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Mahillon M, Brodard J, Kellenberger I, Blouin AG, Schumpp O. A novel weevil-transmitted tymovirus found in mixed infection on hollyhock. Virol J 2023; 20:17. [PMID: 36710353 PMCID: PMC9885571 DOI: 10.1186/s12985-023-01976-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Leaves of hollyhock (Alcea rosea) exhibiting vein chlorosis and yellow mosaic symptoms were collected at public sites in Lausanne and Nyon, two cities of western Switzerland. Diagnostic methods untangled in samples from both sites the mixed infections of a novel isometric virus, tentatively named "Alcea yellow mosaic virus" (AYMV) with the carlavirus Gaillardia latent virus. A new potyvirus was also identified in samples from Nyon. A combination of Illumina, Nanopore and Sanger sequencing was necessary to assemble the full-length genome of AYMV, revealing an exceptionally high cytidine content and other features typically associated with members of the genus Tymovirus. The host range of AYMV was found to be restricted to mallows, including ornamentals as well as economically important plants. Phylogenetic analyses further showed that AYMV belongs to a Tymovirus subclade that also gathers the other mallow-infecting members. The virus was readily transmitted by sap inoculation, and the weevil species Aspidapion radiolus was evidenced as a vector. Transmission assays using another weevil or other insect species did not succeed, and seed transmission was not observed.
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Affiliation(s)
- Mathieu Mahillon
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Isabelle Kellenberger
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Arnaud G. Blouin
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland.
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2
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Determinants of Virus Variation, Evolution, and Host Adaptation. Pathogens 2022; 11:pathogens11091039. [PMID: 36145471 PMCID: PMC9501407 DOI: 10.3390/pathogens11091039] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.
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3
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Wu S, Li X, Wang G. tRNA-like structures and their functions. FEBS J 2021; 289:5089-5099. [PMID: 34117728 DOI: 10.1111/febs.16070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 06/10/2021] [Indexed: 11/27/2022]
Abstract
tRNA-like structures (TLSs) were first identified in the RNA genomes of turnip yellow mosaic virus. Since then, TLSs have been found in many other species including mammals, and the RNAs harboring these structures range from viral genomic RNAs to mRNAs and noncoding RNAs. Some progress has also been made on understanding their functions that include regulation of RNA replication, translation enhancement, RNA-protein interaction, and more. In this review, we summarize the current knowledge about the regulations and functions of these TLSs. Possible future directions of the field are also briefly discussed.
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Affiliation(s)
- Sipeng Wu
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Xiang Li
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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4
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Mizutani Y, Abraham A, Uesaka K, Kondo H, Suga H, Suzuki N, Chiba S. Novel Mitoviruses and a Unique Tymo-Like Virus in Hypovirulent and Virulent Strains of the Fusarium Head Blight Fungus, Fusarium boothii. Viruses 2018; 10:v10110584. [PMID: 30373133 PMCID: PMC6266667 DOI: 10.3390/v10110584] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 11/16/2022] Open
Abstract
Hypovirulence of phytopathogenic fungi are often conferred by mycovirus(es) infections and for this reason many mycoviruses have been characterized, contributing to a better understanding of virus diversity. In this study, three strains of Fusarium head blight fungus (Fusarium boothii) were isolated from Ethiopian wheats as dsRNA-carrying strains: hypovirulent Ep-BL13 (>10, 3 and 2.5 kbp dsRNAs), and virulent Ep-BL14 and Ep-N28 (3 kbp dsRNA each) strains. The 3 kbp-dsRNAs shared 98% nucleotide identity and have single ORFs encoding a replicase when applied to mitochondrial codon usage. Phylogenetic analysis revealed these were strains of a new species termed Fusarium boothii mitovirus 1 in the genus Mitovirus. The largest and smallest dsRNAs in Ep-BL13 appeared to possess single ORFs and the smaller was originated from the larger by removal of its most middle part. The large dsRNA encoded a replicase sharing the highest amino acid identity (35%) with that of Botrytis virus F, the sole member of the family Gammaflexiviridae. Given that the phylogenetic placement, large genome size, simple genomic and unusual 3′-terminal RNA structures were far different from members in the order Tymovirales, the virus termed Fusarium boothii large flexivirus 1 may form a novel genus and family under the order.
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Affiliation(s)
- Yukiyoshi Mizutani
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
| | - Adane Abraham
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya 464-8601, Japan.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan.
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
- Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan.
