1932

Abstract

Superfamily 2 helicase proteins are ubiquitous in RNA biology and have an extraordinarily broad set of functional roles. Central among these roles are the promotion of rearrangements of structured RNAs and the remodeling of ribonucleoprotein complexes (RNPs), allowing formation of native RNA structure or progression through a functional cycle of structures. Although all superfamily 2 helicases share a conserved helicase core, they are divided evolutionarily into several families, and it is principally proteins from three families, the DEAD-box, DEAH/RHA, and Ski2-like families, that function to manipulate structured RNAs and RNPs. Strikingly, there are emerging differences in the mechanisms of these proteins, both between families and within the largest family (DEAD-box), and these differences appear to be tuned to their RNA or RNP substrates and their specific roles. This review outlines basic mechanistic features of the three families and surveys individual proteins and the current understanding of their biological substrates and mechanisms.

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2014-06-02
2024-04-25
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Literature Cited

  1. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H. 1.  et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420:563–73 [Google Scholar]
  2. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R. 2.  et al. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484–88 [Google Scholar]
  3. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D. 3.  et al. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–49 [Google Scholar]
  4. Sigler PB.4.  1975. An analysis of the structure of tRNA. Annu. Rev. Biophys. Bioeng. 4:477–527 [Google Scholar]
  5. Karpel RL, Swistel DG, Miller NS, Geroch ME, Lu C, Fresco JR. 5.  1975. Acceleration of RNA renaturation by nucleic acid unwinding proteins. Brookhaven Symp. Biol. 26:165–74 [Google Scholar]
  6. Herschlag D.6.  1995. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270:20871–74 [Google Scholar]
  7. Russell R.7.  2008. RNA misfolding and the action of chaperones. Front. Biosci. 13:1–20 [Google Scholar]
  8. Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C. 8.  et al. 2007. RNA chaperones, RNA annealers and RNA helicases. RNA Biol. 4:118–30 [Google Scholar]
  9. Pan C, Russell R. 9.  2010. Roles of DEAD-box proteins in RNA and RNP folding. RNA Biol. 7:667–76 [Google Scholar]
  10. Jankowsky E.10.  2011. RNA helicases at work: binding and rearranging. Trends Biochem. Sci. 36:19–29 [Google Scholar]
  11. Linder P, Jankowsky E. 11.  2011. From unwinding to clamping: the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol. 12:505–16 [Google Scholar]
  12. Gorbalenya AE, Koonin EV. 12.  1993. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3:419–29 [Google Scholar]
  13. Fairman-Williams ME, Guenther UP, Jankowsky E. 13.  2010. SF1 and SF2 helicases: family matters. Curr. Opin. Struct. Biol. 20:313–24 [Google Scholar]
  14. Singleton MR, Dillingham MS, Wigley DB. 14.  2007. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76:23–50 [Google Scholar]
  15. Cordin O, Banroques J, Tanner N, Linder P. 15.  2006. The DEAD-box protein family of RNA helicases. Gene 367:17–37 [Google Scholar]
  16. Hilbert M, Karow AR, Klostermeier D. 16.  2009. The mechanism of ATP-dependent RNA unwinding by DEAD box proteins. Biol. Chem. 390:1237–50 [Google Scholar]
  17. Caruthers JM, Johnson ER, McKay DB. 17.  2000. Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase. Proc. Natl. Acad. Sci. USA 97:13080–85 [Google Scholar]
  18. Bono F, Ebert J, Lorentzen E, Conti E. 18.  2006. The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 126:713–25 [Google Scholar]
  19. Andersen C, Ballut L, Johansen J, Chamieh H, Nielsen K. 19.  et al. 2006. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 313:1968–72 [Google Scholar]
  20. Jankowsky E, Gross CH, Shuman S, Pyle AM. 20.  2000. The DExH protein NPH-II is a processive and directional motor for unwinding RNA. Nature 403:447–51 [Google Scholar]
  21. Pang PS, Jankowsky E, Planet PJ, Pyle AM. 21.  2002. The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding. EMBO J. 21:1168–76 [Google Scholar]
  22. Serebrov V, Pyle AM. 22.  2004. Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase. Nature 430:476–80 [Google Scholar]
  23. Büttner K, Nehring S, Hopfner KP. 23.  2007. Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat. Struct. Mol. Biol. 14:647–52 [Google Scholar]
  24. Richards JD, Johnson KA, Liu H, McRobbie AM, McMahon S. 24.  et al. 2008. Structure of the DNA repair helicase Hel308 reveals DNA binding and autoinhibitory domains. J. Biol. Chem. 283:5118–26 [Google Scholar]
  25. Pena V, Jovin SM, Fabrizio P, Orlowski J, Bujnicki JM. 25.  et al. 2009. Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase. Mol. Cell 35:454–66 [Google Scholar]
  26. Zhang L, Xu T, Maeder C, Bud LO, Shanks J. 26.  et al. 2009. Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2. Nat. Struct. Mol. Biol. 16:731–39 [Google Scholar]
  27. Jackson RN, Klauer AA, Hintze BJ, Robinson H, van Hoof A, Johnson SJ. 27.  2010. The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing. EMBO J. 29:2205–16 [Google Scholar]
  28. Weir JR, Bonneau F, Hentschel J, Conti E. 28.  2010. Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proc. Natl. Acad. Sci. USA 107:12139–44 [Google Scholar]
