Genetic analysis of the Chlamydomonas reinhardtii I-CreI mobile intron homing system in Escherichia coli

Genetics

Volumn 147, Issue 4, 1997, Pages 1653-1664

  Seligman, Lenny M ^a,b   Stephens, Kathryn M ^a   Savage, Jeremiah H ^b   Monnat Jr , Raymond J ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b POMONA COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CHLAMYDOMONAS REINHARDTII; ESCHERICHIA COLI; FRAMESHIFT MUTATION; GENETIC ANALYSIS; INTRON; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

ANIMALS; BINDING SITES; CHLAMYDOMONAS REINHARDTII; DNA RESTRICTION ENZYMES; ESCHERICHIA COLI; INTRONS; MODELS, MOLECULAR; MUTAGENESIS; PROTEIN CONFORMATION;

ALGAE; CHLAMYDOMONAS REINHARDTII; CHLOROPHYTA; ESCHERICHIA COLI; EUKARYOTA;

EID: 0030777960     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (48)

1. AAGAARD, C., M. J. AWAYEZ and R. A. GARRETT, 1997 Profile of the DNA recognition site of the archeal homing endonuclease IDmoI. Nucleic Acids Res. 25: 1523-1530.
2. AGGARWAI, A. K., 1995 Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5: 11-19.
3. ANDERSON, J. E., 1993 Restriction endonucleases and modification methylases. Curr. Opin. Struct. Biol. 3: 24-30.
4. BELFORT, M., and P. S. PERLMAN, 1995 Mechanisms of intron mobility. J. Biol. Chem. 270: 30237-30240.
5. BELFORT, M., and R. ROBERTS, 1997 Homing endonucleases - keeping the house in order. Nucleic Acids Res. 25: 3379-3388.
6. BELFORT, M., M. E. REABAN, T. COETZEE and J. Z. DALGAARD, 1995 Prokaryotic introns and inteins: a panoply of form and function. J. Bacteriol. 177: 3897-3903.
7. CHANG, A. C. Y., and S. N. COHEN, 1978 Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134: 1141-1156.
8. DUAN, X., F. S. GIMBLE and F. A. QUIOCHO, 1997 Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Cell 89: 555-564.
9. DÜRRENBERGER, F., and J.-D. ROCHAIX, 1991 Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self-splicing, DNA endonuclease activity and in vivo mobility. EMBO J. 10: 3495-3501.
10. DÜRRENBERGER, F., and J.-D. ROCHAIX, 1993 Characterization of the cleavage site and the recognition sequence of the I-CreI DNA endonuclease encoded by the chloroplast ribosomal intron of Chlamydomonas reinhardtii. Mol. Gen. Genet. 236: 409-414.
11. DÜRRENBERGER, F., A. J. THOMPSON, D. L. HERRIN and J.-D. ROCHAIX, 1996 Double strand break-induced recombination in Chlamydomonas reinhardtii chloroplasts. Nucleic Acids Res. 24: 3323-3331.
12. GIMBLE, F. S., and B.W. STEPHENS, 1995 Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of PI-SceI endonuclease. J. Biol. Chem. 270: 5849-5856.
13. BAD promoter. J. Bacteriol. 177: 4121-4131.
14. HEATH, P. J., K. M. STEPHENS, R. J. MONNAT, JR. and B. L. STODDARD, 1997 The structure of I-CreI: a Group I intron-encoded homing endonuclease. Nature Struct. Biol. 4: 468-476.
15. HENKE, R. M., R. A. BUTOW and P. S. PERLMAN, 1995 Maturase and endonuclease functions depend on separate conserved domains of the bifunctional protein encoded by the group I intron aI4α of yeast mitochondrial DNA. EMBO J. 14: 5094-5099.
16. HENSGENS, L. A. M., L. BONEN, M. DE HAAN, G. VAN DER HORST and L. A. GRIVELL, 1983 Two intron sequences in yeast mitochondrial COX1 gene: homology among URF-containing introns and strain-dependent variation in flanking exons. Cell 32: 379-389.
17. HERRIN, D. L., Y. CHEN and G. W. SCHMIDT, 1990 RNA splicing in Chlamydomonas chloroplasts: self-splicing of 23S preRNA. J. Biol. Chem. 265: 21134-21140.
18. HERZING, L. B. K., and M. S. MEYN, 1993 Novel LacZ-based recombination vectors for mammalian cells. Gene 137: 163-169.
19. HODGES, R., F. B. PERLER, C. J. NOREN and W. E. JACK, 1992 Protein splicing removes intervening sequences in an archaea DNA polymerase. Nucleic Acids Res. 20: 6153-6157.
