novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages
A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolution...
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| Veröffentlicht in: | Archives of virology 2014-09, Vol.159 (9), p.2283-2294 |
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| creator | Mauricio-Castillo, J. A Torres-Herrera, S. I Cárdenas-Conejo, Y Pastor-Palacios, G Méndez-Lozano, J Argüello-Astorga, G. R |
| description | A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolutionary relationship between these viruses. However, recombination analysis indicated that a short segment of SiMSinV DNA-A encompassing the plus-strand replication origin and the 5´-proximal 43 codons of the Rep gene was derived from tomato mottle Taino virus (ToMoTV). Accordingly, the putative cis- and trans-acting replication specificity determinants of SiMSinV were identical to those of ToMoTV but differed from those of CdTV. Modeling of the SiMSinV and CdTV Rep proteins revealed significant differences in the region comprising the small β1/β5 sheet element, where five putative DNA-binding specificity determinants (SPDs) of Rep (i.e., amino acid residues 5, 8, 10, 69 and 71) were previously identified. Computer-assisted searches of public databases led to identification of 33 begomoviruses from three continents encoding proteins with SPDs identical to those of the Rep encoded by SiMSinV. Sequence analysis of the replication origins demonstrated that all 33 begomoviruses harbor potential Rep-binding sites identical to those of SiMSinV. These data support the hypothesis that the Rep β1/β5 sheet region determines specificity of this protein for DNA replication origin sequences. |
| doi_str_mv | 10.1007/s00705-014-2073-8 |
| format | Article |
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A ; Torres-Herrera, S. I ; Cárdenas-Conejo, Y ; Pastor-Palacios, G ; Méndez-Lozano, J ; Argüello-Astorga, G. R</creator><creatorcontrib>Mauricio-Castillo, J. A ; Torres-Herrera, S. I ; Cárdenas-Conejo, Y ; Pastor-Palacios, G ; Méndez-Lozano, J ; Argüello-Astorga, G. R</creatorcontrib><description>A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolutionary relationship between these viruses. However, recombination analysis indicated that a short segment of SiMSinV DNA-A encompassing the plus-strand replication origin and the 5´-proximal 43 codons of the Rep gene was derived from tomato mottle Taino virus (ToMoTV). Accordingly, the putative cis- and trans-acting replication specificity determinants of SiMSinV were identical to those of ToMoTV but differed from those of CdTV. Modeling of the SiMSinV and CdTV Rep proteins revealed significant differences in the region comprising the small β1/β5 sheet element, where five putative DNA-binding specificity determinants (SPDs) of Rep (i.e., amino acid residues 5, 8, 10, 69 and 71) were previously identified. Computer-assisted searches of public databases led to identification of 33 begomoviruses from three continents encoding proteins with SPDs identical to those of the Rep encoded by SiMSinV. Sequence analysis of the replication origins demonstrated that all 33 begomoviruses harbor potential Rep-binding sites identical to those of SiMSinV. These data support the hypothesis that the Rep β1/β5 sheet region determines specificity of this protein for DNA replication origin sequences.</description><identifier>ISSN: 0304-8608</identifier><identifier>EISSN: 1432-8798</identifier><identifier>DOI: 10.1007/s00705-014-2073-8</identifier><identifier>PMID: 24737005</identifier><language>eng</language><publisher>Vienna: Springer-Verlag</publisher><subject>amino acids ; Begomovirus ; Begomovirus - genetics ; Begomovirus - isolation & purification ; Begomovirus - physiology ; Binding Sites ; Biomedical and Life Sciences ; Biomedicine ; Cell cycle ; Chino del tomate virus ; codons ; Computational Biology ; DNA replication ; genes ; Genomes ; Hypotheses ; Infectious Diseases ; Lycopersicon esculentum ; Malvaceae - virology ; Medical Microbiology ; Mexico ; Original Article ; Proteins ; Recombination, Genetic ; replication origin ; sequence analysis ; Sequence Homology, Nucleic Acid ; Sida rhombifolia ; Taino tomato mottle virus ; Virology ; Virus Replication ; Viruses</subject><ispartof>Archives of virology, 2014-09, Vol.159 (9), p.2283-2294</ispartof><rights>Springer-Verlag Wien 2014</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c499t-78fc3753bd3b51d208ae5ab4ebfe8f6c1b6980c50bd5651096138afa331024183</citedby><cites>FETCH-LOGICAL-c499t-78fc3753bd3b51d208ae5ab4ebfe8f6c1b6980c50bd5651096138afa331024183</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00705-014-2073-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00705-014-2073-8$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51297</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24737005$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mauricio-Castillo, J. A</creatorcontrib><creatorcontrib>Torres-Herrera, S. I</creatorcontrib><creatorcontrib>Cárdenas-Conejo, Y</creatorcontrib><creatorcontrib>Pastor-Palacios, G</creatorcontrib><creatorcontrib>Méndez-Lozano, J</creatorcontrib><creatorcontrib>Argüello-Astorga, G. R</creatorcontrib><title>novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages</title><title>Archives of virology</title><addtitle>Arch Virol</addtitle><addtitle>Arch Virol</addtitle><description>A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolutionary relationship between these viruses. However, recombination analysis indicated that a short segment of SiMSinV DNA-A encompassing the plus-strand replication origin and the 5´-proximal 43 codons of