The protein family of RNA helicases

Critical Reviews in Biochemistry and Molecular Biology

Volumn 33, Issue 4, 1998, Pages 259-296

  Lüking, Angelika ^a   Stahl, Ulf ^b   Schmidt, Udo ^b  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

ATP hydrolysis; DEAD DEAH box protein; Mitochondrial RNA splicing; MRNA export; Nuclear pre mRNA splicing; Ribosomal biogenesis; RNA degradation; RNA helicase; Translation initiation; Unwinding of RNA

Indexed keywords

DEAD BOX PROTEIN; DEAH BOX PROTEIN; MESSENGER RNA; RIBOSOME RNA; RNA HELICASE; UNCLASSIFIED DRUG;

CELL DIFFERENTIATION; ENZYME ACTIVITY; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; REVIEW; RNA CONFORMATION; RNA EDITING; RNA GENE; RNA PROCESSING; RNA TRANSPORT; SACCHAROMYCES CEREVISIAE; TRANSLATION INITIATION; VIRUS GENE; VIRUS REPLICATION;

AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; HUMANS; MOLECULAR SEQUENCE DATA; RIBOSOMES; RNA HELICASES;

EID: 0031720383     PISSN: 10409238     EISSN: None     Source Type: Journal    
DOI: 10.1080/10409239891204233     Document Type: Review

References (202)

1. Abramson, R. D., Dever, T. E., Lawson, T. G., Ray, B. K., Thach, R. E., and Merrick, W. C. (1987). The ATP-dependent interaction of eukaryotic initiation factors with mRNA. J. Biol Chem. 262: 3826-3832.
2. Abramson, R. D., Dever, T. E., and Merrick, W. C. (1988). Biochemical evidence supporting a mechanism for cap-independent and internal initiation of eukaryotic mRNA. J. Biol. Chem. 263: 6016-6019.
3. Altamura, N., Dujardin, G., Groudinsky, O., and Slonimski, P. P. (1994). Two adjacent nuclear genes, ISFI and NAM7/UPF1, cooperately participate in mitochondrial functions in Saccharomyces cerevisiae. Mol. Gen. Genet. 242: 49-56.
4. Altamura, N., Groudinsky, O., Dujardin, G., and Slonimski, P. P. (1992). NAM7 nuclear gene encodes a novel member of a family of helicases with a Zn-ligand motif and is involved in mitochondrial functions in Saccharomyces cerevisiae. J. Mol. Biol. 224: 575-587.
5. Altmann, M., Müller, P. P., Wittmer, B., Ruchti, F., Lanker, S., and Trachsel, H. (1993). A Saccharomyces cerevsiae homologue of mammalian translation initiation factor eIF-4B contributes to RNA helicase activity. EMBO J. 12: 3997-4003.
6. Altmann, M., Schmitz, N., Berset, C., and Trachsel, H. (1997). A novel inhibitor of cap-dependent translation initiation in yeast: p20 competes with eIF4G for binding to eIF4E. EMBO J. 16: 1114-1121.
7. Arenas, J. E. and Abelson, J. N. (1997). Prp43: An RNA helicase-like factor involved in spliceosome disassembly. Proc. Natl. Acad. Sci. USA 94: 11798-11802.
8. Bayliss, C. and Condits, R. C. (1996). The vaccinia virus A18R gene product is a DNA-dependent ATPase. J. Biol. Chem. 270: 1550-1556.
9. Ben Asher, E., Groudinsky, O., Dujardin, G., Altamura, N., Kermorgant, M., and Slonimski, P. P. (1989). Novel class of nuclear genes involved in both mRNA splicing and protein synthesis in S. cerevisiae mitochondria. Mol. Gen. Genet. 215: 517-528.
10. Blum, S., Mueller, M., Schmid, S. R., Under, P., and Trachsel, H. (1989). Translation in Saccharomyces cerevisiae: initiation factor 4A-dependent cell-free system. Proc. Natl. Acad. Sci. USA 86: 6043-6046.
11. Böddeker, N., Stade, K., and Franceschi, F. (1997). Characterization of DbpA, an Escherichia coli DEAD box protein with ATP-independent RNA unwinding activity. Nucleic Acids Res. 25: 537-545.
12. Brockdorff, N., Ashworth, A., Kay, G. F., McCabe, V. M., Norris, D. P. C., P. J., Swift, S., and Rastan, S. (1992). The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71: 515-526.
13. Brown, C. J., Henddrich, B. D., Rupert, J. L., Lafreniere, R. G., Xing, Y., Lawrence, J., and Willard, H. F. (1992). The human XIST gene: analysis of a 17-kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71: 527-542.
14. Broyles, S. S. and Moss, B. (1987). Identification of the vaccinia virus gene encoding nucleoside triphosphate phosphohydrolase I, a DNA-dependent ATPase. J. Virology 61: 1738-1742.
15. Buelt, M. K., Glidden, B. J., and Storm, D. R. (1994). Regulation of p68 RNA helicase by Calmudin and protein kinase C. J. Biol. Chem. 269: 29367-29370.
16. Burke, J. M. (1988). Molecular genetics of group I introns, RNA structures and protein factors required for splicing - a review. Gene 73: 273-294.
17. Chang, T.-H., Arenas, J., and Abelson, J. (1990). Identification of five putative RNA helicase genes. Proc. Natl. Acad. Sci. USA 87: 1571-1575.
