Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 50, 2015, Pages E6852-E6861

  Rad, Behzad ^a,b   Forget, Anthony L ^a   Baskin, Ronald J ^a   Kowalczykowski, Stephen C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

BLM; DNA repair; Fluorescence; Recombination; TIRF microscopy

Indexed keywords

DIMER; DNA; DOUBLE STRANDED DNA; FLUORESCENT DYE; HELICASE; MONOMER; RECQ HELICASE; SINGLE STRANDED DNA; VIRUS DNA;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA DENATURATION; DNA REPAIR; DNA REPLICATION; ENZYME ACTIVITY; FLUORESCENCE IMAGING; HOLLIDAY JUNCTION; HOMOLOGOUS RECOMBINATION; MOLECULE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN BINDING; CHEMISTRY; CONFORMATION; ENTEROBACTERIA PHAGE LAMBDA; FLUORESCENCE; GENETICS; METABOLISM; MICROSCOPY; PROCEDURES;

BACTERIOPHAGE LAMBDA; DNA, VIRAL; FLUORESCENCE; FLUORESCENT DYES; MICROSCOPY; NUCLEIC ACID CONFORMATION; RECQ HELICASES;

EID: 84950103610     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1518028112     Document Type: Article

References (72)

1. Singleton MR, Dillingham MS, Wigley D.B. (2007) Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem 76:23-50.
2. Nakayama H, et al (1984) Isolation and genetic characterization of a thymineless death-resistant mutant of Escherichia coli K12: Identification of a new mutation (recQ1) that blocks the RecF recombination pathway. Mol Gen Genet 195(3): 474-480.
3. Bennett RJ, Keck J.L. (2004) Structure and function of RecQ DNA helicases. Crit Rev Biochem Mol Biol 39(2):79-97.
4. Brosh RM, Jr, Bohr VA (2007) Human premature aging, DNA repair and RecQ helicases. Nucleic Acids Res 35(22):7527-7544.
5. Umezu K, Nakayama H. (1993) RecQ DNA helicase of Escherichia coli. Characterization of the helix-unwinding activity with emphasis on the effect of single-stranded DNA-binding protein. J Mol Biol 230(4):1145-1150.
6. Umezu K, Nakayama K, Nakayama H. (1990) Escherichia coli RecQ protein is a DNA helicase. Proc Natl Acad Sci USA 87(14):5363-5367.
7. Harmon FG, Kowalczykowski S.C. (1998) RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination. Genes Dev 12(8):1134-1144.
8. Courcelle J, Hanawalt P.C. (1999) RecQ and RecJ process blocked replication forks prior to the resumption of replication in UV-irradiated Escherichia coli. Mol Gen Genet 262(3):543-551.
9. Handa N, Morimatsu K, Lovett S.T., Kowalczykowski S.C. (2009) Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli. Genes Dev 23(10): 1234-1245.
10. Morimatsu K, Kowalczykowski S.C. (2014) RecQ helicase and RecJ nuclease provide complementary functions to resect DNA for homologous recombination. Proc Natl Acad Sci USA 111(48):E5133-E5142.
11. Adams MD, McVey M, Sekelsky J.J. (2003) Drosophila BLM in double-strand break repair by synthesis-dependent strand annealing. Science 299 (5604):265-267.
12. Hanada K, et al (1997) RecQ DNA helicase is a suppressor of illegitimate recombination in Escherichia coli. Proc Natl Acad Sci USA 94(8):3860-3865.
13. Harmon FG, DiGate RJ, Kowalczykowski S.C. (1999) RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: A conserved mechanism for control of DNA recombination. Mol Cell 3(5):611-620.
14. Suski C, Marians K.J. (2008) Resolution of converging replication forks by RecQ and topoisomerase III. Mol Cell 30(6):779-789.
15. Lopez CR, et al (2005) A role for topoisomerase III in a recombination pathway alternative to RuvABC. Mol Microbiol 58(1):80-101.
16. Harmon FG, Kowalczykowski S.C. (2001) Biochemical characterization of the DNA helicase activity of the escherichia coli RecQ helicase. J Biol Chem 276(1):232-243.
17. Harmon FG, Brockman JP, Kowalczykowski S.C. (2003) RecQ helicase stimulates both DNA catenation and changes in DNA topology by topoisomerase III. J Biol Chem 278(43):42668-42678.
18. Manthei KA, Hill MC, Burke J.E., Butcher SE, Keck J.L. (2015) Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases. Proc Natl Acad Sci USA 112(14):4292-4297.
19. Shereda RD, Bernstein DA, Keck J.L. (2007) A central role for SSB in Escherichia coli RecQ DNA helicase function. J Biol Chem 282(26):19247-19258.
20. Rad B, Kowalczykowski S.C. (2012) Efficient coupling of ATP hydrolysis to translocation by RecQ helicase. Proc Natl Acad Sci USA 109(5):1443-1448.
