Bypass of a protein barrier by a replicative DNA helicase (original) (raw)

References

  1. Patel, S. S. & Picha, K. M. Structure and function of hexameric helicases. Annu. Rev. Biochem. 69, 651–697 (2000)
    Article CAS Google Scholar
  2. Enemark, E. J. & Joshua-Tor, L. On helicases and other motor proteins. Curr. Opin. Struct. Biol. 18, 243–257 (2008)
    Article CAS Google Scholar
  3. Egelman, E. H., Yu, X., Wild, R., Hingorani, M. M. & Patel, S. S. Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases. Proc. Natl Acad. Sci. USA 92, 3869–3873 (1995)
    Article ADS CAS Google Scholar
  4. Kaplan, D. L. & O’Donnell, M. Twin DNA pumps of a hexameric helicase provide power to simultaneously melt two duplexes. Mol. Cell 15, 453–465 (2004)
    Article CAS Google Scholar
  5. Fu, Y. V. et al. Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase. Cell 146, 931–941 (2011)
    Article CAS Google Scholar
  6. Kaplan, D. L., Davey, M. J. & O’Donnell, M. Mcm4,6,7 uses a “pump in ring” mechanism to unwind DNA by steric exclusion and actively translocate along a duplex. J. Biol. Chem. 278, 49171–49182 (2003)
    Article CAS Google Scholar
  7. Fanning, E. & Zhao, K. SV40 DNA replication: from the A gene to a nanomachine. Virology 384, 352–359 (2009)
    Article CAS Google Scholar
  8. Fanning, E., Zhao, X. & Jiang, X. in DNA Tumor Viruses (eds Damania, B. & Pipas, J. M. ) 1–24 (Springer US, 2009)
    Book Google Scholar
  9. Wessel, R., Schweizer, J. & Stahl, H. Simian virus 40 T-antigen DNA helicase is a hexamer which forms a binary complex during bidirectional unwinding from the viral origin of DNA replication. J. Virol. 66, 804–815 (1992)
    CAS PubMed PubMed Central Google Scholar
  10. Weisshart, K. et al. Two regions of simian virus 40 large T antigen determine cooperativity of double-hexamer assembly on the viral origin of DNA replication and promote hexamer interactions during bidirectional origin DNA unwinding. J. Virol. 73, 2201–2211 (1999)
    CAS PubMed PubMed Central Google Scholar
  11. Barbaro, B. A., Sreekumar, K. R., Winters, D. R., Prack, A. E. & Bullock, P. A. Phosphorylation of simian virus 40 large T antigen on Thr 124 selectively promotes double-hexamer formation on subfragments of the viral core origin. J. Virol. 74, 8601–8613 (2000)
    Article CAS Google Scholar
  12. Smelkova, N. V. & Borowiec, J. A. Dimerization of simian virus 40 T-antigen hexamers activates T-antigen DNA helicase activity. J. Virol. 71, 8766–8773 (1997)
    CAS PubMed PubMed Central Google Scholar
  13. Alexandrov, A. I., Botchan, M. R. & Cozzarelli, N. R. Characterization of simian virus 40 T-antigen double hexamers bound to a replication fork. J. Biol. Chem. 277, 44886–44897 (2002)
    Article CAS Google Scholar
  14. SenGupta, D. J. & Borowiec, J. A. Strand-specific recognition of a synthetic DNA replication fork by the SV40 large tumor antigen. Science 256, 1656–1661 (1992)
    Article ADS CAS Google Scholar
  15. Morris, P. D. et al. Hepatitis C virus NS3 and simian virus 40 large T antigen helicases displace streptavidin from 5′-biotinylated oligonucleotides but not from 3′-biotinylated oligonucleotides: evidence for directional bias in translocation on single-stranded DNA. Biochemistry 41, 2372–2378 (2002)
    Article CAS Google Scholar
  16. Goetz, G. S., Dean, F. B., Hurwitz, J. & Matson, S. W. The unwinding of duplex regions in DNA by the simian virus 40 large tumor antigen-associated DNA helicase activity. J. Biol. Chem. 263, 383–392 (1988)
    CAS PubMed Google Scholar
  17. Enemark, E. J. & Joshua-Tor, L. Mechanism of DNA translocation in a replicative hexameric helicase. Nature 442, 270–275 (2006)
    Article ADS CAS Google Scholar
  18. Li, D. et al. Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen. Nature 423, 512–518 (2003)
    Article ADS CAS Google Scholar
  19. Gai, D., Zhao, R., Li, D., Finkielstein, C. V. & Chen, X. S. Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell 119, 47–60 (2004)
    Article CAS Google Scholar
  20. Gomez-Lorenzo, M. G. et al. Large large T antigen on the simian virus 40 origin of replication: a 3D snapshot prior to DNA replication. EMBO J. 22, 6205–6213 (2003)
    Article CAS Google Scholar
  21. Cuesta, I. et al. Conformational rearrangements of SV40 large large T antigen during early replication events. J. Mol. Biol. 397, 1276–1286 (2010)
    Article CAS Google Scholar
  22. Borowiec, J. A. & Hurwitz, J. ATP stimulates the binding of simian virus 40 (SV40) large tumor antigen to the SV40 origin of replication. Proc. Natl Acad. Sci. USA 85, 64–68 (1988)
    Article ADS CAS Google Scholar
