the virus is readily transmissible by mechanical inoculation. Localized transmission by flea beetles may occur in the field.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology and Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
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van Roon AMM, Bink HHJ, Plaisier JR, Pleij CWA, Abrahams JP, Pannu NS. Crystal Structure of an Empty Capsid of Turnip Yellow Mosaic Virus. J Mol Biol 2004; 341:1205-14. [PMID: 15321716 DOI: 10.1016/j.jmb.2004.06.085] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 06/24/2004] [Accepted: 06/30/2004] [Indexed: 11/26/2022]
Abstract
Empty capsids (artificial top component) of turnip yellow mosaic virus were co-crystallized with an encapsidation initiator RNA hairpin. No clear density was observed for the RNA, but there were clear differences in the conformation of a loop of the coat protein at the opening of the pentameric capsomer (formed by five A-subunits) protruding from the capsid, compared to the corresponding loop in the intact virus. Further differences were found at the N terminus of the A-subunit. These differences have implications for the mechanism of decapsidation of the virus, required for infection.
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Affiliation(s)
- Anne-Marie M van Roon
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Bink HHJ, Roepan SK, Pleij CWA. Two histidines of the coat protein of turnip yellow mosaic virus at the capsid interior are crucial for viability. Proteins 2004; 55:236-44. [PMID: 15048817 DOI: 10.1002/prot.10600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
RNA-coat protein interactions in turnip yellow mosaic virus (TYMV) have been shown to involve low pK proton-donating groups. Two different types of interaction have been proposed. In the so-called type I interaction, protonated C-residues interact with acidic amino acids at low pH, thereby providing a rationale for the high C-content (38%) of the genomic RNA. The type II interaction involves charged histidines interacting with phosphates of the RNA backbone. Site-directed mutagenesis of the TYMV coat protein and subsequent in vivo analysis were performed to distinguish between these two types of RNA-protein interaction. The results reveal a prominent role for the histidines H68 and H180, since mutation to an alanine residue inhibits symptom development on secondary leaves, indicating that spreading of the virus in the plant is blocked. Viral RNA and coat protein synthesis are not altered, showing that these two histidines may play a role in the process of RNA encapsidation. Overexpression of the TYMV coat protein in Escherichia coli leads to the formation of bona fide capsids, showing that the two histidines are not critical in capsid assembly. Mutagenesis of the acidic amino acids D11, E135, and D143 to alanine apparently did not interfere with virus viability. The functional role of the histidines during the infection cycle is discussed in terms of the structure of the coat protein, both at the level of amino acid sequence conservation among the members of the Tymoviridae family and as the three-dimensional structure of the coat protein.
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Affiliation(s)
- Hugo H J Bink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands
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Gowda S, Satyanarayana T, Ayllón MA, Moreno P, Flores R, Dawson WO. The conserved structures of the 5' nontranslated region of Citrus tristeza virus are involved in replication and virion assembly. Virology 2003; 317:50-64. [PMID: 14675624 DOI: 10.1016/j.virol.2003.08.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The genomic RNA of different isolates of Citrus tristeza virus (CTV) reveals an unusual pattern of sequence diversity: the 3' halves are highly conserved (homology >90%), while the 5' halves show much more dissimilarity, with the 5' nontranslated region (NTR) containing the highest diversity (homology as low as 42%). Yet, positive-sense sequences of the 5' NTR were predicted to fold into nearly identical structures consisting of two stem-loops (SL1 and SL2) separated by a short spacer region. The predicted most stable secondary structures of the negative-sense sequences were more variable. We introduced mutations into the 5' NTR of a CTV replicon to alter the sequence and/or the predicted secondary structures with or without additional compensatory changes designed to restore predicted secondary structures, and examined their effect on replication in transfected protoplasts. The results suggested that the predicted secondary structures of the 5' NTR were more important for replication than the primary structure. Most mutations that were predicted to disrupt the secondary structures fail to replicate, while compensatory mutations were allowed replication to resume. The 5' NTR mutations that were tolerated by the CTV replicon were examined in the full-length virus for effects on replication and production of the multiple subgenomic RNAs. Additionally, the ability of these mutants to produce virions was monitored by electron microscopy and by passaging the progeny nucleocapsids to another batch of protoplasts. Some of the mutants with compensatory sequence alterations predicted to rebuild similar secondary structures allowed replication at near wild-type levels but failed to passage, suggesting that the 5' NTR contains sequences required for both replication and virion assembly.
