Group II intron splicing factors derived by diversification of an ancient RNA-binding domain

EMBO Journal

Volumn 22, Issue 15, 2003, Pages 3919-3929

  Ostheimer, Gerard J ^a   Williams Carrier, Rosalind ^a   Belcher, Susan ^a   Osborne, Erin ^a,b   Gierke, Jennifer ^a,c   Barkan, Alice ^a  

^a UNIVERSITY OF OREGON   (United States)

^b GEOPHYSICAL LABORATORY   (United States)

^c 8520 University Green   (United States)

Author keywords

Chloroplast; CRM domain; Group II intron; UPF 0044

Indexed keywords

PROTEIN; PROTEIN CAF1; PROTEIN CAF2; PROTEIN CRS2; RIBONUCLEOPROTEIN; RNA; UNCLASSIFIED DRUG;

ARTICLE; CHLOROPLAST; GENETIC CODE; HOST; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; RIBOSOME; RNA BINDING; RNA SPLICING;

AMINO ACID SEQUENCE; BASE SEQUENCE; CHLOROPLASTS; DNA PRIMERS; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PLANT PROTEINS; PRECIPITIN TESTS; RNA SPLICING; RNA-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TWO-HYBRID SYSTEM TECHNIQUES; ZEA MAYS;

ZEA MAYS;

EID: 0042525906     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg372     Document Type: Article

References (51)

