title: DNA-binding specificity determinants of replication proteins encoded by eukaryotic ssDNA viruses are adjacent to widely separated RCR conserved motifs.
abstract: Eukaryotic ssDNA viruses encode a rolling-circle replication (RCR) initiation protein, Rep, which binds to iterated DNA elements functioning as essential elements for virus-specific replication. By using the iterons of all known circoviruses, nanoviruses and nanovirus-like satellites as heuristic devices, we have identified certain amino acid residues that presumably determine the DNA-binding specificity of their Rep proteins. These putative "specificity determinants" (SPDs) cluster in two discrete protein regions, which are adjacent to distinct conserved motifs. A comparable distribution of SPDs was uncovered in the Rep protein of geminiviruses. Modeling of the tertiary structure of diverse Rep proteins showed that SPD regions interact to form a small beta-sheet element that has been proposed to be critical for high-affinity DNA-binding of Rep. Our findings indicate that eukaryotic circular ssDNA viruses have a common ancestor and suggest that SPDs present in replication initiators from a huge variety of viral and plasmid RCR systems are associated with the same conserved motifs.
authors.affiliation: División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa San José 2055, CP 78216 San Luis Potosí, México.
authors.forename: Aurora
authors.initials: A
authors.lastname: Londoño
authors.forename: Lina
authors.initials: L
authors.lastname: Riego-Ruiz
authors.forename: Gerardo R
authors.initials: GR
authors.lastname: Argüello-Astorga
mesh_terms: D000595:Amino Acid Sequence; D017925:Circovirus / Q000235:genetics*; D017124:Conserved Sequence; D004277:DNA, Single-Stranded; D004279:DNA, Viral / Q000235:genetics / Q000378:metabolism; D004720:Endonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017791:Geminiviridae / Q000235:genetics*; D015967:Gene Expression Regulation, Viral / Q000502:physiology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D025682:Nanovirus / Q000235:genetics*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism*; D014779:Virus Replication / Q000502:physiology*
chemical_list: D004277:DNA, Single-Stranded; D004279:DNA, Viral; D014764:Viral Proteins; D004720:Endonucleases