Unwinding of the ssDNA/ssRNA duplex by p33 in an in vitro strand separation assay. (A) Schematic representation of the known domains in the tombusvirus replication proteins p33 and p92pol. Note that the N-terminal segment in p92pol contains the same sequence as in p33 due to the overlapping expression strategy of TBSV genome, while the C-terminal region of p92pol carries the RdRp domain. TMD, trans-membrane domains; P, phosphorylation sites; RPR, arginine-proline-rich RNA-binding domain; S1 and S2 are subdomains of the p33:p33/p92 interaction domain. The closely related TCV p88 is similar to p92pol and carries the p33 similarity domain as well as the RdRp domain. P88C is an N-terminally truncated p88 derivative, which has strong RdRp activity in vitro. (B) Scheme of the strand separation assay showing the hybridized ssDNA/ssRNA duplex. The 5′ end labeled, 21 base ssDNA oligo was annealed to the unlabeled DI-72(−)RNA prior to the addition of purified recombinant p33. (C) In vitro strand separation assay with p33 using an ssDNA oligo/ssRNA template duplex. Lane 1: 5′ end labeled-ssDNA oligo; Lanes 2 and 8: annealed ssDNA/ssRNA, no p33; Lane 3: annealed ssDNA/ssRNA template plus 4 pmol purified recombinant TBSV MBP-p33; Lane 4: annealed ssDNA/ssRNA plus 4 pmol purified recombinant TCV MBP-p88C; Lanes 5–7: annealed ssDNA/ssRNA plus 0.4, 1 and 4 pmol purified recombinant MBP-Ded1p, respectively. The assay was performed in the absence of ATP. The 32P-labeled free ssDNA and ssDNA/ssRNA duplex were separated on non-denaturing 5% acrylamide gels. Quantification of the ssDNA/ssRNA duplex was done with ImageQuant. Bottom image shows an SDS-PAGE analysis of purified recombinant proteins used in these assays. Each experiment was repeated at least three times. (D) In vitro strand separation assay with recombinant proteins using an ssDNA oligo/ssRNA template duplex in the absence of ATP. Lane 1: 5′ end labeled-ssDNA oligo; Lanes 2–3: annealed ssDNA/ssRNA, plus 1 and 4 pmol of p88; Lanes 4–6: annealed ssDNA/ssRNA template plus 0.4, 1 and 4 pmol purified recombinant TBSV MBP-p33; Lanes 7–8: annealed ssDNA/ssRNA plus 1 and 4 pmol purified recombinant TCV MBP-p88C; Lanes 9–11: annealed ssDNA/ssRNA plus 0.4, 1 and 4 pmol purified recombinant MBP-Ded1p, respectively; Lane 12: annealed ssDNA/ssRNA, no p33. The percentage of unwound ssDNA/ssRNA duplex is shown. The lower image shows a shorter exposure for the ssDNA/ssRNA duplex. (E) In vitro strand separation assay with recombinant proteins using an ssDNA oligo/ssRNA template duplex in the presence of ATP. Lane 1: 5′ end labeled-ssDNA oligo; Lane 2: annealed ssDNA/ssRNA, no p33; Lanes 3–4: annealed ssDNA/ssRNA, plus 1 and 4 pmol of p88; Lanes 5–6: annealed ssDNA/ssRNA template plus 1 and 4 pmol purified recombinant TBSV MBP-p33; Lane 7: annealed ssDNA/ssRNA, no p33; Lanes 8–9: annealed ssDNA/ssRNA plus 1 and 4 pmol purified recombinant TCV MBP-p88C; lanes 10–11: annealed ssDNA/ssRNA plus 1 and 4 pmol purified recombinant MBP-Ded1p, respectively; Lane 12: annealed ssDNA/ssRNA, no p33. The percentage of unwound ssDNA/ssRNA duplex is shown. See additional details in panel C.