Roles of DEAD-box proteins in RNA and RNP folding

RNA Biology

Volumn 7, Issue 6, 2010, Pages 667-676

  Pan, Cynthia ^a   Russell, Rick ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

DEAD box protein; Group I intron; Misfolded RNA; Pre mRNA splicing; RNA chaperone; RNA folding; RNA helicase; RNA unwinding; RNA protein interaction; RNP remodeling

Indexed keywords

ADENOSINE TRIPHOSPHATE; DEAD BOX PROTEIN; FUNGAL PROTEIN; RIBONUCLEOPROTEIN; RNA; RNA HELICASE;

CONFORMATIONAL TRANSITION; GENE STRUCTURE; HUMAN; INTRON; NEUROSPORA CRASSA; NONHUMAN; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW;

EID: 78751676793     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.7.6.13571     Document Type: Review

References (149)

1. Noller HF. RNA structure: reading the ribosome. Science 2005; 309:1508-14.
2. Carthew RW, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs. Cell 2009; 136:642-55.
3. Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009; 136:701-18.
4. Collins K. The biogenesis and regulation of telomerase holoenzymes. Nat Rev Mol Cell Biol 2006; 7:484-94.
5. Esakova O, Krasilnikov AS. Of proteins and RNA: The RNase P/MRP family. RNA 2010.
6. Doudna JA, Batey RT. Structural insights into the signal recognition particle. Annu Rev Biochem 2004; 73:539-57.
7. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008; 320:1344-9.
8. Amaral PP, Dinger ME, Mercer TR, Mattick JS. The eukaryotic genome as an RNA machine. Science 2008; 319:1787-9.
9. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223-7.
10. Weinberg Z, Perreault J, Meyer MM, Breaker RR. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature 2009; 462:656-9.
11. Sigler PB. An analysis of the structure of tRNA. Annu Rev Biophys Bioeng 1975; 4:477-527.
12. Herschlag D. RNA chaperones and the RNA folding problem. J Biol Chem 1995; 270:20871-4.
13. Schroeder R, Barta A, Semrad K. Strategies for RNA folding and assembly. Nat Rev Mol Cell Biol 2004; 5:908-19.
14. Levin JG, Guo J, Rouzina I, Musier-Forsyth K. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. Prog Nucleic Acid Res Mol Biol 2005; 80:217-86.
15. Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C, Mayer O, et al. RNA chaperones, RNA annealers and RNA helicases. RNA Biol 2007; 4:118-30.
16. Russell R. RNA misfolding and the action of chaperones. Front Biosci 2008; 13:1-20.
17. Fairman-Williams ME, Guenther UP, Jankowsky E. SF1 and SF2 helicases: family matters. Curr Opin Struct Biol 2010; 20:313-24.
18. Linder P. Dead-box proteins: a family affair - active and passive players in RNP-remodeling. Nucleic Acids Res 2006; 34:4168-80.
19. Jankowsky E, Fairman ME. RNA helicases - one fold for many functions. Curr Opin Struct Biol 2007; 17:316-24.
20. Lambowitz AM, Zimmerly S. Group II Introns: Mobile Ribozymes that Invade DNA. Cold Spring Harb Perspect Biol 2010.
21. Potratz JP, Tijerina P, Russell R. Mechanisms of DEAD-box proteins in ATP-dependent processes. In: Jankowsky E, Ed. RNA helicases: Royal Society of Chemistry 2010; 61-98.
22. Zingler N, Solem A, Pyle AM. Protein-facilitated ribozyme folding and catalysis. Nucleic Acids Symp Ser (Oxf) 2008; 67-8.
23. Cordin O, Banroques J, Tanner NK, Linder P. The DEAD-box protein family of RNA helicases. Gene 2006; 367:17-37.
24. Del Campo M, Lambowitz AM. Structure of the yeast DEAD box protein Mss116p reveals two wedges that crimp RNA. Mol Cell 2009; 35:598-609.
25. Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 2006; 125:287-300.
26. Bono F, Ebert J, Lorentzen E, Conti E. The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 2006; 126:713-25.
27. von Moeller H, Basquin C, Conti E. The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner. Nat Struct Mol Biol 2009; 16:247-54.
28. Andersen CB, Ballut L, Johansen JS, Chamieh H, Nielsen KH, Oliveira CL, et al. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 2006; 313:1968-72. (Pubitemid 44498005)
29. Collins R, Karlberg T, Lehtio L, Schutz P, van den Berg S, Dahlgren LG, et al. The DEXD/H-box RNA helicase DDX19 is regulated by an {alpha}-helical switch. J Biol Chem 2009; 284:10296-300.
30. 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.