18. Cheng, J., Fogel-Petrovic, M., and Maquat, L. E. (1990). Translation to near the distal end of the penultimate exon is required for normal levels of spliced triosephosphate isomerase mRNA. Mol. Cell. Biol. 10: 5215-5225.
19. Chuang, R.-Y., Weaver, P. L., Liu, Z., and Chang, T.-H. (1997). Requirement of the DEAD-box protein Ded1p for messenger RNA translation. Science 275: 1468-1471.
20. Claude, A., Arenas, J. E., and Hurwitz, J. (1991). The isolation and characterization of a RNA helicase from nuclear extracts of HeLa cells. J. Biol. Chem. 266: 10358-10367.
21. Company, M., Arenas, J., and Abelson, J. (1991). Requirement of the RNA helicase-like protein PRP22 for release of messenger RNA from spliceosomes. Nature 349: 487-493.
22. Conrad-Webb, H., Perlman, P. S., Zhu, H., and Butow, R. A. (1990). The nuclear SUV3-1 mutation affects a variety of post-transcriptional processes in yeast mitochondria. Nucleic Acids Res. 18: 1369-1376.
23. Conroy, S. C., Dever, T. E., Owens, C. L., and Merrick, W. C. (1990). Characterization of the 46,000 dalton subunit of the eIF-4A. Arch. Biochem. Biophys. 282: 363-371.
24. Czaplinski, K., Weng, Y., Hagan, K. W., and Peltz, S. W. (1995). Purification and characterization of the Upf1 protein: a factor involved in translation and mRNA degradation. RNA 1: 610-623.
25. Dalbadie-McFarland, G. and Abelson, J. N. (1990). A helicase-like protein required for mRNA splicing in yeast. Proc. Natl. Acad. Sci. USA 87: 4263-4240.
26. Daugeron, M. C. and Linder, P. (1998). DbpTp, a putative ATP-dependent RNA helicase from Saccharomyces cerevisiae, is required for 60S ribosomal subunit assembly. RNA 4: 566-581.
27. de la Cruz, J., lost, I, Kressler, D., and Linder, P. (1997). The p20 and Ded1 proteins have antagonistic roles in eIF4E-dependent translation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 94: 5201-5206.
28. de la Cruz, J., Kressler, D., Tollervey, D., and Under, P. (1998). Doblp (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae. EMBO J. 17: 1128-1140.
29. de Valoir, T., Tucker, M. A., Belikoff, E. J., Camp, L. A., Bolduc,C., and Beckingham, K. (1991). A second maternally expressed Drosophila gene encodes a putative RNA helicase of the "DEAD box" family. Proc. Natl. Acad. Sci. USA 88: 2113-2117.
30. Dmochowska, A., Golik, P., and Stepien, P. (1995). The novel nuclear gene DSS-1 of Saccharomyces cerevisiae is necessary for mitochondrial biogenesis. Curr. Genet. 28: 108-112.
31. Dykstra, C. C., Kitada, K., Clark, A. B., Hamataka, R. K., and Sugino, A. (1991). Cloning and characterizing of DST2, the gene for DNA strand transfer protein b from Saccharomyces cerevisiae. Mol. Cell. Biol. 11: 2583-2592.
32. Eichler, D. C. and Craig, N. (1994). Processing of eukaryotic ribosomal RNA. Prog. Nucleic Acids Res. Mol. Biol. 49: 197-239.
33. Fathi, Z. and Condit, R. C. (1991a). Genetic and molecular biological characterization of a vaccinia virus temperature-sensitve complementation group affecting a virion component. Virology 181: 258-272.
34. Fathi, Z. and Condit, R. C. (1991b). Phenotypic characterization of a vaccinia virus temperatursensitive complementation group affecting a virion component. Virology 181: 273-276.
35. Fernández, A., Laín, S., and García, A. (1995). RNA helicase activity of the plum pox potyvirus CI protein expressed in Escherichia coli. Mapping of an RNA binding domain. Nucleic Acids Res. 23: 1327-1332.
36. Flores-Rozas, H. and Hurwitz, J. (1993). Characterization of a new RNA helicase from nuclear extracts of Hela cells which translocates in the 5′ to 3′ direction. J. Biol. Chem. 268: 21372-21383.
37. Ford, M. J., Anton, I. A., and Lane, D. P. (1988). Nuclear protein with sequence homology to translation initiation factor eIF-4A. Nature 322: 736-738.
38. Fornerod, M., Ohno, M., Yoshida, M., and Mattaj, I. W. (1997). CRM1 is an export receptor for leucine-rich nuclear export signals. Cell 90: 1051-1060.
39. 1-ATPase, and other nucleotidebinding proteins. Proc. Natl. Acad. Sci. USA 83:907-911.
40. Fuller-Pace, F. V. (1994). RNA helicases: modulators of RNA structure. Trends Cell Biol. 4: 271-274.
41. Fuller-Pace, F. V., Nicol, S. M., Reid, A. D., and Lane, D. P. (1993). DbpA; a DEAD box protein specifically activated by 23S rRNA. EMBO J. 12: 3619-3626.
42. Gershon, P. D. and Moss, B. (1990). Early transcription factor subunits are encoding by vaccinia virus late genes. Proc. Natl. Acad. Sci. USA 87: 4401-4405.
43. Golubovsky, M. D. and Ivanov, Y. N. (1972). Autosomal mutation in Drosophlla melanogaster killing the males and connected with female sterility. Dros. Info. Serv. 49: 117.
