Modes of binding and activation of Mcm4/6/7 helicase on a bubble structure
Initiation of DNA replication is associated with localized melting of duplex DNA near replication origins. Helicases are loaded onto replication forks through the melted region, induced by initiator binding, in bacteria (32). We previously reported that Mcm4/6/7 can be loaded onto a bubble-like structure and can serve as a DNA helicase at the forks (13). The ability of Mcm4/6/7 to unwind the bubble substrate but not the conventional duplex DNA (Figures 2 and 13) indicates that Mcm can be loaded through the single-stranded segment of the bubble. Furthermore, the Mcm4/6/7 complex displays marked preference for thymine-rich sequences within the single-stranded segment for helicase activation (13). The results in this report indicate that helicase action of Mcm4/6/7 on synthetic bubbles may depend on the presence of an unpaired region of sufficient length (at least 40 nt), which may permit assembly of a double-hexameric complex on the substrate DNA, similar to SV40 T-antigen protein (Figure 2A) (21). When one strand of the single-stranded segment in T-rich bubble was replaced by guanine-rich sequences, the efficiency of unwinding was significantly reduced.
Our footprinting analyses showed that Mcm4/6/7 strongly protects 25 nt single-stranded DNA segment adjacent to each branch point and proximal to 5′ ends of both strands of the bubble. At each fork, one Mcm4/6/7 complex is likely to encircle the single-stranded DNA strand and two hexamers may bind symmetrically to the bubble substrate, forming a double hexameric structure on the bubble (see schematic drawing of Figure 1A). Efficient unwinding into both directions may require simultaneous activation of both hexamers which may sit at the center while extruding the unwound single-stranded DNA through the rings. This may closely resemble the proposed modes of binding and helicase actions of T-antigen (21). Although we cannot totally exclude the possibility that one Mcm4/6/7 hexamer at each fork unwinds the duplex independently, ring-shaped structures of mouse and archea MCM, as revealed by electron microscopy, bear much similarity to the recently solved structure of the SV40 large T-antigen (4,6), and are in favor of the double-hexameric structure of mouse Mcm on a bubble DNA.