  29. Halbach F, Rode M, Conti E. 29.  2012. The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome. RNA 18:124–34 [Google Scholar]
  30. He Y, Andersen GR, Nielsen KH. 30.  2010. Structural basis for the function of DEAH helicases. EMBO Rep. 11:180–86 [Google Scholar]
  31. Walbott H, Mouffok S, Capeyrou R, Lebaron S, Humbert O. 31.  et al. 2010. Prp43p contains a processive helicase structural architecture with a specific regulatory domain. EMBO J. 29:2194–204 [Google Scholar]
  32. Johnson SJ, Jackson RN. 32.  2013. Ski2-like RNA helicase structures: common themes and complex assemblies. RNA Biol. 10:33–43 [Google Scholar]
  33. Bernstein J, Patterson DN, Wilson GM, Toth EA. 33.  2008. Characterization of the essential activities of Saccharomyces cerevisiae Mtr4p, a 3′→5′ helicase partner of the nuclear exosome. J. Biol. Chem. 283:4930–42 [Google Scholar]
  34. Jia H, Wang X, Anderson JT, Jankowsky E. 34.  2012. RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex. Proc. Natl. Acad. Sci. USA 109:7292–97 [Google Scholar]
  35. Schwer B.35.  2008. A conformational rearrangement in the spliceosome sets the stage for Prp22-dependent mRNA release. Mol. Cell 30:743–54 [Google Scholar]
  36. Lohman TM, Bjornson KP. 36.  1996. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65:169–214 [Google Scholar]
  37. Rogers GW, Richter NJ, Merrick WC. 37.  1999. Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A. J. Biol. Chem. 274:12236–44 [Google Scholar]
  38. Rogers GJ, Lima W, Merrick W. 38.  2001. Further characterization of the helicase activity of eIF4A substrate specificity. J. Biol. Chem. 276:12598–608 [Google Scholar]
  39. Bizebard T, Ferlenghi I, Iost I, Dreyfus M. 39.  2004. Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases. Biochemistry 43:7857–66 [Google Scholar]
  40. Yang Q, Jankowsky E. 40.  2006. The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases. Nat. Struct. Mol. Biol. 13:981–86 [Google Scholar]
  41. Halls C, Mohr S, Del Campo M, Yang Q, Jankowsky E, Lambowitz A. 41.  2007. Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis–dependent and –independent mechanisms, and general RNA chaperone activity. J. Mol. Biol. 365:835–55 [Google Scholar]
  42. Yang Q, Del Campo M, Lambowitz AM, Jankowsky E. 42.  2007. DEAD-box proteins unwind duplexes by local strand separation. Mol. Cell 28:253–63 [Google Scholar]
  43. Chen Y, Potratz J, Tijerina P, Del Campo M, Lambowitz A, Russell R. 43.  2008. DEAD-box proteins can completely separate an RNA duplex using a single ATP. Proc. Natl. Acad. Sci. USA 105:20203–8 [Google Scholar]
  44. Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD, De La Cruz EM. 44.  2010. Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proc. Natl. Acad. Sci. USA 107:4046–50 [Google Scholar]
  45. Cao W, Coman MM, Ding S, Henn A, Middleton ER. 45.  et al. 2011. Mechanism of Mss116 ATPase reveals functional diversity of DEAD-box proteins. J. Mol. Biol. 409:399–414 [Google Scholar]
  46. Liu F, Putnam A, Jankowsky E. 46.  2008. ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding. Proc. Natl. Acad. Sci. USA 105:20209–14 [Google Scholar]
  47. Henn A, Bradley MJ, De La Cruz EM. 47.  2012. ATP utilization and RNA conformational rearrangement by DEAD-box proteins. Annu. Rev. Biophys. 41:247–67 [Google Scholar]
  48. Russell R, Jarmoskaite I, Lambowitz AM. 48.  2012. Toward a molecular understanding of RNA remodeling by DEAD-box proteins. RNA Biol. 10:44–55 [Google Scholar]
  49. Mallam AL, Del Campo M, Gilman B, Sidote DJ, Lambowitz AM. 49.  2012. Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p. Nature 490:121–25 [Google Scholar]
  50. Benz J, Trachsel H, Baumann U. 50.  1999. Crystal structure of the ATPase domain of translation initiation factor 4A from Saccharomyces cerevisiae: the prototype of the DEAD box protein family. Structure 7:671–79 [Google Scholar]
  51. Rudolph MG, Heissmann R, Wittmann JG, Klostermeier D. 51.  2006. Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain. J. Mol. Biol. 361:731–43 [Google Scholar]
  52. Napetschnig J, Kassube SA, Debler EW, Wong RW, Blobel G, Hoelz A. 52.  2009. Structural and functional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19. Proc. Natl. Acad. Sci. USA 106:3089–94 [Google Scholar]
  53. Schütz P, Karlberg T, van den Berg S, Collins R, Lehtiö L. 53.  et al. 2010. Comparative structural analysis of human DEAD-box RNA helicases. PLoS ONE 5:0012791 [Google Scholar]
  54. Story RM, Li H, Abelson JN. 54.  2001. Crystal structure of a DEAD box protein from the hyperthermophile Methanococcus jannaschii. Proc. Natl. Acad. Sci. USA 98:1465–70 [Google Scholar]
  55. Shi H, Cordin O, Minder CM, Linder P, Xu RM. 55.  2004. Crystal structure of the human ATP-dependent splicing and export factor UAP56. Proc. Natl. Acad. Sci. USA 101:17628–33 [Google Scholar]
  56. Cheng Z, Coller J, Parker R, Song H. 56.  2005. Crystal structure and functional analysis of DEAD-box protein Dhh1p. RNA 11:1258–70 [Google Scholar]
  57. Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. 57.  2006. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125:287–300 [Google Scholar]
  58. Collins R, Karlberg T, Lehtiö L, Schütz P, van den Berg S. 58.  et al. 2009. The DEXD/H-box RNA helicase DDX19 is regulated by an α-helical switch. J. Biol. Chem. 284:10296–300 [Google Scholar]
  59. Del Campo M, Lambowitz A. 59.  2009. Structure of the yeast DEAD-box protein Mss116p reveals two wedges that crimp RNA. Mol. Cell 35:598–609 [Google Scholar]