44. Gorbalenya, A. E. and Koonin, E. V. (1989). Viral proteins containing the purine NTP-binding sequence pattern. Nucleic Acids Res. 17: 8413-8440.
45. Gorbalenya, A. E. and Koonin, E. Y. (1991). Endonuclease (R) subunit of type-I and type-in restriction modification enzymes contain a helicase-like domain. FEBS Lett. 291: 277-281.
46. Gorbalenya, A. E., Koonin, E. V., Donchenko, A. P. and Blinov, V. M. (1988a). A conserved NTP-motif in putative helicases. Nature 333: 22.
47. Gorbalenya, A. E., Koonin, E. V., Donchenko, A. P., and Blinov, V. M. (1988b). A novel superfamily of nucleoside triphosphate-binding motif containing proteins which are probably involved in duplex unwinding in DNA and RNA replication and recombination. FEBS Lett. 235: 16-24.
48. Gorbalenya, A. E., Koonin, E. V., Donchenko, A. P., and Blinov, V. M. (1989). Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 17: 4713-4730.
49. Grifo, J. A., Tahara, S. M., Abramson, R. D., Satler, C. A., and Merrick, W. C. (1984). RNA-stimulated ATPase activity of eukaryotic initiation factors. J. Biol. Chem. 259: 8648-8654.
50. Grivell, L. A. (1995). Nucleo-mitochondrial interactions in mitochondrial gene expression. Crit. Rev. Biochem. Mol. Biol. 30: 121-164.
51. Gros, C. and Wengler, G. (1996). Identification of an RNA-stimulated NTPase in the predicted helicase sequence of the Rubella virus nonstructural polyprotein. Virology 217: 367-372.
52. Gururajan, R., Mathews, L., Longo, F. J. and Weeks, D. L. (1994). An3 mRNA encodes an RNA helicase that colocalizes with nucleoli in Xenopus oocytes in a stage-specific manner. Proc. Natl. Acad. Sci. USA 91: 2056-2060.
53. Gururajan, R., Perry O'Keefe, H., Melton, D. A., and Weeks, D. L. (1991). The Xenopus localized messenger RNA An3 may encode an ATP-dependent RNA helicase. Nature 349: 717-719.
54. Gururajan, R. and Weeks, D. L. (1997). An3 protein encoded by a localized maternal mRNA in Xenopus laevis is an ATPase with substrate-specific RNA helicase activity. Biochim. Biophys. Acta 1350: 169-182.
55. Hagan, K. W., Ruiz-Echevarría, M. J., Quan, Y., and Peltz, S. W. (1995). Characterization of cis-acting sequences and decay intermediates involved in nonsense-mediated mRNA turnover. Mol. Cell. Biol. 15: 809-823.
56. Hajduk, S. L., Harris, M. E., and Pollard, V. W. (1993). RNA editing in kinetoplastid mitochondria. FASEB J. 7: 54-63.
57. Hamm, J. and Lammond, A. I. (1998). Spliceosome assembly: the unwinding role of DEAD-box proteins. Curr. Biol. 8: 532-534.
58. Hay, B., Jan, L. Y., and Jan, Y. N. (1988). A protein component of Drosophila polar granules is encoded by vasa and has extensive sequence similarity to ATP-dependent helicases. Cell 55: 577-587.
59. He, F. and Jacobson, A. (1995). Identification of a novel component of the nonsense-mediated mRNA decay pathway using an interacting protein screen. Genes Dev. 9: 437-454.
60. Hershey, J. W. B. (1991). Translational control in mammalian cells. Annu. Rev. Biochem. 60:117-755.
61. Hirling, H., Scheffner, M., Restle, T., and Stahl, H. (1989). RNA helicase activity associated with the human p68 protein. Nature 339: 562-564.
62. Hodgeman, T. C. (1988). A new superfamily of replicative proteins. Nature 333: 22-23.
63. Houghton, M., Selby, M., Weiner, A., and Choo, Q. L. (1994). Hepatits C virus: structure, protein products and processing of the polyprotein precursor. Curr. Stud. Hematol. Blood Transfus. 61: 1-11.
64. 0-Thalassemia gene: A premature termination codon causes β-mRNA deficiency without affecting cytoplasmic β-mRNA stability. Blood 64: 23-32.
65. Iggo, R. D., Jamieson, D.J., MacNeill, S. A., Southgate, J., McPheat, J., and Lane, D. P. (1991). p68 RNA helicase: identification of a nucleolar form and cloning of related genes containing a conserved intron in yeasts. Mol. Cell. Biol. 11: 1326-1333.
66. Iggo, R. D. and Lane, D. P. (1989). Nuclear protein p68 is an RNA-dependent ATPase. EMBO J. 8: 1827-1831.
67. Jamieson, D. J. and Beggs, J. D. (1991). A suppressor of yeast spp81/dedl mutations encodes a very similar putative ATP-dependent RNA helicase. Mol. Microbiol. 5: 805-812.
68. Jamieson, D. J., Rahe, B., Pringle, J., and Beggs, J. D. (1991). A suppressor of a yeast splicing mutation (prp8-l) encodes a putative ATP-dependent RNA helicase. Nature 349: 715-717.
69. Jaramillo, M., Dever, T. E., Merrick, W. C., and Sonenberg, N. (1991). RNA unwinding in translation: assembly of helicase complex intermediates comprising eukaryotic initiation factors eIF-2F and eIF-4B. Mol Cell Biol. 11: 5992-5997.
