Superfamily 2 helicases

Frontiers in Bioscience

Volumn 17, Issue 6, 2012, Pages 2070-2088

  Byrd, Alicia K ^a   Raney, Kevin D ^a  

^a UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

Author keywords

DEAD box; DEAH; DExH; Helicase; Review H4R molecular pharmacology; Superfamily 2

Indexed keywords

EID: 84860370125     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/4038     Document Type: Review

References (168)

1. Margaret E. Fairman-Williams, Ulf Peter Guenther, Eckhard Jankowsky: SF1 and SF2 helicases: family matters. Curr Opin Struct Biol 20, 313-324 (2010).
2. Timothy M. Lohman, Eric. J. Tomko, Colin. G. Wu: Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nat Rev Mol Cell Biol 9, 391-401 (2008). (Pubitemid 351574201)
3. Anna Marie Pyle: Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biochem 37, 317-336 (2008).
4. Martin R. Singleton, Mark S. Dillingham, Dale B. Wigley: Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem 76, 23- 50 (2007).
5. Alexander E. Gorbalenya, Eugene V. Koonin, Alexi P. Donchenko, Vladimir M. Blinov: Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res 17, 4713-4730 (1989). (Pubitemid 19165040)
6. Alexander E. Gorbalenya, Eugene V. Koonin: Helicases: amino acid sequence comparisons and structure-function relationships. Curr Opin Struct Biol 3, 419-429 (1993). (Pubitemid 23207576)
7. Olivier Cordin, Josette Banroques, N. Kyle Tanner, Patrick Linder: The DEAD-box protein family of RNA helicases. Gene 367, 17-37 (2006). (Pubitemid 43286737)
8. Mark S. Dillingham, Dale B. Wigley, Martin R. Webb: Direct measurement of single-stranded DNA translocation by PcrA helicase using the fluorescent base analogue 2-aminopurine. Biochemistry 41, 643- 51 (2002). (Pubitemid 34062036)
9. Mark S. Dillingham, Dale B. Wigley, Martin R. Webb: Demonstration of unidirectional singlestranded DNA translocation by PcrA helicase: measurement of step size and translocation speed. Biochemistry 39, 205-212 (2000). (Pubitemid 30033335)
10. Panos Soultanas, Mark S. Dillingham, Paul Wiley, Martin R. Webb, Dale B. Wigley: Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism. EMBO J 19, 3799-3810 (2000). (Pubitemid 30462137)
11. Vaishnavi Rajagopal, Madhura Gurjar, Mikhail K. Levin, Smita S. Patel: The Protease Domain Increases the Translocation Stepping Efficiency of the Hepatitis C Virus NS3-4A Helicase. J Biol Chem 285, 17821-17832 (2010).
12. Jin Yu, Wei Cheng, Carlos Bustamante, George Oster: Coupling Translocation with Nucleic Acid Unwinding by NS3 Helicase. J Mol Biol 404, 439- 455 (2010).
13. Dennis L. Matlock, Laxmi Yeruva, Alicia K. Byrd, Samuel G. Mackintosh, Clint Langston, Carrie Brown, Craig E. Cameron, Christopher J. Fischer, Kevin D. Raney: Investigation of Translocation, DNA Unwinding, and Protein Displacement by NS3h, the Helicase Domain from the Hepatitis C Virus Helicase. Biochemistry 49, 2097-2109 (2010).
14. Sua Myong, Ivan Rasnik, Chirlmin Joo, Timopthy M. Lohman, Taekjip Ha: Repetitive shuttling of a motor protein on DNA. Nature 437, 1321-1325 (2005). (Pubitemid 41568672)
15. Eric J. Tomko, Christopher J. Fischer, Anita Niedziela-Majka, Timothy M. Lohman: A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNA. Mol Cell 26, 335-347 (2007). (Pubitemid 46687098)
16. Ralf Seidel, Joost G. Bloom, Cees Dekker, Mark D. Szczelkun: Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I. EMBO J 27, 1388-1398 (2008). (Pubitemid 351655181)
17. Sua Myong, Sheng Cui, Peter V. Cornish, Axel Kirchhofer, Michaela U. Gack, Jae U. Jung, Karl-Peter Hopfner, Taekjip Ha: Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA. Science 323, 1070-1074 (2009).
18. Yongli Zhang, Corey L. Smith, Anjanabha Saha, Stephan W. Grill, Shirley Mihardja, Steven B. Smith, Bradley R. Cairns, Craig L. Peterson, Carlos Bustamante: DNA Translocation and Loop Formation Mechanism of Chromatin Remodeling by SWI/SNF and RSC. Mol Cell 24, 559-568 (2006). (Pubitemid 350284224)
19. Martin Zofall, Jim Persinger, Stefan R. Kassabov, Blaine Bartholomew: Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat Struct Mol Biol 13, 339-346 (2006). (Pubitemid 43873505)
20. Quansheng Yang, Eckhard Jankowsky: The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases. Nat Struct Mol Biol 13, 981-986 (2006). (Pubitemid 44684849)
21. Quansheng Yang, Mark Del Campo, Alan M. Lambowitz, Eckhard Jankowsky: DEAD-Box Proteins Unwind Duplexes by Local Strand Separation. Mol Cell 28, 253-263 (2007). (Pubitemid 47610740)
22. J. E. Walker, M. Saraste, M. J. Runswick, N. J. Gay: Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1, 945-951 (1982).
