Genome-wide comprehensive analysis of human helicases

Communicative and Integrative Biology

Volumn 4, Issue 1, 2011, Pages 118-137

  Umate, Pavan ^a   Tuteja, Narendra ^a   Tuteja, Renu ^a  

^a INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY ICGEB   (India)

Author keywords

DEAD box; DHX and DDX helicases; Human helicases; MCM proteins; RecQ helicases; RNA helicases

Indexed keywords

EID: 79951703153     PISSN: None     EISSN: 19420889     Source Type: Journal    
DOI: 10.4161/cib.13844     Document Type: Article

References (111)

1. Compton SA, Tolun G, Kamath-Loeb AS, Loeb LA, Griffith JD. The Werner syndrome protein binds replication fork and holliday junction DNAs as an oligomer. J Biol Chem 2008; 283:24478-83.
2. Hartung F, Plchova H, Puchta H. Molecular characterization of RecQ homologues in Arabidopsis thaliana. Nucleic Acids Res 2000; 28:4275-82.
3. Tuteja N, Tuteja R. Prokaryotic and eukaryotic DNA helicases. Essential molecular motor proteins for cellular machinery. Eur J Biochem 2004; 271:1835-48.
4. Tuteja R. Genome wide identification of Plasmodium falciparum helicases: a comparison with human host. Cell Cycle 2010; 9:104-20.
5. Umate P, Tuteja R, Tuteja N. Genome-wide analysis of helicase gene family from rice and Arabidopsis: a comparison with yeast and human. Plant Mol Biol 2010; 73:449-65.
6. Tanner NK, Cordin O, Banroques J, Doere M, Linder P The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis. Mol Cell 2003; 11:127-38.
7. Tuteja N, Tuteja R. Unravelling DNA helicases. Motif, structure, mechanism and function. Eur J Biochem 2004; 271:1849-63.
8. Tanner NK, Linder P. DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol Cell 2001; 8:251-62.
9. Caruthers JM, McKay DB. Helicase structure and mechanism. Curr Opin Struct Biol 2002; 12:123-33.
10. Hogbom M, Collins R, van den Berg S, Jenvert RM, Karlberg T, Kotenyova T, et al. Crystal structure of conserved domains 1 and 2 of the human DEAD-box helicase DDX3X in complex with the mononucleotide AMP. J Mol Biol 2007; 372:150-9.
11. Gorbalenya AE, Koonin EV. Helicases: amino acid sequence comparisons and structure-function relationships. Curr Opin Struct Biol 1993; 3:419-29.
12. Laggerbauer B, Achsel T, Luhrmann R. The human U5-200 kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. Proc Natl Acad Sci USA 1998; 95:4188-92.
13. Raghunathan PL, Guthrie C. RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Curr Biol 1998; 8:847-55.
14. Fairman ME, Maroney PA, Wang W, Bowers HA, Gollnick P, Nilsen TW, et al. Protein displacement by DExH/D "RNA helicases" without duplex unwinding. Science 2004; 304:730-4.
15. Shen H, Zheng X, Shen J, Zhang L, Zhao R, Green MR. Distinct activities of the DExD/H-box splicing factor hUAP56 facilitate stepwise assembly of the splicesome. Genes Dev 2008; 22:1796-803.
16. Rozen F, Edery I, Meerovitch K, Dever TE, Merrick WC, Sonenberg N. Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F Mol Cell Biol 1990; 10:1134-44.
17. Thomas AA, van Aalzum L, Voorma HO. RNA unwinding by eukaryotic initiation factor 4A and nucleotide modification. Biochem Int 1992; 27:17-23.
18. Wang Y, Wagner JD, Guthrie C. The DEAH-box splicing factor Prp16 unwinds RNA duplexes in vitro. Curr Biol 1998; 8:441-51.
19. Yang Q, Jankowsky E. ATP- and ADP-dependent modulation of RNA unwinding and strand annealing activities by the DEAD-box protein DED1. Biochemistry 2005; 44:13591-601.
20. Rocak S, Linder P. DEAD-box proteins: The driving forces behind RNA metabolism. Nat Rev Mol Cell Biol 2004; 5:232-41.
21. Cordin O, Banroques J, Tanner NK, Linder P. The DEAD-box protein family of RNA helicases. Gene 2006; 367:17-37.