70. Jin, L. and Peterson, D. L. (1995). Expression, isolation, and characterization of the Hepatitis C virus ATPase/RNA helicase. Arch. Biochem. Biophys. 323: 47-53.
71. Jones, P. G., Mitta, M., Kim, Y., Jiang, W., and Inouye, M. (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.
72. Kadaré, G. and Haenni, A. L. (1997). Virus encoded RNA helicases, J. Virol. 71:2583-2590.
73. Kalman, M., Murphy, H., and Cashel, M. (1991). rhlB, a new Escherichia coli K-12 gene with an RNA helicase-like protein sequence motif, one of the least five such possible genes in a prokaryote. New Biol. 3: 886-895.
74. Kim, D. W., Gwack, Y., Han, J. H., and Choe, J. (1995). C-terminal domain of the hepatitis C virus protein contains an RNA helicase activity. Biochem. Biophys. Res. Commun. 215:160-166.
75. Kim, J., Ljungdahl, P. O., and Fink, G. R. (1990). kern mutations affect nuclear fusion in Saccharomyces cerevisiae. Genetics 126: 799-812.
76. Kim, S. H., Smith, J., Claude, A., and Lin, R. J. (1992). The purified yeast pre-mRNA splicing factor PRP2 is an RNA-dependent NTPase. EMBO J. 11: 2319-2326.
77. King, P. S. and Beggs, J. D. (1990). Interaction of the PRP2 protein with pre-mRNA splicing complexes in Saccharomyces cerevisiae. Nucleic Acids Res. 18: 6559-6564.
78. Kipling, D., Tambini, C., and Kearsey, S. E. (1991). rar mutations which increase artificial chromosome stability in Saccharomyces cerevisiae identify transcription and recombination proteins. Nucleic Acids Res. 19: 1385-1391.
79. Klug, A. and Schwabe, J. W. (1995). Protein motifs 5. Zinc fingers. FASEB J. 9: 597-604.
80. Komiya, T., Itoh, K., Ikenishi, K., and Furusawa, M. (1994). Isolation and characterization of a novel gene of the DEAD box protein family which is specifically expressed in germ cells of Xenopus laevis. Dev. Biol. 162: 354-363.
81. Komiya, T. and Tanigawa, Y. (1995). Cloning of a gene of the DEAD box protein family which is specifically expressed in germ cells in rats. Biochem. Biophys. Res. Commun. 207: 405-410.
82. Koonin, E. V. (1991). Similarities in RNA helicases. Nature 352: 290.
83. Koonin, E. V. (1992). A new group of putative RNA helicases. Trends Biochem. Sci. 17:495-497.
84. Koonin, E. V. and Senkevich, T. G. (1992). Vaccinia virus encodes four putative DNA and/or RNA helicases distantly related to each other. J. Gen.Virol. 73: 989-993.
85. Kozak, M. (1989). The scanning model for translation: An update. J. Cell. Biol. 108: 229-241.
86. Krämer, A. (1996). The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu. Rev. Biochem. 65: 367-409.
87. Kressler, D., de la Cruz, J., Rojo, M., and Linder, P. (1997). Fa11p is an essential DEAD-box protein involved in 40S-ribosomal-subunit biogenesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 17: 7283-7294.
88. Kressler, D., de la Cruz, J., Rojo, M., and Linder, P. (1998). Dbp6p is an essential putative ATP-dependent RNA helicase required for the 60S-ribosomal-subunit assembly in Saccharomyces cerevisiae. Mol. Cell. Biol. 18: 1855-1865.
89. Kuroda, M. I., Kernan, M. J., Kreber, R., Ganetzky, B., and Baker, B. S. (1991). The maleless protein associates with the X chromosme to regulate dosage compensation in Drosophila. Cell 66: 935-947.
90. Laggerbauer, B., Achsel, T., and Lührmann, R. (1998). The human U5-200kD DEXH-box protein unwinds U4/U6 duplices in vitro. Proc. Natl. Acad. Sci. USA 95: 4188-4192.
91. Lain,S.,Riechmann, J.L.,and Garcia, J. A. (1990). RNA helicase: a novel activity associated with a protein encoded by a postive strand RNA virus. Nucleic Acids Res. 18: 7003-7006.
92. Lambowitz, A. M. and Belfort, M. (1993). Introns as mobile genetic elements. Annu. Rev. Biochem. 62: 587-622.
93. Lambowitz, A. M., Caprara, M. G., Zimmerly, S., and Perlman, P. S. (1998). Group I and group II ribozymes as RNPs: Clues to the past and guides to the future. In: T. Cech (ed.) The RNA World, 2nd edition, Cold Spring Harbor Labo-ratory Press, Cold Spring Harbor, NY, in press.
94. Lambowitz, A. M. and Perlman, P. S. (1990). Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 15: 440-444.
95. Lamm, G. M. and Lamond, A. I. (1993). Non-snRNP protein splicing factors. Biochim. Biophys. Acta 1173: 247-265.
96. Lamond, A. I. (1993). The spliceosome. Bio Essays 15: 595-603.
97. Lane, D. P. and Hoeffler, W. K. (1980). SV40 large T shares an antigenic determinant with a cellular protein of molecular weight 68,000. Nature 288 167-170.
98. Larimer, F. W., Hsu, C. L., Maupin, M. K., and Stevens, A. (1992). Characterization of the XRN1 gene encoding a 5'-3'exoribonuclease: sequence data and analysis of disparate protein and mRNA levels of the gene-disrupted yeast cells. Gene 120: 51-57.