23. Bojana Lucic, Ying Zhang, Oliver King, Ramiro Mendoza-Maldonado, Matteo Berti, Frank H. Niesen, Nicola A. Burgess-Brown, Ashley C. W. Pike, Christopher D. O. Cooper, Opher Gileadi, Alessandro Vindigni: A prominent beta-hairpin structure in the winged-helix domain of RECQ1 is required for DNA unwinding and oligomer formation. Nucleic Acids Res 39, 1703-1717 (2011).
24. Meltem Muftuoglu, Tomasz Kulikowicz, Gad Beck, Jae Wan Lee, Jason Piotrowski, Vilhelm A. Bohr: Intrinsic ssDNA Annealing Activity in the CTerminal Region of WRN. Biochemistry 47, 10247- 10254 (2008).
25. Eckhard Jankowsky, Margaret E. Fairman: RNA helicases - one fold for many functions. Curr Opin Struct Biol 17, 316-324 (2007). (Pubitemid 47021361)
26. Smita S. Patel, K. M. Picha: Structure and function of hexameric helicases. Annu Rev Biochem 69, 651-697 (2000).
27. Eckhard Jankowsky, Margaret E. Fairman: Remodeling of ribonucleoprotein complexes with DExH/D RNA helicases. Nucleic Acids Res 34, 4181- 4188 (2006). (Pubitemid 44542197)
28. Margaret E. Fairman, Patricia A. Maroney, Wen Wang, Heath A. Bowers, Paul Gollnick, Timothy W. Nilsen, Eckhard Jankowsky: Protein displacement by DExH/D RNA helicases without duplex unwinding. Science 304, 730-734 (2004). (Pubitemid 38560878)
29. Richard J. Bennett, James L. Keck: Structure and Function of RecQ DNA Helicases. Crit Rev Biochem Mol Biol 39, 79-97 (2004). (Pubitemid 38888058)
30. Frances V. Fuller-Pace: DExD/H box RNA helicases: multifunctional proteins with important roles in transcriptional regulation. Nucleic Acids Res 34, 4206-4215 (2008). (Pubitemid 44542200)
31. Alexandra. Lusser, James T. Kadonaga: Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25, 1192-1200 (2003). (Pubitemid 37499319)
32. Anja J. van Brabant, Rodica Stan, Nathan A. Ellis: DNA helicases, genomic instability, and heman genetic disease. Annu Rev Genom Human Genet 1, 409-459 (2000).
33. Nathan A. Ellis: DNA helicases in inherited human disorders. Curr Opin Gen Dev 7, 354-363 (1997). (Pubitemid 27292287)
34. Manuel Hilbert, Anne R. Karow, Dagmar Klostermeier: The mechanism of ATP-dependent RNA unwinding by DEAD box proteins. Biol Chem 390, 1237-1250 (2009).
35. Jacob K. Grohman, Mark Del Campo, Hari Bhaskaran, Pilar Tijerina, Alan M. Lambowitz, Rick Russell: Probing the Mechanisms of DEAD-Box Proteins as General RNA Chaperones: The CTerminal Domain of CYT-19 Mediates General Recognition of RNA. Biochemistry 46, 3013-3022 (2007). (Pubitemid 46449125)
36. Pilar Tijerina, Hari Bhaskaran, Rick Russell: Nonspecific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone. Proc Natl Acad Sci U S A 103, 16698-16703 (2006). (Pubitemid 44737316)
37. Fei Liu, Andrea Putnam, Eckhard Jankowsky: ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding. Proc Natl Acad Sci U S A 105, 20209-20214 (2008).
38. N. Kyle Tanner, Olivier Cordin, Josette Banroques, Monique Doere, Patrick Linder: The Q Motif: A Newly Identified Motif in DEAD Box Helicases May Regulate ATP Binding and Hydrolysis. Mol Cell 11, 127-138 (2003). (Pubitemid 36126596)
39. Ruairi Collins, Tobias Karlberg, Lari Lehtio, Patrick Schutz, Susanne van den Berg, Lars Goran Dahlgren, Martin Hammarstrom, Johan Weigelt, Herwig Schuler: The DEXD/H-box RNA Helicase DDX19 Is Regulated by an alpha-Helical Switch. J Biol Chem 284, 10296-10300 (2009).
40. Christian B. F. Andersen, Lionel Ballut, Jesper S. Johansen, Hala Chamieh, Klaus H. Nielsen, Cristiano L. P. Oliveira, Jan Skov Pedersen, Bertrand Seraphin, Herve Le Hir, Gregers Rom Andersen: Structure of the Exon Junction Core Complex with a Trapped DEAD-Box ATPase Bound to RNA. Science 313, 1968-1972 (2006). (Pubitemid 44498005)
41. Mark Del Campo, Alan M. Lambowitz: Structure of the Yeast DEAD Box Protein Mss116p Reveals Two Wedges that Crimp RNA. Mol Cell 35, 598-609 (2009).
42. Fulvia Bono, Judith Ebert, Esben Lorentzen, Elena Conti: The Crystal Structure of the Exon Junction Complex Reveals How It Maintains a Stable Grip on mRNA. Cell 126, 713-725 (2006). (Pubitemid 44233638)
43. Toru Sengoku, Osamu Nureki, Akira Nakamura, Satoru Kobayashi, Shigeyuki Yokoyama: Structural Basis for RNA Unwinding by the DEAD-Box Protein Drosophila Vasa. Cell 125, 287-300 (2006).
