An allosteric-feedback mechanism for protein-assisted group I intron splicing

RNA

Volumn 13, Issue 2, 2007, Pages 211-222

  Caprara, Mark G ^a   Chatterjee, Piyali ^a,b   Solem, Amanda ^a,c   Brady Passerini, Kristina L ^a,d   Kaspar, Benjamin J ^a  

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

^b LERNER RESEARCH INSTITUTE   (United States)

^c YALE UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Group I introns; RNA folding; RNA protein interactions; RNP assembly

Indexed keywords

CYTOCHROME B; PROTEIN; PROTEIN I ANII; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; BINDING SITE; COMPLEX FORMATION; CONTROLLED STUDY; FEEDBACK SYSTEM; GENE MUTATION; INTRON; NONHUMAN; PRIORITY JOURNAL; PROTEIN RNA BINDING; RNA PROBE; RNA SPLICING; RNA STRUCTURE;

ALLOSTERIC REGULATION; ASPERGILLUS NIDULANS; BASE SEQUENCE; CYTOCHROMES B; FEEDBACK, BIOCHEMICAL; FUNGAL PROTEINS; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA PRECURSORS; RNA SPLICE SITES; RNA SPLICING; RNA, CATALYTIC; RNA, FUNGAL; RNA-DIRECTED DNA POLYMERASE;

EMERICELLA NIDULANS;

EID: 33846437819     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.307907     Document Type: Article

References (42)