31. Cordin O, Tanner NK, Doere M, Linder P, Banroques J. The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity. EMBO J 2004; 23:2478-87.
32. Banroques J, Doere M, Dreyfus M, Linder P, Tanner NK. Motif III in superfamily 2 "helicases" helps convert the binding energy of ATP into a high-affinity RNA binding site in the yeast DEAD-box protein Ded1. J Mol Biol 2010; 396:949-66.
33. Lorsch JR, Herschlag D. The DEAD box protein eIF4A. (1) A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry 1998; 37:2180-93.
34. Polach KJ, Uhlenbeck OC. Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA. Biochemistry 2002; 41:3693-702.
35. Theissen B, Karow AR, Kohler J, Gubaev A, Klostermeier D. Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase. Proc Natl Acad Sci USA 2008; 105:548-53.
36. Karow AR, Klostermeier D. A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN. Nucleic Acids Res 2009; 37:4464-71.
37. Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD, De La Cruz EM. Pathway of ATP utilization and duplex rRNA unwinding by the DEADbox helicase, DbpA. Proc Natl Acad Sci USA 2010; 107:4046-50.
38. Henn A, Cao W, Hackney DD, De La Cruz EM. The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA. J Mol Biol 2008; 377:193-205.
39. Singleton MR, Dillingham MS, Wigley DB. Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem 2007; 76:23-50.
40. Lohman TM, Tomko EJ, Wu CG. Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nat Rev Mol Cell Biol 2008; 9:391-401.
41. Rossler OG, Straka A, Stahl H. Rearrangement of structured RNA via branch migration structures catalysed by the highly related DEAD-box proteins p68 and p72. Nucleic Acids Res 2001; 29:2088-96.
42. Chamot D, Colvin KR, Kujat-Choy SL, Owttrim GW. RNA structural rearrangement via unwinding and annealing by the cyanobacterial RNA helicase, CrhR. J Biol Chem 2005; 280:2036-44.
43. Rogers GW Jr, Richter NJ, Merrick WC. Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A. J Biol Chem 1999; 274:12236-44.
44. Rogers GW Jr, Lima WF, Merrick WC. Further characterization of the helicase activity of eIF4A. Substrate specificity. J Biol Chem 2001; 276:12598-608.
45. Chen Y, Potratz JP, Tijerina P, Del Campo M, Lambowitz AM, Russell R. DEAD-box proteins can completely separate an RNA duplex using a single ATP. Proc Natl Acad Sci USA 2008; 105:20203-8.
46. Liu F, Putnam A, Jankowsky E. ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding. Proc Natl Acad Sci USA 2008; 105:20209-14.
47. Jarmoskaite I, Russell R. DEAD-box proteins as RNA helicases and chaperones. Wiley Interdisciplinary Reviews: RNA 2010.
48. Yao N, Reichert P, Taremi SS, Prosise WW, Weber PC. Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease-helicase. Structure 1999; 7:1353-63.
49. Buttner K, Nehring S, Hopfner KP. Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat Struct Mol Biol 2007; 14:647-52.
50. He Y, Andersen GR, Nielsen KH. Structural basis for the function of DEAH helicases. EMBO Rep 2010; 11:180-6.
51. Jackson RN, Klauer AA, Hintze BJ, Robinson H, van Hoof A, Johnson SJ. The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing. EMBO J 2010; 29:2205-16.
52. Weir JR, Bonneau F, Hentschel J, Conti E. Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proc Natl Acad Sci USA 2010; 107:12139-44.
53. Rogers GW Jr, Richter NJ, Lima WF, Merrick WC. Modulation of the helicase activity of eIF4A by eIF4B, eIF4H and eIF4F. J Biol Chem 2001; 276:30914-22.
54. Bizebard T, Ferlenghi I, Iost I, Dreyfus M. Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases. Biochemistry 2004; 43:7857-66.
55. Tijerina P, Bhaskaran H, Russell R. 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 2006; 103:16698-703.
56. Yang Q, Jankowsky E. The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases. Nat Struct Mol Biol 2006; 13:981-6. (Pubitemid 44684849)
57. Grohman JK, Del Campo M, Bhaskaran H, Tijerina P, Lambowitz AM, Russell R. Probing the mechanisms of DEAD-box proteins as general RNA chaperones: the C-terminal domain of CYT-19 mediates general recognition of RNA. Biochemistry 2007; 46:3013-22.