99. Lasko, P. F. and Ashburner, M. (1988). The product of the Drosophila gene vasa is very similar to eukaryotic initiation factor 4A. Nature 335: 611-617.
100. Lasko, P. F. and Ashburner, M. (1990). Posterior localization of vasa protein correlates with, but is not sufficient for, pole cell development. Genes Dev. 4: 905-922.
101. Laughrea, M. and Moore, P. B. (1978). On the relationship between the binding of ribosomal protein S1 to the 30S subunit of Escherichia coli and the 3′ terminus of 16S RNA. J. Mol. Biol. 121:411-430.
102. Lee, C-G., Chang, K., A., Kuroda, M. I., and Hurwitz, J. (1997). The NTPase/helicase activities of Drosophila maleless, an essential factor in dosage compensation. EMBO J. 16:2671 - 681.
103. Lee, C.-G. and Hurwitz, J. (1992). A new RNA helicase isolated from Hela cells that catalytically translocated in the 3′ to 5′ direction. J. Biol. Chem. 267: 4398-4407.
104. Lee, C.-G. and Hurwitz, J. (1993). Human RNA helicase A is homologous to the maleless protein of Drosophila.J. Biol. Chem. 268:16822-16830.
105. Leeds, P., Peltz, S.W., Jacobson, A., and Culbertson, M. R. (1991). The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev. 5: 2303-2314.
106. Leroy, P., Alzari, P., Sassoon, D., Wolgemuth, D., and Fellous, M. (1989). The protein encoded by a murine male germ cell-specific transcript is a putative ATP-dependent RNA helicase. Cell 57: 549-559.
107. Liang, L., Diehl-Jones, W., and Lasko, P. (1994). Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-bindig and helicase activities. Development 120:1201-1211.
108. Liang, S., Hitomi, M., Hu, Y. H., Liu, Y., and Tartakoff, A. M. (1996). A DEAD-box-family protein is required for nucleocytoplasmic transport of yeast mRNA. Mol Cell. Biol. 16: 5139-5146.
109. Lin, R.-J., Lustig, A. J., and Abelson, J. N. (1987). Splicing of yeast nuclear pre-mRNA in vitro requires a functional 40S spliceosome and several extrinsic factors. Genes Dev. 1: 7-18.
110. Linder, P., Lasko, P. F., Ashburner, M., Leroy, P., Nielsen, P. P., Nishi, K., Schnier, J., and Slonimski, P. P. (1989). Birth of the D-E-A-D box. Nature 337: 121-122.
111. Linder, P. and Prat, A. (1990). Baker's yeast, the new work horse in protein synthesis studies: Analyzing eukaryotic translation initiation. Bio Essays 12: 519-527.
112. Linder, P. and Slonimski, P. P. (1988). Sequence of the genes TIF1 and TIF2 from Saccharomyces cerevisiae coding for a translation initiation factor. Nucleic Acids Res. 16: 10359.
113. Linder, P. and Slonimski, P. P. (1989). An essential yeast protein, encoded by the duplicated genes Tif 1 and Tif2 and homologous to the mammalian translation initiation factor eIF4A, can suppress a mitochondrial missense mutation. Proc. Natl. Acad. Sci. USA 86:2286-2290.
114. Lu, K. P. and Means, A. R. (1993). Regulation of the cell cycle by calcium and calmodulin. Endocrin. Rev. 14: 40-58.
115. Lucchesi, J. C. and Manning, J. E. (1987). Gene dosage compensation in Drosophila melanogaster. Adv. Genet 24: 371-429.
116. Madhani, H. D. and Guthrie, C. (1994a). Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet. 28: 1-26.
117. Madhani, H. D. and Guthrie, C. (1994b). Genetic interaction between the yeast RNA helicase homolog Prp16 and spliceosomal snRNAs identify candidate ligands for the Prp 16 RNA-dependent ATPase. Genetics 137: 677-687.
118. + gene encoding a putative RNA helicase is essential for nitrogen starvation-induced G1 arrest and initiation of sexual development in the fission yeast Schizosaccharomyces pombe. Mol. Gen. Genet. 244: 456-464.
119. Mahowald, A. P. (1971). Polar granules of Drosophila. III. The continuity of polar granules during the life-cycle of Drosohpila. J. Exp. Zool. 176: 329-344.
120. Mahowald, A. P. (1992). Germ plasm revisited and illuminated. Science 255: 1216-1217.
121. Margossian, S.P. and Butow, R. A. (1996). RNA trunover and the control of mitochondrial gene expression. Trends Biochem. Sci 21: 392-396.
122. Margossian, S. P., Li, H., Zassenhaus, H. P., and Butow, R. A. (1996). The DExH box protein Suv3p is a component of a yeast mitochondrial 3′- to- 'Exoribonuclease that suppresses group I intron toxicty. Cell 84: 199-209.
123. Maison, S. W. and Kaiser-Rogers, K. A. (1990). DNA helicases. Annu. Rev. Biochem. 59: 289-329.
124. Mehlin, H., Daneholt, B., and Skoglund, U. (1992). Translocation of a specific premessenger ribonucleoprotein particle through the nuclear pore studied with electron microscope tomography. Cell 69: 605-613.
125. Michel, F., Umesono, K., and Ozeki, H. (1989). Comparative and functional anatomy of group II catalytic introns: a review. Gene 82: 5-30.
