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Loading mechanisms of ring helicases at replication origins.

Soultanas P - Mol. Microbiol. (2012)

Bottom Line: Bidirectional loading of two ring helicases at a replication origin is achieved by strictly regulated and intricately choreographed mechanisms, often through the action of replication initiation and helicase-loader proteins.Current structural and biochemical data reveal a wide range of different helicase-loading mechanisms.Here we review advances in this area and discuss their implications.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. soultanas@nottingham.ac.uk

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Related in: MedlinePlus

A. Helicase loader-mediated loading in A. aeolicus. A schematic diagram showing directional helicase loader-mediated and DnaA-mediated loading mechanisms on the 5′ and 3′ strands, respectively, based upon the A. aeolicus system (Duderstadt et al., 2011). The DnaA filament is shown to wrap double-stranded DNA around the outside with flexible helicase-interacting domains (domain I) projecting out from the filament. The filament extends into the 5′ strand of the melted DUE but in this case with the ssDNA in the interior of the filament. The helicase loader (green) forms a continuous heterofilament with the ATP-end of the DnaA-ssDNA filament, by docking the arginine from its Box VII into the ATP binding site of the DnaA, and delivers the helicase (brown) in the correct orientation onto the 5′ strand. The interactions of the flexible N-terminal DnaA domains with the helicase deliver it onto the 3′ strand in the opposite direction. A side-view of the Bacillus stearothermophilus DnaB helicase is shown with the characteristic two-tier (N-terminal and C-terminal tiers) ring structure of bacterial helicases (Bailey et al., 2007).B. Organization of the E. coli oriC. The relative positions of DnaA binding sites (R, I and τ sites), NAP (Nucleoid Associated Proteins) binding sites for IHF and FIS and the DUE are indicated. Binding of IHF between the R1 and R5 sites sharply bends the DNA, as indicated in the inset showing the crystal structure of IHF binding and bending double-stranded DNA.C. DnaA-mediated helicase loading in E. coli. A schematic model showing how two ring helicases are directionally loaded onto the E. coli oriC (Ozaki and Katayama, 2012). The DUE is cooperatively melted via binding of DnaA and IHF and the first helicase is loaded onto the bottom (A-rich) strand directionally. Subsequent translocation forward (in the 5′–3′ direction) melts a larger segment of the duplex allowing loading of the second helicase in the top (T-rich) strand and in the opposite direction. In both cases loading is mediated by the flexible N-terminal helicase-interacting domains of DnaA projecting out of the filament. For the sake of simplicity no helicase loader is depicted but it may participate indirectly in the process by binding onto the C-terminal tier of the helicase ring forcing opening of the ring for loading to proceed.
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fig02: A. Helicase loader-mediated loading in A. aeolicus. A schematic diagram showing directional helicase loader-mediated and DnaA-mediated loading mechanisms on the 5′ and 3′ strands, respectively, based upon the A. aeolicus system (Duderstadt et al., 2011). The DnaA filament is shown to wrap double-stranded DNA around the outside with flexible helicase-interacting domains (domain I) projecting out from the filament. The filament extends into the 5′ strand of the melted DUE but in this case with the ssDNA in the interior of the filament. The helicase loader (green) forms a continuous heterofilament with the ATP-end of the DnaA-ssDNA filament, by docking the arginine from its Box VII into the ATP binding site of the DnaA, and delivers the helicase (brown) in the correct orientation onto the 5′ strand. The interactions of the flexible N-terminal DnaA domains with the helicase deliver it onto the 3′ strand in the opposite direction. A side-view of the Bacillus stearothermophilus DnaB helicase is shown with the characteristic two-tier (N-terminal and C-terminal tiers) ring structure of bacterial helicases (Bailey et al., 2007).B. Organization of the E. coli oriC. The relative positions of DnaA binding sites (R, I and τ sites), NAP (Nucleoid Associated Proteins) binding sites for IHF and FIS and the DUE are indicated. Binding of IHF between the R1 and R5 sites sharply bends the DNA, as indicated in the inset showing the crystal structure of IHF binding and bending double-stranded DNA.C. DnaA-mediated helicase loading in E. coli. A schematic model showing how two ring helicases are directionally loaded onto the E. coli oriC (Ozaki and Katayama, 2012). The DUE is cooperatively melted via binding of DnaA and IHF and the first helicase is loaded onto the bottom (A-rich) strand directionally. Subsequent translocation forward (in the 5′–3′ direction) melts a larger segment of the duplex allowing loading of the second helicase in the top (T-rich) strand and in the opposite direction. In both cases loading is mediated by the flexible N-terminal helicase-interacting domains of DnaA projecting out of the filament. For the sake of simplicity no helicase loader is depicted but it may participate indirectly in the process by binding onto the C-terminal tier of the helicase ring forcing opening of the ring for loading to proceed.