1. Adams, P.L., Stahley, M.R., Gill, M.L., Kosek, A.B., Wang, J., and Strobel, S.A. 2004. Crystal structure of a group I intron splicing intermediate. RNA 10: 1867-1887.
2. Allain, F.H., Gubser, C.C., Howe, P.W., Nagai, K., Neuhaus, D., and Varani, G. 1996. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formulation. Nature 380: 646-650.
3. Avis, J.M., Allain, F.H., Howe, P.W., Varani, G., Nagai, K., and Neuhaus, D. 1996. Solution structure of the N-terminal RNP domain of U1A protein: The role of C-terminal residues in structure stability and RNA binding. J. Mol. Biol. 257: 398-411.
4. Bartley, L.E., Zhuang, X., Das, R., Chu, S., and Herschlag, D. 2003. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. J. Mol. Biol. 328: 1011-1026.
5. Batey, R.T. and Williamson, J.R. 1998. Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15. RNA 4: 984-997.
6. Bokinsky, G., Nivon, L.G., Liu, S., Chai, G., Hong, M., Weeks, K.M., and Zhuang, X. 2006. Two distinct binding modes of a protein cofactor with its target RNA. J. Mol. Biol. 361: 771-784.
7. Buchmueller, K.L., Webb, A.E., Richardson, D.A., and Weeks, K.M. 2000. A collapsed nonnative RNA folding state. Nat. Struct. Biol. 7: 362-366.
8. Caprara, M.G. and Waring, R.B. 2005. Group I Introns and their maturases: Uninvited, but welcome guests. In Homing endonucleases and inteins (eds. M. Belfort et al.). Springer-Verlag, Heidelberg.
9. Caprara, M.G., Mohr, G., and Lambowitz, A.M. 1996. A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core. J. Mol. Biol. 257: 512-531.
10. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., and Doudna, J.A. 1996. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273: 1678-1685.
11. Chatterjee, P., Brady, K.L., Solem, A., Ho, Y., and Caprara, M.G. 2003. Functionally distinct nucleic acid binding sites for a group I intron encoded RNA maturase/DNA homing endonuclease. J. Mol. Biol. 329: 239-251.
12. DiNitto, J.P. and Huber, P.W. 2003. Mutual induced fit binding of Xenopus ribosomal protein L5 to 5S rRNA. J. Mol. Biol. 330: 979-992.
13. Downing, M.E., Brady, K.L., and Caprara, M.G. 2005. A C-terminal fragment of an intron-encoded maturase is sufficient for promoting group I intron splicing. RNA 11: 437-446.
14. Ehresmann, C., Baudin, F., Mougel, M., Romby, P., Ebel, J.P., and Ehresmann, B. 1987. Probing the structure of RNAs in solution. Nucleic Acids Res. 15: 9109-9128.
15. Geese, W.J. and Waring, R.B. 2001. A comprehensive characterization of a group IB intron and its encoded maturase reveals that protein-assisted splicing requires an almost intact intron RNA. J. Mol. Biol. 308: 609-622.
16. Golden, B.L., Kim, H., and Chase, E. 2005. Crystal structure of a phage Twort group I ribozyme-product complex. Nat. Struct. Mol. Biol. 12: 82-89.
17. Gubser, C.C. and Varani, G. 1996. Structure of the polyadenylation regulatory element of the human U1A pre-mRNA 3′-untranslated region and interaction with the U1A protein. Biochemistry 35: 2253-2267.
18. Guo, F., Gooding, A.R., and Cech, T.R. 2004. Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site. Mol. Cell 16: 351-362.
19. Hainzl, T., Huang, S., and Sauer-Eriksson, A.E. 2005. Structural insights into SRP RNA: An induced fit mechanism for SRP assembly. RNA 11: 1043-1045.
20. Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K., and Pease, L.R. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51-59.
21. Ho, Y., Kim, S.J., and Waring, R.B. 1997. A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease. Proc. Natl. Acad. Sci. 94: 8994-8999.
22. Kuglstatter, A., Oubridge, C., and Nagai, K. 2002. Induced structural changes of 7SL RNA during the assembly of human signal recognition particle. Nat. Struct. Biol. 9: 740-744.
23. Lambowitz, A.M., Caprara, M.G., Zimmerly, S., and Perlman, P.S. 1999. Group I and group II ribozymes as RNPs: Clues to the past and guides to the future. In The RNA World II (eds. R.F. Gesteland et al.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
24. Leulliot, N. and Varani, G. 2001. Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture. Biochemistry 40: 7947-7956.
25. Longo, A., Leonard, C.W., Bassi, G.S., Berndt, D., Krahn, J.M., Hall, T.M., and Weeks, K.M. 2005. Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase. Nat. Struct. Mol. Biol. 12: 779-787.
26. Maeder, C. and Draper, D.E. 2005. A small protein unique to bacteria organizes rRNA tertiary structure over an extensive region of the 50 S ribosomal subunit. J. Mol. Biol. 354: 436-446.
27. Michel, F. and Westhof, E. 1990. Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216: 585-610.
28. Mohr, S., Stryker, J.M., and Lambowitz, A.M. 2002. A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell 109: 769-779.
29. Peattie, D.A. 1979. Direct chemical method for sequencing RNA. Proc. Natl. Acad. Sci. 76: 1760-1764.
30. Petrov, A., Meskauskas, A., and Dinman, J.D. 2004. Ribosomal protein L3: Influence on ribosome structure and function. RNA Biol. 1: 59-65.
31. Rajkowitsch, L., Semrad, K., Mayer, O., and Schroeder, R. 2005. Assays for the RNA chaperone activity of proteins. Biochem. Soc. Trans. 33: 450-456.
32. Russell, R., Millett, I.S., Doniach, S., and Herschlag, D. 2000. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nat. Struct. Biol. 7: 367-370.
33. Saldanha, R.J., Patel, S.S., Surendran, R., Lee, J.C., and Lambowitz, A.M. 1995. Involvement of Neurospora mitochondrial tyrosyl-tRNA synthetase in RNA splicing. A new method for purifying the protein and characterization of physical and enzymatic properties pertinent to splicing. Biochemistry 34: 1275-1287.
34. Solem, A., Chatterjee, P., and Caprara, M.G. 2002. A novel mechanism for protein-assisted group I intron splicing. RNA 8: 412-425.
35. Sorrentino, S., Naddeo, M., Russo, A., and D'Alessio, G. 2003. Degradation of double-stranded RNA by human pancreatic ribonuclease: Crucial role of noncatalytic basic amino acid residues. Biochemistry 42: 10182-10190.
36. Thirumalai, D. and Hyeon, C. 2005. RNA and protein folding: Common themes and variations. Biochemistry 44: 4957-4970.
37. Tompa, P. and Csermely, P. 2004. The role of structural disorder in the function of RNA and protein chaperones. FASEB J. 18: 1169-1175.
38. Webb, A.E. and Weeks, K.M. 2001. A collapsed state functions to selfchaperone RNA folding into a native ribonucleoprotein complex. Nat. Struct. Biol. 8: 135-140.
39. Woodson, S.A. 2000. Compact but disordered states of RNA. Nat. Struct. Biol. 7: 349-352.
40. Woodson, S.A. 2005. Structure and assembly of group I introns. Curr. Opin. Struct. Biol. 15: 324-330.
41. Wu, M. and Tinoco Jr., I. 1998. RNA folding causes secondary structure rearrangement. Proc. Natl. Acad. Sci. 95: 11555-11560.
42. Zarrinkar, P.P. and Williamson, J.R. 1994. Kinetic intermediates in RNA folding. Science 265: 918-924.