126. Milburn, S. C., Hershey, J. W. B., Davies, M. V., Kellcher, K., and Kaufman, R. J. (1990). Cloning and sequencing of eukaryotic initiation factor 4B cDNA: sequence determination identifies a common RNA recognition motif. EMBO J. 9: 2783-2790.
127. Missel, A. and Göringer, H. U. (1994). Trypanosoma brucei mitochondria contain RNA helicase activity. Nucleic Acids Res. 22: 4050-4056.
128. Missel, A., Souza, A. E., Nörskau, G. and Göringer, H. U. (1997). Disruption of a gene encoding a novel mitochondrial DEAD-box protein in Trypanosoma brucei affects edited mRNAs. Mol. Cell. Biol. 17: 4895-4903.
129. Moazed, D. and Noller, H. F. (1991). Sites of the CCA end of peptidyl-tRNA with 23S rRNA. Proc. Natl. Acad. Sci. USA 88: 3725-3728.
130. Moore, M. J., Query, C. C., and Sharp, P. A. (1993). Splicing of precursors to messenger RNAs by the spliceosome. In: R. F. Gesteland and J. F. Atkins (eds.) The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 303-357.
131. Nicol, S. M. and Fuller-Pace, F. V. (1995). The "DEAD box" protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA. Proc. Natl. Acad. Sci. USA 92: 11681-11685.
132. Nielsen, P. J. and Trachsel, H. (1988). The mouse protein synthesis initiation factor 4A gene family includes two related functional genes which are differentially expressed. EMBO J. 7:2097-2105.
133. Niemer, I., Schmelzer, C., and Borner, G. V. (1995). Overexpression of DEAD box protein pMSS 116 promotes ATP-dependent splicing of a yeast group II intron in vitro. Nucleic Acids Res. 23: 2966-2972.
134. Nierhaus, K. H. (1991). The side-by-side model of two tRNA molecules allowing the alpha-helical conformation of the nascent polypeptide during the ribosomal transpeptidation. Biochimie 73: 947-60.
135. Nishi, K., Morel-Deville, F., Hershey, J. W. B., Leighton, T., and Schnier, J. (1988). An eIF-4A-like protein is a suppressor of an Escherichia coli mutant defective in 50S ribosome subunit assembly. Nature 336: 496-498.
136. Noller, H. F. (1991). Ribosomal RNA and translation. Annu. Rev. Biochem. 60: 191-227.
137. O'Day, C. L., Chavanikamannil, F., and Abelson, J. N. (1996a). 18S rRNA processing requires the RNA helicase-like protein Rpr3. Nucleic Acids Res. 24: 3201-3207.
138. O'Day, C. L., Dalbadie-McFarland, G., and Abelson, J. N. (1996b). The Saccharomyces cerevisiae Prp5 protein has RNA-dependent ATPase activity with specificity for U2 small nuclear RNA. J. Biol. Chem. 271: 33261-33267.
139. Ohno, M. and Shimura, Y. (1996). A human RNA helicase-like protein, HRH1, facilitates nuclear export of spliced mRNA by releasing RNA from spliceosome. Genes Dev. 10: 997-1007.
140. Ono, Y., Ohno, M., and Shimura, Y. (1994). Identification of a putative RNA helicase (HRHI), a human homolog of yeast Prp22. Mol. Cell. Biol. 14:6711-7620.
141. Owttrim, G. W., Hofmann, S., and Kuhlemeier, C. (1991). Divergent genes for translation initiation factor eIF-4A are coordinately expressed in tobacco. Nucleic Acids Res. 19: 5491-5496.
142. Pacha, R. F., Meis, R., and Condit, R. C. (1990). Structure and expression of the vaccinia virus gene which prevents virus-induced breakdown of RNA. J. Virol. 64: 3853-3863.
143. Paoletti, E., Rosemond-Hornbeak, H., and Moss, B. (1974). Two nucleic acid-dependent nucleoside triphosphate phosphohydrolases from vaccinia virus. Purification and characterization. J. Biol. Chem. 249: 3273-3280.
144. Patterson, L. F., Harvey, M., and Lasko, P. F. ( 1992). Dbp73D, a Drosophila gene expressed in ovary, encodes a novel DEAD box protein. Nucleic Acids Res. 20: 3063-3067.
145. Pause, A., Méthot, N., and Sonenberg, N. (1993). The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation factor 4A is required for RNA binding and ATP hydrolysis. Mol. Cell. Biol. 13: 6789-6798.
146. Pause, A. and Sonenberg, N. (1992). Mutational analysis of a DEAD box RNA helicase: the mammalian translation initiation factor eIF-4A. EMBO J. 11: 2643-2654.
147. Peltz, S. W., Feng, H., Welch, E., and Jacobson, A. (1994). Nonsense-mediated mRNA decay in yeast. Prog. Nucleic Acids Res. Mol. Biol. 47: 271-298.
148. Plumpton, M., McGarvey, M., and Beggs, J. D. (1994). A dominant negative mutation in the conserved RNA helicase motif 'SAT' causes splicing factor PRP2 to stall in spliceosomes. EMBO J. 13: 879-887.
149. Prat, A., Schmid, S. R., Buser, P., Blum, S., Trachsel, H., Nielsen, P. J., and Linder, P. (1990). Expression of translation initiation factor eIF-4A from yeast and mouse in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1050: 140-145.