  60. von Moeller H, Basquin C, Conti E. 60.  2009. The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner. Nat. Struct. Mol. Biol. 16:247–54 [Google Scholar]
  61. Lorsch JR, Herschlag D. 61.  1998. The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry 37:2180–93 [Google Scholar]
  62. Iost I, Dreyfus M, Linder P. 62.  1999. Ded1p, a DEAD-box protein required for translation initiation in Saccharomyces cerevisiae, is an RNA helicase. J. Biol. Chem. 274:17677–83 [Google Scholar]
  63. Polach KJ, Uhlenbeck OC. 63.  2002. Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA. Biochemistry 41:3693–702 [Google Scholar]
  64. Cordin O, Tanner NK, Doère M, Linder P, Banroques J. 64.  2004. The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity. EMBO J. 23:2478–87 [Google Scholar]
  65. Banroques J, Cordin O, Doère M, Linder P, Tanner NK. 65.  2008. A conserved phenylalanine of motif IV in superfamily 2 helicases is required for cooperative, ATP-dependent binding of RNA substrates in DEAD-box proteins. Mol. Cell. Biol. 28:3359–71 [Google Scholar]
  66. Theissen B, Karow A, Köhler J, Gubaev A, Klostermeier D. 66.  2008. Cooperative binding of ATP and RNA induces a closed conformation in a DEAD-box RNA helicase. Proc. Natl. Acad. Sci. USA 105:548–53 [Google Scholar]
  67. Karow AR, Klostermeier D. 67.  2009. A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN. Nucleic Acids Res. 37:4464–71 [Google Scholar]
  68. Rössler OG, Straka A, Stahl H. 68.  2001. Rearrangement of structured RNA via branch migration structures catalysed by the highly related DEAD-box proteins p68 and p72. Nucleic Acids Res. 29:2088–96 [Google Scholar]
  69. Yang Q, Jankowsky E. 69.  2005. ATP- and ADP-dependent modulation of RNA unwinding and strand annealing activities by the DEAD-box protein DED1. Biochemistry 44:13591–601 [Google Scholar]
  70. Uhlmann-Schiffler H, Jalal C, Stahl H. 70.  2006. Ddx42p: a human DEAD box protein with RNA chaperone activities. Nucleic Acids Res. 34:10–22 [Google Scholar]
  71. Garcia I, Albring MJ, Uhlenbeck OC. 71.  2012. Duplex destabilization by four ribosomal DEAD-box proteins. Biochemistry 51:10109–18 [Google Scholar]
  72. Rozen F, Edery I, Meerovitch K, Dever TE, Merrick WC, Sonenberg N. 72.  1990. Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F. Mol. Cell. Biol. 10:1134–44 [Google Scholar]
  73. Huang Y, Liu ZR. 73.  2002. The ATPase, RNA unwinding, and RNA binding activities of recombinant p68 RNA helicase. J. Biol. Chem. 277:12810–15 [Google Scholar]
  74. Rocak S, Emery B, Tanner NK, Linder P. 74.  2005. Characterization of the ATPase and unwinding activities of the yeast DEAD-box protein Has1p and the analysis of the roles of the conserved motifs. Nucleic Acids Res. 33:999–1009 [Google Scholar]
  75. Jarmoskaite I, Russell R. 75.  2011. DEAD-box proteins as RNA helicases and chaperones. WIREs RNA 2:135–52 [Google Scholar]
  76. Tijerina P, Bhaskaran H, Russell R. 76.  2006. 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. USA 103:16698–703 [Google Scholar]
  77. Grohman J, Del Campo M, Bhaskaran H, Tijerina P, Lambowitz A, Russell R. 77.  2007. Probing the mechanisms of DEAD-box proteins as general RNA chaperones: the C-terminal domain of CYT-19 mediates general recognition of RNA. Biochemistry 46:3013–22 [Google Scholar]
  78. Mallam AL, Jarmoskaite I, Tijerina P, Del Campo M, Seifert S. 78.  et al. 2011. Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail. Proc. Natl. Acad. Sci. USA 108:12254–59 [Google Scholar]
  79. Steimer L, Wurm JP, Linden MH, Rudolph MG, Wöhnert J, Klostermeier D. 79.  2013. Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera. Nucleic Acids Res. 41:6259–72 [Google Scholar]
  80. Klostermeier D.80.  2013. Rearranging RNA structures at 75°C? Toward the molecular mechanism and physiological function of the Thermus thermophilus DEAD-box helicase Hera. Biopolymers 99:1137–46 [Google Scholar]
  81. Kossen K, Karginov FV, Uhlenbeck OC. 81.  2002. The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA. J. Mol. Biol. 324:625–36 [Google Scholar]
  82. Hardin JW, Hu YX, McKay DB. 82.  2010. Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif. J. Mol. Biol. 402:412–27 [Google Scholar]
  83. Folkmann AW, Noble KN, Cole CN, Wente SR. 83.  2011. Dbp5, Gle1-IP6 and Nup159: a working model for mRNP export. Nucleus 2:540–48 [Google Scholar]
  84. Andreou AZ, Klostermeier D. 84.  2013. The DEAD-box helicase eIF4A: paradigm or the odd one out?. RNA Biol. 10:19–32 [Google Scholar]
  85. Jankowsky E, Gross CH, Shuman S, Pyle AM. 85.  2001. Active disruption of an RNA–protein interaction by a DExH/D RNA helicase. Science 291:121–25 [Google Scholar]
  86. Fairman M, Maroney P, Wang W, Bowers H, Gollnick P. 86.  et al. 2004. Protein displacement by DExH/D “RNA helicases” without duplex unwinding. Science 304:730–34 [Google Scholar]
  87. Jankowsky E, Bowers H. 87.  2006. Remodeling of ribonucleoprotein complexes with DExH/D RNA helicases. Nucleic Acids Res. 34:4181–88 [Google Scholar]
  88. Bowers HA, Maroney PA, Fairman ME, Kastner B, Lührmann R. 88.  et al. 2006. Discriminatory RNP remodeling by the DEAD-box protein DED1. RNA 12:903–12 [Google Scholar]
  89. Strunk BS, Karbstein K. 89.  2009. Powering through ribosome assembly. RNA 15:2083–104 [Google Scholar]
  90. Shajani Z, Sykes MT, Williamson JR. 90.  2011. Assembly of bacterial ribosomes. Annu. Rev. Biochem. 80:501–26 [Google Scholar]
  91. Jagessar KL, Jain C. 91.  2010. Functional and molecular analysis of Escherichia coli strains lacking multiple DEAD-box helicases. RNA 16:1386–92 [Google Scholar]