22. Linder P Dead-box proteins: A family affair-active and passive players in RNP-remodeling. Nucleic Acids Res 2006; 34:4168-80.
23. Tuteja N, Tuteja R. DNA helicases as molecular motors: an insight. Physica Acta 2006; 372:70-83.
24. de la Cruz J, Kressler D, Linder P. Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem Sci 1999; 24:192-8.
25. Daugeron MC, Linder P. Are DEAD-box proteins becoming respectable helicases? Nat Struct Biol 2000; 7:97-9.
26. Jankowsky E, Gross CH, Shumann S, Pyle AM. The DExH protein NPH-II is a processive and directional motor for unwinding RNA. Nature 2000; 403:447-51.
27. Aubourg S, Kreis M, Lecharny A. The DEAD-box RNA helicase family in Arabidopsis thaliana. Nucleic Acids Res 1999; 27:628-36.
28. Boudet N, Aubourg S, Toffano-Nioche C, Kreis M, Lecharny A. Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis and Drosophila. Genome Res 2001; 11:2101-14.
29. Abdelhaleem M, Maltais L, Wain H. The human DDX and DHX gene families of putative RNA helicases. Genomics 2003; 81:618-22.
30. Staley JP, Guthrie C. Mechanical devices of the spliceosome: Motors, clocks, springs and things. Cell 1998; 92:315-26.
31. Gencheva M, Kato M, Newo AN, Lin RJ. Contribution of DEAH-box protein DHX16/hPRP2 in human pre-mRNA splicing. Biochem J 2010; 429:25-32.
32. Pisareva VP, Pisarev AV, Komar AA, Hellen CU, Pestova TV. Translation initiation on mammalian mRNAs with structured 5' UTRs requires DExH-box protein DHX29. Cell 2008; 135:1237-50.
33. Chakraborty P, Grosse F. WRN helicase unwinds Okazaki fragment-like hybrids in a reaction stimulated by the human DHX9 helicase. Nucleic Acids Res 2010; 38:4722-30.
34. Huang M, Mitchell BS. Guanine nucleotide depletion mediates translocation of nucleolar proteins, including RNA helicase A (DHX-9). Nucleosides Nucleotides Nucleic Acids 2008; 27:704-11.
35. Alli Z, Ackerley C, Chen Y, Al-Saud B, Abdelhaleem M. Nuclear and mitochondrial localization of the putative RNA helicase DHX32. Exp Mol Pathol 2006; 81:245-8.
36. Chen Y, Alli Z, Ackerley C, Al-Saud B, Abdelhaleem M. Altered distribution of heat shock protein 60 (Hsp60) with dysregulated expression of DHX32. Exp Mol Pathol 2007; 82:256-61.
37. Fu JJ, Li LY, Lu GX Molecular cloning and characterization of human DDX36 and mouse Ddx36 genes, New members of the DEAD/H box superfamily. Acta Biochim Biophys Sinica 2002; 34:655-61.
38. Vaughn JP, Creacy SD, Routh ED, Joyner-Butt C, Jenkins GS, Pauli S, et al. The DEXH protein product of the DHX36 gene is the major source of tetramolecular quadruplex G4-DNA resolving activity in HeLa cell lysates. J Biol Chem 2005; 280:38117-20.
39. Lee JH, Rho SB, Chun T GABAA receptor-associated protein (GABARAP) induces apoptosis by interacting with DEAD (Asp-Glu-Ala-Asp/His) box polypeptide 47 (DDX 47). Biotechnol Lett 2005; 27:623-8.
40. Uhlmann-Schiffler H, Jalal C, Stahl H. Ddx42p-a human DEAD box protein with RNA chaperone activities. Nucleic Acids Res 2006; 34:10-22.
41. Mulhern O, Bowie AG. Unexpected roles for DEAD-box protein 3 in viral RNA sensing pathways. Eur J Immunol 2010; 40:933-5.
42. Chen CY, Yedavalli VR, Jeang KT A method to study the role of DDX3 RNA helicase in HIV-1. Methods Mol Biol 2010; 587:281-9.
43. Lee CS, Dias AP, Jedrychowski M, Patel AH, Hsu JL. Reed R. Human DDX3 functions in translation and interacts with the translation initiation factor eIF3. Nucleic Acids Res 2008; 36:4708-18.
44. Franca R, Belfiore A, Spadari S, Maga G. Human DEAD-box ATPase DDX3 shows a relaxed nucleoside substrate specificity. Proteins 2007; 67:1128-37.
45. waf1/cip1 promoter, is a candidate tumor suppressor. Cancer Res 2006; 66:6579-88.
46. Rosner A, Rinkevich B. The DDX3 subfamily of the DEAD box helicases: divergent roles as unveiled by studying different organisms and in vitro assays. Curr Med Chem 2007; 14:2517-25.