150. Py, B., Higgins, C. F., Krisch, H. M., and Carpousis, A. J. (1996). A DEAD-box RNA helicase in the Escherichia coli degradosome. Nature 381: 169-172.
151. Raghunathan, P. L. and Guthrie, C. (1998). RNA unwinding in U4-U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Curr. Biol. 8: 847-855.
152. Ray, B. K., Lawson, T. G., Kramer, J. C., Cladaras, M. H., Grifo, J. A., Abramson, R. D., Merick, W. C., and Thach, R. E. (1985). ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors. J. Biol. Chem. 260: 7651-7658.
153. Rhoads, R. E. (1991) Initiation: mRNA and 60S subunit binding. In: H. Trachsel (ed.) Translation in Eukaryotes, CRC Press, Boca Raton, Florida, pp. 109-148.
154. Ripmaster, T. L., Vaughn, G. P., and Woolford, J. L. Jr. (1992). A putative ATP-dependent RNA helicase involved in Saccharomyces cerevisiae ribosome assembly. Proc. Natl. Acad. Sci. USA 89: 11131-11135.
155. Roussell, D. L. and Bennett, K. L. (1993). glh-1, a germ-line putative RNA helicase from Caenorhabditis, has four zinc fingers. Proc. Natl. Acad. Sci USA 90: 9300-9304.
156. Roy, J., Kyunghoon, K., Maddock, J., Anthony, J. G. and Woolford, J. L. Jr. (1995). The final stages of spliceosome maturation require Spp2p that can interact with the DEAH box protein Prp2p and promte step 1 of splicing. RNA 1: 375-390.
157. Rozen, F., Edery, I., Meeovitch, K., Dever, T. E., Merrick, W. C., and Sonenberg, N. (1990). Bidirectional RNA helicase activity of eukaryotic translation initiation factors 4A and 4F. Mol. Cell. Biol. 10: 1134-1144.
158. Rozen, F., Pelltier, J., Trachsel, H., and Sonenberg, N. (1989). A lysine substitution in the ATP binding site of eukaryotic initiation factor 4A abrogates nucleotide-binding activity. Mol. Cell. Biol. 9: 4061-4063.
159. Ruby, S. W. and Abelson, J. (1991). Pre-mRNA splicing in yeast. Trends Genet. 7: 79-85.
160. Sachs, A. B. and Davis, R. W. (1990). Translation initiation and ribosomal biogenesis: Involvement of a putaive rRNA helicase and RPL46. Science 241: 1077-1079.
161. Schmid, S. R. and Linder, P. (1991). Translation initiation factor 4A from Saccharomyces cerevisiae: analysis of residues conserved in the D-E-A-D family of RNA helicases. Mol. Cell. Biol. 11: 3463-3471.
162. Schmid, S. R. and Linder, P. (1992). D-E-A-D protein family of putative RNA helicases. Mol Microbiol. 6: 283-291.
163. Schwer, B. and Guthrie, C. (1991). PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 349: 494-499.
164. Seedorf, M. and Silver, P. A. (1997). Importin/ karyopherin protein family members required for mRNA export from the nucleus. Proc. Natl. Acad. Sci. USA 94: 8590-8595.
165. Séraphin, B., Boulet, A., Simon, M., and Faye, G. (1987). Construction of a yeast strain devoid of mitochondrial introns and its use to screen nuclear genes involved in mitochondrial splicing. Proc. Natl. Acad. Sci. USA 84: 6810-6814.
166. Séraphin, B., Simon, M., Boulet, A., and Paye, G. (1989). Mitochondrial splicing requires a protein from a novel helicase family. Nature 337: 84-87.
167. Shuman, S. (1992). Vaccina virus RNA helicase: An essential enzyme related to the DE-H family of RNA-dependent NTPases. Proc. Natl. Acad. Sci. USA 89: 10935-10939.
168. Shuman, S. (1993). Vaccina virus RNA helicase. Directionality and substrate specifity. J. Biol. Chem. 268: 11798-11802.
169. Snay-Hodge, C. A., Colot, H. V., Goldstein, A. L., and Cole, C. N. (1998). Dbp5p/rat8p is a yeast nuclear pore-associated DEAD-box protein essential for RNA export. EMBO J. 17: 2663-2676.
170. Sollner-Webb, B. (1996). Trypanosome RNA editing: resolved. Science 273: 1182-1183.
171. Sonenberg, N. (1988). Cap-binding proteins of eukaryotic messenger RNA: functions in initiation and control of translation. Prog. Nucleic Acids Res. Mol. Biol. 35: 173-207.
172. Song, Y., Kim, S., and Kirn, J. (1995). ROK1, a high-copy-number plasmid suppressor of kem1, encodes a putative ATP-dependent RNA helicase in Saccharomyces cerevisiae. Gene 166: 151-154.
173. Stade, K., Ford, C. S., Guthrie, C., and Weis, K. (1997). Exportin 1 (Crm Ip) is an essential nuclear export factor. Cell 90: 1041-1050.
174. Staley, J. P. and Guthrie, C. (1998). Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92: 315-326.
175. Stepien, P. P., Kokot, L., Leski, T., and Bartnik, E. (1995). The suv3 nuclear gene product is required for the in vivo processing of the yeast mitochondrial 21S rRNA transcripts containing the r1 intron. Curr. Genet. 27: 234-238.