  92. Lehnik-Habrink M, Rempeters L, Kovács Á, Wrede C, Baierlein C. 92.  et al. 2013. DEAD-Box RNA helicases in Bacillus subtilis have multiple functions and act independently from each other. J. Bacteriol. 195:534–44 [Google Scholar]
  93. Fuller-Pace FV, Nicol SM, Reid AD, Lane DP. 93.  1993. DbpA: a DEAD box protein specifically activated by 23S rRNA. EMBO J. 12:3619–26 [Google Scholar]
  94. Tsu C, Kossen K, Uhlenbeck O. 94.  2001. The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA 7:702–9 [Google Scholar]
  95. Diges C, Uhlenbeck O. 95.  2001. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 20:5503–12 [Google Scholar]
  96. Wang S, Hu Y, Overgaard MT, Karginov FV, Uhlenbeck OC, McKay DB. 96.  2006. The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold. RNA 12:959–67 [Google Scholar]
  97. Elles LM, Uhlenbeck OC. 97.  2008. Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype. Nucleic Acids Res. 36:41–50 [Google Scholar]
  98. Elles LM, Sykes MT, Williamson JR, Uhlenbeck OC. 98.  Sharpe 2009. A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Res. 37:6503–14 [Google Scholar]
  99. Charollais J, Pflieger D, Vinh J, Dreyfus M, Iost I. 99.  2003. The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli. Mol. Microbiol. 48:1253–65 [Google Scholar]
  100. Trubetskoy D, Proux F, Allemand F, Dreyfus M, Iost I. 100.  2009. SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly, is specifically targeted to 23S rRNA in vivo. Nucleic Acids Res. 37:6540–49 [Google Scholar]
  101. Proux F, Dreyfus M, Iost I. 101.  2011. Identification of the sites of action of SrmB, a DEAD-box RNA helicase involved in Escherichia coli ribosome assembly. Mol. Microbiol. 82:300–11 [Google Scholar]
  102. Jones PG, Mitta M, Kim Y, Jiang W, Inouye M. 102.  1996. Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli. Proc. Natl. Acad. Sci. USA 93:76–80 [Google Scholar]
  103. Iost I, Bizebard T, Dreyfus M. 103.  2013. Functions of DEAD-box proteins in bacteria: current knowledge and pending questions. Biochim. Biophys. Acta 1829:866–77 [Google Scholar]
  104. Charollais J, Dreyfus M, Iost I. 104.  2004. CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Res. 32:2751–59 [Google Scholar]
  105. Jiang W, Hou Y, Inouye M. 105.  1997. CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J. Biol. Chem. 272:196–202 [Google Scholar]
  106. Awano N, Xu C, Ke H, Inoue K, Inouye M, Phadtare S. 106.  2007. Complementation analysis of the cold-sensitive phenotype of the Escherichia coli csdA deletion strain. J. Bacteriol. 189:5808–15 [Google Scholar]
  107. Phadtare S.107.  2011. Unwinding activity of cold shock proteins and RNA metabolism. RNA Biol. 8:394–97 [Google Scholar]
  108. Jain C.108.  2008. The E. coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly. RNA 14:381–89 [Google Scholar]
  109. Martin R, Straub AU, Doebele C, Bohnsack MT. 109.  2013. DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol. 10:4–18 [Google Scholar]
  110. Weaver PL, Sun C, Chang TH. 110.  1997. Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3. Mol. Cell. Biol. 17:1354–65 [Google Scholar]
  111. Pertschy B, Schneider C, Gnädig M, Schäfer T, Tollervey D, Hurt E. 111.  2009. RNA helicase Prp43 and its co-factor Pfa1 promote 20 to 18S rRNA processing catalyzed by the endonuclease Nob1. J. Biol. Chem. 284:35079–91 [Google Scholar]
  112. Bohnsack MT, Martin R, Granneman S, Ruprecht M, Schleiff E, Tollervey D. 112.  2009. Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis. Mol. Cell 36:583–92 [Google Scholar]
  113. Lebaron S, Papin C, Capeyrou R, Chen YL, Froment C. 113.  et al. 2009. The ATPase and helicase activities of Prp43p are stimulated by the G-patch protein Pfa1p during yeast ribosome biogenesis. EMBO J. 28:3808–19 [Google Scholar]
  114. de la Cruz J, Kressler D, Tollervey D, Linder P. 114.  1998. Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae. EMBO J. 17:1128–40 [Google Scholar]
  115. Lamanna AC, Karbstein K. 115.  2011. An RNA conformational switch regulates pre-18S rRNA cleavage. J. Mol. Biol. 405:3–17 [Google Scholar]
  116. Young CL, Khoshnevis S, Karbstein K. 116.  2013. Cofactor-dependent specificity of a DEAD-box protein. Proc. Natl. Acad. Sci. USA 110:E2668–76 [Google Scholar]
  117. Watkins NJ, Bohnsack MT. 117.  2012. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. WIREs RNA 3:397–414 [Google Scholar]
  118. Liang XH, Fournier MJ. 118.  2006. The helicase Has1p is required for snoRNA release from pre-rRNA. Mol. Cell. Biol. 26:7437–50 [Google Scholar]
  119. Bohnsack MT, Kos M, Tollervey D. 119.  2008. Quantitative analysis of snoRNA association with pre-ribosomes and release of snR30 by Rok1 helicase. EMBO Rep. 9:1230–36 [Google Scholar]
  120. Kos M, Tollervey D. 120.  2005. The putative RNA helicase Dbp4p is required for release of the U14 snoRNA from preribosomes in Saccharomyces cerevisiae. Mol. Cell 20:53–64 [Google Scholar]
  121. Granneman S, Bernstein KA, Bleichert F, Baserga SJ. 121.  2006. Comprehensive mutational analysis of yeast DEXD/H box RNA helicases required for small ribosomal subunit synthesis. Mol. Cell. Biol. 26:1183–94 [Google Scholar]
  122. Colley A, Beggs JD, Tollervey D, Lafontaine DL. 122.  2000. Dhr1p, a putative DEAH-box RNA helicase, is associated with the box C+D snoRNP U3. Mol. Cell. Biol. 20:7238–46 [Google Scholar]
  123. Lebaron S, Froment C, Fromont-Racine M, Rain JC, Monsarrat B. 123.  et al. 2005. The splicing ATPase Prp43p is a component of multiple preribosomal particles. Mol. Cell. Biol. 25:9269–82 [Google Scholar]