44. Yingfeng Chen, Jeffrey P. Potratz, Pilar Tijerina, Mark Del Campo, Alan M. Lambowitz, Rick Russell: DEAD-box proteins can completely separate an RNA duplex using a single ATP. Proc Natl Acad Sci U S A 105, 20203-20208 (2008).
45. Jon R. Lorsch, Daniel Herschlag: The DEAD Box Protein eIF4A. 1. A Minimal Kinetic and Thermodynamic Framework Reveals Coupled Binding of RNA and Nucleotide. Biochemistry 37, 2180-2193 (1998). (Pubitemid 28119291)
46. Kevin J. Polach, Olke C. Uhlenbeck: Cooperative Binding of ATP and RNA Substrates to the DEAD/H Protein DbpA. Biochemistry 41, 3693-3702 (2002). (Pubitemid 34224682)
47. Olivier Cordin, N. Kyle Tanner, Monique Doere, Patrick Linder, Josette Banroques: The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity. EMBO J 23, 2478-2487 (2004). (Pubitemid 38988220)
48. Isabelle Iost, Marc Dreyfus, Patrick Linder: Ded1p, a DEAD-box Protein Required for Translation Initiation in Saccharomyces cerevisiae, Is an RNA Helicase. J Biol Chem 274, 17677-17683 (1999).
49. Arnon Henn, Wenxiang Cao, David D. Hackney, Enrique M. De La Cruz: The ATPase Cycle Mechanism of the DEAD-box rRNA Helicase, DbpA. J Mol Biol 377, 193-205 (2008).
50. Arnon Henn, Wenxiang Cao, N Licciardello, S. E Heitkamp, David D. Hackney, Enrique M. De La Cruz: Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proc Natl Acad Sci U S A 107, 4046-4050 (2010).
51. Xuying Wang, Huijue Jia, Eckhard Jankowsky, James T. Anderson: Degradation of hypomodified tRNAiMet in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p. RNA 14, 107- 116 (2008).
52. William R. Widner, Reed B. Wickner: Evidence that the SKI antiviral system of Saccharomyces cerevisiae acts by blocking expression of viral mRNA. Mol Cell Biol 13, 4331-4341 (1993). (Pubitemid 23187662)
53. Ryan N. Jackson, A. Alejandra Klauer, Bradley J. Hintze, Howard Robinson, Ambro van Hoof, Sean J. Johnson: The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing. EMBO J 29, 2205-2216 (2010).
54. Justin T. Brown, Xinxue Bai, Arlen W. Johnson: The yeast antiviral proteins Ski2p, Ski3p, and Ski8p exist as a complex in vivo. RNA 6, 449-457 (2000). (Pubitemid 30161288)
55. Tamas I. Orban, Elisa Izaurralde: Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA 11, 459-469 (2005). (Pubitemid 40397179)
56. John R. Weir, Fabien Bonneau, Jendrik Hentschel, Elena Conti: Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proc Natl Acad Sci U S A 107, 12139-12144 (2010).
57. Eckhard Jankowsky, Christian H. Gross, Stewart Shuman, Anna Marie Pyle: The DExH protein NPH-II is a processive and directional motor for unwinding RNA. Nature 403, 447-451 (2000). (Pubitemid 30073096)
58. Kevin D. Raney, Suresh D. Sharma, Ibrahim M. Moustafa, Craig E. Cameron: Hepatitis C Virus Nonstructural Protein 3 (HCV NS3): A Multifunctional Antiviral Target. J Biol Chem 285, 22725-22731 (2010).
59. Jane Kawaoka, Anna M. Pyle: Choosing beteen DNA and RNA: the polymer specificity of RNA helicase NPH-II. Nucleic Acids Res 33, 644-649 (2005). (Pubitemid 40360994)
60. Jane Kawaoka, Eckhard Jankowsky, Anna M. Pyle: Backbone tracking by the SF2 helicase NPH-II. Nat Struct Mol Biol 11, 526-530 (2004). (Pubitemid 38691919)
61. Rudolf K. F. Beran, Michael M. Bruno, Heath A. Bowers, Eckhard Jankowsky, Anna Marie Pyle: Robust Translocation Along a Molecular Monorail: the NS3 Helicase from Hepatitis C Virus Traverses Unusually Large Disruptions in its Track. J Mol Biol 358, 974-982 (2006).
62. Chun Chung Wang, Zhi Shun Huang, Pei Ling Chiang, Chien Tsun Chen, Huey Nan Wu: Analysis of the nucleoside triphosphatase, RNA triphosphatase, and unwinding activities of the helicase domain of dengue virus NS3 protein. FEBS Letters 583, 691-696 (2009).
63. Joseph L. Kim, Kurt A. Morgenstern, James P. Griffith, Maureen D. Dwyer, John A. Thomson, Mark A. Murcko, Chao Lin, Paul R. Caron: Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Structure 6, 89- 100 (1998). (Pubitemid 28084402)
64. Meigang Gu, Charles M. Rice: Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism. Proc Natl Acad Sci U S A 107, 521-528 (2010).