  23. Sclafani, R. A., Fletcher, R. J. & Chen, X. S. Two heads are better than one: regulation of DNA replication by hexameric helicases. Genes Dev. 18, 2039–2045 (2004)
    Article CAS Google Scholar
  24. Takahashi, T. S., Wigley, D. B. & Walter, J. C. Pumps, paradoxes and ploughshares: mechanism of the MCM2–7 DNA helicase. Trends Biochem. Sci. 30, 437–444 (2005)
    Article CAS Google Scholar
  25. Yardimci, H., Loveland, A. B., Habuchi, S., van Oijen, A. M. & Walter, J. C. Uncoupling of sister replisomes during eukaryotic DNA replication. Mol. Cell 40, 834–840 (2010)
    Article CAS Google Scholar
  26. Yardimci, H., Loveland, A. B., van Oijen, A. M. & Walter, J. C. Single-molecule analysis of DNA replication in Xenopus egg extracts. Methods 57, 179–186 (2012)
    Article CAS Google Scholar
  27. Stillman, B. W. & Gluzman, Y. Replication and supercoiling of simian virus 40 DNA in cell extracts from human cells. Mol. Cell. Biol. 5, 2051–2060 (1985)
    Article CAS Google Scholar
  28. Wobbe, C. R., Dean, F., Weissbach, L. & Hurwitz, J. In vitro replication of duplex circular DNA containing the simian virus 40 DNA origin site. Proc. Natl Acad. Sci. USA 82, 5710–5714 (1985)
    Article ADS CAS Google Scholar
  29. Bullock, P. A., Seo, Y. S. & Hurwitz, J. Initiation of simian virus 40 DNA synthesis in vitro. Mol. Cell. Biol. 11, 2350–2361 (1991)
    Article CAS Google Scholar
  30. Murakami, Y. & Hurwitz, J. Functional interactions between SV40 large T antigen and other replication proteins at the replication fork. J. Biol. Chem. 268, 11008–11017 (1993)
    CAS PubMed Google Scholar
  31. Kim, S., Dallmann, H. G., McHenry, C. S. & Marians, K. J. Coupling of a replicative polymerase and helicase: a τ-DnaB interaction mediates rapid replication fork movement. Cell 84, 643–650 (1996)
    Article CAS Google Scholar
  32. Stano, N. M. et al. DNA synthesis provides the driving force to accelerate DNA unwinding by a helicase. Nature 435, 370–373 (2005)
    Article ADS CAS Google Scholar
  33. Chen, L. et al. Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase. Biochemistry 30, 11018–11025 (1991)
    Article CAS Google Scholar
  34. Seinsoth, S., Uhlmann-Schiffler, H. & Stahl, H. Bidirectional DNA unwinding by a ternary complex of large T antigen, nucleolin and topoisomerase I. EMBO Rep. 4, 263–268 (2003)
    Article CAS Google Scholar
  35. Barker, S., Weinfeld, M. & Murray, D. DNA-protein crosslinks: their induction, repair, and biological consequences. Mutat. Res. 589, 111–135 (2005)
    Article CAS Google Scholar
  36. Anand, R. P. et al. Overcoming natural replication barriers: differential helicase requirements. Nucleic Acids Res. 40, 1091–1105 (2011)
    Article Google Scholar
  37. Wu, C., Roy, R. & Simmons, D. T. Role of single-stranded DNA binding activity of large T antigen in simian virus 40 DNA replication. J. Virol. 75, 2839–2847 (2001)
    Article CAS Google Scholar
  38. Eki, T., Matsumoto, T., Murakami, Y. & Hurwitz, J. The replication of DNA containing the simian virus 40 origin by the monopolymerase and dipolymerase systems. J. Biol. Chem. 267, 7284–7294 (1992)
    CAS PubMed Google Scholar
  39. Ishimi, Y., Claude, A., Bullock, P. & Hurwitz, J. Complete enzymatic synthesis of DNA containing the SV40 origin of replication. J. Biol. Chem. 263, 19723–19733 (1988)
    CAS PubMed Google Scholar
  40. Wold, M. S., Li, J. J. & Kelly, T. J. Initiation of simian virus 40 DNA replication in vitro: large-tumor-antigen- and origin-dependent unwinding of the template. Proc. Natl Acad. Sci. USA 84, 3643–3647 (1987)
    Article ADS CAS Google Scholar
  41. Wang, I.-N. Lysis timing and bacteriophage fitness. Genetics 172, 17–26 (2005)
    Article Google Scholar
  42. Thomason, L. C., Oppenheim, A. B. & Court, D. L. Modifying bacteriophage lambda with recombineering. Methods Mol Biol. 501, 239–251 (2009)
    Article CAS Google Scholar
  43. Kuhn, H. & Frank-Kamenetskii, M. D. Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases. Nucleic Acids Res. 36, e40 (2008)
    Article Google Scholar
  44. Loparo, J. J., Kulczyk, A. W., Richardson, C. C. & van Oijen, A. M. Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange. Proc. Natl Acad. Sci. USA 108, 3584–3589 (2011)
    Article ADS CAS Google Scholar
  45. MacMillan, A. M., Chen, L. & Verdine, G. L. Synthesis of an oligonucleotide suicide substrate for DNA methyltransferases. J. Org. Chem. 57, 2989–2991 (1992)
    Article CAS Google Scholar
  46. Tanner, N. A. & van Oijen, A. M. in Single Molecule Tools, Part B:Super-Resolution, Particle Tracking, Multiparameter, and Force Based Methods (ed. Walter, N. G. ) 259–278 (Academic, 2010)

Download references