  124. Combs DJ, Nagel RJ, Ares M, Stevens SW. 124.  2006. Prp43p is a DEAH-box spliceosome disassembly factor essential for ribosome biogenesis. Mol. Cell. Biol. 26:523–34 [Google Scholar]
  125. Leeds NB, Small EC, Hiley SL, Hughes TR, Staley JP. 125.  2006. The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis. Mol. Cell. Biol. 26:513–22 [Google Scholar]
  126. Tanaka N, Schwer B. 126.  2006. Mutations in PRP43 that uncouple RNA-dependent NTPase activity and pre-mRNA splicing function. Biochemistry 45:6510–21 [Google Scholar]
  127. Tanaka N, Aronova A, Schwer B. 127.  2007. Ntr1 activates the Prp43 helicase to trigger release of lariat-intron from the spliceosome. Genes Dev. 21:2312–25 [Google Scholar]
  128. Guenther UP, Jankowsky E. 128.  2009. Helicase multitasking in ribosome assembly. Mol. Cell 36:537–38 [Google Scholar]
  129. Cordin O, Beggs JD. 129.  2013. RNA helicases in splicing. RNA Biol. 10:83–95 [Google Scholar]
  130. Chang TH, Tung L, Yeh FL, Chen JH, Chang SL. 130.  2013. Functions of the DExD/H-box proteins in nuclear pre-mRNA splicing. Biochim. Biophys. Acta 1829:764–74 [Google Scholar]
  131. Semlow DR, Staley JP. 131.  2012. Staying on message: ensuring fidelity in pre-mRNA splicing. Trends Biochem. Sci. 37:263–73 [Google Scholar]
  132. Ruby SW, Chang TH, Abelson J. 132.  1993. Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA. Genes Dev. 7:1909–25 [Google Scholar]
  133. Kistler AL, Guthrie C. 133.  2001. Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for Sub2, an essential spliceosomal ATPase. Genes Dev. 15:42–49 [Google Scholar]
  134. Shen H, Zheng X, Shen J, Zhang L, Zhao R, Green MR. 134.  2008. Distinct activities of the DExD/H-box splicing factor hUAP56 facilitate stepwise assembly of the spliceosome. Genes Dev. 22:1796–803 [Google Scholar]
  135. O'Day CL, Dalbadie-McFarland G, Abelson J. 135.  1996. The Saccharomyces cerevisiae Prp5 protein has RNA-dependent ATPase activity with specificity for U2 small nuclear RNA. J. Biol. Chem. 271:33261–67 [Google Scholar]
  136. Perriman R, Barta I, Voeltz GK, Abelson J, Ares M. 136.  2003. ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA. Proc. Natl. Acad. Sci. USA 100:13857–62 [Google Scholar]
  137. Perriman RJ, Ares M. 137.  2007. Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing. Genes Dev. 21:811–20 [Google Scholar]
  138. Abu Dayyeh BK, Quan TK, Castro M, Ruby SW. 138.  2002. Probing interactions between the U2 small nuclear ribonucleoprotein and the DEAD-box protein, Prp5. J. Biol. Chem. 277:20221–33 [Google Scholar]
  139. Perriman R, Ares M. 139.  2010. Invariant U2 snRNA nucleotides form a stem loop to recognize the intron early in splicing. Mol. Cell 38:416–27 [Google Scholar]
  140. Staley JP, Guthrie C. 140.  1999. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell 3:55–64 [Google Scholar]
  141. Strauss EJ, Guthrie C. 141.  1994. Prp28, a “DEAD-box” protein, is required for the first step of mRNA splicing in vitro. Nucleic Acids Res. 22:3187–93 [Google Scholar]
  142. Warkocki Z, Odenwälder P, Schmitzová J, Platzmann F, Stark H. 142.  et al. 2009. Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components. Nat. Struct. Mol. Biol. 16:1237–43 [Google Scholar]
  143. Lardelli RM, Thompson JX, Yates JR, Stevens SW. 143.  2010. Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing. RNA 16:516–28 [Google Scholar]
  144. Liu HL, Cheng SC. 144.  2012. The interaction of Prp2 with a defined region of the intron is required for the first splicing reaction. Mol. Cell. Biol. 32:5056–66 [Google Scholar]
  145. Ohrt T, Prior M, Dannenberg J, Odenwälder P, Dybkov O. 145.  et al. 2012. Prp2-mediated protein rearrangements at the catalytic core of the spliceosome as revealed by dcFCCS. RNA 18:1244–56 [Google Scholar]
  146. Ohrt T, Odenwälder P, Dannenberg J, Prior M, Warkocki Z. 146.  et al. 2013. Molecular dissection of step 2 catalysis of yeast pre-mRNA splicing investigated in a purified system. RNA 19:902–15 [Google Scholar]
  147. Mefford MA, Staley JP. 147.  2009. Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps. RNA 15:1386–97 [Google Scholar]
  148. Hilliker AK, Mefford MA, Staley JP. 148.  2007. U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing. Genes Dev. 21:821–34 [Google Scholar]
  149. Tseng CK, Liu HL, Cheng SC. 149.  2011. DEAH-box ATPase Prp16 has dual roles in remodeling of the spliceosome in catalytic steps. RNA 17:145–54 [Google Scholar]
  150. Schwer B, Gross CH. 150.  1998. Prp22, a DExH-box RNA helicase, plays two distinct roles in yeast pre-mRNA splicing. EMBO J. 17:2086–94 [Google Scholar]
  151. Wagner JD, Jankowsky E, Company M, Pyle AM, Abelson JN. 151.  1998. The DEAH-box protein PRP22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes. EMBO J. 17:2926–37 [Google Scholar]
  152. Tanaka N, Schwer B. 152.  2005. Characterization of the NTPase, RNA-binding, and RNA helicase activities of the DEAH-box splicing factor Prp22. Biochemistry 44:9795–803 [Google Scholar]
  153. Arenas JE, Abelson JN. 153.  1997. Prp43: an RNA helicase–like factor involved in spliceosome disassembly. Proc. Natl. Acad. Sci. USA 94:11798–802 [Google Scholar]
  154. Martin A, Schneider S, Schwer B. 154.  2002. Prp43 is an essential RNA-dependent ATPase required for release of lariat-intron from the spliceosome. J. Biol. Chem. 277:17743–50 [Google Scholar]
  155. Tsai RT, Fu RH, Yeh FL, Tseng CK, Lin YC. 155.  et al. 2005. Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev. 19:2991–3003 [Google Scholar]