65. Nanhua Yao, Paul Reichert, S Shane Taremi, Winifred W. Prosise, Patricia C. Weber: Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease-helicase. Structure 7, 1353-1363 (1999). (Pubitemid 29529876)
66. Sophie Dumont, Wei Cheng, Victor Serebrov, Rudolf K. Beran, Ignacio Tinoco, Anna Marie Pyle, Carlos Bustamante: RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature 439, 105-108 (2006). (Pubitemid 43053637)
67. Alan J. Tackett, Yingfeng Chen, Craig E. Cameron, Kevin D. Raney: Multiple Full-length NS3 Molecules Are Required for Optimal Unwinding of Oligonucleotide DNA in vitro. J Biol Chem 280, 10797-10806 (2005). (Pubitemid 40395943)
68. Victor Serebrov, Anna Marie Pyle: Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase. Nature 430, 476-480 (2004). (Pubitemid 38987912)
69. Sua Myong, Michael M. Bruno, Anna Marie Pyle, Taekjip Ha: Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase. Science 317, 513-516 (2007). (Pubitemid 47196115)
70. Victor Serebrov, Rudolf K. Beran, Anna Marie Pyle: Establishing a mechanistic basis for the large kinetic steps of the NS3 helicase. J Biol Chem 284, 2512-2521 (2009).
71. Todd C. Appleby, Robert Anderson, Olga Fedorova, Anna M. Pyle, Ruth Wang, Xiaohong Liu, Katherine M. Brendza, John R. Somoza: Visualizing ATP-Dependent RNA Translocation by the NS3 Helicase from HCV. J Mol Biol 405, 1139-1153 (2011).
72. Rafael Sanjuan, Ignacio Marin: Tracing the Origin of the Compensasome: Evolutionary History of DEAH Helicase and MYST Acetyltransferase Gene Families. Mol Biol Evol 18, 330-343 (2001). (Pubitemid 32225082)
73. Jovanka T. Koo, Juno Choe, Steve L. Moseley: HrpA, a DEAH-box RNA helicase, is involved in mRNA processing of a fimbrial operon in Escherichia coli. Mol Microbiol 52, 1813-1826 (2004). (Pubitemid 38822687)
74. Helene Walbott, Saida Mouffok, Regine Capeyrou, Simon Lebaron, Odile Humbert, Herman van Tilbeurgh, Yves Henry, Nicolas Leulliot: Prp43p contains a processive helicase structural architecture with a specific regulatory domain. EMBO J 29, 2194- 2204 (2010).
75. Jeffrey A. Toretsky, Verda Erkizan, Amy Levenson, Ogan D. Abaan, Jeffrey D. Parvin, Timothy P. Cripe, Anna M. Rice, Sean Bong Lee, Aykut Uren: Oncoprotein EWS-FLI1 Activity Is Enhanced by RNA Helicase A. Cancer Res 66, 5574- 5581 (2006). (Pubitemid 43927107)
76. Chee Gun Lee, Vera da Costa Soares, Carol Newberger, Katia Manova, Elizabeth Lacy, Jerard Hurwitz: RNA helicase A is essential for normal gastrulation. Proc Natl Acad Sci U S A 95, 13709- 13713 (1998). (Pubitemid 28523037)
77. Melissa A. Mefford, Jonathan P. Staley: Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps. RNA 15, 1386-1397 (2009).
78. Beate Schwer: A Conformational Rearrangement in the Spliceosome Sets the Stage for Prp22- Dependent mRNA Release. Mol Cell 30, 743-754 (2008). (Pubitemid 351815129)
79. Simon Lebaron, Carine Froment, Micheline Fromont-Racine, Jean Christophe Rain, Bernard Monsarrat, Michele Caizergues-Ferrer, Yves Henry: The Splicing ATPase Prp43p Is a Component of Multiple Preribosomal Particles. Mol Cell Biol 25, 9269-9282 (2005). (Pubitemid 41507829)
80. Nina B. Leeds, Eliza C. Small, Shawna L. Hiley, Timothy R. Hughes, Jonathan P. Staley: The Splicing Factor Prp43p, a DEAH Box ATPase, Functions in Ribosome Biogenesis. Mol Cell Biol 26, 513-522 (2006). (Pubitemid 43089764)
81. Rong Tzong Tsai, Ru Huei Fu, Fu Lung Yeh, Chi Kang Tseng, Yu Chieh Lin, Yu hsin Huang, Soo Chen Cheng: Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev 19, 2991-3003 (2005).
82. Naoko Tanaka, Anna Aronova, Beate Schwer: Ntr1 activates the Prp43 helicase to trigger release of lariat-intron from the spliceosome. Genes Dev 21, 2312-2325 (2007). (Pubitemid 47443337)
83. Arnold Martin, Susanne Schneider, Beate Schwer: Prp43 Is an Essential RNA-dependent ATPase Required for Release of Lariat-Intron from the Spliceosome. J Biol Chem 277, 17743-17750 (2002). (Pubitemid 34967580)
84. Jaime E. Arenas, John N. Abelson: Prp43: An RNA helicase-like factor involved in spliceosome disassembly. Proc Nat Acad Sci U S A 94, 11798- 11802 (1997).
85. Katharina Buttner, Sebastian Nehring, Karl Peter Hopfner: Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat Struct Mol Biol 14, 647-652 (2007). (Pubitemid 47037060)
86. Dahai Luo, Ting Xu, Randall P. Watson, Daniella Scherer-Becker, Aruna Sampath, Wolfgang Jahnke, Sui Sum Yeong, Chern Hoe Wang, Siew Pheng Lim, Alex Strongin, Subhash G. Vasudevan, Julien Lescar: Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein. EMBO J 27, 3209-3219(2008).