Mentions: In A. aeolicus, the DnaC helicase loader cooperates with the replication initiator DnaA to load two ring helicases at the replication origin. The DnaA and DnaC nucleoprotein filaments described above are directional. One end of the filament terminates with a protein molecule (DnaA or DnaC) presenting an ATP-bound active site in the open state, defined as the ATP-end, and the opposite end of the filament terminates with a protein molecule presenting the arginine finger of Box VII, defined as the R-end (Fig. 1B and Mott et al., 2008). Initial binding of DnaA molecules to DnaA boxes, via the C-terminal domain IV, at the oriC forms a directional right-handed helical filament with the DNA double helix wrapped around the outside of the filament and the ATP-end directed towards the DUE. The constrained positive supercoiling induces compensatory negative supercoiling and weakening of the double helix within the DUE. Partial melting of the DUE at the ATP-end of the filament exposes the two DNA strands and the DnaA filament invades one of the strands forming an extended filament, with the single-stranded DNA bound along the contiguous network of the α3/α4 and α5/α6 helices inside the DnaA filament (Fig. 2A and Duderstadt et al., 2011). Therefore, the role of DnaA is initially to destabilize and actively melt the DUE at the replication origin.


Loading mechanisms of ring helicases at replication origins.

Soultanas P - Mol. Microbiol. (2012)