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5
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Green KJ, Mollov D, Tran LT, Alvarez-Quinto RA, Ochoa JB, Quito-Avila DF, Karasev AV. Characterization of a New Tymovirus Causing Stunting and Chlorotic Mosaic in Naranjilla (Solanum quitoense). PLANT DISEASE 2018; 102:911-918. [PMID: 30673388 DOI: 10.1094/pdis-10-17-1534-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Naranjilla ("little orange"), also known as lulo (Solanum quitoense Lam.), is a perennial shrub species cultivated in the Andes for fresh fruit and juice production. In 2015, a naranjilla plant exhibiting stunting, mosaic, and chlorotic spots was sampled in the Pastaza province of Ecuador and maintained under greenhouse conditions. An infectious agent was mechanically transmitted to indicator plants and was subjected to biological and molecular characterization. Spherical particles approximately 30 nm in diameter, composed of a single 20-kDa capsid protein, were observed under an electron microscope in infected naranjilla plants. High-throughput sequencing conducted on inoculated Nicotiana benthamiana plants produced a single sequence contig sharing the closest relationship with several tymoviruses. The entire 6,245-nucleotide genome of a new tymovirus was amplified using reverse-transcription polymerase chain reaction and resequenced with the Sanger methodology. The genome had three open reading frames typical of tymoviruses, and displayed a whole-genome nucleotide identity level with the closest tymovirus, Eggplant mosaic virus, at 71% (90% coverage). This tymovirus from naranjilla was able to systemically infect eggplant, tamarillo, N. benthamiana, and naranjilla. In naranjilla, it produced mosaic, chlorotic spots, and stunting, similar to the symptoms observed in the original plant. The virus was unable to infect potato and tobacco and unable to systemically infect pepper plants, replicating only in inoculated leaves. We concluded that this virus represented a new tymovirus infecting naranjilla, and proposed the tentative name Naranjilla chlorotic mosaic virus (NarCMV).
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Affiliation(s)
- Kelsie J Green
- Department of Entomology, Plant Pathology and Nematology (EPPN), University of Idaho, Moscow
| | - Dimitre Mollov
- United States Department of Agriculture-Agricultural Research Service, National Germplasm Resources Laboratory, Beltsville, MD
| | | | - Robert A Alvarez-Quinto
- Centro de Investigaciones Biotecnológicas del Ecuador and Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Jose B Ochoa
- Instituto Nacional Autónomo de Investigaciones Agropecuarias, Quito, Ecuador
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador and Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral
| | - Alexander V Karasev
- Department of EPPN and Bioinformatics and Computational Biology Program, University of Idaho
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6
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Blawid R, Hayashi EAI, Rezende JAM, Kitajima EW, Nagata T. A highly divergent isolate of tomato blistering mosaic virus from Solanum violaefolium. Virus Genes 2016; 52:294-8. [PMID: 26810401 DOI: 10.1007/s11262-016-1288-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
The complete genome of a tymovirus infecting Solanum violaefolium was sequenced. The genome comprised 6284 nt, with a 5'-UTR of 137 nt and a comparatively longer 3'-UTR of 121 nt. Sequence analysis confirmed three ORFs encoding a movement protein, a polyprotein, and a coat protein (CP). The isolate was considered to be the Tomato blistering mosaic virus (ToBMV) based on a CP amino acid sequence identity of 95.3 %. The nucleotide sequence of the complete genome of the S. violaefolium isolate, however, differed markedly from the other two reported ToBMV isolates, with identities of 76.6 and 76.3 %, below one of the demarcation criteria of the genus Tymovirus (overall genome identity of 80 %). No recombination signals were detected in the genome of this isolate. The high identity of the CP amino acid sequence and similar host responses suggest that the S. violaefolium isolate belongs to the same species as the Tomato blistering mosaic virus. The sequence analysis of this ToBMV isolate thus suggests that the demarcation criterion of 80 % overall genome sequence identity in the genus Tymovirus may require revision.
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Affiliation(s)
- Rosana Blawid
- Departamento de Biologia Celular, Universidade de Brasília, UnB, Brasília, DF, Brazil
| | | | - Jorge Alberto Marques Rezende
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Cx. Postal 9, Piracicaba, SP, 13418-900, Brazil
| | - Elliot W Kitajima
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Cx. Postal 9, Piracicaba, SP, 13418-900, Brazil
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Universidade de Brasília, UnB, Brasília, DF, Brazil.