87. Vilhelm A. Bohr: Rising from the RecQ-age: the role of human RecQ helicases in genome maintenance. Trends Biochem Sci 33, 609-620 (2008).
88. Peter McGlynn, Robert G. Lloyd: Recombinational repair and restart of damaged replication forks. Nat Rev Mol Cell Biol 3, 859-870 (2002). (Pubitemid 35285276)
89. Robert M. Brosh, Jr., Vilhelm A. Ohr: Human premature aging, DNA repair and RecQ helicases. Nucleic Acids Res 35, 7527-7544 (2007).
90. Nathan A. Ellis, Joanna Groden, Tian Zhang Ye, Joel Straughen, David J. Lennon, Susan Ciocci, Maria Proytcheva, James German: The Bloom's syndrome gene product is homologous to RecQ helicases. Cell 83, 655-666 (1995).
91. Chang En Yu, Junko Oshima, Ying Hui Fu, Ellen M. Wijsman, Fuki Hisama, Reid Alisch, Shellie Matthews, Jun Nakura, Tetsuro Miki, Samir Ouais, George M. Martin, John Mulligan, Gerard D. Schellenberg: Positional cloning of the Werner's syndrome gene. Science 272, 258-262 (1996). (Pubitemid 26119137)
92. Saori Kitao, Akira Shimamoto, Makoto Goto, Robert W. Miller, William A. Smithson, Noralane M. Lindor, Yasuhiro Furuichi: Mutations in RECQL4 cause a subset of cases of Rothmund-Thomson syndrome. Nat Genet 22, 82-84 (1999). (Pubitemid 29214810)
93. Payam Mohaghegh, Julia K. Karow, Robert M. Brosh, Jr., Vilhelm A. Bohr, Ian D. Hickson: The Bloom's and Werner's syndrome proteins are DNA structure-specific helicases. Nucleic Acids Res 29, 2843-2849 (2001). (Pubitemid 32685049)
94. Y. Wu, A. Suhasini, R. Brosh: Welcome the Family of FANCJ-like Helicases to the Block of Genome Stability Maintenance Proteins. Cell Mol Life Sci 66, 1209-1222 (2009).
95. Jana Rudolf, Christophe Rouillon, Ulrich Schwarz-Linek, Malcolm F. White: The helicase XPD unwinds bubble structures and is not stalled by DNA lesions removed by the nucleotide excision repair pathway. Nucleic Acids Res 38, 931-941 (2010).
96. Alan R. Lehmann: The xeroderma pigmentosum group D (XPD) gene: one gene, two functions, three diseases. Genes Dev 15, 15-23 (2001). (Pubitemid 32060677)
97. Masayoshi Honda, Jeehae Park, Robert A. Pugh, Taekjip Ha, Maria Spies: Single-Molecule Analysis Reveals Differential Effect of ssDNA-Binding Proteins on DNA Translocation by XPD Helicase. Mol Cell 35, 694-703 (2009).
98. Li Fan, Jill O. Fuss, Quen J. Cheng, Andrew S. Arvai, Michal Hammel, Victoria A. Roberts, Priscilla K. Cooper, John A. Tainer: XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations. Cell 133, 789-800 (2008). (Pubitemid 351715395)
99. Huanting Liu, Jana Rudolf, Kenneth A. Johnson, Stephen A. McMahon, Muse Oke, Lester Carter, Anne Marie McRobbie, Sara E. Brown, James H. Naismith, Malcolm F. White: Structure of the DNA Repair Helicase XPD. Cell 133, 801-812 (2008). (Pubitemid 351707686)
100. Stephanie C Wolski, Jochen Kuper, Petra Hanzelmann, James J Truglio, Deborah L. Croteau, Bennett Kisker Caroline Van Houten: Crystal structure of the FeS cluster-containing necleotide excision repair helicase XPD. PLoS Biol 6, 1332- 1342 (2008). (Pubitemid 351888315)
101. Robert A. Pugh, Masayoshi Honda, Haley Leesley, Alvin Thomas, Yuyen Lin, Mark J. Nilges, Isaac K. O. Cann, Maria Spies: The Iron-containing Domain Is Essential in Rad3 Helicases for Coupling of ATP Hydrolysis to DNA Translocation and for Targeting the Helicase to the Single-stranded DNADouble- stranded DNA Junction. J Biol Chem 283, 1732-1743 (2008).