21. Rad B, Kowalczykowski S.C. (2012) Translocation of E. coli RecQ helicase on singlestranded DNA. Biochemistry 51(13):2921-2929.
22. Sarlós K., Gyimesi M, Kovács M (2012) RecQ helicase translocates along single-stranded DNA with a moderate processivity and tight mechanochemical coupling. Proc Natl Acad Sci USA 109(25):9804-9809.
23. Gyimesi M, et al (2012) Complex activities of the human Bloom's syndrome helicase are encoded in a core region comprising the RecA and Zn-binding domains. Nucleic Acids Res 40(9):3952-3963.
24. Nimonkar AV, et al (2011) BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair. Genes Dev 25(4): 350-362.
25. Cejka P, et al (2010) DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1 and Mre11-Rad50-Xrs2. Nature 467 (7311):112-116.
26. Niu H, et al (2010) Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae. Nature 467 (7311):108-111.
27. Li N, et al (2010) Multiple Escherichia coli RecQ helicase monomers cooperate to unwind long DNA substrates: A fluorescence cross-correlation spectroscopy study. J Biol Chem 285(10):6922-6936.
28. Xu HQ, et al (2003) The Escherichia coli RecQ helicase functions as a monomer. J Biol Chem 278(37):34925-34933.
29. Zhang XD, et al (2006) Escherichia coli RecQ is a rapid, efficient, and monomeric helicase. J Biol Chem 281(18):12655-12663.
30. Joo C, Balci H, Ishitsuka Y., Buranachai C, Ha T. (2008) Advances in single-molecule fluorescence methods for molecular biology. Annu Rev Biochem 77:51-76.
31. Bianco PR, et al (2001) Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 409 (6818):374-378.
32. Spies M, Amitani I, Baskin R.J., Kowalczykowski S.C. (2007) RecBCD enzyme switches lead motor subunits in response to chi recognition. Cell 131(4):694-705.
33. Spies M, et al (2003) A molecular throttle: The recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell 114(5):647-654.
34. Fili N, et al (2010) Visualizing helicases unwinding DNA at the single molecule level. Nucleic Acids Res 38(13):4448-4457.
35. Handa N, Bianco PR, Baskin R.J., Kowalczykowski S.C. (2005) Direct visualization of RecBCD movement reveals cotranslocation of the RecD motor after chi recognition. Mol Cell 17(5):745-750.
36. Greene EC, Mizuuchi K. (2002) Direct observation of single MuB polymers: Evidence for a DNA-dependent conformational change for generating an active target complex. Mol Cell 9(5):1079-1089.
37. Amitani I, Liu B, Dombrowski C.C., Baskin RJ, Kowalczykowski S.C. (2010) Watching individual proteins acting on single molecules of DNA. Methods Enzymol 472:261-291.
38. Forget AL, Dombrowski CC, Amitani I, Kowalczykowski S.C. (2013) Exploring protein DNA interactions in 3D using in situ construction, manipulation and visualization of individual DNA dumbbells with optical traps, microfluidics and fluorescence microscopy. Nat Protoc 8(3):525-538.
39. Fili N, Toseland CP, Dillingham M.S., Webb MR, Molloy J.E. (2011) A single-molecule approach to visualize the unwinding activity of DNA helicases. Methods Mol Biol 778: 193-214.
40. Dillingham MS, et al (2008) Fluorescent single-stranded DNA binding protein as a probe for sensitive, real-time assays of helicase activity. Biophys J 95(7):3330-3339.
41. Bell JC, Plank JL, Dombrowski C.C., Kowalczykowski S.C. (2012) Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA. Nature 491 (7423): 274-278.
42. Eggleston AK, Rahim NA, Kowalczykowski S.C. (1996) A helicase assay based on the displacement of fluorescent, nucleic acid-binding ligands. Nucleic Acids Res 24(7): 1179-1186.
43. Kowalczykowski S, Steinhardt J. (1977) Kinetics of hemoglobin S gelation followed by continuously sensitive low-shear viscosity. J Mol Biol 115(2):201-213.
44. Nielsen AE (1964) Kinetics of Precipitation (MacMillan, New York), p 153.
45. Oosawa F, Asakura S. (1975) Thermodynamics of the Polymerization of Protein (Academic, New York) p 204.
46. Jensen DE, von Hippel PH (1976) DNA "melting" proteins. I. Effects of bovine pancreatic ribonuclease binding on the conformation and stability of DNA. J Biol Chem 251(22):7198-7214.
