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

Journal of Molecular Biology

Volumn 274, Issue 3, 1997, Pages 353-364

  Costa, Maria ^a   Fontaine, Jean Marc ^b   Loiseaux De Goër, Susan ^b   Michel, François ^a  

^a CENTRE DE GÉNÉTIQUE MOLÉCULAIRE   (France)

^b STATION BIOLOGIQUE   (France)

Author keywords

Gel electrophoresis; Group II intron; Non denaturing; Ribozyme; RNA conformation; RNA melting curve

Indexed keywords

MAGNESIUM; MITOCHONDRIAL DNA;

ALGA; ARTICLE; CONTROLLED STUDY; ESTERIFICATION; INTRON; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; RIBOSOME SUBUNIT; RNA CONFORMATION; RNA SPLICING;

PYLAIELLA LITTORALIS;

EID: 0031555476     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1416     Document Type: Article

References (36)

1. Banerjee, A. R., Jaeger, J. A. & Turner, D. H. (1993). Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry, 32, 153-163.
2. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K. H., Golden, B. L., Kundrot, C. E., Cech, T. R. & Doudna, J. A. (1996). Crystal structure of a group I ribozyme domain - principles of RNA packing. Science, 273, 1678-1685.
3. Cech, T. R. & Herschlag, D. (1996). Group I ribozymes: substrate recognition, catalytic strategies, and comparative mechanistic analysis. In Nucleic Acids and Molecular Biology (Eckstein, F. & Lilley, D. M. J., eds), vol. 10, pp. 1-17, Springer-Verlag, Berlin.
4. Chanfreau, G. & Jacquier, A. (1993). Interaction of intronic boundaries is required for the second splicing step efficiency of a group II intron. EMBO J. 12, 5173-5180.
5. Chanfreau, G. & Jacquier, A. (1996). An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J. 15, 3466-3476.
6. Chin, K. & Pyle, A. M. (1995). Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5′-splice site selection. RNA, 1, 391-406.
7. Cole, P. E., Yang, S. K. & Crothers, D. M. (1972). Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry, 11, 4358-4368.
8. Costa, M. & Michel, F. (1995). Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14, 1276-1285.
9. Costa, M. & Michel, F. (1997). Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution. EMBO J. 16, 3289-3302.
10. Costa, M., Dème, E., Jacquier, A. & Michel, F. (1997). Multiple tertiary interactions involving domain II of group II self-splicing introns. J. Mol. Biol. 267, 520-536.
11. Daniels, D. L., Michels, W. J., Jr. & Pyle, A. M. (1996). Two competing pathways for self-splicing by group II introns: a quantitative analysis of in vitro reaction rates and products. J. Mol. Biol. 256, 31-49.
12. Davila-Aponte, J. A., Huss, V. A. R., Sogin, M. L. & Cech, T. R. (1991). A self-splicing group I intron in the nuclear pre-rRNA of the green alga, Ankistrodesmus stipitatus. Nucl. Acids Res. 19, 4429-4436.
13. Draper, D. E. (1996). Strategies for RNA folding. Trends Biochem. Sci. 21, 145-149.
14. Fontaine, J.-M., Rousvoal, S., Leblanc, C., Kloareg, B. & Loiseaux-de Goër, S. (1995). The mitochondrial LSU rDNA of the brown alga Pylaiella littoralis reveals α-proteobacterial features and is split by four group IIB introns with an atypical phylogeny. J. Mol. Biol. 251, 378-389.
15. Fontaine, J.-M., Goux, D., Kloareg, B. & Loiseaux-de Goër, S. (1997). The reverse-transcriptase-like proteins encoded by group II introns in the mitochondrial genome of the brown alga Pylaiella littoralis belong to two different lineages which apparently coevolved with the group II ribozyme lineages. J. Mol. Evol. 44, 33-42.
16. Harris-Kerr, C. L., Zhang, M. & Peebles, C. L. (1993). The phylogenetically predicted base-pairing interaction between α and α′ is required for group II splicing in vitro. Proc. Natl Acad. Sci. USA, 90, 10658-10662.
17. Hebbar, S. K., Belcher, S. M. & Perlman, P. S. (1992). A maturase-encoding group IIA intron of yeast mitochondria self-splices in vitro. Nucl. Acids Res. 20, 1747-1754.
18. Jacquier, A. & Jacquesson-Breuleux, N. (1991). Splice site selection and role of the lariat in a group II intron. J. Mol. Biol. 219, 415-428.
19. Jacquier, A. & Michel, F. (1987). Multiple exon-binding sites in class II self-splicing introns. Cell, 50, 17-29.
20. Jacquier, A. & Michel, F. (1990). Base-pairing interactions involving the 5′ and 3′-terminal nucleotides of group II introns. J. Mol. Biol. 213, 437-447.
21. 2+, and in the presence of substrate. Biochemistry, 29, 10147-10158.
22. Jaeger, L., Westhof, E. & Michel, F. (1993). Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3′ terminal intron components. J. Mol. Biol. 234, 331-346.
23. Jarrell, K. A., Peebles, C. L., Dietrich, R. C., Romiti, S. L. & Perlman, P. S. (1988). Group II intron self-splicing. Alternative reaction conditions yield novel products. J. Biol. Chem. 263, 3432-3439.
24. Kwakman, J. H. J. M., Konings, D. A. M., Hogeweg, P., Pel, H. J. & Grivell, L. A. (1990). Structural analysis of a group II intron by chemical modifications and minimal energy calculations. J. Biomol. Struct. Dynam. 8, 413-430.
25. Lambowitz, A. M. & Belfort, M. (1993). Introns as mobile genetic elements. Annu. Rev. Biochem. 62, 587-622.
26. Latham, J. A. & Cech, T. R. (1989). Defining the inside and outside of a catalytic RNA molecule. Science, 245, 276-282.
27. Michel, F. & Ferat, J.-L. (1995). Structure and activities of group II introns. Annu. Rev. Biochem. 64, 435-461.
28. Michel, F., Umesono, K. & Ozeki, H. (1989). Comparative and functional anatomy of group II catalytic introns-a review. Gene, 82, 5-30.
29. Peebles, C. L., Perlman, P. S., Mecklenburg, K. L., Petrillo, M. L., Tabor, J. H., Jarrell, K. A. & Cheng, H.-L. (1986). A self-splicing RNA excises an intron lariat. Cell, 44, 213-223.
30. Pyle, A. M. (1993). Ribozymes: a distinct class of metalloenzymes. Science, 261, 709-714.
31. ++ ions in the tertiary structure. Biochemistry, 36, 4718-4730.
32. Schmidt, U., Riederer, B., Mörl, M., Schmelzer, C. & Stahl, U. (1990). Self-splicing of the mobile group II intron of the filamentous fungus Podospora anserina (CO1I1) in vitro. EMBO J. 9, 2289-2298.
33. Ile of the purple bacterium Azoarcus. RNA, 2, 74-83.
34. van der Veen, R., Arnberg, A. C., van der Horst, G., Bonen, L., Tabak, H. F. & Grivell, L. A. (1986). Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Cell, 44, 225-234.
35. Woodson, S. A. & Cech, T. R. (1991). Alternative secondary structures in the 5′ exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA. Biochemistry, 30, 2042-2050.
36. Zimmerly, S., Guo, H., Eskes, R., Yang, J., Perlman, P. S. & Lambowitz, A. M. (1995). A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell, 83, 529-538.