102. Jana Rudolf, Vasso Makrantoni, W. John Ingledew, Michael J. R. Stark, Malcolm F. White: The DNA Repair Helicases XPD and FancJ Have Essential Iron-Sulfur Domains. Mol Cell 23, 801-808 (2006). (Pubitemid 44344515)
103. Rachel Litman, Min Peng, Zhe Jin, Fan Zhang, Junran Zhang, Simon Powell, Paul R. Andreassen, Sharon B. Cantor: BACH1 is critical for homologous recombination and appears to be the Fanconi anemia gene product FANCJ. Cancer Cell 8, 255-265 (2005). (Pubitemid 41317595)
104. Sharon B. Cantor, Daphne W. Bell, Shridar Ganesan, Elizabeth M. Kass, Ronny Drapkin, Steven Grossman, Doke C. R. Wahrer, Dennis C. Sgroi, William S. Lane, Daniel A. Haber, David M. Livingston: BACH1, a Novel Helicase-like Protein, Interacts Directly with BRCA1 and Contributes to Its DNA Repair Function. Cell 105, 149-160 (2001). (Pubitemid 32323924)
105. Alexey Bochkarev, Elena Bochkareva, Lori Frappier, Aled M. Edwards: The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding. EMBO J 18, 4498-4504 (1999). (Pubitemid 29391259)
106. Iain D. Kerr, Ross I. M. Wadsworth, Liza Cubeddu, Wulf Blankenfeldt, James H. Naismith, Malcolm F. White: Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein. EMBO J 22, 2561- 2570 (2003). (Pubitemid 36712354)
107. Margaret M. Kasten, Cedric R. Clapier, Bradley R. Cairns: Snap Shot: Chromatin Remodeling: SWI/SNF. Cell 144, 310-310 (2011).
108. Cedric R. Clapier, Bradley R. Cairns: The Biology of Chromatin Remodeling Complexes. Annu Rev Biochem 78, 273-304 (2009).
109. Liling Tang, Eva Nogales, Claudio Ciferri: Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription. Prog Biophys Mol Biol 102, 122- 128 (2010).
110. Diana C. Hargreaves, Gerald R. Crabtree: ATPdependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res 21, 396-420 (2011).
111. Elisabetta Citterio, Vincent Van Den Boom, Gavin Schnitzler, Roland Kanaar, Edgar Bonte, Robert E. Kingston, Jan H. J. Hoeijmakers, Wim Vermeulen: ATP-Dependent Chromatin Remodeling by the Cockayne Syndrome B DNA Repair- Transcription-Coupling Factor. Mol Cell Biol 20, 7643-7653 (2000).
112. Jeffrey A. Jeddeloh, Trevor L. Stokes, Eric J. Richards: Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22, 94-97 (1999). (Pubitemid 29214813)
113. Andrei Alexeev, Alexander Mazin, Stephen C. Kowalczykowski: Rad54 protein possesses chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat Struct Mol Biol 10, 182-186 (2003). (Pubitemid 36297987)
114. Martin J. Law, Karen M. Lower, Hsiao P. J. Voon, Jim R. Hughes, David Garrick, Vip Viprakasit, Matthew Mitson, Marco De Gobbi, Marco Marra, Andrew Morris, Aaron Abbott, Steven P. Wilder, Stephen Taylor, Guilherme M. Santos, Joe Cross, Helena Ayyub, Steven Jones, Jiannis Ragoussis, Daniela Rhodes, Ian Dunham, Douglas R. Higgs, Richard J. Gibbons: ATR-X Syndrome Protein Targets Tandem Repeats and Influences Allele- Specific Expression in a Size-Dependent Manner. Cell 143, 367-378 (2010).
115. Nathalie G. Berube, Cecilia A. Smeenk, David J. Picketts: Cell cycle-dependent phosphorylation of the ATRX protein correlates with changes in nuclear matrix and chromatin association. Hum Mol Genet 9, 539-547 (2000). (Pubitemid 30154012)
116. Lee H. Wong, James D. McGhie, Marcus Sim, Melissa A. Anderson, Soyeon Ahn, Ross D. Hannan, Amee J. George, Kylie A. Morgan, Jeffrey R. Mann, K. H. A. Choo: ATRX interacts with H3.3 in maintaining telomere structural integrity in pluripotent embryonic stem cells. Genome Res 20, 351-360 (2010).
117. Gregory D. Bowman: Mechanisms of ATPdependent nucleosome sliding. Current Opinion in Structural Biology 20, 73-81 (2010).
118. K. E van Holde, T. D. Yager: Models for chromatin remodeling: a critical comparison. Biochem Cell Biol 81, 169-172 (2003).
119. Ralf Strohner, Malte Wachsmuth, Karoline Dachauer, Jacek Mazurkiewicz, Julia Hochstatter, Karsten Rippe, Gernot Langst: A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat Struct Mol Biol 12, 683-690 (2005). (Pubitemid 43086274)
120. Anjanabha Saha, Jacqueline Wittmeyer, Bradley R. Cairns: Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev 16, 2120-2134 (2002).
121. Giuseppe Lia, Elise Praly, Helder Ferreira, Chris Stockdale, Yuk Ching Tse-Dinh, David Dunlap, Vincent Croquette, David Bensimon, Tom Owen- Hughes: Direct Observation of DNA Distortion by the RSC Complex. Mol Cell 21, 417-425 (2006). (Pubitemid 43163536)
122. Shou Wei Ding: RNA-based antiviral immunity. Nat Rev Immunol 10, 632-644 (2010).
123. Emily Bernstein, Amy A. Caudy, Scott M. Hammond, Gregory J. Hannon: Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363-366 (2001). (Pubitemid 32151243)
124. Harris S. Soifer, Masayuki Sano, Kumi Sakurai, Pritsana Chomchan, Pal Saetrom, Mark A. Sherman, Michael A. Collingwood, Mark A. Behlke, John J. Rossi: A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs. Nucleic Acids Res 36, 6511-6522 (2008).