47. Botlagunta M, Vesuna F, Mironchik Y, Raman A, Lisok A, Winnard P Jr, et al. Oncogenic role of DDX3 in breast cancer biogenesis. Oncogene 2008; 27:3912.
48. Yedavalli VS, Neuveut C, Chi YH, Kleiman L, Jeang KT. Requirement of DDX3 DEAD box RNA helicase for HIV-1 Rev-RRE export function. Cell 2004; 119:381-92.
49. Abdelhaleem M. RNA helicases: regulators of differentiation. Clin Biochem 2005; 38:499-503.
50. Rauschendorf MA, Zimmer J, Hanstein R, Dickemann C, Vogt PH. Complex transcriptional control of the AZFa gene DDX3Y in human testis. Int J Androl 2011; 34:84-96.
51. Margossian SP, Li H, Zassenhaus HP, Butow RA. The DExH box protein Suv3p is a component of yeast mitochondrial 3'-to-5' exoribonuclease that suppresses group I intron toxicity. Cell 1996; 84:199-209.
52. Minczuk M, Piwowarski J, Papworth MA, Awiszus K, Schalinski S, Dziembowski A, et al. Localisation of the human Suv3p helicase in the mitochondrial matrix and its preferential unwinding of dsDNA. Nucleic Acids Res 2002; 30:5074-86.
53. Dziembowski A, Piwowarski J, Hoser R, Minczuk M, Dmochowska A, Siep M, et al. The yeast mitochondrial degradosome. Its composition, interplay between RNA helicase and RNase activities and the role in mitochondrial RNA metabolism. J Biol Chem 2003; 278 :1603-11.
54. Khidr L, Wu G, Davila A, Procaccio V, Wallace D, Lee WH. Role of SUV3 helicase in maintaining mitochondrial homeostasis in human cells. J Biol Chem 2008; 283:27064-73.
55. Shu Z, Vijayakumar S, Chen CF, Chen PL, Lee WH. Purified human SUV3p exhibits multiple-substrate unwinding activity upon conformational change. Biochemistry 2004; 43:4781-90.
56. Pereira M, Mason P, Szczesny RJ, Maddukuri L, Dziwura S, Jedrzejczak R, et al. Interaction of human SUV3 RNA/DNA helicase with BLM helicase; loss of the SUV3 gene results in mouse embryonic lethality. Mech Ageing Dev 2007; 128:609-17.
57. Dziembowski A, Malewicz M, Minczuk M, Golik P, Dmochowska A, Stepien PP The yeast nuclear gene DSS1, which codes for a putative RNase II, is necessary for the function of the mitochondrial degradosome in processing and turnover of RNA. Mol Gen Genet 1998; 260:108-14.
58. Bjergbaek L, Cobb JA, Gasser SM. RecQ helicases and genome stability: lessons from model organisms and human disease. Swiss Med Wkly 2002; 132:433-42.
59. Shen JC, Gray MD, Oshima J, Kamath-Loeb AS, Fry M, Loeb LA. Werner syndrome protein. I. DNA helicase and dna exonuclease reside on the same polypeptide. J Biol Chem 1998; 273:34139-44.
60. Puranam KL, Blackshear PJ. Cloning and characterization of RECQL, a potential human homologue of the Escherichia coli DNA helicase RecQ. J Biol Chem 1994; 269:29838-45.
61. Yan H, Chen CY, Kobayashi R, Newport J. Replication focus-forming activity 1 and the Werner syndrome gene product. Nat Genet 1998; 19:375-8.
62. Cogoni C, Macino G. Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase. Science 1999; 286:2342-4.
63. Pike ACW, Shrestha B, Popuri V, Burgess-Brown N, Muzzolini L, Costantini S, et al. Structure of the human RECQ1 helicase reveals a putative strand-separation pin. Proc Natl Acad Sci USA 2009; 106:1039-44.
64. Rossi ML, Ghosh AK, Kulikowicz T, Croteau DL, Bohr VA. Conserved helicase domain of human RecQ4 is required for strand annealing-independent DNA unwinding. DNA Repair (Amst) 2010; 9:796-804.
65. Thangavel S, Mendoza-Maldonado R, Tissino E, Sidorova JM, Yin J, Wang W, et al. Human RECQ1 and RECQ4 helicases play distinct roles in DNA replication initiation. Mol Cell Biol 2010; 30:1382-96.
66. Bugreev DV, Brosh RM Jr, Mazin AV. RECQ1 possesses DNA branch migration activity. J Biol Chem 2008; 283:20231-42.