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Guo S, Kierzek E, Chen G, Zhou YJ, Wong SM. TMV mutants with poly(A) tracts of different lengths demonstrate structural variations in 3'UTR affecting viral RNAs accumulation and symptom expression. Sci Rep 2015; 5:18412. [PMID: 26678425 PMCID: PMC4683447 DOI: 10.1038/srep18412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022] Open
Abstract
The upstream pseudoknots domain (UPD) of Tobacco mosaic virus (TMV) is located at the 3'-untranslated region (UTR). It plays an important role in virus replication and translation. To determine the importance of UPD and 3'-UTR, and the effects of introduced RNA elements in TMV 3'-UTR, a series of TMV mutants with internal poly(A) tract upstream of UPD was constructed for structural analysis by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). TMV(24A+UPD) and TMV(42A+UPD) formed a similar structure as that of TMV 3'-UTR, but TMV(62A+UPD) structures altered by the introduced poly(A) tract. In addition, TMV(24A+UPD) had a higher viral RNAs accumulation than TMV in N. benthamiana protoplasts, and induced lethal symptoms in the infected plants. TMV(62A+UPD) showed a drastically reduced accumulation, its coat protein was undetectable in protoplasts, and the inoculated plants remained symptomless. This study analyzed the structures of 3'-UTR of TMV and found that the longer poly(A) tract introduced upstream of UPD reduced viral RNAs accumulation and induced milder symptoms in N. benthamiana. In conclusion, different lengths of the internal poly(A) tract introduced into the TMV 3'UTR lead to structural variations that affect virus accumulation and symptom expression.
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Affiliation(s)
- Song Guo
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Yi-Jun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing 210014, PRC
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
- Temasek Life Sciences Laboratory, Singapore, Republic of Singapore
- National University of Singapore Research Institute in Suzhou, Jiangsu, PRC
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8
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Hull R. Replication of Plant Viruses. PLANT VIROLOGY 2014. [PMCID: PMC7184227 DOI: 10.1016/b978-0-12-384871-0.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses co-infecting cells. Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses coinfecting cells.
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9
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Chen IH, Cheng JH, Huang YW, Lin NS, Hsu YH, Tsai CH. Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants. Virology 2013; 444:64-70. [PMID: 23768785 PMCID: PMC7111917 DOI: 10.1016/j.virol.2013.05.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/20/2013] [Accepted: 05/22/2013] [Indexed: 12/30/2022]
Abstract
Bamboo mosaic virus (BaMV) has a positive-sense single-stranded RNA genome with a 5' cap and a 3' poly(A) tail. To characterize polyadenylation activity in the BaMV replicase complex, we performed the in vitro polyadenylation with various BaMV templates. We conducted a polyadenylation activity assay for BaMV RNA by using a partially purified BaMV replicase complex. The results showed that approximately 200 adenylates at the 3' end of the RNA were generated on the endogenous RNA templates. Specific fractions derived from uninfected Nicotiana benthamiana plants enhanced the polyadenylation activity, implying that host factors are involved in polyadenylation. Furthermore, polyadenylation can be detected in newly synthesized plus-strand RNA in vitro when using the exogenous BaMV minus-strand minigenome. For polyadenylation on the exogenous plus-strand minigenome, the 3' end requires at least 4A to reach 22% polyadenylation activity. The results indicate that the BaMV replicase complex recognizes the 3' end of BaMV for polyadenylation.
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Affiliation(s)
- I-Hsuan Chen
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jai-Hong Cheng
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Na-Sheng Lin
- The Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
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10
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Mini-genome rescue of Crimean-Congo hemorrhagic fever virus and research into the evolutionary patterns of its untranslated regions. Virus Res 2013; 177:22-34. [PMID: 23891575 DOI: 10.1016/j.virusres.2013.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 07/04/2013] [Accepted: 07/05/2013] [Indexed: 11/23/2022]
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a member of genus Nairovirus, family Bunyaviridae, which are distributed widely in Africa, Europe and Asia with several genotypes. As a BSL-4 level pathogen, the requirement of high-level biosafety facilities severely constrains researches on live virus manipulation. In this study, we developed a helper-virus-independent mini-genome rescue system for the Chinese YL04057 strain. Based on the enhanced green fluorescent protein (EGFP)-derived mini-genome plasmids, this polymerase I driven system permits easy observation and quantification. Unlike previous report, gradually reduced levels of activity of the CCHFV L, M and S untranslated regions (UTRs) were observed in our system. We also demonstrated that the UTRs at both ends were indispensable for mini-genome background expression. In addition, we phylogentically analyzed all six UTRs of CCHFV and showed that L-UTRs were clustered together approximately corresponding to their original geographical continents. The UTRs of M segment showed a similar branch structure to its open reading frames (ORFs), and nearly an identical tree was generated with 5' UTRs of S segment compared with its ORFs. However, the 3' UTRs of S segment formed new divergent groups. Compatibility tests of YL04057 strain nucleocapsid protein and L protein expression plasmids with Nigerian strain IbAr10200 mini-genomes revealed lower compatibility of L-UTRs without an obvious effect on M-UTRs. Moreover, we demonstrated that the L-UTRs could tolerate certain nucleotide mutations. This system may provide a foundation for future studies of the viral replication cycle, pathogenic mechanisms and evolutionary patterns of CCHFV.