125. Noah C. Welker, Tuhin S. Maity, Xuecheng Ye, P. Joseph Aruscavage, Ammie A. Krauchuk, Qinghua Liu, Brenda L. Bass: Dicer's Helicase Domain Discriminates dsRNA Termini to Promote an Altered Reaction Mode. Molecular Cell 41, 589-599 (2011).
126. Mitsutoshi Yoneyama, Mika Kikuchi, Takashi Natsukawa, Noriaki Shinobu, Tadaatsu Imaizumi, Makoto Miyagishi, Kazunari Taira, Shizuo Akira, Takashi Fujita: The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat Immun 5, 730-737 (2004). (Pubitemid 39023305)
127. Veit Hornung, Jana Ellegast, Sarah Kim, Krzysztof Brzozka, Andreas Jung, Hiroki Kato, Hendrik Poeck, Shizuo Akira, Karl Klaus Conzelmann, Martin Schlee, Stefan Endres, Gunther Hartmann: 5'-Triphosphate RNA Is the Ligand for RIG-I. Science 314, 994-997 (2006).
128. Andreas Pichlmair, Oliver Schulz, Choon Ping Tan, Tanja I. Naslund, Peter Liljestrom, Friedemann Weber, Caetano Reis e Sousa: RIG-I-Mediated Antiviral Responses to Single-Stranded RNA Bearing 5'-Phosphates. Science 314, 997-1001 (2006). (Pubitemid 44749946)
129. Aaron J. Shatkin, James L. Manley: The ends of the affair: Capping and polyadenylation. Nat Struct Mol Biol 7, 838-842 (2000).
130. Sheng Cui, Katherina Eisenacher, Axel Kirchhofer, Krzysztof Brzozka, Alfred Lammens, Katja Lammens, Takashi Fujita, Karl-Klaus Conzelmann, Anne Krug, Karl-Peter Hopfner: The Cterminal regulatory domain is the RNA 5'- triphosphate sensor of RIG-I. Mol Cell 29, 169-179 (2008). (Pubitemid 351172822)
131. Eva Sisakova, Marie Weiserova, Cees Dekker, Ralf Seidel, Mark D. Szczelkun: The interrelationship of helicase and nuclease domains during DNA translocation by the molecular motor EcoR124I. J Mol Biol 384, 1273-1286 (2008).
132. Piero R. Bianco, Cuiling Xu, Min Chi: Type I restriction endonucleases are true catalytic enzymes. Nucleic Acids Res 37, 3377-3390 (2009).
133. Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis: REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38, D234-D236 (2010).
134. Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis: REBASE-enzymes and genes for DNA restriction and modification. Nucleic Acids Res 35, D269-D270 (2007). (Pubitemid 46056212)
135. Graham P. Davies, Ina Martin, Shane S. Sturrock, Andrew Cronshaw, Noreen E. Murray, David T. F. Dryden: On the structure and operation of type I DNA restriction enzymes. J Mol Biol 290, 565- 579 (1999). (Pubitemid 29324840)
136. Noreen E. Murray: Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle). Microbiol Mol Biol Rev 64, 412-434 (2000). (Pubitemid 30412679)
137. Robert Yuan, Thomas A. Bickle, Walter Ebbers, Christine Brack: Multiple steps in DNA recognition by restriction endonuclease from E. coli K. Nature 256, 556-560 (1975).
138. Srivani Sistla, Desirazu N. Rao: S-Adenosyl-Lmethionine- Dependent Restriction Enzymes. Crit Rev Biochem Mol Biol 39, 1-19 (2004).
139. Pavel Janscak, Agnes Abadjieva, Keith Firman: The Type I Restriction Endonuclease R.EcoR124I: Over-production and Biochemical Properties. J Mol Biol 257, 977-991 (1996). (Pubitemid 26117084)
140. Keith Firman, Mark D. Szczelkun: Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement. EMBO J 19, 2094-2102 (2000). (Pubitemid 30237584)
141. John Rosamond, Brian Endlich, Stuart Linn: Electron microscopic studies of the mechanism of action of the restriction endonuclease of Escherichia coli B. J Mol Biol 129, 619-635 (1979). (Pubitemid 9188540)
142. F. William Studier, Pradip K. Bandyopadhyay: Model for how type I restriction enzymes select cleavage sites in DNA. Proc Natl Acad Sci U S A 85, 4677-4681 (1988).
143. Jurg Dreier, Maria P. MacWilliams, Thomas A. Bickle: DNA Cleavage by the Type IC Restriction- Modification Enzyme EcoR124II. J Mol Biol 264, 722-733 (1996). (Pubitemid 27013556)
144. Mark D. Szczelkun: Kinetic Models of Translocation, Head-On Collision, and DNA Cleavage by Type I Restriction Endonucleases. Biochemistry 41, 2067-2074 (2002). (Pubitemid 34132281)
145. Joo Seop Park, Michael T. Marr, Jeffrey W. Roberts: E. coli Transcription Repair Coupling Factor (Mfd Protein) Rescues Arrested Complexes by Promoting Forward Translocation. Cell 109, 757-767 (2002). (Pubitemid 34722270)
146. Abigail J. Smith, Mark D. Szczelkun, Nigel J. Savery: Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase. Nucleic Acids Res 35, 1802-1811 (2007). (Pubitemid 47061651)
147. Peter McGlynn, Abdulwahab A. Al-Deib, Joing Liu, Kenneth J. Marians, Robert G. Lloyd: The DNA replication protein PriA and the recombination protein RecG bind D-loops. J Mol Biol 270, 212-221 (1997). (Pubitemid 27296682)
148. Joing Liu, Kenneth J. Marians: PriA-directed Assembly of a Primosome on D Loop DNA. J Biol Chem 274, 25033-25041 (1999).
