Mechanism of DNA Interaction and Translocation by the Replicase of a Circular Rep-Encoding Single-Stranded DNA Virus

Abstract

CRESS-DNA viruses encompass a significant portion of the biosphere’s virome. However, little is known about the structure of Rep responsible for initiating the RCR of CRESS-DNA viruses.

A Structural Perspective of Reps from CRESS-DNA Viruses and Their Bacterial Plasmid Homologues

“…Viruses 2022, 14, 37 2 of 17 domain (OD) in the middle, and (3) an ATPase domain (AD) at the C-terminus [14,20]. Relaxes and Reps bind to ori and deform the dsDNA to form a cruciform structure.…”

“…Crystal structures of Relaxases and Reps in complex with their ssDNA substrate define how these proteins attain sequence specificity; however, there is lack of structural information on ori recognition, cruciform formation, and ssDNA ligation. The OD serves to oligomerize Relaxases and Reps into hexamers and acts as the conduit for ssDNA translocation in Reps [20,21]. The AD of Reps are members of the Super Family 3 (SF3), which belong to the ATPases Associated with diverse cellular Activities (AAA+) families [20,22].…”

“…The OD serves to oligomerize Relaxases and Reps into hexamers and acts as the conduit for ssDNA translocation in Reps [20,21]. The AD of Reps are members of the Super Family 3 (SF3), which belong to the ATPases Associated with diverse cellular Activities (AAA+) families [20,22]. The AD is responsible for the helicase activity of Rep. Reps are not true replicases, as they initiate replication but are not responsible for DNA elongation.…”

“…Porcine circovirus type 2 (PCV2) may be regarded as the prototypical member of CRESS-DNA viruses as it is the most commonly studied member. We recently determined the structure of the PCV2 Rep in complex with ssDNA and adenosine diphosphate (ADP) [20]. The structure demonstrated a lock washer-like hexamer whose central channel was occupied by a hexanucleotide ssDNA.…”

“…Furthermore, we demonstrated that PCV2 Rep exhibited basal NTPase activity. In conjunction with the literature describing the structure of PCV2 ED and PCV2 ED bound to ssDNA, there are now atomic coordinates describing the full-length PCV2 Rep [20,[28][29][30]. Our PCV2 Rep structure inspired us to ask: how conserved are the primary and tertiary structures of Reps, how conserved are the functional centers of Reps, and are there distinctions between Reps that may shed light on their functional activity?…”