176. Stepien, P. P., Margossian, S. P., Landsman, D., and Butow, R.A. (1992). The nuclear gene suv3 affecting mitochondrial post-transcriptional processes encodes a putative ATP-dependent RNA helicase. Proc. Natl. Acad. Sci. USA 89: 6813-6817.
177. Strauss, E. and Guthrie, C. (1991). A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family. Genes Dev. 5:629-641.
178. Strauss, E. and Guthrie, C. (1994). PRP28, a 'DEAD-box' protein, is required for the first step of mRNA splicing in vitro. Nucleic Acids Res. 22: 3187-3193.
179. Strome, S. (1992). The germ of the issue. Nature 358: 368-369.
180. Sudo, K., Takahashi, E., and Nakamura, Y. (1995). Isolation and mapping of the human EIF4A2 gene homologous to the murine protein synthesis initiation factor 4A-II gene Eif4a2. Cytogenet. Cell Genet. 71: 385-388.
181. Szer, W., Hermoso, J. M., and Boublik, M. (1976). Destabilization of the secondary structure of RNA by ribosomal protein S1 from Escherichia coli. Biochem. Biophys. Res. Comm. 70: 957-964.
182. Takeshita, K., Forget, B. G., Scaarpa, A., and Benz, E. J. (1984). Intranuclear defect in β-globin mRNA accumulation due to a premature translation termination codon. Blood 64: 13-22.
183. Tang, H., Gaietta, G. M., Fischer, W. H., Ellisman, M. H., and Wong, S. F. (1997). A cellular cofactor for the constitutive transport element of type D retrovirus. Science 276: 1412-1415.
184. Teigelkamp, S., McGarvey, M., Plumpton, M., and Beggs, J. D. (1994). The splicing factor PRP2, a putative RNA helicase, interacts directly with the pre-mRNA. EMBO J. 13: 888-897.
185. Tishkoff, D. X., Johnson, A. W., and Kolodner, R. D. (1991). Molecular and genetic analysis of the gene encoding the Saccharomyces cerevisiae strand exchange protein Sepl. Mol. Cell. Biol. 11: 2593-2608.
186. Toone, W. M., Rudd, K. E., and Friesen, J. D. (1991). deaD, a new Escherichia coli gene encoding a presumed ATP-dependent RNA helicase, can suppress a mutation in rpsB gene encoding ribosomal Protein S2. J. Bacterial. 173: 3291-3302.
187. + RNA export. EMBO J. 17: 2651-2662.
188. Oilman, K. S., Powers, M. A., and Forbes, D. J. (1997). Nuclear export receptors: from importin to exportin. Cell 90: 967-970.
189. Umen, J. G. and Guthrie, C. (1995a). Prp16p, S1u7p, and PrpSp interact with the 3′ splice site in two distinct stages during the second catalytic step of pre-mRNA splicing. RNA 1: 584-597.
190. Umen, J. G. and Guthrie, C. (1995b). The second catalytic step of pre-mRNA splicing. RNA 1: 869-885.
191. Venema, J., Bousquet-Antonelli, C., Gelugne, J.-P., Caizergues-Ferrer, M., and Tollervey, D. (1997). Rok1 is a putative RNA helicase required for rRNA processing. Mol. Cell. Biol. 17: 3398-3407.
192. Voorma, H. O., Thomas, A. A. M., and van Heugten, H. A. A. (1994). Initiation of protein synthesis in eukaryotes. Mol. Biol. Rep. 19: 139-145.
193. Wagner, J. D. O., Jankowsky, E., Company, M., Pyle, A. M., and Abelson, J. N. (1998). The DEAH-box protein PRP22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA. EMBO J. 17: 2926-2937.
194. Walker, J. E., Saraste, M., Runswick, M. J., and Gay, N. J. (1982). Distantly related sequence in the a- and b-subunits of ATP synthase, myosin, kinase and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
195. Wang, Y., Wagner, J. D. O., and Guthrie, C. (1998). The DEAH-box splicing factor Prp 16 unwinds RNA duplexes in vitro. Curr. Biol, 8: 441-451.
196. Warrener, P. and Collett, M. S. (1995). Pestivirus NS3 (p80) protein possesses RNA helicase activity. J. Virol. 69: 1720-1726.
197. Wassarman, D. A. and Steitz, J. A. (1991). Alive with DEAD proteins. Nature 349: 463-464.
198. 3. Mol. Cell. Biol. 17: 1354-1365.
199. Will, C. L., and Lührmann, R. (1997). Protein functions in pre-mRNA splicing. Curr. Opin. Cell Biol. 9: 320-328.
200. Yánez, R. J., M., R. J., Boursnell, M., Rodríguez, J. F., and Vinuela, E. (1993). Two putative African swine fever virus helicases similar to yeast 'DEAH' pre-mRNA processing proteins and vaccinia virus ATPases D11L and D6R. Gene 134: 161-174.
201. Zassenhaus, H. P., Farrelly, F., Hudspeth, M. E., Grossman, L. I, and Butow, R. A. (1983). Transcriptional analysis of the Saccharomyces cerevisiae mitochondrial var1 gene: anomalous hybridization of RNA from AT-rich regions. Mol. Cell. Biol. 3: 1615-1624.
202. Zhu, H., Conrad-Webb, H., Liao, X. S., Perlman, P.S., and Butow, R. A. (1989). Functional expression of a yeast mitochondrial intron-encoded protein requires RNA processing at a conserved dodecamer sequence at the 3′end of the gene. Mol. Cell. Biol. 9: 1507-1512.