  156. Laggerbauer B, Achsel T, Lührmann R. 156.  1998. The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. Proc. Natl. Acad. Sci. USA 95:4188–92 [Google Scholar]
  157. Raghunathan PL, Guthrie C. 157.  1998. RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Curr. Biol. 8:847–55 [Google Scholar]
  158. Mozaffari-Jovin S, Santos KF, Hsiao HH, Will CL, Urlaub H. 158.  et al. 2012. The Prp8 RNase H-like domain inhibits Brr2-mediated U4/U6 snRNA unwinding by blocking Brr2 loading onto the U4 snRNA. Genes Dev. 26:2422–34 [Google Scholar]
  159. Hahn D, Kudla G, Tollervey D, Beggs JD. 159.  2012. Brr2p-mediated conformational rearrangements in the spliceosome during activation and substrate repositioning. Genes Dev. 26:2408–21 [Google Scholar]
  160. Nielsen KH, Staley JP. 160.  2012. Spliceosome activation: U4 is the path, stem I is the goal, and Prp8 is the keeper. Let's cheer for the ATPase Brr2. ! Genes Dev. 26:2461–67 [Google Scholar]
  161. Mozaffari-Jovin S, Wandersleben T, Santos KF, Will CL, Lührmann R, Wahl MC. 161.  2013. Inhibition of RNA helicase Brr2 by the C-terminal tail of the spliceosomal protein Prp8. Science 341:80–84 [Google Scholar]
  162. Zaher HS, Green R. 162.  2009. Fidelity at the molecular level: lessons from protein synthesis. Cell 136:746–62 [Google Scholar]
  163. Hopfield JJ.163.  1974. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci. USA 71:41305–9 [Google Scholar]
  164. Ninio J.164.  1975. Kinetic amplification of enzyme discrimination. Biochimie 57:587–95 [Google Scholar]
  165. Bhaskaran H, Russell R. 165.  2007. Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone. Nature 449:1014–18 [Google Scholar]
  166. Xu YZ, Query CC. 166.  2007. Competition between the ATPase Prp5 and branch region–U2 snRNA pairing modulates the fidelity of spliceosome assembly. Mol. Cell 28:838–49 [Google Scholar]
  167. Yang F, Wang XY, Zhang ZM, Pu J, Fan YJ. 167.  et al. 2013. Splicing proofreading at 5′ splice sites by ATPase Prp28p. Nucleic Acids Res. 41:4660–70 [Google Scholar]
  168. Burgess S, Couto JR, Guthrie C. 168.  1990. A putative ATP binding protein influences the fidelity of branchpoint recognition in yeast splicing. Cell 60:705–17 [Google Scholar]
  169. Konarska MM, Query CC. 169.  2005. Insights into the mechanisms of splicing: more lessons from the ribosome. Genes Dev. 19:2255–60 [Google Scholar]
  170. Villa T, Guthrie C. 170.  2005. The Isy1p component of the NineTeen Complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing. Genes Dev. 19:1894–904 [Google Scholar]
  171. Mayas RM, Maita H, Staley JP. 171.  2006. Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat. Struct. Mol. Biol. 13:482–90 [Google Scholar]
  172. Mayas RM, Maita H, Semlow DR, Staley JP. 172.  2010. Spliceosome discards intermediates via the DEAH box ATPase Prp43p. Proc. Natl. Acad. Sci. USA 107:10020–25 [Google Scholar]
  173. Koodathingal P, Novak T, Piccirilli JA, Staley JP. 173.  2010. The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5′ splice site cleavage during pre-mRNA splicing. Mol. Cell 39:385–95 [Google Scholar]
  174. Lambowitz AM, Zimmerly S. 174.  2011. Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb. Perspect. Biol. 3:a003616 [Google Scholar]
  175. Mohr S, Stryker J, Lambowitz A. 175.  2002. A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell 109:769–79 [Google Scholar]
  176. Séraphin B, Simon M, Boulet A, Faye G. 176.  1989. Mitochondrial splicing requires a protein from a novel helicase family. Nature 337:84–87 [Google Scholar]
  177. Huang H, Rowe C, Mohr S, Jiang Y, Lambowitz A, Perlman P. 177.  2005. The splicing of yeast mitochondrial group I and group II introns requires a DEAD-box protein with RNA chaperone function. Proc. Natl. Acad. Sci. USA 102:163–68 [Google Scholar]
  178. Köhler D, Schmidt-Gattung S, Binder S. 178.  2010. The DEAD-box protein PMH2 is required for efficient group II intron splicing in mitochondria of Arabidopsis thaliana. Plant Mol. Biol. 72:459–67 [Google Scholar]
  179. Asakura Y, Galarneau E, Watkins KP, Barkan A, van Wijk KJ. 179.  2012. Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific group II introns and affect chloroplast ribosome biogenesis. Plant Physiol. 159:961–74 [Google Scholar]
  180. Russell R, Millett I, Doniach S, Herschlag D. 180.  2000. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nat. Struct. Biol. 7:367–70 [Google Scholar]
  181. Russell R, Das R, Suh H, Travers K, Laederach A. 181.  et al. 2006. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J. Mol. Biol. 363:531–44 [Google Scholar]
  182. Russell R, Herschlag D. 182.  2001. Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. J. Mol. Biol. 308:839–51 [Google Scholar]
  183. Sinan S, Yuan X, Russell R. 183.  2011. The Azoarcus group I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins. J. Biol. Chem. 286:37304–12 [Google Scholar]
  184. Del Campo M, Tijerina P, Bhaskaran H, Mohr S, Yang Q. 184.  et al. 2007. Do DEAD-box proteins promote group II intron splicing without unwinding RNA?. Mol. Cell 28:159–66 [Google Scholar]
  185. Del Campo M, Mohr S, Jiang Y, Jia H, Jankowsky E, Lambowitz A. 185.  2009. Unwinding by local strand separation is critical for the function of DEAD-box proteins as RNA chaperones. J. Mol. Biol. 389:674–93 [Google Scholar]
  186. Bifano A, Caprara M. 186.  2008. A DExH/D-box protein coordinates the two steps of splicing in a group I intron. J. Mol. Biol. 383:667–82 [Google Scholar]
