Photocrosslinking of 4-thio uracil-containing RNAs supports a side-by- side arrangement of domains 5 and 6 of a group II intron

RNA

Volumn 5, Issue 2, 1999, Pages 318-329

  Podar, Mircea ^a,b   Perlman, Philip S ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

Author keywords

4 thio uracil; Crosslinking; Group II introns; RNA structure; Self splicing

Indexed keywords

4 THIOURACIL; MAGNESIUM ION; MITOCHONDRIAL DNA; RNA;

ARTICLE; CROSS LINKING; INTRON; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA SEQUENCE; RNA SPLICING; RNA STRUCTURE; ULTRAVIOLET RADIATION;

BASE SEQUENCE; CROSS-LINKING REAGENTS; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA SPLICING; RNA, FUNGAL; THIOURACIL; ULTRAVIOLET RAYS;

EID: 0033065716     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299981724     Document Type: Article

References (39)

1. Abramovitz DL, Friedman RA, Pyle AM. 1996. Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science 271:1413-1416.
2. Bartholomew B, Dahmus ME, Meares CF. 1986. RNA contacts sub-units IIo and IIc in HeLa RNA polymerase II transcription complexes. J Biol Chem 261:14226-14231.
3. Boulanger SC, Belcher SM, Schmidt U, Dib-Hajj SD, Schmidt T, Perlman PS. 1995. Studies of point mutants define essential nucleotides in the domain 5 substructure of a group II intron. Mol Cell Biol 15:4479-4488.
4. Boulanger SC, Faix PH, Yang H, Zhuo J, Franzen JS, Peebles CL, Perlman PS. 1996. Length changes in the joining segment between domains 5 and 6 of a group II intron inhibit self-splicing and alter 3′ splice site selection. Mol Cell Biol 16:5896-5904.
5. Chanfreau G, Jacquier A. 1994. Catalytic site components common to both splicing steps of a group II intron. Science 266:1383-1387.
6. Chanfreau G, Jacquier A. 1996. An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J 15:3466-3476.
7. Chu VT, Liu Q, Podar M, Perlman PS, Pyle AM. 1998. More than one way to splice an RNA: Branching without a bulge and splicing without branching in group II introns. RNA 4:1186-1202.
8. Costa M, Christian EL, Michel F. 1998. Differential chemical probing of a group II self-splicing intron identifies bases involved in tertiary interactions and supports an alternative secondary structure model of domain V. RNA 4:1055-1068.
9. Costa M, Deme E, Jacquier A, Michel F. 1997. Multiple tertiary interactions involving domain II of group II self-splicing introns. J Mol Biol 267:520-536.
10. Costa M, Michel F. 1995. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J 14:1276-1285.
11. Dib-Hajj SD, Boulanger SC, Hebbar SK, Peebles CL, Franzen JF, Perlman PS. 1993. Domain 5 interacts with domain 6 and influences the second transesterification reaction of group II intron self-splicing. Nucleic Acids Res 21:1797-1804.
12. Franzen JS, Zhang M, Chay TR, Peebles CL. 1994. Thermal activation of a group II intron ribozyme reveals multiple conformational states. Biochemistry 33:11315-11326.
13. Gaur RK, McLaughlin LW, Green MR. 1997. Functional group substitutions of the branchpoint adenosine in a nuclear pre-mRNA and a group II intron. RNA 3:861-869.
14. Hebbar SK, Belcher SM, Perlman PS. 1992. A maturase-encoding group IIA intron of yeast mitochondria self-splices in vitro. Nucleic Acids Res 20:1747-1754.
15. Jacquier A. 1996. Group II introns: Elaborate ribozymes. Biochimie 78:474-487.
16. Jarrell KA, Dietrich RC, Perlman PS. 1988. Group II intron domains 5 facilitates a trans-splicing reaction. Mol Cell Biol 8:2361-2366.
17. Jarrell KA, Peebles CL, Dietrich RC, Romiti SL, Perlman PS. 1988. Group II intron self-splicing: Alternative reaction conditions yield novel products. J Biol Chem 263:3432-3439.