58. Mohr G, Del Campo M, Mohr S, Yang Q, Jia H, Jankowsky E, et al. Function of the C-terminal domain of the DEAD-box protein Mss116p analyzed in vivo and in vitro. J Mol Biol 2008; 375:1344-64.
59. Diges CM, Uhlenbeck OC. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J 2001; 20:5503-12.
60. Wang S, Hu Y, Overgaard MT, Karginov FV, Uhlenbeck OC, McKay DB. 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 2006; 12:959-67.
61. Klostermeier D, Rudolph MG. A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility. Nucleic Acids Res 2009; 37:421-30.
62. Fuller-Pace FV, Nicol SM, Reid AD, Lane DP. DbpA: a DEAD box protein specifically activated by 23S rRNA. EMBO J 1993; 12:3619-26.
63. Sharpe Elles LM, Sykes MT, Williamson JR, Uhlenbeck OC. A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Res 2009; 37:6503-14.
64. Serra MJ, Turner DH. Predicting thermodynamic properties of RNA. Methods Enzymol 1995; 259:242-61.
65. Tinoco I Jr, Bustamante C. How RNA folds. J Mol Biol 1999; 293:271-81.
66. Pan T, Sosnick T. RNA folding during transcription. Annu Rev Biophys Biomol Struct 2006; 35:161-75.
67. Zhang L, Bao P, Leibowitz MJ, Zhang Y. Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the self-splicing Candida intron. RNA 2009; 15:1986-92.
68. Chadalavada DM, Cerrone-Szakal AL, Bevilacqua PC. Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions. RNA 2007; 13:2189-201.
69. Baldwin RL, Rose GD. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 1999; 24:26-33.
70. Gartland WJ, Sueoka N. Two interconvertible forms of tryptophanyl sRNA in E. coli. Proc Natl Acad Sci USA 1966; 55:948-56.
71. Lindahl T, Adams A, Fresco JR. Renaturation of transfer ribonucleic acids through site binding of magnesium. Proc Natl Acad Sci USA 1966; 55:941-8.
72. Uhlenbeck OC, Chirikjian JG, Fresco JR. Oligonucleotide binding to the native and denatured conformers of yeast transfer RNA-3 Lea. J Mol Biol 1974; 89:495-504.
73. Madore E, Florentz C, Giege R, Lapointe J. Magnesium-dependent alternative foldings of active and inactive Escherichia coli tRNA(Glu) revealed by chemical probing. Nucleic Acids Res 1999; 27:3583-8.
74. Weidner H, Yuan R, Crothers DM. Does 5S RNA function by a switch between two secondary structures? Nature 1977; 266:193-4.
75. Woodson SA, Cech TR. Alternative secondary structures in the 5′ exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA. Biochemistry 1991; 30:2042-50.
76. Woodson SA, Emerick VL. An alternative helix in the 26S rRNA promotes excision and integration of the Tetrahymena intervening sequence. Mol Cell Biol 1993; 13:1137-45.
77. Pichler A, Schroeder R. Folding problems of the 5′ splice site containing the P1 stem of the group I thymidylate synthase intron: substrate binding inhibition in vitro and mis-splicing in vivo. J Biol Chem 2002; 277:17987-93.
78. Duncan CD, Weeks KM. SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA. Biochemistry 2008; 47:8504-13.
79. Chadalavada DM, Senchak SE, Bevilacqua PC. The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. J Mol Biol 2002; 317:559-75.
80. Roth A, Breaker RR. The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 2009; 78:305-34.
81. Storz G, Altuvia S, Wassarman KM. An abundance of RNA regulators. Annu Rev Biochem 2005; 74:199-217.
82. Staley JP, Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs and things. Cell 1998; 92:315-26.
83. Noble SM, Guthrie C. Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations. Genetics 1996; 143:67-80.
84. Edwalds-Gilbert G, Kim DH, Kim SH, Tseng YH, Yu Y, Lin RJ. Dominant negative mutants of the yeast splicing factor Prp2 map to a putative cleft region in the helicase domain of DExD/H-box proteins. RNA 2000; 6:1106-19.
85. Lardelli RM, Thompson JX, Yates JR, 3rd, Stevens SW. Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing. RNA 2010; 16:516-28.
86. Staley JP, Guthrie C. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol Cell 1999; 3:55-64.
87. Chen JY, Stands L, Staley JP, Jackups RR Jr, Latus LJ, Chang TH. Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor. Mol Cell 2001; 7:227-32.
88. Konarska MM, Vilardell J, Query CC. Repositioning of the reaction intermediate within the catalytic center of the spliceosome. Mol Cell 2006; 21:543-53.