1. Barkan, A. (1989) Tissue-dependent plastid RNA splicing in maize. Plant Cell, 1, 437-445.
2. Barkan, A. and Martienssen, R.A. (1991) Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1. Proc. Natl Acad. Sci. USA, 88, 3502-3506.
3. Bassi, G.S., de Oliviera, D.M., White, M.F. and Weeks, K.M. (2002) Recruitment of intron-encoded and co-opted proteins in splicing of the bI3 group I intron RNA. Proc. Natl Acad. Sci. USA, 99, 128-133.
4. Bonen, L. and Vogel, J. (2001) The ins and outs of group II introns. Trends Genet., 17, 322-331.
5. Brangeon, J. et al. (2000) Defective splicing of the first nad4 intron is associated with lack of several complex I subunits in the Nicotinia sylvestris NMS1 nuclear mutant. Plant J., 21, 269-280.
6. Cech, T.R. (1986) The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cell, 44, 207-210.
7. Clodi, E., Semrad, K. and Schroeder, R. (1999) Assaying RNA chaperone activity in vivo using a novel RNA folding trap. EMBO J., 18, 3776-3782.
8. Coetzee, T., Herschlag, D. and Belfort, M. (1994) Eschericia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes Dev., 8, 1575-1588.
9. Collins, C.A. and Guthrie, C. (2000) The question remains: is the spliceosome a ribozyme. Nat. Struct. Biol., 7, 850-854.
10. Dai, L. and Zimmerly, S. (2002) Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res., 30, 1091-1102.
11. Dai, L. and Zimmerly, S. (2003) ORF-less and reverse-transcriptase-encoding group II introns in achaebacteria, with a pattern of homing into related group II intron ORFs. RNA, 9, 14-19.
12. Eickbush, T.H. (1999) Mobile introns: retrohoming by complete reverse splicing. Curr. Biol., 9, R11-R14.
13. Emanuelsson, O., Nielsen, H., Brunak, S. and von Heijne, G. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol., 300, 1005-1016.
14. Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature, 340, 245-246.
15. Goldschmidt-Clermont, M., Girard-Bascou, J., Choquet, Y. and Rochaix, J.-D. (1990) Trans-splicing mutants of Chlamydomonas reinhardtii. Mol. Gen. Genet., 223, 417-425.
16. Gordon, P.M. and Piccirilli, J. (2001) Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis. Nat. Struct. Biol., 8, 893-898.
17. Gordon, P.M., Sontheimer, E.J. and Piccirilli, J.A. (2000) Metal ion catalysis during the exon-ligation step of nuclear pre-mRNA splicing: extending the parallels between the spliceosome and group II introns. RNA, 6, 199-205.
18. Guo, Q. and Lambowitz, A.M. (1992) A tyrosyl-tRNA synthetase binds specifically to the group I intron catalytic core. Genes Dev., 6, 1357-1372.
19. Herschlag, D. (1995) RNA chaperones and the RNA folding problem. J. Biol. Chem., 270, 20871-20874.
20. Higgins, D., Thompson, J., Gibson, T., Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
21. Ho, Y. and Waring, R. (1999) The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing. J. Mol. Biol., 292, 987-1001.
22. Jenkins, B.D. and Barkan, A. (2001) Recruitment of a peptidyl-tRNA hydrolase as a facilitator of group II intron splicing in chloroplasts. EMBO J., 20, 872-879.
23. Jenkins, B.D., Kulhanek, D.J. and Barkan, A. (1997) Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors. Plant Cell, 9, 283-296.
24. 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 Gesteland, R.F., Cech, T.R. and Atkins, J.F. (eds), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 451-485.
25. Matsuura, M. et al. (1997) A bacterial group II intron encoding reverse transcriptase, maturase and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron. Genes Dev., 11, 2910-2924.
26. Menninger, J. (1976) Peptidyl-transfer RNA dissociates during protein synthesis from ribosomes of Eschericia coli. J. Biol. Chem., 251, 3392-3398.
27. Michel, F. and Ferat, J.-L. (1995) Structure and actvities of group II introns. Annu. Rev. Biochem., 64, 435-461.
28. Michel, F., Umesono, K. and Ozeki, H. (1989) Comparative and functional anatomy of group II catalytic introns - a review. Gene, 82, 5-30.
29. 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.
30. Nilsen, T.W. (1998) RNA-RNA interactions in nuclear pre-mRNA splicing. In Simons, R.W. and Grunberg-Manago, M. (eds), RNA Structure and Function. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 279-307.
31. Ostheimer, G.J., Barkan, A. and Matthews, B.W. (2002) Crystal structure of E.coli YhbY: a representative of a novel class of RNA binding proteins. Structure, 10, 1593-1601.
32. Perron, K., Goldschmidt-Clermont, M. and Rochaix, J.-D. (1999) A factor related to pseudouridine synthases is required for chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO J., 18, 6481-6490.
33. Qin, P.Z. and Pyle, A.M. (1998) The architectural organization and mechanistic functions of group II intron structural elements. Curr. Opin. Struct. Biol., 8, 301-308.
34. Rivier, C., Goldschmidt-Clermont, M. and Rochaix, J.-D. (2001) Identification of an RNA-protein complex involved in chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO J., 20, 1765-1773.
35. Schmitt, E., Mechulam, Y., Fromant, M., Plateau, P. and Blanquet, S. (1997) Crystal structure at 1.2 Å resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase. EMBO J., 16, 4760-4769.
36. Seraphin, B., Simon, M., Boulet, A. and Faye, G. (1989) Mitochondrial splicing requires a protein from a novel helicase family. Nature, 337, 84-87.
37. Sharp, P.A. (1991) 'Five easy pieces'. Science, 254, 663.
38. Solem, A., Chatterjee, P. and Caprara, M. (2002) A novel mechanism for protein-assisted group I intron splicing. RNA, 8, 412-425.
39. Sontheimer, E.J., Sun, S. and Piccirilli, J. (1997) Metal ion catalysis during splicing of premessenger RNA. Nature, 388, 801-805.
40. Swisher, J.F., Su, L.J., Brenowitz, M., Anderson, V.E. and Pyle, A.M. (2002) Productive folding to the native state by a group II intron ribozyme. J. Mol. Biol., 315, 297-310.
41. Till, B., Schmitz-Linneweber, C., Williams-Carrier, R. and Barkan, A. (2001) CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin. RNA, 7, 1227-1238.
42. Toor, N., Hausner, G. and Zimmerly, S. (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA, 7, 1142-1152.
43. Toro, N. (2003) Bacteria and Archaea group II introns: additional mobile genetic elements in the envronment. Environ. Microbiol., 5, 143-151.
44. Valadkhan, S. and Manley, J.L. (2001) Splicing-related catalysis by protein-free snRNAs. Nature, 413, 701-707.
45. 2+-dependent chemistry at the catalytic core? Cell, 109, 149-152.
46. Vogel, J., Borner, T. and Hess, W. (1999) Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plants mutants. Nucleic Acids Rev., 27, 3866-3874.
47. Waldsich, C., Grossberger, R. and Schroeder, R. (2002) RNA chaperone StpA loosens interaction of the tertiary structure in the td group I intron in vivo. Genes Dev., 16, 2300-2312.
48. Wardleworth, B.J., Kvaratskhelia, M. and White, M.F. (2000) Site-directed mutagenesis of the yeast resolving enzyme CceI reveals catalytic residues and relationship with the intron-splicing factor Mrs1. J. Biol. Chem., 275, 23725-23728.
49. Weeks, K.M. (1997) Protein-facilitated RNA folding. Curr. Opin. Struct. Biol., 7, 336-342.
50. Weeks, K.M. and Cech, T.R. (1995) Efficient protein-facilitated splicing of the yeast mitochondrial bI5 intron. Biochemistry, 34, 7728-7738.
51. Willis, M.A., Krajewski, W., Chalamasetty, V.R., Retty, P., A., H. and Herzberg, O. (2002) Structure of HI1333 (YhbY), a putative RNA-binding protein from Haemophilus influenzae. Proteins, 49, 423-426.