A. Helicase loader-mediated loading in A. aeolicus. A schematic diagram showing directional helicase loader-mediated and DnaA-mediated loading mechanisms on the 5′ and 3′ strands, respectively, based upon the A. aeolicus system (Duderstadt et al., 2011). The DnaA filament is shown to wrap double-stranded DNA around the outside with flexible helicase-interacting domains (domain I) projecting out from the filament. The filament extends into the 5′ strand of the melted DUE but in this case with the ssDNA in the interior of the filament. The helicase loader (green) forms a continuous heterofilament with the ATP-end of the DnaA-ssDNA filament, by docking the arginine from its Box VII into the ATP binding site of the DnaA, and delivers the helicase (brown) in the correct orientation onto the 5′ strand. The interactions of the flexible N-terminal DnaA domains with the helicase deliver it onto the 3′ strand in the opposite direction. A side-view of the Bacillus stearothermophilus DnaB helicase is shown with the characteristic two-tier (N-terminal and C-terminal tiers) ring structure of bacterial helicases (Bailey et al., 2007).B. Organization of the E. coli oriC. The relative positions of DnaA binding sites (R, I and τ sites), NAP (Nucleoid Associated Proteins) binding sites for IHF and FIS and the DUE are indicated. Binding of IHF between the R1 and R5 sites sharply bends the DNA, as indicated in the inset showing the crystal structure of IHF binding and bending double-stranded DNA.C. DnaA-mediated helicase loading in E. coli. A schematic model showing how two ring helicases are directionally loaded onto the E. coli oriC (Ozaki and Katayama, 2012). The DUE is cooperatively melted via binding of DnaA and IHF and the first helicase is loaded onto the bottom (A-rich) strand directionally. Subsequent translocation forward (in the 5′–3′ direction) melts a larger segment of the duplex allowing loading of the second helicase in the top (T-rich) strand and in the opposite direction. In both cases loading is mediated by the flexible N-terminal helicase-interacting domains of DnaA projecting out of the filament. For the sake of simplicity no helicase loader is depicted but it may participate indirectly in the process by binding onto the C-terminal tier of the helicase ring forcing opening of the ring for loading to proceed.
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Show All Figures
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fig02: A. Helicase loader-mediated loading in A. aeolicus. A schematic diagram showing directional helicase loader-mediated and DnaA-mediated loading mechanisms on the 5′ and 3′ strands, respectively, based upon the A. aeolicus system (Duderstadt et al., 2011). The DnaA filament is shown to wrap double-stranded DNA around the outside with flexible helicase-interacting domains (domain I) projecting out from the filament. The filament extends into the 5′ strand of the melted DUE but in this case with the ssDNA in the interior of the filament. The helicase loader (green) forms a continuous heterofilament with the ATP-end of the DnaA-ssDNA filament, by docking the arginine from its Box VII into the ATP binding site of the DnaA, and delivers the helicase (brown) in the correct orientation onto the 5′ strand. The interactions of the flexible N-terminal DnaA domains with the helicase deliver it onto the 3′ strand in the opposite direction. A side-view of the Bacillus stearothermophilus DnaB helicase is shown with the characteristic two-tier (N-terminal and C-terminal tiers) ring structure of bacterial helicases (Bailey et al., 2007).B. Organization of the E. coli oriC. The relative positions of DnaA binding sites (R, I and τ sites), NAP (Nucleoid Associated Proteins) binding sites for IHF and FIS and the DUE are indicated. Binding of IHF between the R1 and R5 sites sharply bends the DNA, as indicated in the inset showing the crystal structure of IHF binding and bending double-stranded DNA.C. DnaA-mediated helicase loading in E. coli. A schematic model showing how two ring helicases are directionally loaded onto the E. coli oriC (Ozaki and Katayama, 2012). The DUE is cooperatively melted via binding of DnaA and IHF and the first helicase is loaded onto the bottom (A-rich) strand directionally. Subsequent translocation forward (in the 5′–3′ direction) melts a larger segment of the duplex allowing loading of the second helicase in the top (T-rich) strand and in the opposite direction. In both cases loading is mediated by the flexible N-terminal helicase-interacting domains of DnaA projecting out of the filament. For the sake of simplicity no helicase loader is depicted but it may participate indirectly in the process by binding onto the C-terminal tier of the helicase ring forcing opening of the ring for loading to proceed.
Mentions: In A. aeolicus, the DnaC helicase loader cooperates with the replication initiator DnaA to load two ring helicases at the replication origin. The DnaA and DnaC nucleoprotein filaments described above are directional. One end of the filament terminates with a protein molecule (DnaA or DnaC) presenting an ATP-bound active site in the open state, defined as the ATP-end, and the opposite end of the filament terminates with a protein molecule presenting the arginine finger of Box VII, defined as the R-end (Fig. 1B and Mott et al., 2008). Initial binding of DnaA molecules to DnaA boxes, via the C-terminal domain IV, at the oriC forms a directional right-handed helical filament with the DNA double helix wrapped around the outside of the filament and the ATP-end directed towards the DUE. The constrained positive supercoiling induces compensatory negative supercoiling and weakening of the double helix within the DUE. Partial melting of the DUE at the ATP-end of the filament exposes the two DNA strands and the DnaA filament invades one of the strands forming an extended filament, with the single-stranded DNA bound along the contiguous network of the α3/α4 and α5/α6 helices inside the DnaA filament (Fig. 2A and Duderstadt et al., 2011). Therefore, the role of DnaA is initially to destabilize and actively melt the DUE at the replication origin.

Bottom Line: Bidirectional loading of two ring helicases at a replication origin is achieved by strictly regulated and intricately choreographed mechanisms, often through the action of replication initiation and helicase-loader proteins.Current structural and biochemical data reveal a wide range of different helicase-loading mechanisms.Here we review advances in this area and discuss their implications.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. soultanas@nottingham.ac.uk

Show MeSH
Related in: MedlinePlus