149. Christian J. Rudolph, Amy L. Upton, Lynda Harris, Robert G. Lloyd: Pathological replication in cells lacking RecG DNA translocase. Mol Microbiol 73, 352-366 (2009).
150. Christian J. Rudolph, Amy L. Upton, Geoffrey S. Briggs, Robert G. Lloyd: Is RecG a general guardian of the bacterial genome? DNA Repair 9, 210-223 (2010).
151. Robert G. Lloyd: Conjugational recombination in resolvase-deficient ruvC mutants of Escherichia coli K-12 depends on recG. J Bacteriol 173, 5414- 5418 (1991).
152. Jing Zhang, Akeel A. Mahdi, Geoffrey S. Briggs, Robert G. Lloyd: Promoting and Avoiding Recombination: Contrasting Activities of the Escherichia coli RuvABC Holliday Junction Resolvase and RecG DNA Translocase. Genetics 185, 23-37 (2010).
153. Robert G. Lloyd, G. J. Sharples: Dissociation of synthetic Holliday junctions by E. coli RecG protein. EMBO J 12, 17-22 (1993). (Pubitemid 23042378)
154. Peter McGlynn, Robert G. Lloyd: Modulation of RNA Polymerase by (p)ppGpp Reveals a RecGDependent Mechanism for Replication Fork Progression. Cell 101, 35-45 (2000).
155. Simon D. Vincent, Akeel A. Mahdi, Robert G. Lloyd: The RecG Branch Migration Protein of Escherichia coli Dissociates R-loops. J Mol Biol 264, 713-721 (1996). (Pubitemid 27013555)
156. Tsuneaki Asai, Tokio Kogoma: D-loops and Rloops: alternative mechanisms for the initiation of chromosome replication in Escherichia coli. J Bacteriol 176, 1807-1812 (1994). (Pubitemid 24103526)
157. Tsuneaki Asai, Tokio Kogoma: Roles of ruvA, ruvC and recG Gene Functions in Normal and DNA Damage-Inducible Replication of the Escherichia coli Chromosome. Genetics 137, 895-902 (1994). (Pubitemid 24235605)
158. Hisao Masai, Taku Tanaka, Daisuke Kohda: Stalled replication forks: Making ends meet for recognition and stabilization. Bioessays 32, 687-697 (2010).
159. Toshimi Mizukoshi, Taku Tanaka, Ken ichi Arai, Daisuke Kohda, Hisao
160. Amanda V. Gregg, Peter McGlynn, Razieh P. Jaktaji, Robert G. Lloyd: Direct Rescue of Stalled DNA Replication Forks via the Combined Action of PriA and RecG Helicase Activities. Mol Cell 9, 241- 251 (2002). (Pubitemid 34195551)
161. Ashley C. W. Pike, Binesh Shrestha, Venkateswarlu Popuri, Nicola Burgess-Brown, Laura Muzzolini, Silvia Costantini, Alessandro Vindigni, Opher Gileadi: Structure of the human RECQ1 helicase reveals a putative strand-separation pin. Proc Natl Acad Sci U S A 106, 1039-1044 (2009).
162. Martin R. Singleton, Sarah Scaife, Dale B. Wigley: Structural Analysis of DNA Replication Fork Reversal by RecG. Cell 107, 79-89 (2001). (Pubitemid 32972039)
163. K. Saikrishnan, B. Powell, N. J. Cook, M. R. Webb, D. B. Wigley: Mechanistic basis of 5'-3' translocation in SF1B helicases. Cell 137, 849-859 (2009).
164. Coralie Halls, Sabine Mohr, Mark Del Campo, Quansheng Yang, Eckhard Jankowsky, Alan M. Lambowitz: Involvement of DEAD-box Proteins in Group I and Group II Intron Splicing. Biochemical Characterization of Mss116p, ATP Hydrolysisdependent and -independent Mechanisms, and General RNA Chaperone Activity. J Mol Biol 365, 835-855 (2007). (Pubitemid 46001664)
165. Yuliang Wu, Jr Brosh: Distinct roles of RECQ1 in the maintenance of genomic stability. DNA Repair 9, 315-324 (2010).
166. Harald Durr, Christian Korner, Marisa Muller, Volker Hickmann, Karl Peter Hopfner: X-Ray Structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase Core and Its Complex with DNA. Cell 121, 363-373 (2005). (Pubitemid 40692297)
167. Tatsuya Nishino, Kayoko Komori, Daisuke Tsuchiya, Yoshizumi Ishino, Kosuke Morikawa: Crystal Structure and Functional Implications of Pyrococcus furiosus Hef Helicase Domain Involved in Branched DNA Processing. Structure 13, 143-153 (2005). (Pubitemid 40092482)
168. Mikalai Lapkouski, Santosh Panjikar, Pavel Janscak, Ivana Kuta Smatanova, Jannette Carey, Rudiger Ettrich, Eva Csefalvay: Structure of the motor subunit of type I restriction-modification complex EcoR124I. Nat Struct Mol Biol 16, 94-95 (2009).