A novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages
- 361 Downloads
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.
KeywordsReplication Origin Genomic Component Tomato Yellow Leaf Curl Sardinia Virus Identical Iterative Element Iteron Sequence
We thank Salvador Ambriz-Granados for his technical assistance, and Dr. Samuel Lara González (IPICYT) for his valuable advices on protein modeling. We also thank two anonymous reviewers for thoughtful comments and suggestions. GPP was supported by a postdoctoral fellowship from the Consejo Nacional de Ciencia y Tecnología (CONACYT, Mexico). This research was supported by a CONACYT grant (SEP-84004) to GRAA.
- 2.Andrade EC, Manhani GG, Alfenas PF, Calegario RF, Fontes EP, Zerbini FM (2006) Tomato yellow spot virus, a tomato-infecting begomovirus from Brazil with a closer relationship to viruses from Sida sp., forms pseudorecombinants with begomoviruses from tomato but not from Sida. J Gen Virol 87:3687–3696CrossRefPubMedGoogle Scholar
- 4.Arguello-Astorga GR, Ruiz-Medrano R (2001) An iteron-related domain is associated to Motif 1 in the replication proteins of geminiviruses: identification of potential interacting amino acid–base pairs by a comparative approach. Arch Virol 146:465–485Google Scholar
- 18.Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, Richardson DC (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375–W383Google Scholar
- 21.DeLano WL (2002) The PyMol molecular graphics system. Schrodinger, New York. http://www.pymol.org
- 28.Gregorio-Jorge J, Bernal-Alcocer A, Bañuelos-Hernandez B, Alpuche-Solís AG, Hernandez-Zepeda C, Moreno-Valenzuela O, Frías-Treviño G, Argüello-Astorga GR (2010) Analysis of a new strain of Euphorbia mosaic virus with distinct replication specificity unveils a lineage of begomoviruses with short Rep sequences in the DNA-B intergenic region. Virol J 7:275PubMedCentralCrossRefPubMedGoogle Scholar
- 30.Ha C, Coombs S, Revill P, Harding R, Vu M, Dale J (2008) Molecular characterization of begomoviruses and DNA satellites from Vietnam: additional evidence that the New World geminiviruses were present in the Old World prior to continental separation. J Gen Virol 89:312–326CrossRefPubMedGoogle Scholar
- 40.Martin DP, Lefeuvre P, Varsani A, Hoareau M, Semegni J-Y, Dijoux B, Vincent C, Reynaud B, Lett JM (2011) Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks. PLOS Pathogens 7(9):e1002203. doi: 10.1371/journal.ppat.1002203 PubMedCentralCrossRefPubMedGoogle Scholar
- 43.Melgarejo TA, Kon T, Rojas MR, Paz-Carrasco L, Zerbini FM, Gilbertson RL (2013) Characterization of a new world monopartite begomovirus causing leaf curl disease of tomato in Ecuador and Peru reveals a new direction in geminivirus evolution. J Virol 87:5397–5413PubMedCentralCrossRefPubMedGoogle Scholar
- 48.Ramos PL, Guevara-Gonzalez RG, Peral R, Ascencio-Ibañez JT, Polston JE, Arguello-Astorga GR, Vega-Arreguin JC, Rivera-Bustamante RF (2003) Tomato mottle Taino virus pseudorecombines with PYMV but not with ToMoV: implications for the delimitation of cis- and trans-acting replication specificity determinants. Arch Virol 148:1697–1712CrossRefPubMedGoogle Scholar