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Affiliation(s)
- Siddarame Gowda
- Department of Plant Pathology, University of Florida, Citrus Research and Education Center, Lake Alfred, FL 33850, USA
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Bink HHJ, Schirawski J, Haenni AL, Pleij CWA. The 5'-proximal hairpin of turnip yellow mosaic virus RNA: its role in translation and encapsidation. J Virol 2003; 77:7452-8. [PMID: 12805444 PMCID: PMC164824 DOI: 10.1128/jvi.77.13.7452-7458.2003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RNA genome of turnip yellow mosaic virus (TYMV) consists of more than 6,000 nucleotides. During a study of the roles of the two hairpins located in its 90-nucleotide 5' untranslated region, it was observed that stabilization of the 5'-proximal hairpin leads to a delay in the development of symptoms on plants. This delay in symptom development for both locally and systemically infected leaves was found to be dependent on a change in the free energy of the hairpin caused by introduced mutations. A protoplast transfection assay revealed that the accumulation of plus-strand full-length RNA and subgenomic RNA, as well as protein expression levels, was affected by hairpin stability. Stabilization of this hairpin inhibited translation. A model is proposed in which a destabilized 5'-proximal hairpin allows maximal translation of the viral proteins. It is suggested that this hairpin may exist in close proximity to the 5' cap as long as its stability is low enough to enable translation. However, at an acidic pH, the hairpin structure becomes more stable and is functionally transformed into the initiation signal for viral packaging. Slightly acidic conditions can be found in chloroplasts, where TYMV assembly is driven by a low pH generated by active photosynthesis.
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Affiliation(s)
- Hugo H J Bink
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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Bink HHJ, Hellendoorn K, van der Meulen J, Pleij CWA. Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA. Proc Natl Acad Sci U S A 2002; 99:13465-70. [PMID: 12361978 PMCID: PMC129696 DOI: 10.1073/pnas.202287499] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 5' UTR of turnip yellow mosaic virus RNA contains two conserved hairpins with internal loops consisting of C.C and C.A mismatches. In this article, evidence is presented indicating that the 5' proximal hairpin functions as an encapsidation initiation signal. Extensive mutagenesis studies on this hairpin and sequencing of virus progeny showed a clear preference for C.C and C.A mismatches within the internal loop. The importance of these mismatches lies in their pH-dependent protonation and stable base pair formation. Encapsidation efficiency was found to be severely affected for several mutants lacking the protonatable mismatches in the internal loop of the 5' proximal hairpin. Furthermore, gel mobility-shift assays were performed with various RNA hairpins and empty capsids with a hole. Protonatable hairpins containing C.C and/or C.A pairs were found to bind specifically to the interior of the protein shell under acidic conditions (pH 4.5) in the presence of spermidine. Based on these results we propose that this binding of protonated cytosines to the coat protein of turnip yellow mosaic virus may represent a new motif in RNA-protein interactions.
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Affiliation(s)
- Hugo H J Bink
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2300 RA Leiden, The Netherlands
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de Smit MH, Gultyaev AP, Hilge M, Bink HHJ, Barends S, Kraal B, Pleij CWA. Structural variation and functional importance of a D-loop-T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs. Nucleic Acids Res 2002; 30:4232-40. [PMID: 12364602 PMCID: PMC140539 DOI: 10.1093/nar/gkf539] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Valine-accepting tRNA-like structures (TLSs) are found at the 3' ends of the genomic RNAs of most plant viruses belonging to the genera Tymovirus, Furovirus, Pomovirus and Pecluvirus, and of one Tobamovirus species. Sequence alignment of these TLSs suggests the existence of a tertiary D-loop-T-loop interaction consisting of 2 bp, analogous to those in the elbow region of canonical tRNAs. The conserved G(18).Psi(55) pair of regular tRNAs is found to covary in these TLSs between G.U (possibly also modified to G.Psi) and A.G. We have mutated the relevant bases in turnip yellow mosaic virus (TYMV) and examined the mutants for symptom development on Chinese cabbage plants and for accumulation of genetic reversions. Development of symptoms is shown to rely on the presence of either A.G or G.U in the original mutants or in revertants. This finding supports the existence and functional importance of this tertiary interaction. The fact that only G.U and A.G are accepted at this position appears to result from steric and energetic limitations related to the highly compact nature of the elbow region. We discuss the implications of these findings for the various possible functions of the valine-accepting TLS.