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Chen XS, Brown CM. Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes. Nucleic Acids Res 2012; 40:8862-73. [PMID: 22821558 PMCID: PMC3467077 DOI: 10.1093/nar/gks684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/15/2012] [Accepted: 06/20/2012] [Indexed: 01/14/2023] Open
Abstract
Messenger ribonucleic acids (RNAs) contain a large number of cis-regulatory RNA elements that function in many types of post-transcriptional regulation. These cis-regulatory elements are often characterized by conserved structures and/or sequences. Although some classes are well known, given the wide range of RNA-interacting proteins in eukaryotes, it is likely that many new classes of cis-regulatory elements are yet to be discovered. An approach to this is to use computational methods that have the advantage of analysing genomic data, particularly comparative data on a large scale. In this study, a set of structural discovery algorithms was applied followed by support vector machine (SVM) classification. We trained a new classification model (CisRNA-SVM) on a set of known structured cis-regulatory elements from 3'-untranslated regions (UTRs) and successfully distinguished these and groups of cis-regulatory elements not been strained on from control genomic and shuffled sequences. The new method outperformed previous methods in classification of cis-regulatory RNA elements. This model was then used to predict new elements from cross-species conserved regions of human 3'-UTRs. Clustering of these elements identified new classes of potential cis-regulatory elements. The model, training and testing sets and novel human predictions are available at: http://mRNA.otago.ac.nz/CisRNA-SVM.
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Affiliation(s)
- Xiaowei Sylvia Chen
- Department of Biochemistry and Genetics Otago, University of Otago, Dunedin 9054, New Zealand.
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12
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Blueberry latent virus: an amalgam of the Partitiviridae and Totiviridae. Virus Res 2010; 155:175-80. [PMID: 20888379 DOI: 10.1016/j.virusres.2010.09.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/20/2010] [Accepted: 09/21/2010] [Indexed: 11/24/2022]
Abstract
A new, symptomless virus was identified in blueberry. The dsRNA genome of the virus, provisionally named Blueberry latent virus (BBLV), codes for two putative proteins, one without any similarities to virus proteins and an RNA-dependent RNA polymerase. More than 35 isolates of the virus from different cultivars and geographic regions were partially or completely sequenced. BBLV, found in more than 50% of the material tested, has high degree of homogeneity as isolates show more than 99% nucleotide identity between them. Phylogenetic analysis clearly shows a close relationship between BBLV and members of the Partitiviridae, although its genome organization is related more closely to members of the Totiviridae. Transmission studies from three separate crosses showed that the virus is transmitted very efficiently by seed. These properties suggest that BBLV belongs to a new family of plant viruses with unique genome organization for a plant virus but signature properties of cryptic viruses including symptomless infection and very efficient vertical transmission.
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13
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Dreher TW. Viral tRNAs and tRNA-like structures. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:402-14. [PMID: 21956939 DOI: 10.1002/wrna.42] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Viruses commonly exploit or modify some aspect of tRNA biology. Large DNA viruses, especially bacteriophages, phycodnaviruses, and mimiviruses, produce their own tRNAs, apparently to adjust translational capacity during infection. Retroviruses recruit specific host tRNAs for use in priming the reverse transcription of their genome. Certain positive-strand RNA plant viral genomes possess 3'-tRNA-like structures (TLSs) that are built quite differently from authentic tRNAs, and yet efficiently recapitulate several properties of tRNAs. The structures and roles of these TLSs are discussed, emphasizing the variety in both structure and function.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology and Center for Genome Research and Bioinformatics, Oregon State University, Corvallis, OR 97331, USA.
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14
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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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