  187. Russell R, Jarmoskaite I, Lambowitz AM. 187.  2013. Toward a molecular understanding of RNA remodeling by DEAD-box proteins. RNA Biol. 10:44–55 [Google Scholar]
  188. Mohr S, Matsuura M, Perlman P, Lambowitz A. 188.  2006. A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone. Proc. Natl. Acad. Sci. USA 103:3569–74 [Google Scholar]
  189. Solem A, Zingler N, Pyle A. 189.  2006. A DEAD protein that activates intron self-splicing without unwinding RNA. Mol. Cell 24:611–17 [Google Scholar]
  190. Fedorova O, Solem A, Pyle AM. 190.  2010. Protein-facilitated folding of group II intron ribozymes. J. Mol. Biol. 397:799–813 [Google Scholar]
  191. Potratz JP, Del Campo M, Wolf RZ, Lambowitz AM, Russell R. 191.  2011. ATP-dependent roles of the DEAD-box protein Mss116p in group II intron splicing in vitro and in vivo. J. Mol. Biol. 411:661–79 [Google Scholar]
  192. Zingler N, Solem A, Pyle AM. 192.  2010. Dual roles for the Mss116 cofactor during splicing of the ai5γ group II intron. Nucleic Acids Res. 38:6602–9 [Google Scholar]
  193. Karunatilaka KS, Solem A, Pyle AM, Rueda D. 193.  2010. Single-molecule analysis of Mss116-mediated group II intron folding. Nature 467:935–39 [Google Scholar]
  194. Potratz JP, Russell R. 194.  2012. RNA catalysis as a probe for chaperone activity of DEAD-box helicases. Methods Enzymol. 511:111–30 [Google Scholar]
  195. Waldsich C, Pyle AM. 195.  2008. A kinetic intermediate that regulates proper folding of a group II intron RNA. J. Mol. Biol. 375:572–80 [Google Scholar]
  196. Aitken CE, Lorsch JR. 196.  2012. A mechanistic overview of translation initiation in eukaryotes. Nat. Struct. Mol. Biol. 19:568–76 [Google Scholar]
  197. Svitkin YV, Pause A, Haghighat A, Pyronnet S, Witherell G. 197.  et al. 2001. The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5′ secondary structure. RNA 7:382–94 [Google Scholar]
  198. Rogers GW, Richter NJ, Lima WF, Merrick WC. 198.  2001. Modulation of the helicase activity of eIF4A by eIF4B, eIF4H, and eIF4F. J. Biol. Chem. 276:30914–22 [Google Scholar]
  199. Schütz P, Bumann M, Oberholzer AE, Bieniossek C, Trachsel H. 199.  et al. 2008. Crystal structure of the yeast eIF4A–eIF4G complex: an RNA-helicase controlled by protein–protein interactions. Proc. Natl. Acad. Sci. USA 105:9564–69 [Google Scholar]
  200. Marintchev A, Edmonds KA, Marintcheva B, Hendrickson E, Oberer M. 200.  et al. 2009. Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation. Cell 136:447–60 [Google Scholar]
  201. Hilbert M, Kebbel F, Gubaev A, Klostermeier D. 201.  2011. eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism. Nucleic Acids Res. 39:2260–70 [Google Scholar]
  202. Rajagopal V, Park EH, Hinnebusch AG, Lorsch JR. 202.  2012. Specific domains in yeast translation initiation factor eIF4G strongly bias RNA unwinding activity of the eIF4F complex toward duplexes with 5′-overhangs. J. Biol. Chem. 287:20301–12 [Google Scholar]
  203. Sun Y, Atas E, Lindqvist L, Sonenberg N, Pelletier J, Meller A. 203.  2012. The eukaryotic initiation factor eIF4H facilitates loop-binding, repetitive RNA unwinding by the eIF4A DEAD-box helicase. Nucleic Acids Res. 40:6199–207 [Google Scholar]
  204. Lindqvist L, Imataka H, Pelletier J. 204.  2008. Cap-dependent eukaryotic initiation factor-mRNA interactions probed by cross-linking. RNA 14:960–69 [Google Scholar]
  205. von der Haar T, McCarthy JE. 205.  2002. Intracellular translation initiation factor levels in Saccharomyces cerevisiae and their role in cap-complex function. Mol. Microbiol. 46:531–44 [Google Scholar]
  206. Kolupaeva VG, Lomakin IB, Pestova TV, Hellen CU. 206.  2003. Eukaryotic initiation factors 4G and 4A mediate conformational changes downstream of the initiation codon of the encephalomyocarditis virus internal ribosomal entry site. Mol. Cell. Biol. 23:687–98 [Google Scholar]
  207. de Breyne S, Yu Y, Unbehaun A, Pestova TV, Hellen CU. 207.  2009. Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites. Proc. Natl. Acad. Sci. USA 106:9197–202 [Google Scholar]
  208. Hilliker A, Gao Z, Jankowsky E, Parker R. 208.  2011. The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex. Mol. Cell 43:962–72 [Google Scholar]
  209. Pisareva VP, Pisarev AV, Komar AA, Hellen CU, Pestova TV. 209.  2008. Translation initiation on mammalian mRNAs with structured 5′UTRs requires DExH-box protein DHX29. Cell 135:1237–50 [Google Scholar]
  210. Abaeva IS, Marintchev A, Pisareva VP, Hellen CU, Pestova TV. 210.  2011. Bypassing of stems versus linear base-by-base inspection of mammalian mRNAs during ribosomal scanning. EMBO J. 30:115–29 [Google Scholar]
  211. Hartman TR, Qian S, Bolinger C, Fernandez S, Schoenberg DR, Boris-Lawrie K. 211.  2006. RNA helicase A is necessary for translation of selected messenger RNAs. Nat. Struct. Mol. Biol. 13:509–16 [Google Scholar]
  212. Ranji A, Shkriabai N, Kvaratskhelia M, Musier-Forsyth K, Boris-Lawrie K. 212.  2011. Features of double-stranded RNA–binding domains of RNA helicase A are necessary for selective recognition and translation of complex mRNAs. J. Biol. Chem. 286:5328–37 [Google Scholar]
  213. Lasko P.213.  2013. The DEAD-box helicase Vasa: evidence for a multiplicity of functions in RNA processes and developmental biology. Biochim. Biophys. Acta 1829:810–16 [Google Scholar]
  214. Carrera P, Johnstone O, Nakamura A, Casanova J, Jäckle H, Lasko P. 214.  2000. VASA mediates translation through interaction with a Drosophila yIF2 homolog. Mol. Cell 5:181–87 [Google Scholar]
