Kinetic characterization of group II intron folding and splicing

Methods in Molecular Biology

Volumn 848, Issue , 2012, Pages 91-111

  Fedorova, Olga ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Folding; Group II intron; Kinetics; Ribozyme

Indexed keywords

MESSENGER RNA; RIBOZYME;

ARTICLE; BIOCATALYSIS; CHEMISTRY; CONFORMATION; GENETICS; INTRON; KINETICS; METABOLISM; RNA SPLICING;

BIOCATALYSIS; INTRONS; KINETICS; NUCLEIC ACID CONFORMATION; RNA SPLICING; RNA, CATALYTIC; RNA, MESSENGER;

ANIMALIA; BACTERIA (MICROORGANISMS); FUNGI;

EID: 84858240582     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-545-9_7     Document Type: Article

References (27)

1. Lehmann, K., and Schmidt, U. (2003) Group II introns: structure and catalytic versatility of large natural ribozymes. Crit. Rev. Biochem. Mol. Biol. 38 : 249-303. (Pubitemid 36793893)
2. Pyle, A.M., Lambowitz, A.M. (2006) Group II introns: ribozymes that splice RNA and invade DNA. in The RNA world, R.F. Gesteland, Cech T.R., Atkins J.F. (ed) Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York, 469-506.
3. Lambowitz, A.M., Zimmerly, S. (2004) Mobile group II introns. Annu Rev Genet. 38 : 1-35. (Pubitemid 40013722)
4. Michel, F., K. Umesono, and H. Ozeki (1989) Comparative and functional anatomy of group II catalytic introns-a review. Gene 82 : 5-30. (Pubitemid 19248654)
5. Qin, P.Z. and A.M. Pyle (1998) The architectural organization and mechanistic function of group II intron structural elements. Curr. Opin. Struct.Biol. 8 : 301-308. (Pubitemid 28321356)
6. Pyle, A.M., Fedorova, O., Waldsich, C. (2007) Folding of group II introns: a model system for large, multidomain RNAs? Trends Biochem. Sci. 32 : 138-145. (Pubitemid 46367692)
7. Fedorova, O., Su, L.J., Pyle, A.M. (2002) Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions. Methods 28 : 323-335. (Pubitemid 35373845)
8. Jarrell, K.A., R.C. Dietrich, and P.S. Perlman (1988) Group II Intron Domain 5 facilitates a trans-splicing reaction. Mol. Cell. Biol. 8 : 2361-2366.
9. Franzen, J.S., M. Zhang, and C.L. Peebles (1993) Kinetic analysis of the 5'-splice junction hydrolysis of a Group II intron promoted by Domain 5. Nucleic Acids Res. 21 : 627-634. (Pubitemid 23155554)
10. Pyle, A.M. and J.B. Green (1994) Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate. Biochemistry 33 : 2716-2725. (Pubitemid 24099684)
11. Chin, K. and A.M. Pyle, (1995) Branch-point attack in group II introns is a highly reversible transesterification, providing a possible proofreading mechanism for 5'-splice site selection. RNA 1 : 391-406.
12. Fedorova, O., Mitros T., Pyle A.M. (2003) Domains 2 and 3 interact to form critical elements of the group II intron active site. J. Mol. Biol. 330 : 197-209. (Pubitemid 36773696)
13. Zingler, N., Solem, A., Pyle, A.M. (2010) Dual roles for the Mss116 cofactor during splicing of the ai5{gamma} group II intron. Nucleic Acids Res. 38 : 6602-6609.
14. Su, L.J., Waldsich, C., and Pyle, A.M. (2005) An obligate intermediate along the slow folding pathway of a group II intron ribozyme. Nucleic Acids Res. 33 : 6674-6687. (Pubitemid 41830475)
15. Fedorova, O., Waldsich, C., Pyle A.M. (2007) Group II Intron Folding under Nearphysiological Conditions: Collapsing to the Near-native State. J. Mol. Biol. 366 : 1099-1114. (Pubitemid 46186386)
16. Steiner, M., Karunatilaka, K.S., Sigel, R.K., Rueda, D. (2008) Single-molecule studies of group II intron ribozymes. Proc Natl Acad Sci USA 105 : 13853-13858.
17. Toor, N., G. Hausner, and S. Zimmerly (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7 : 1142-52. (Pubitemid 32726912)
18. Toro, N., Molina-Sánchez,M.D., Fernández-López, M.(2002) Identification and characterization of bacterial class E group II introns. Gene 299 : 245-250. (Pubitemid 35379846)
19. Simon, D.M., Clarke, N.A., McNeil, B.A., Johnson, I., Pantuso, D., Dai, L., Chai, D., Zimmerly, S. (2008) Group II introns in eubacteria and archaea: ORF-less introns and new varieties. RNA 14 : 1704-1713.
20. Toor, N., Robart, A.R., Christianson, J., Zimmerly, S. (2006) Self-splicing of a group IIC intron: 5' exon recognition and alternative 5' splicing events implicate the stem-loop motif of a transcriptional terminator. Nucleic Acids Res. 34 : 6461-6471. (Pubitemid 46017943)
21. Jarrell, K.A., Peebles, C.L., Dietrich, R.C., Romiti, S.L., Perlman, P.S. (1988) Group II intron selfsplicing: Alternative reaction conditions yield novel products. J. Biol. Chem. 263 : 3432-3439. (Pubitemid 18072804)
22. Daniels, D., W.J. Michels, and A.M. Pyle (1996) Two competing pathways for selfsplicing by group II introns; a quantitative analysis of in-vitro reaction rates and products. J. Mol. Biol. 256 : 31-49. (Pubitemid 26104208)
23. Costa, M., Fontaine, J.M., Goer, S.L, Michel, F. (1997) A group II self-splicing intron from the Brown Alga Pylaiella littoralis is active at unusually low magnesium concentrations and forms populations of molecules with a uniform conformation. J. Mol. Biol. 274 : 353-364. (Pubitemid 27520624)
24. Mullineux, S.T., Costa, M., Bassi, G.S., Michel, F., Hausner, G. (2010) A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions. RNA, 16 : 1818-1831.
25. Adamidi, C., Fedorova, O., Pyle, A.M. (2003) A group II intron inserted into a bacterial heatshock operon shows autocatalytic activity and unusual thermostability. Biochemistry 423409-1 8 : 3409-3418. (Pubitemid 36368634)
26. Swisher, J., Su, L.J., Brenowitz, M., Anderson, V.E., Pyle, A.M. (2002) Productive Folding to the Native State by a Group II Intron Ribozyme. J. Mol. Biol. 315 : 297-310. (Pubitemid 34729341)
27. Rangan, P., Masquida, B., Westhof, E. & Woodson, S.A. (2003). Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl. Acad. Sci. USA 100 : 1574-1579. (Pubitemid 36254489)