Do DEAD-box Proteins Promote Group II Intron Splicing Without Unwinding RNA?

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2007 Oct 16

PMID 17936712

Citations 42

Authors

Mark Del Campo

Pilar Tijerina

Hari Bhaskaran

Sabine Mohr

Quansheng Yang

Eckhard Jankowsky

Rick Russell

Alan M Lambowitz

Affiliations

Soon will be listed here.

Abstract

The DEAD-box protein Mss116p promotes group II intron splicing in vivo and in vitro. Here we explore two hypotheses for how Mss116p promotes group II intron splicing: by using its RNA unwinding activity to act as an RNA chaperone or by stabilizing RNA folding intermediates. We show that an Mss116p mutant in helicase motif III (SAT/AAA), which was reported to stimulate splicing without unwinding RNA, retains ATP-dependent unwinding activity and promotes unfolding of a structured RNA. Its unwinding activity increases sharply with decreasing duplex length and correlates with group II intron splicing activity in quantitative assays. Additionally, we show that Mss116p can promote ATP-independent RNA unwinding, presumably via single-strand capture, also potentially contributing to DEAD-box protein RNA chaperone activity. Our findings favor the hypothesis that DEAD-box proteins function in group II intron splicing as in other processes by using their unwinding activity to act as RNA chaperones.

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References

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 U S A. 2006; 103(45):16698-703. PMC: 1636518. DOI: 10.1073/pnas.0603127103. View

Seraphin B, Simon M, Boulet A, Faye G . Mitochondrial splicing requires a protein from a novel helicase family. Nature. 1989; 337(6202):84-7. DOI: 10.1038/337084a0. View

Fedorova O, Waldsich C, Pyle A . Group II intron folding under near-physiological conditions: collapsing to the near-native state. J Mol Biol. 2007; 366(4):1099-114. PMC: 2274780. DOI: 10.1016/j.jmb.2006.12.003. View

Shelton V, Sosnick T, Pan T . Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry. 1999; 38(51):16831-9. DOI: 10.1021/bi991699s. View

Nolte A, Chanfreau G, Jacquier A . Influence of substrate structure on in vitro ribozyme activity of a group II intron. RNA. 1998; 4(6):694-708. PMC: 1369651. DOI: 10.1017/s1355838298980165. View

Herschlag D . RNA chaperones and the RNA folding problem. J Biol Chem. 1995; 270(36):20871-4. DOI: 10.1074/jbc.270.36.20871. View

Tanner N, Linder P . DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol Cell. 2001; 8(2):251-62. DOI: 10.1016/s1097-2765(01)00329-x. View

Halls C, Mohr S, Del Campo M, Yang Q, Jankowsky E, Lambowitz A . 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. 2006; 365(3):835-55. PMC: 1832103. DOI: 10.1016/j.jmb.2006.09.083. View

Saldanha R, Chen B, Wank H, Matsuura M, Edwards J, Lambowitz A . RNA and protein catalysis in group II intron splicing and mobility reactions using purified components. Biochemistry. 1999; 38(28):9069-83. DOI: 10.1021/bi982799l. View

10.

Zhuang X, Kim H, Pereira M, Babcock H, Walter N, Chu S . Correlating structural dynamics and function in single ribozyme molecules. Science. 2002; 296(5572):1473-6. DOI: 10.1126/science.1069013. View

11.

Russell R, Das R, Suh H, Travers K, Laederach A, Engelhardt M . The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J Mol Biol. 2006; 363(2):531-44. DOI: 10.1016/j.jmb.2006.08.024. View

12.

Pyle A, Fedorova O, Waldsich C . Folding of group II introns: a model system for large, multidomain RNAs?. Trends Biochem Sci. 2007; 32(3):138-45. DOI: 10.1016/j.tibs.2007.01.005. View

13.

Grohman J, Del Campo M, Bhaskaran H, Tijerina P, Lambowitz A, 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(11):3013-22. PMC: 2271177. DOI: 10.1021/bi0619472. View

14.

Esteban J, Walter N, Kotzorek G, Heckman J, Burke J . Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme. Proc Natl Acad Sci U S A. 1998; 95(11):6091-6. PMC: 27590. DOI: 10.1073/pnas.95.11.6091. View

15.

Mohr S, Matsuura M, Perlman P, Lambowitz A . A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone. Proc Natl Acad Sci U S A. 2006; 103(10):3569-74. PMC: 1450124. DOI: 10.1073/pnas.0600332103. View

16.

Solem A, Zingler N, Pyle A . A DEAD protein that activates intron self-splicing without unwinding RNA. Mol Cell. 2006; 24(4):611-7. DOI: 10.1016/j.molcel.2006.10.032. View

17.

Waldsich C, Pyle A . A folding control element for tertiary collapse of a group II intron ribozyme. Nat Struct Mol Biol. 2006; 14(1):37-44. DOI: 10.1038/nsmb1181. View

18.

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(41):13591-601. DOI: 10.1021/bi0508946. View

19.

Schroeder R, Barta A, Semrad K . Strategies for RNA folding and assembly. Nat Rev Mol Cell Biol. 2004; 5(11):908-19. DOI: 10.1038/nrm1497. View

20.

Mohr S, Stryker J, Lambowitz A . A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell. 2002; 109(6):769-79. DOI: 10.1016/s0092-8674(02)00771-7. View