67. Sekelsky JJ, Brodsky MH, Rubin GM. Hawley RS. Drosophila and human RecQ5 exist in different isoforms generated by alternative splicing. Nucleic Acids Res 1999; 27:3762-9.
68. Aygün O, Svejstrup J, Liu Y. A RECQ5-RNA polymerase II association identified by targeted proteomic analysis of human chromatin. Proc Natl Acad Sci USA 2008; 105:8580-4.
69. Zheng L, Kanagaraj R, Mihaljevic B, Schwendener S, Sartori AA, Gerrits B, et al. MRE11 complex links RECQ5 helicase to sites of DNA damage. Nucleic Acids Res 2009; 37:2645-57.
70. Schwendener S, Raynard S, Paliwal S, Cheng A, Kanagaraj R, Shevelev I, et al. Physical interaction of RECQ5 helicase with RAD51 facilitates its anti-recombinase activity. J Biol Chem 2010; 285:15739-45.
71. Blundred R, Myers K, Helleday T, Goldman AS, Bryant HE. Human RECQL5 overcomes thymidine-induced replication stress. DNA Repair (Amst) 2010; 9:964-75.
72. Watt PM, Hickson ID, Borts RH, Louis EJ. SGS1, a homologue of the Bloom's and Werner's syndrome genes, is required for maintenance of genome stability in Saccharomyces cerevisiae. Genetics 1996; 144:935-45.
73. van Brabant AJ, Ye T, Sanz M, German IJ, Ellis NA, Holloman WK Binding and melting of D-loops by the Bloom syndrome helicase. Biochemistry 2000; 39:14617-25.
74. Angloff S, McDonald JP, Bendixen C, Arthur L, Rothstein R. The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol Cell Biol 1994; 14:8391-8.
75. Wu L, Davies SL, North PS, Goulaouic H, Riou JF, Turley H, et al. The Bloom's syndrome gene product interacts with topoisomerase III. J Biol Chem 2000; 275:9636-44.
76. Wu L, Davies SL, Levitt NC, Hickson ID. Potential role for the BLM helicase in recombinational repair via a conserved interaction with RAD51. J Biol Chem 2001; 276:19375-81.
77. Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, et al. Analysis of human transcriptomes. Nat Genet 1999; 23:387-8.
78. Kearsey SE, Labib K. MCM proteins: evolution, properties and role in DNA replication. Biochim Biophys Acta 1998; 1398:113-36.
79. Forsburg SL. Eukaryotic MCM proteins: beyond replication initiation. Microbiol Mol Biol Rev 2004; 68:109-31.
80. Bell SP, Dutta A. DNA replication in eukaryotic cells. Annu Rev Biochem 2002; 71:333-74.
81. 1-phase and are required to establish, but not maintain, the S-phase checkpoint. Mol Biol Cell 2001; 12:3658-67.
82. Feger G, Vaessin H, Su TT, Wolff E, Jan LY, Jan YN. dpa, a member of the MCM family, is required for mitotic DNA replication but not endoreplication in Drosophila. EMBO J 1995; 14:5387-98.
83. Springer PS, McCombie WR, Sundaresan V, Martienssen RA. Gene trap tagging of PROLIFERA and essential MCM2-3-5 like gene in Arabidopsis. Science 1995; 268:877-80.
84. Maiorano D, Lutzmann M, Méchali M. MCM proteins and DNA replication. Curr Opin Cell Biol 2006; 18:130-6.
85. Gozuacik D, Chami M, Lagorce D, Faivre J, Murakami Y, Poch O, et al. Identification and functional characterization of a new member of the human Mcm protein family: hMcm8. Nucleic Acids Res 2003; 31:570-9.
86. Johnson EM, Kinoshita Y, Daniel DC. A new member of the MCM protein family encoded by the human MCM8 gene, located contrapodal to GCD10 at chromosome band 20p12.3-13. Nucleic Acids Res 2003; 31:2915-25.
87. Maiorano D, Cuvier O, Danis E, Méchali M. MCM8 is an MCM2-7-related protein that functions as a DNA helicase during replication elongation and not initiation. Cell 2005; 120:315-28.
88. Volkening M, Hoffmann I. Involvement of human MCM8 in prereplication complex assembly by recruiting hcdc6 to chromatin. Mol Cell Biol 2005; 25:1560-8.
89. Lutzmann M, Maiorano D, Méchali M. Identification of full genes and proteins of MCM9, a novel, vertebrate-specific member of the MCM2-8 protein family. Gene 2005; 362:51-6.
