Do DEAD-Box Proteins Promote Group II Intron Splicing without Unwinding RNA?

Molecular Cell

Volumn 28, Issue 1, 2007, Pages 159-166

  Del Campo, Mark ^a   Tijerina, Pilar ^a   Bhaskaran, Hari ^a   Mohr, Sabine ^a   Yang, Quansheng ^b   Jankowsky, Eckhard ^b   Russell, Rick ^a   Lambowitz, Alan M ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

RNA

Indexed keywords

DEAD BOX PROTEIN; MUTANT PROTEIN; PROTEIN MSS116P; RIBOZYME; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; GENE MUTATION; INTRON; NONHUMAN; PROTEIN PURIFICATION; QUANTITATIVE ASSAY; REACTION TIME; RNA CLEAVAGE; RNA SPLICING; RNA STRUCTURE; TETRAHYMENA THERMOPHILA;

DEAD-BOX RNA HELICASES; INTRONS; MUTATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; RECOMBINANT FUSION PROTEINS; RNA; RNA SPLICING; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 34948833173     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2007.07.028     Document Type: Article

References (23)

1. Esteban J.A., Walter N.G., Kotzorek G., Heckman J.E., and Burke J.M. Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme. Proc. Natl. Acad. Sci. USA 95 (1998) 6091-6096
2. Fedorova O., Waldsich C., and Pyle A.M. Group II intron folding under near-physiological conditions: collapsing to the near-native state. J. Mol. Biol. 366 (2007) 1099-1114
3. Grohman J.K., Del Campo M., Bhaskaran H., Tijerina P., Lambowitz A.M., and 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 46 (2007) 3013-3022
4. Halls C., Mohr S., Del Campo M., Yang Q., Jankowsky E., and Lambowitz A.M. 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 (2007) 835-855
5. Herschlag D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270 (1995) 20871-20874
6. Huang, H.R. (2004) Functional studies of intron- and nuclear-encoded splicing factors in the mitochondria of Saccharomyces cerevisiae, PhD thesis, The University of Texas Southwestern Medical Center, Dallas, Texas.
7. Huang H.R., Rowe C.E., Mohr S., Jiang Y., Lambowitz A.M., and Perlman P.S. 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 (2005) 163-168
8. Lambowitz A.M., Caprara M.G., Zimmerly S., and Perlman P.S. Group I and group II ribozymes as RNPs: clues to the past and guides to the future. In: Gesteland R.F., Cech T.R., and Atkins J.F. (Eds). The RNA World (1999), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 451-485
9. Mohr S., Stryker J.M., and Lambowitz A.M. A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell 109 (2002) 769-779
10. Mohr S., Matsuura M., Perlman P.S., and Lambowitz A.M. 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 (2006) 3569-3574
11. Nolte A., Chanfreau G., and Jacquier A. Influence of substrate structure on in vitro ribozyme activity of a group II intron. RNA 4 (1998) 694-708
12. Pyle A.M., Fedorova O., and Waldsich C. Folding of group II introns: a model system for large, multidomain RNAs?. Trends Biochem. Sci. 32 (2007) 138-145
13. Russell R., Das R., Suh H., Travers K., Laederach A., Engelhardt M., and Herschlag D. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J. Mol. Biol. 363 (2006) 531-544
14. Saldanha R., Chen B., Wank H., Matsuura M., Edwards J., and Lambowitz A.M. RNA and protein catalysis in group II intron splicing and mobility reactions using purified components. Biochemistry 38 (1999) 9069-9083
15. Schroeder R., Barta A., and Semrad K. Strategies for RNA folding and assembly. Nat. Rev. Mol. Cell Biol. 5 (2004) 908-919
16. Séraphin B., Simon M., Boulet A., and Faye G. Mitochondrial splicing requires a protein from a novel helicase family. Nature 337 (1989) 84-87
17. Shelton V.M., Sosnick T.R., and Pan T. Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry 38 (1999) 16831-16839
18. Solem A., Zingler N., and Pyle A.M. A DEAD protein that activates intron self-splicing without unwinding RNA. Mol. Cell 24 (2006) 611-617
19. Tanner N.K., and Linder P. DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol. Cell 8 (2001) 251-262
20. Tijerina P., Bhaskaran H., and Russell R. Non-specific 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 (2006) 16698-16703
21. Yang Q., and Jankowsky E. ATP- and ADP-dependent modulation of RNA unwinding and strand annealing activities by the the DEAD-box protein Ded1. Biochemistry 44 (2005) 13591-13601
22. Waldsich C., and Pyle A.M. A folding control element for tertiary collapse of a group II intron ribozyme. Nat. Struct. Mol. Biol. 14 (2007) 37-44
23. Zhuang X., Kim H., Pereira M.J., Babcock H.P., Walter N.G., and Chu S. Correlating structural dynamics and function in single ribozyme molecules. Science 296 (2002) 1473-1476