Abstract
The evolutionarily conserved DExD/H-box proteins are essential for all RNA-related biological processes. They are thought to modulate the structure and function of specific RNAs and/or ribonucleoprotein particles by using their intrinsic RNA-dependent ATPase activities to achieve the desired conformational changes. A number of DExD/H-box proteins have been shown to unwind short RNA duplexes in vitro, a hallmark of the so-called RNA helicases or unwindases. However, some are unable to do so, perhaps because of requirements for cofactors. Here, we present a “solid-state” method that may allow investigators to overcome such problems.
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References
Tanner, N. K. and Linder, P. (2001) DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol. Cell 8, 251–262.
Staley, J. P. and Guthrie, C. (1998) Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92, 315–326.
Fuller-Pace, F. V. (1994) RNA helicases: modulators of RNA structure. Trends Cell. Biol. 4, 271–274.
Schwer, B. and Gross, C. H. (1998) Prp22, a DExH-box RNA helicase, plays two distinct roles in yeast pre-mRNA splicing. EMBO J. 17, 2086–2094.
Tseng, S. S., Weaver, P. L., Liu, Y., Hitomi, M., Tartakoff, A. M., and Chang, T.-H. (1998) Dbp5p, a cytosolic RNA helicase, is required for poly(A)+ RNA export. EMBO J. 17, 2651–2662.
Rozen, F., Edery, I., Meerovitch, K., Dever, T. E., Merrick, W. C., and Sonenberg, N. (1990) Bidirectional RNA helicase activity of eukaryotic translation initiation factor 4A and 4F. Mol. Cell. Biol. 10, 1134–1144.
Hirling, H., Scheffner, M., Restle, T., and Stahl, H. (1989) RNA helicase activity associated with the human p68 protein. Nature 339, 562–564.
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.
Liang, L., Diehl-Jones, W., and Lasko, P. (1994) Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities. Development 120, 1201–1211.
Wang, Y., Wagner, J. D., and Guthrie, C. (1998) The DEAH-box splicing factor Prp16 unwinds RNA duplexes in vitro. Curr. Biol. 8, 441–451.
Laggerbauer, B., Achsel, T., and Lührmann, R. (1998) The human U5–200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. Proc. Natl. Acad. Sci. USA 95, 4188–4192.
Jankowsky, E., Gross, C. H., Shuman, S., and Pyle, A. M. (2000) The DExH protein NPH-II is a processive and directional motor for unwinding RNA. Nature 403, 447–451.
de la Cruz, J., Kressler, D., and Linder, P. (1999) Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem. Sci. 24, 192–198.
Gutell, R. R., Larsen, N., and Woese, C. R. (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58, 10–26.
Staley, J. P. and Guthrie, C. (1999) An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell 3, 55–64.
Lorsch, J. R. and Herschlag, D. (1998) The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes. Biochemistry 37, 2194–2206.
Lorsch, J. R. and Herschlag, D. (1998) The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry 37, 2180–2193.
Schwer, B. (2001) A new twist on RNA helicases: DExH/D box proteins as RNPases. Nat. Struct. Biol. 8, 113–116.
Kistler, A. L. and Guthrie, C. (2001) Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for Sub2, an essential spliceosomal ATPase. Genes Dev. 15, 42–49.
Jankowsky, E., Gross, C. H., Shuman, S., and Pyle, A. M. (2001) Active disruption of an RNA-protein interaction by a DExH/D RNA helicase. Science 291, 121–125.
Chen, J. Y., Stands, L., Staley, J. P., Jackups, R. R., Latus, L. J., and Chang, T.-H. (2001) 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 7, 227–232.
Strauss, E. J. 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.
Rogers, G. W., Jr., Richter, N. J., and Merrick, W. C. (1999) Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A. J. Biol. Chem. 274, 12,236–12,244.
Ray, B. K., Lawson, T. G., Kramer, J. C., Cladaras, M. H., Grifo, J. A., et al. (1985) ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors. J. Biol. Chem. 260, 7651–7658.
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-4F and eIF-4B. Mol. Cell. Biol. 11, 5992–5997.
Schmitt, C., von Kobbe, C., Bachi, A., Pante, N., Rodrigues, J. P., Boscheron, C., et al. (1999) Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p. EMBO J. 18, 4332–4347.
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.
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© 2004 Humana Press Inc., Totowa, NJ
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Tseng-Rogenski, S.S., Chang, TH. (2004). RNA Unwinding Assay for DExD/H-Box RNA Helicases. In: Schoenberg, D.R. (eds) mRNA Processing and Metabolism. Methods in Molecular Biology™, vol 257. Humana Press. https://doi.org/10.1385/1-59259-750-5:093
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DOI: https://doi.org/10.1385/1-59259-750-5:093
Publisher Name: Humana Press
Print ISBN: 978-1-58829-225-4
Online ISBN: 978-1-59259-750-5
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