89. Mefford MA, Staley JP. Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps. RNA 2009; 15:1386-97.
90. Schwer B. A conformational rearrangement in the spliceosome sets the stage for Prp22-dependent mRNA release. Mol Cell 2008; 30:743-54. (Pubitemid 351815129)
91. 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.
92. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinformatics 2002; 3:2.
93. Leontis NB, Westhof E. Analysis of RNA motifs. Curr Opin Struct Biol 2003; 13:300-8.
94. Hodak JH, Downey CD, Fiore JL, Pardi A, Nesbitt DJ. Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET. Proc Natl Acad Sci USA 2005; 102:10505-10.
95. Fiore JL, Kraemer B, Koberling F, Edmann R, Nesbitt DJ. Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop-receptor tertiary interaction. Biochemistry 2009; 48:2550-8.
96. Zarrinkar PP, Williamson JR. Kinetic intermediates in RNA folding. Science 1994; 265:918-24.
97. Sclavi B, Sullivan M, Chance MR, Brenowitz M, Woodson SA. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 1998; 279:1940-3.
98. Rook MS, Treiber DK, Williamson JR. Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape. J Mol Biol 1998; 281:609-20.
99. Russell R, Herschlag D. New pathways in folding of the Tetrahymena group I RNA enzyme. J Mol Biol 1999; 291:1155-67.
100. Russell R, Millett IS, Doniach S, Herschlag D. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nat Struct Biol 2000; 7:367-70.
101. Russell R, Zhuang X, Babcock HP, Millett IS, Doniach S, Chu S, et al. Exploring the folding landscape of a structured RNA. Proc Natl Acad Sci USA 2002; 99:155-60. (Pubitemid 34060333)
102. Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc Natl Acad Sci USA 2007; 104:7045-50.
103. Shcherbakova I, Mitra S, Laederach A, Brenowitz M. Energy barriers, pathways and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol 2008; 12:655-66.
104. Pan J, Woodson SA. Folding intermediates of a self-splicing RNA: mispairing of the catalytic core. J Mol Biol 1998; 280:597-609.
105. Russell R, Das R, Suh H, Travers KJ, Laederach A, Engelhardt MA, et al. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J Mol Biol 2006; 363:531-44.
106. Wan Y, Suh H, Russell R, Herschlag D. Multiple unfolding events during native folding of the Tetrahymena group I ribozyme. J Mol Biol 2010; 400:1067-77.
107. Treiber DK, Rook MS, Zarrinkar PP, Williamson JR. Kinetic intermediates trapped by native interactions in RNA folding. Science 1998; 279:1943-6.
108. Jiang YF, Xiao M, Yin P, Zhang Y. Monovalent cations use multiple mechanisms to resolve ribozyme misfolding. RNA 2006; 12:561-6.
109. Duncan CD, Weeks KM. Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding. Biochemistry 2010; 49:5418-25.
110. Rangan P, Masquida B, Westhof E, Woodson SA. Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc Natl Acad Sci USA 2003; 100:1574-9.
111. Chauhan S, Caliskan G, Briber RM, Perez-Salas U, Rangan P, Thirumalai D, et al. RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. J Mol Biol 2005; 353:1199-209.
112. Chauhan S, Behrouzi R, Rangan P, Woodson SA. Structural rearrangements linked to global folding pathways of the Azoarcus group I ribozyme. J Mol Biol 2009; 386:1167-78.
113. Roh JH, Guo L, Kilburn JD, Briber RM, Irving T, Woodson SA. Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle x-ray scattering. J Am Chem Soc 2010; 132:10148-54.
114. Coetzee T, Herschlag D, Belfort M. Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes Dev 1994; 8:1575-88.
115. Clodi E, Semrad K, Schroeder R. Assaying RNA chaperone activity in vivo using a novel RNA folding trap. EMBO J 1999; 18:3776-82. (Pubitemid 29308856)
116. Rajkowitsch L, Semrad K, Mayer O, Schroeder R. Assays for the RNA chaperone activity of proteins. Biochem Soc Trans 2005; 33:450-6.
117. Waldsich C, Grossberger R, Schroeder R. RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo. Genes Dev 2002; 16:2300-12.
118. Mayer O, Waldsich C, Grossberger R, Schroeder R. Folding of the td pre-RNA with the help of the RNA chaperone StpA. Biochem Soc Trans 2002; 30:1175-80.
