Archives of Virology

, Volume 159, Issue 9, pp 2283–2294 | Cite as

A novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages

  • J. A. Mauricio-Castillo
  • S. I. Torres-Herrera
  • Y. Cárdenas-Conejo
  • G. Pastor-Palacios
  • J. Méndez-Lozano
  • G. R. Argüello-AstorgaEmail author
Original Article


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.


Replication Origin Genomic Component Tomato Yellow Leaf Curl Sardinia Virus Identical Iterative Element Iteron Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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.

Supplementary material

705_2014_2073_MOESM1_ESM.pdf (355 kb)
Supplementary material 1 (PDF 354 kb)
705_2014_2073_MOESM2_ESM.pdf (738 kb)
Supplementary material 2 (PDF 738 kb)


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Copyright information

© Springer-Verlag Wien 2014

Authors and Affiliations

  • J. A. Mauricio-Castillo
    • 1
  • S. I. Torres-Herrera
    • 2
  • Y. Cárdenas-Conejo
    • 2
  • G. Pastor-Palacios
    • 2
  • J. Méndez-Lozano
    • 3
  • G. R. Argüello-Astorga
    • 2
    Email author
  1. 1.Unidad Académica de Agronomía, Universidad Autónoma de ZacatecasZacatecasMexico
  2. 2.División de Biología MolecularInstituto Potosino de Investigación Científica y TecnológicaSan Luis PotosíMexico
  3. 3.Instituto Politécnico Nacional, CIIDIR Unidad SinaloaGuasaveMexico

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