47. Jensen DE, Kelly RC, von Hippel PH (1976) DNA "melting" proteins. II. Effects of bacteriophage T4 gene 32-protein binding on the conformation and stability of nucleic acid structures. J Biol Chem 251(22):7215-7228.
48. Lucic B, et al (2011) A prominent β-hairpin structure in the winged-helix domain of RECQ1 is required for DNA unwinding and oligomer formation. Nucleic Acids Res 39(5):1703-1717.
49. Hishida T, et al (2004) Role of the Escherichia coli RecQ DNA helicase in SOS signaling and genome stabilization at stalled replication forks. Genes Dev 18(15):1886-1897.
50. Byrd AK, Raney K.D. (2004) Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA. Nat Struct Mol Biol 11(6):531-538.
51. Levin MK, Wang YH, Patel S.S. (2004) The functional interaction of the hepatitis C virus helicase molecules is responsible for unwinding processivity. J Biol Chem 279(25): 26005-26012.
52. Byrd AK, Raney K.D. (2005) Increasing the length of the single-stranded overhang enhances unwinding of duplex DNA by bacteriophage T4 Dda helicase. Biochemistry 44(39):12990-12997.
53. Levin MK, Patel S.S. (1999) The helicase from hepatitis C virus is active as an oligomer. J Biol Chem 274(45):31839-31846.
54. Dou SX, Wang PY, Xu H.Q., Xi X.G. (2004) The DNA binding properties of the Escherichia coli RecQ helicase. J Biol Chem 279(8):6354-6363.
55. Kowalczykowski SC, Lonberg N, Newport J.W., Paul LS, von Hippel PH (1980) On the thermodynamics and kinetics of the cooperative binding of bacteriophage T4-coded gene 32 (helix destabilizing) protein to nucleic acid lattices. Biophys J 32(1):403-418.
56. Duderstadt KE, Chuang K, Berger J.M. (2011) DNA stretching by bacterial initiators promotes replication origin opening. Nature 478 (7368):209-213.
57. Dueber EL, Corn JE, Bell S.D., Berger J.M. (2007) Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science 317 (5842):1210-1213.
58. Gaudier M, Schuwirth BS, Westcott S.L., Wigley D.B. (2007) Structural basis of DNA replication origin recognition by an ORC protein. Science 317 (5842):1213-1216.
59. Dodson M, Dean FB, Bullock P, Echols H., Hurwitz J. (1987) Unwinding of duplex DNA from the SV40 origin of replication by T antigen. Science 238 (4829):964-967.
60. Dean FB, et al (1987) Simian virus 40 (SV40) DNA replication: SV40 large T antigen unwinds DNA containing the SV40 origin of replication. Proc Natl Acad Sci USA 84(1): 16-20.
61. Gauss P, Park K, Spencer T.E., Hacker K.J. (1994) DNA helicase requirements for DNA replication during bacteriophage T4 infection. J Bacteriol 176(6):1667-1672.
62. Barry J, Alberts B. (1994) Purification and characterization of bacteriophage T4 gene 59 protein. ADNA helicase assembly protein involved in DNA replication. J Biol Chem 269(52):33049-33062.
63. Bernstein DA, Zittel MC, Keck J.L. (2003) High-resolution structure of the E. coli RecQ helicase catalytic core. EMBO J 22(19):4910-4921.
64. Zhu Z, Chung WH, Shim E.Y., Lee SE, Ira G. (2008) Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134(6):981-994.
65. Nimonkar AV, Ozsoy AZ, Genschel J, Modrich P., Kowalczykowski S.C. (2008) Human exonuclease 1 and BLM helicase interact to resect DNA and initiate DNA repair. Proc Natl Acad Sci USA 105(44):16906-16911.
66. Wu L, Hickson I.D. (2003) The Bloom's syndrome helicase suppresses crossing over during homologous recombination. Nature 426 (6968):870-874.
67. Cejka P, Plank JL, Bachrati C.Z., Hickson ID, Kowalczykowski S.C. (2010) Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1-Top3. Nat Struct Mol Biol 17(11):1377-1382.
68. Cejka P, Kowalczykowski S.C. (2010) The full-length Saccharomyces cerevisiae Sgs1 protein is a vigorous DNA helicase that preferentially unwinds holliday junctions. J Biol Chem 285(11):8290-8301.
69. Schneider CA, Rasband WS, Eliceiri K.W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9(7):671-675.
70. Sambrook J, Fritsch EF, Maniatis T. (1989) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY), 2nd Ed.
71. Forget AL, Kowalczykowski S.C. (2012) Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search. Nature 482 (7385):423-427.
72. Doyle PS, Ladoux B, Viovy J.L. (2000) Dynamics of a tethered polymer in shear flow. Phys Rev Lett 84(20):4769-4772.