90. Lutzmann M, Méchali M. MCM9 binds Cdt1 and is required for the assembly of prereplication complexes. Mol Cell 2008; 31:190-200.
91. Homesley L, Lei M, Kawasaki Y, Sawyer S, Christensen T, Tye BK. Mcm10 and the MCM2-7 complex interact to initiate DNA synthesis and to release replication factors from origins. Genes Dev 2000; 14:913-26.
92. Maine GT, Sinha P, Tye BK. Mutants of S. cerevisiae defective in the maintenance of minichromosomes. Genetics 1984; 106:365-85.
93. Wohlschlegel JA, Dhar SK, Prokhorova TA, Dutta A, Walter JC. Xenopus Mcm10 binds to origins of DNA replication after Mcm2-7 and stimulates origin binding of Cdc45. Mol Cell 2002; 9:1-20.
94. Xu X, Rochette PJ, Feyissa EA, Su TV, Liu Y MCM10 mediates RECQ4 association with MCM2-7 helicase complex during DNA replication. EMBO J 2009; 28:3005-14.
95. Sharma A, Kaur M, Kar A, Ranade SM, Saxena S. Ultraviolet radiation stress triggers the downregulation of essential replication factor MCM10. J Biol Chem 2010; 285:8352-62.
96. Guzder SN, Sung P, Bailly V, Prakash L, Prakash S. RAD25 is a DNA helicase required for DNA repair and RNA polymerase II transcription. Nature 1994; 369:578-81.
97. Sung P, Bailly V, Weber C, Thompson LH, Prakash L, Prakash S. Human xeroderma pigmentosum group D gene encodes a DNA helicase. Nature 1993; 365:852-5.
98. Zurita M, Merino C. The transcriptional complexity of the TFIIH complex. Trends Genet 2003; 19:578-84.
99. Dubaele S, Proietti De Santis L, Bienstock RJ, Keriel A, Stefanini M, Van Houten B, et al. Basal transcription defect discriminates between xeroderma pigmentosum and trichothiodystrophy in XPD patients. Mol Cell 2003; 11:1635-46.
100. Gibbons R. Alpha thalassaemia-mental retardation, X linked. Orphanet J Rare Dis 2006; 1:15.
101. Ivessa AS, Zhou JQ, Zakian VA. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell 2000; 100:479-89.
102. Garcia PL, Liu Y, Jiricny J, West SC, Janscak P. Human RECQ5b, a protein with DNA helicase and strand-annealing activities in a single polypeptide. EMBO J 2004; 23:2882-91.
103. Korhonen JA, Gaspari M, Falkenberg M. TWINKLE has 5'-3' DNA helicase activity and is specifically stimulated by mitochondrial single-stranded DNA-binding protein. J Biol Chem 2003; 278:48627-32.
104. Spelbrink JN, Li FY, Tiranti V, Nikali K, Yuan QP, Tariq M, et al. Human mitochondrial DNA deletions associated with mutations in the gene encoding Twinkle, a phage T7 gene 4-like protein localized in mitochondria. Nat Genet 2001; 28:223-31.
105. Cantor SB, Bell DW, Ganesan S, Kass EM, Drapkin R, Grossman S, et al. BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function. Cell 2001; 105:149-60.
106. Gupta R, Sharma S, Doherty KM, Sommers JA, Cantor SB, Brosh RM Jr. Inhibition of BACH1 (FANCJ) helicase by backbone discontinuity is overcome by increased motor ATPase or length of loading strand. Nucleic Acids Res 2006; 34:6673-83.
107. Cantor S, Drapkin R, Zhang F, Lin Y, Han J, Pamidi S, et al. The BRCA1-associated protein BACH1 is a DNA helicase targeted by clinically relevant inactivating mutations. Proc Natl Acad Sci USA 2004; 101:2357-62.
108. Tuteja N, Huang NW, Skopac D, Tuteja R, Hrvatic S, Zhang J, et al. Human DNA helicase IV is nucleolin, an RNA helicase modulated by phosphorylation. Gene 1995; 160:143-8.
109. Tuteja R, Tuteja N. Nucleolin: a multifunctional major nucleolar phosphoprotein. Crit Rev Biochem Mol Biol 1998; 33:407-36.
110. Barber LJ, Youds JL, Ward JD, McIlwraith MJ, O'Neil NJ, Petalcorin MI, et al. RTEL1 maintains genomic stability by suppressing homologous recombination. Cell 2008; 135:261-71.
111. Chavez A, Tsou AM, Johnson FB. Telomeres do the (un)twist: Helicase actions at chromosome termini. Biochim Biophys Acta 2009; 1792:329-40.