18. Jestin JL, Deme E, Jacquier A. 1997. Identification of structural elements critical for interdomain interactions in a group II self-splicing intron. EMBO J 16:2945-2954.
19. Koch JL, Boulanger SC, Dib-Hajj SD, Hebbar SK, Perlman PS. 1992. Group II introns deleted for multiple substructures retain self-splicing activity. Mol Cell Biol 12:1950-1958.
20. Konforti BB, Abramovitz DL, Duarte CM, Karpeisky A, Beigelman L, Pyle AM. 1998. Ribozyme catalysis from the major groove of group II intron domain 5. Mol Cell 1:433-441.
21. Lambowitz AM, Caprara MG, Zimmerly S, Perlman PS. 1999. Group I and group II ribozymes as RNPs: Clues to the past and guides to the future. In: Gesteland R, Cech TR, Atkins J, eds. The RNA world, 2nd ed. Cold Spring Harbor New York: Cold Spring Harbor Laboratory Press. In press.
22. Liu Q, Green J, Khodadadi A, Haeberli P, Beigelman L, Pyle A. 1997. Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities. J Mol Biol 267:163-171.
23. Michel F, Ferat JL. 1995. Structure and activities of group II introns. Ann Rev Biochem 64:435-461.
24. Michel F, Umesono K, Ozeki H. 1989. Comparative and functional anatomy of group II catalytic introns - a review. Gene 82:5-30.
25. Michels WJ Jr, Pyle AM. 1995. 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 34:2965-2977.
26. Milligan JF, Uhlenbeck OC. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180:51-62.
27. Mueller MW, Stocker P, Hetzer M, Schweyen RJ. 1991. Fate of the junction phosphate in alternating forward and reverse self-splicing reactions of group II intron RNA. J Mol Biol 222:145-154.
28. Peebles CL, Zhang M, Perlman PS, Franzen JF. 1995. Catalytically critical nucleotides in domain 5 of a group II intron. Proc Natl Acad Sci USA 92:4422-4426.
29. Perlman P, Podar M. 1996. Reactions catalyzed by group II introns in vitro. Methods Enzymol 264:66-86.
30. Podar M. 1997. Biochemical, molecular, and genetic investigations of the structure and mechanism of a group II intron catalytic RNA. Ph.D. Dissertation, University of Texas Southwestern Medical Center, Dallas, Texas.
31. Podar M, Chu VT, Pyle AM, Perlman PS. 1998. Group II intron splicing in vivo by first-step hydrolysis. Nature 391:915-918.
32. 2+-dependent crosslink traps an active form of domain 3 of a self-splicing group II intron. RNA 1:828-840.
33. Podar M, Perlman PS, Padgett RA. 1995. Stereochemical selectivity of group II intron splicing, reverse splicing, and hydrolysis reactions. Mol Cell Biol 15:4466-4478.
34. Podar M, Zhuo J, Zhang M, Franzen JS, Perlman PS, Peebles CL. 1998. Domain 5 binds near a highly conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron. RNA 4:151-166.
35. Pyle A. 1996. Catalytic reaction mechanisms and structural features of group II intron ribozymes. In: Eckstein F, Lilley DMJ, eds. Nucleic Acids and Molecular Biology. Vol. 10. New York: Springer Verlag. pp 75-107.
36. 2+ ions in the tertiary structure. Biochemistry 36:4718-4730.
37. Schmidt U, Maue I, Lehmann K, Belcher SM, Stahl U, Perlman PS. 1998. Mutant alleles of the MRS2 gene of yeast nuclear DNA suppress mutations in the catalytic core of a mitochondrial group II intron. J Mol Biol 282:525-541.
38. Schmidt U, Podar M, Stahl U, Perlman PS. 1996. Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: Phenotypes and suppressor mutations. RNA 2:1161-1172.
39. van der Veen R, Arnberg AC, van der Horst G, Bonen L, Tabak HF, Grivell LA. 1986. Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Cell 44:225-234.