Multiple tertiary interactions involving domain II of group II self-splicing introns

Journal of Molecular Biology

Volumn 267, Issue 3, 1997, Pages 520-536

  Costa, Maria ^a   Dème, Elise ^b   Jacquier, Alain ^b   Michel, François ^a  

^a CENTRE DE GÉNÉTIQUE MOLÉCULAIRE   (France)

^b INSTITUT PASTEUR   (France)

Author keywords

GNRA loops; Group II introns; Ribozyme; RNA conformation; RNA structure

Indexed keywords

RIBOZYME; RNA;

ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ESTERIFICATION; EXON; HYDROLYSIS; INTRON; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; RNA CONFORMATION; RNA SPLICING; RNA STRUCTURE; TEMPERATURE;

EID: 0031552355     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0882     Document Type: Article

References (42)

1. Abramovitz D. L., Friedman R. A., Pyle A. M. Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science. 271:1996;1410-1413.
2. Altura R., Rymond B., Seraphin B., Rosbash M. Sequence requirements for branch formation in a group II self-splicing intron. Nucl. Acids Res. 17:1989;335-354.
3. Augustin S., Müller M. W., Schweyen R. J. Reverse self-splicing of group II intron RNAs in vitro. Nature. 343:1990;383-386.
4. Banerjee A. R., Jaeger J. A., Turner D. H. Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry. 32:1993;153-163.
5. Cate J. H., Gooding A. R., Podell E., Zhou K. H., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science. 273:1996;1678-1685.
6. Chanfreau G., Jacquier A. Interaction of intronic boundaries is required for the second splicing step efficiency of a group II intron. EMBO J. 12:1993;5173-5180.
7. Chanfreau G., Jacquier A. Catalytic site components common to both splicing steps of a group II intron. Science. 266:1994;1383-1387.
8. Chanfreau G., Jacquier A. An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J. 15:1996;3466-3476.
9. Chin K., Pyle A.-M. Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5′-splice site selection. RNA. 1:1995;391-406.
10. Costa M., Michel F. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14:1995;1276-1285.
11. Costa M., Michel F. Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution. EMBO J. 1997.
12. Daniels D. L., Michels W. J., Jr, Pyle A. M. Two competing pathways for self-splicing by group II introns: a quantitative analysis of in vitro reaction rates and products. J. Mol. Biol. 256:1996;31-49.
13. Dichtl B., Pan T., Di Renzo A. B., Uhlenbeck O. C. Replacement of RNA hairpins by in vitro selected tetranucleotides. Nucl. Acids Res. 21:1993;531-535.
14. Franzen J. S., Zhang M. C., Peebles C. L. Kinetic analysis of the 5′ splice junction hydrolysis of a group-II intron promoted by domain-5. Nucl. Acids Res. 21:1993;627-634.
15. Hebbar S. K., Belcher S. M., Perlman P. S. A maturase-encoding group IIA intron of yeast mitochondria self-splices in vitro. Nucl. Acids Res. 20:1992;1747-1754.
16. Jacquier A., Jacquesson-Breuleux N. Splice site selection and role of the lariat in a group II intron. J. Mol. Biol. 219:1991;415-428.
17. Jacquier A., Michel F. Multiple exon-binding sites in class II self-splicing introns. Cell. 50:1987;17-29.
18. Jacquier A., Michel F. Base-pairing interactions involving the 5′ and 3′-terminal nucleotides of group II introns. J. Mol. Biol. 213:1990;437-447.
19. Jacquier A., Rosbash M. Efficient trans-splicing of a yeast mitochondrial RNA group II intron implicates a strong 5′ exon-intron interaction. Science. 234:1986;1099-1104.
20. Jaeger L., Westhof E., Michel F. 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. 234:1993;331-346.
21. Jaeger L., Michel F., Westhof E. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol. 236:1994;1271-1276.
22. Jarrell K. A., Peebles C. L., Dietrich R. C., Romiti S. L., Perlman P. S. Group II intron self-splicing. Alternative reaction conditions yield novel products. J. Biol. Chem. 263:1988;3432-3439.
23. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl Acad. Sci. USA. 82:1985;488-492.
24. Leblanc C., Boyen C., Richard O., Bonnard G., Grienenberger J. M., Kloareg B. Complete sequence of the mitochondrial DNA of the rhodophyte Chondrus crispus (Gigartinales). Gene content and genome organization. J. Mol. Biol. 250:1995;484-495.
25. Michel F., Ferat J.-L. Structure and activities of group II introns. Annu. Rev. Biochem. 64:1995;435-461.
26. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:1990;585-610.
27. Michel F., Jacquier A., Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 64:1982;867-881.
28. Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns-a review. Gene. 82:1989;5-30.
29. Michels W. J., Pyle A. M. Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships. Biochemistry. 34:1995;2965-2977.
30. Murphy F. L., Cech T. R. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. J. Mol. Biol. 236:1994;49-63.
31. Peebles C. L., Zhang M., Perlman P. S., Franzen J. S. Catalytically critical nucleotides in domain 5 of a group II intron. Proc. Natl Acad. Sci. USA. 92:1995;4422-4426.
32. Pley H. W., Flaherty K. M., MacKay D. B. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature. 372:1994;111-113.
33. Pyle A. M., Green J. B. Building a kinetic framework for group II intron ribozyme activity: quantitation of inter-domain binding and chemical rate. Biochemistry. 33:1994;2716-2725.
34. Robineau S., Bergantino E., Carignani G., Michel F., Netter P. Suppressors of cis -acting splicing-deficient mutations that affect the ribozyme core of a group II intron. J. Mol. Biol. 267:1997;537-547.
35. Schmelzer C., Schmidt C., May K., Schweyen R. J. Determination of functional domains in intron bI1 of yeast mitochondrial RNA by studies of mitochondrial mutations and a nuclear suppressor. EMBO J. 2:1983;2047-2052.
36. Schmidt U., Sagebarth R., Schmelzer C., Stahl U. Self-splicing of a Podospora anserina group IIA intron in vitro. Effects of 3′-terminal intron alterations on cleavage at the 5′ and 3′ splice site. J. Mol. Biol. 231:1993;559-568.
37. Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 81:1995;991-1002.
38. Steitz T. A., Steitz J. A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA. 90:1993;6498-6502.
39. Suchy M., Schmelzer C. Restoration of the self-splicing activity of a defective group II intron by a small trans-acting RNA. J. Mol. Biol. 222:1991;179-187.
40. Tuerk C., Gauss P., Thermes C., Groebe D. R., Gayle M., Guild N., Stormo G., d'Aubenton-Carafa Y., Uhlenbeck O. C., Tinoco I., Jr et al. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. Natl Acad. Sci. USA. 85:1988;1364-1368.
41. van der Veen R., Kwakman J. H. J. M., Grivell L. A. Mutations at the lariat acceptor site allow self-splicing of a group II intron without lariat formation. EMBO J. 6:1987;1079-1084.
42. Yang J., Zimmerly S., Perlman P. S., Lambowitz A. M. Efficient integration of an intron RNA into double-stranded DNA by reverse splicing. Nature. 381:1996;332-335.