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Affiliation(s)
- Maarten H de Smit
- Group Genexpress, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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Hemenway CL, Lommel SA. Manipulating plant viral RNA transcription signals. GENETIC ENGINEERING 2001; 22:171-95. [PMID: 11501376 DOI: 10.1007/978-1-4615-4199-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- C L Hemenway
- Departments of Biochemistry Box 7622 & Plant Pathology Box 7616, North Carolina State University, Raleigh, NC 27695, USA
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Bernal JJ, Jiménez I, Moreno M, Hord M, Rivera C, Koenig R, Rodríguez-Cerezo E. Chayote mosaic virus, a New Tymovirus Infecting Cucurbitaceae. PHYTOPATHOLOGY® 2000; 90:1098-104. [PMID: 18944472 DOI: 10.1094/phyto.2000.90.10.1098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chayote mosaic virus (ChMV) is a putative tymovirus isolated from chayote crops in Costa Rica. ChMV was characterized at the host range, serological, and molecular levels. ChMV was transmitted mechanically and induced disease symptoms mainly in Cucurbitaceae hosts. Asymptomatic infections were detected in other host families. Serologically, ChMV is related to the Andean potato latent virus (APLV) and the Eggplant mosaic virus (EMV), both members of the genus Tymovirus infecting solanaceous hosts in the Caribbean Basin and South America. The sequence of the genomic RNA of ChMV was determined and its genetic organization was typical of tymoviruses. Comparisons with other tymoviral sequences showed that ChMV was a new member of the genus Tymovirus. The phylogenetic analyses of the coat protein gene were consistent with serological comparisons and positioned ChMV within a cluster of tymoviruses infecting mainly cucurbit or solanaceous hosts, including APLV and EMV. Phylogenetic analyses of the replicase protein gene confirmed the close relationship of ChMV and EMV. Our results suggest that ChMV is related to two tymoviruses (APLV and EMV) of proximal geographical provenance but with different natural host ranges. ChMV is the first cucurbit-infecting tymovirus to be fully characterized at the genomic level.
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Melchers WJ, Bakkers JM, Bruins Slot HJ, Galama JM, Agol VI, Pilipenko EV. Cross-talk between orientation-dependent recognition determinants of a complex control RNA element, the enterovirus oriR. RNA (NEW YORK, N.Y.) 2000; 6:976-987. [PMID: 10917594 PMCID: PMC1369974 DOI: 10.1017/s1355838200000480] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The coxsackie B3 virus oriR is an element of viral RNA thought to promote the assembly of a ribonucleoprotein complex involved in the initiation of genome replication. The mutual orientation of its two helical domains X and Y is determined by a kissing interaction between the loops of these domains. Here, a genetic approach was worked out to identify spatial orientation-dependent recognition signals in these helices. Spatial orientation changes (due to linear and rotational shifts) were introduced by appropriate insertions/deletions of a single base pair into one or both of the domains, and phenotypic consequences caused by these mutations were studied. The insertion of a base pair into domain Y caused a defect in viral reproduction that could be suppressed by a base-pair insertion into domain X. Similarly, a defect in viral replication caused by a base-pair deletion from domain X could be suppressed by a base-pair deletion from domain Y. Thus, certain areas of the two domains should cross-talk to one another in the sense that a change of space position of one of them required an adequate reply (change of space position) from the other. Phenotypic effects of the local rotation of one or more base pairs (and of some other mutations) in either domain X or domain Y suggested that the two most distal base pairs of these domains served as orientation-dependent recognizable signals. The results were also consistent with the notion that the recognition of the distal base pair of domain Y involved a mechanism similar to the intercalation of an amino acid residue.
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Affiliation(s)
- W J Melchers
- University Medical Center Nijmegen, Department of Medical Microbiology, The Netherlands.
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