the Rep gene was derived from tomato mottle Taino virus (ToMoTV). Accordingly, the putative cis- and trans-acting replication specificity determinants of SiMSinV were identical to those of ToMoTV but differed from those of CdTV. Modeling of the SiMSinV and CdTV Rep proteins revealed significant differences in the region comprising the small β1/β5 sheet element, where five putative DNA-binding specificity determinants (SPDs) of Rep (i.e., amino acid residues 5, 8, 10, 69 and 71) were previously identified. Computer-assisted searches of public databases led to identification of 33 begomoviruses from three continents encoding proteins with SPDs identical to those of the Rep encoded by SiMSinV. Sequence analysis of the replication origins demonstrated that all 33 begomoviruses harbor potential Rep-binding sites identical to those of SiMSinV. These data support the hypothesis that the Rep β1/β5 sheet region determines specificity of this protein for DNA replication origin sequences.</description><subject>amino acids</subject><subject>Begomovirus</subject><subject>Begomovirus - genetics</subject><subject>Begomovirus - isolation & purification</subject><subject>Begomovirus - physiology</subject><subject>Binding Sites</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cell cycle</subject><subject>Chino del tomate virus</subject><subject>codons</subject><subject>Computational Biology</subject><subject>DNA replication</subject><subject>genes</subject><subject>Genomes</subject><subject>Hypotheses</subject><subject>Infectious Diseases</subject><subject>Lycopersicon esculentum</subject><subject>Malvaceae - virology</subject><subject>Medical Microbiology</subject><subject>Mexico</subject><subject>Original Article</subject><subject>Proteins</subject><subject>Recombination, Genetic</subject><subject>replication origin</subject><subject>sequence analysis</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Sida rhombifolia</subject><subject>Taino tomato mottle virus</subject><subject>Virology</subject><subject>Virus Replication</subject><subject>Viruses</subject><issn>0304-8608</issn><issn>1432-8798</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkc-K1TAUh4sozjj6AG404MZN9aRp2nQpg_9gwIXOupymp70Z0qQmaeG-lk9oLncUcSFuTkjynd9J-IriOYc3HKB9G3MBWQKvywpaUaoHxSWvRVWqtlMPi0sQUJeqAXVRPInxDiAfCPm4uKjqVrQA8rL44fxOlg00-8XvJmyRmegtJhrZFPzCohmRae8SGhfZuiVMZiemTSwZupGlgC6WqJNxMwu0WqMz4R2LK2kzGW3SkY2UKCzGoUuRpQMmdsAcQru3ex5k3Egr5eKSPeYdi7RTQMtm8nPA9ZAzLbPGEc4UnxaPJrSRnt2vV8Xth_ffrj-VN18-fr5-d1PquutS2apJi1aKYRSD5GMFCkniUNMwkZoazYemU6AlDKNsJIeu4ULhhEJwqGquxFXx-py7Bv99o5j6xURN1qIjv8Wey6ZRtRSy-w9UKlnJVvKMvvoLvfNbcPkjJ6rpRKOgyhQ_Uzr4GANN_RrMguHYc-hP7vuz-z6770_u-9N7X9wnb8NC4--OX7IzUJ2BmK_cTOGP0f9IfXlumtD3OAcT-9uvVQYAuGhEDeIn7N3GoQ</recordid><startdate>20140901</startdate><enddate>20140901</enddate><creator>Mauricio-Castillo, J. 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A</au><au>Torres-Herrera, S. I</au><au>Cárdenas-Conejo, Y</au><au>Pastor-Palacios, G</au><au>Méndez-Lozano, J</au><au>Argüello-Astorga, G. R</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages</atitle><jtitle>Archives of virology</jtitle><stitle>Arch Virol</stitle><addtitle>Arch Virol</addtitle><date>2014-09-01</date><risdate>2014</risdate><volume>159</volume><issue>9</issue><spage>2283</spage><epage>2294</epage><pages>2283-2294</pages><issn>0304-8608</issn><eissn>1432-8798</eissn><abstract>A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolutionary relationship between these viruses. However, recombination analysis indicated that a short segment of SiMSinV DNA-A encompassing the plus-strand replication origin and the 5´-proximal 43 codons of the Rep gene was derived from tomato mottle Taino virus (ToMoTV). Accordingly, the putative cis- and trans-acting replication specificity determinants of SiMSinV were identical to those of ToMoTV but differed from those of CdTV. Modeling of the SiMSinV and CdTV Rep proteins revealed significant differences in the region comprising the small β1/β5 sheet element, where five putative DNA-binding specificity determinants (SPDs) of Rep (i.e., amino acid residues 5, 8, 10, 69 and 71) were previously identified. Computer-assisted searches of public databases led to identification of 33 begomoviruses from three continents encoding proteins with SPDs identical to those of the Rep encoded by SiMSinV. Sequence analysis of the replication origins demonstrated that all 33 begomoviruses harbor potential Rep-binding sites identical to those of SiMSinV. These data support the hypothesis that the Rep β1/β5 sheet region determines specificity of this protein for DNA replication origin sequences.</abstract><cop>Vienna</cop><pub>Springer-Verlag</pub><pmid>24737005</pmid><doi>10.1007/s00705-014-2073-8</doi><tpages>12</tpages></addata></record> |
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| ispartof | Archives of virology, 2014-09, Vol.159 (9), p.2283-2294 |
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| subjects | amino acids Begomovirus Begomovirus - genetics Begomovirus - isolation & purification Begomovirus - physiology Binding Sites Biomedical and Life Sciences Biomedicine Cell cycle Chino del tomate virus codons Computational Biology DNA replication genes Genomes Hypotheses Infectious Diseases Lycopersicon esculentum Malvaceae - virology Medical Microbiology Mexico Original Article Proteins Recombination, Genetic replication origin sequence analysis Sequence Homology, Nucleic Acid Sida rhombifolia Taino tomato mottle virus Virology Virus Replication Viruses |
| title | novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages |
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