  215. Johnstone O, Lasko P. 215.  2004. Interaction with eIF5B is essential for Vasa function during development. Development 131:4167–78 [Google Scholar]
  216. Daugeron MC, Prouteau M, Lacroute F, Séraphin B. 216.  2011. The highly conserved eukaryotic DRG factors are required for efficient translation in a manner redundant with the putative RNA helicase Slh1. Nucleic Acids Res. 39:2221–33 [Google Scholar]
  217. Gross T, Siepmann A, Sturm D, Windgassen M, Scarcelli J. 217.  et al. 2007. The DEAD-box RNA helicase Dbp5 functions in translation termination. Science 315:646–49 [Google Scholar]
  218. Bolger TA, Folkmann AW, Tran EJ, Wente SR. 218.  2008. The mRNA export factor Gle1 and inositol hexakisphosphate regulate distinct stages of translation. Cell 134:624–33 [Google Scholar]
  219. Tieg B, Krebber H. 219.  2013. Dbp5: from nuclear export to translation. Biochim. Biophys. Acta 1829:791–98 [Google Scholar]
  220. Takyar S, Hickerson RP, Noller HF. 220.  2005. mRNA helicase activity of the ribosome. Cell 120:49–58 [Google Scholar]
  221. Qu X, Wen JD, Lancaster L, Noller HF, Bustamante C, Tinoco I. 221.  2011. The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature 475:118–21 [Google Scholar]
  222. Hardwick SW, Luisi BF. 222.  2013. Rarely at rest: RNA helicases and their busy contributions to RNA degradation, regulation and quality control. RNA Biol. 10:56–70 [Google Scholar]
  223. Py B, Higgins CF, Krisch HM, Carpousis AJ. 223.  1996. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381:169–72 [Google Scholar]
  224. Coburn GA, Miao X, Briant DJ, Mackie GA. 224.  1999. Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes Dev. 13:2594–603 [Google Scholar]
  225. Schneider C, Tollervey D. 225.  2013. Threading the barrel of the RNA exosome. Trends Biochem. Sci. 38:485–93 [Google Scholar]
  226. Halbach F, Reichelt P, Rode M, Conti E. 226.  2013. The yeast Ski complex: crystal structure and RNA channeling to the exosome complex. Cell 154:814–26 [Google Scholar]
  227. Jia H, Wang X, Liu F, Guenther UP, Srinivasan S. 227.  et al. 2011. The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex. Cell 145:890–901 [Google Scholar]
  228. Tran H, Schilling M, Wirbelauer C, Hess D, Nagamine Y. 228.  2004. Facilitation of mRNA deadenylation and decay by the exosome-bound, DExH protein RHAU. Mol. Cell 13:101–11 [Google Scholar]
  229. Fuller-Pace FV.229.  2013. The DEAD box proteins DDX5 (p68) and DDX17 (p72): multi-tasking transcriptional regulators. Biochim. Biophys. Acta 1829:756–63 [Google Scholar]
  230. Cloutier SC, Ma WK, Nguyen LT, Tran EJ. 230.  2012. The DEAD-box RNA helicase Dbp2 connects RNA quality control with repression of aberrant transcription. J. Biol. Chem. 287:26155–66 [Google Scholar]
  231. Ma WK, Cloutier SC, Tran EJ. 231.  2013. The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly. J. Mol. Biol. 425:3824–38 [Google Scholar]
  232. Lund MK, Guthrie C. 232.  2005. The DEAD-box protein Dbp5p is required to dissociate Mex67p from exported mRNPs at the nuclear rim. Mol. Cell 20:645–51 [Google Scholar]
  233. Tran EJ, Zhou Y, Corbett AH, Wente SR. 233.  2007. The DEAD-box protein Dbp5 controls mRNA export by triggering specific RNA:protein remodeling events. Mol. Cell 28:850–59 [Google Scholar]
  234. Taniguchi I, Ohno M. 234.  2008. ATP-dependent recruitment of export factor Aly/REF onto intronless mRNAs by RNA helicase UAP56. Mol. Cell. Biol. 28:601–8 [Google Scholar]
  235. Strässer K, Masuda S, Mason P, Pfannstiel J, Oppizzi M. 235.  et al. 2002. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417:304–8 [Google Scholar]
  236. Fullam A, Schröder M. 236.  2013. DExD/H-box RNA helicases as mediators of anti-viral innate immunity and essential host factors for viral replication. Biochim. Biophys. Acta 1829:854–65 [Google Scholar]
  237. Kruse E, Voigt C, Leeder WM, Göringer HU. 237.  2013. RNA helicases involved in U-insertion/deletion-type RNA editing. Biochim. Biophys. Acta 1829:835–41 [Google Scholar]
  238. Li F, Herrera J, Zhou S, Maslov DA, Simpson L. 238.  2011. Trypanosome REH1 is an RNA helicase involved with the 3′–5′ polarity of multiple gRNA-guided uridine insertion/deletion RNA editing. Proc. Natl. Acad. Sci. USA 108:3542–47 [Google Scholar]
  239. Hernandez A, Madina BR, Ro K, Wohlschlegel JA, Willard B. 239.  et al. 2010. REH2 RNA helicase in kinetoplastid mitochondria: ribonucleoprotein complexes and essential motifs for unwinding and guide RNA (gRNA) binding. J. Biol. Chem. 285:1220–28 [Google Scholar]
  240. Millevoi S, Moine H, Vagner S. 240.  2012. G-quadruplexes in RNA biology. WIREs RNA 3:495–507 [Google Scholar]
  241. Sexton AN, Collins K. 241.  2011. The 5′ guanosine tracts of human telomerase RNA are recognized by the G-quadruplex binding domain of the RNA helicase DHX36 and function to increase RNA accumulation. Mol. Cell. Biol. 31:736–43 [Google Scholar]
  242. Lattmann S, Stadler MB, Vaughn JP, Akman SA, Nagamine Y. 242.  2011. The DEAH-box RNA helicase RHAU binds an intramolecular RNA G-quadruplex in TERC and associates with telomerase holoenzyme. Nucleic Acids Res. 39:9390–404 [Google Scholar]
  243. Lattmann S, Giri B, Vaughn JP, Akman SA, Nagamine Y. 243.  2010. Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU. Nucleic Acids Res. 38:6219–33 [Google Scholar]
  244. Chakraborty P, Grosse F. 244.  2011. Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair 10:654–65 [Google Scholar]
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