119. Schroeder R, Grossberger R, Pichler A, Waldsich C. RNA folding in vivo. Curr Opin Struct Biol 2002; 12:296-300.
120. Mohr S, Stryker JM, Lambowitz AM. A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell 2002; 109:769-79.
121. Huang HR, Rowe CE, Mohr S, Jiang Y, Lambowitz AM, Perlman PS. 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 2005; 102:163-8.
122. Seraphin B, Simon M, Boulet A, Faye G. Mitochondrial splicing requires a protein from a novel helicase family. Nature 1989; 337:84-7.
123. Mohr S, Matsuura M, Perlman PS, Lambowitz AM. A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone. Proc Natl Acad Sci USA 2006; 103:3569-74.
124. Bifano AL, Caprara MG. A DExH/D-box protein coordinates the two steps of splicing in a group I intron. J Mol Biol 2008; 383:667-82.
125. Bhaskaran H, Russell R. Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone. Nature 2007; 449:1014-8. (Pubitemid 350014602)
126. Del Campo M, Tijerina P, Bhaskaran H, Mohr S, Yang Q, Jankowsky E, et al. Do DEAD-box proteins promote group II intron splicing without unwinding RNA? Mol Cell 2007; 28:159-66.
127. Yang Q, Fairman ME, Jankowsky E. DEAD-box-protein-assisted RNA structure conversion towards and against thermodynamic equilibrium values. J Mol Biol 2007; 368:1087-100.
128. Landry SJ, Jordan R, McMacken R, Gierasch LM. Different conformations for the same polypeptide bound to chaperones DnaK and GroEL. Nature 1992; 355:455-7.
129. Zhu X, Zhao X, Burkholder WF, Gragerov A, Ogata CM, Gottesman ME, et al. Structural analysis of substrate binding by the molecular chaperone DnaK. Science 1996; 272:1606-14.
130. Schmid D, Baici A, Gehring H, Christen P. Kinetics of molecular chaperone action. Science 1994; 263:971-3.
131. Alfano C, McMacken R. Heat shock protein-mediated disassembly of nucleoprotein structures is required for the initiation of bacteriophage lambda DNA replication. J Biol Chem 1989; 264:10709-18.
132. Diamant S, Ben-Zvi AP, Bukau B, Goloubinoff P. Size-dependent disaggregation of stable protein aggregates by the DnaK chaperone machinery. J Biol Chem 2000; 275:21107-13.
133. Bukau B, Weissman J, Horwich A. Molecular chaperones and protein quality control. Cell 2006; 125:443-51.
134. Saibil HR. Chaperone machines in action. Curr Opin Struct Biol 2008; 18:35-42.
135. Barends TR, Werbeck ND, Reinstein J. Disaggregases in 4 dimensions. Curr Opin Struct Biol 2010; 20:46-53.
136. Bowers HA, Maroney PA, Fairman ME, Kastner B, Luhrmann R, Nilsen TW, et al. Discriminatory RNP remodeling by the DEAD-box protein DED1. RNA 2006; 12:903-12.
137. 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.
138. Uhlmann-Schiffler H, Jalal C, Stahl H. Ddx42p - a human DEAD box protein with RNA chaperone activities. Nucleic Acids Res 2006; 34:10-22.
139. Perriman R, Barta I, Voeltz GK, Abelson J, Ares M Jr. ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA. Proc Natl Acad Sci USA 2003; 100:13857-62.
140. Lund MK, Guthrie C. The DEAD-box protein Dbp5p is required to dissociate Mex67p from exported mRNPs at the nuclear rim. Mol Cell 2005; 20:645-51.
141. Tran EJ, Zhou Y, Corbett AH, Wente SR. The DEAD-box protein Dbp5 controls mRNA export by triggering specific RNA:protein remodeling events. Mol Cell 2007; 28:850-9.
142. Stewart M. Ratcheting mRNA out of the nucleus. Mol Cell 2007; 25:327-30.
143. Linder P. mRNA export: RNP remodeling by DEAD-box proteins. Curr Biol 2008; 18:297-9.
144. Strahm Y, Fahrenkrog B, Zenklusen D, Rychner E, Kantor J, Rosbach M, et al. The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr 255p. EMBO J 1999; 18:5761-77.
145. Weirich CS, Erzberger JP, Flick JS, Berger JM, Thorner J, Weis K. Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export. Nat Cell Biol 2006; 8:668-76.
146. 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. (Pubitemid 41443687)
147. Halls C, Mohr S, Del Campo M, Yang Q, Jankowsky E, Lambowitz AM. 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 2007; 365:835-55.
148. Jankowsky E. RNA helicases at work: binding and rearranging. Trends in Biochemical Sciences 2010; In press.
149. Lehnert V, Jaeger L, Michel F, Westhof E. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem Biol 1996; 3:993-1009.