20. HOLLOWAY, B., and K. B. LOW, 1996 F-prime and R-prime factors, pp. 2413-2420 in Escherichia coli and Salmonella: Cellular and Molecular Biology, Ed. 2, edited by F. C. NEIDHARDT, R. I. CURTISS, J. L. INGRAHAM, E. C. C. LIN, K B. LOW, JR., et al. ASM Press, Washington, D.C.
21. HOLMES, D. S., and M. QUIGLEY, 1981 A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 114: 193-197.
22. JASIN, M., 1996 Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet 12: 224-228.
23. KUNKEL, T. A., J. D. ROBERTS and R. A. ZAKOUR, 1987 Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154: 367-382.
24. LAMBOWITZ, A. M., and M. BELFORT, 1993 Introns as mobile genetic elements. Annu. Rev. Biochem. 62: 587-622.
25. LEMIEUX, C., J. BOULANGER, C. OTIS and M. TURMEL, 1989 Nucleotide sequence of the chloroplast large subunit rRNA gene from Chlamydomonas reinhardtii. Nucleic Acids Res. 17: 7997.
26. MICHEL, F., A. JACQUIER and B. DUJON, 1982 Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie 64: 867-881.
27. MILLER, J. H., 1992 A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, Ed. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
28. MONNAT, R. J., JR., A. F. M. HACKMANN and T. A. CHIAVEROTTI, 1992 Nucleotide sequence analysis of human hypoxanthine phosphoribosyltransferase gene deletions. Genomics 13: 777-787.
29. MONTEILHET, C., A. PERRIN, A. THIERRY, L. COLLEAUX and B. DUJON, 1990 Purification and characterization of the in vitro activity of I-SceI, a novel and highly specific endonuclease encoded by a group I intron. Nucleic Acids Res. 18: 1407-1413.
30. MUELLER, J. E., M. BRYK, N. LOIZOS and M. BELFORT, 1993 Homing endonucleases, pp. 111-143 in Nucleases, Ed. 2, edited by S. M. LINN, R. S. LLOYD and R. J. ROBERTS. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. PAKULA, A. A., and R. T. SAUER, 1989 Genetic analysis of protein stability and function. Annu. Rev. Genet. 23: 289-310.
32. PERRIN, A., M. BUCKLE and B. DUJON, 1993 Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions. EMBO J. 12: 2939-2947.
33. PIETROKOVSKI, S., 1994 Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Sci. 3: 2340-2350.
34. PIETROKOVSKI, S., 1997 Modular organization of inteins and C-terminal autocatalytic domains. Protein Sci. (in press).
35. PLESSIS, A., A. PERRIN, J. E. HABER and B. DUJON, 1992 Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus. Genetics 130: 451-460.
36. ROBERTS, R., and S. HALFORD, 1993 Type II restriction endonucleases, pp.35-88 in Nucleases, Ed.2, edited by S. LINN, R, LLOYD and R. J. ROBERTS. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
37. ROCHAIX, J. D., and P. MALNOE, 1978 Anatomy of the chloroplast ribosomal DNA of Chlamydomonas reinhardtii. Cell 15: 661-670.
38. ROCHAIX, J. D., M. RAHIRE and F. MICHEL, 1985 The chloroplast ribosomal intron of Chlamydomonas reinhardtii codes for a polypeptide related to mitochondrial maturases. Nucleic Acids Res. 13: 975-984.
39. SAMBROOK, J., E. F. FRITSCH and T. MANIATIS, 1989 Molecular Cloning: A Laboratory Manual, Ed. 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
40. SCHAAPER, R. M., 1988 Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: role of mismatch repair. Proc. Natl. Acad. Sci. USA 85: 8126-8130.
41. SELIGMAN, L.. and C. MANOIL, 1994 An amphipathic sequence determinant of membrane protein topology. J. Biol. Chem. 269: 19888-19896.
42. STAHL, F., W. WENDE, A. JELTSCH and A. PINGOUD, 1996 Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein. Proc. Natl. Acad. Sci. USA 93: 6175-6180.
43. STEPHENS, K. M., R. J. MONNAT, JR., P. J. HEATH and B. L. STODDARD, 1997 Crystallization and preliminary X-ray studies of I-CreI: a group I intron-encoded endonuclease from C. reinhardtii. Proteins: SFG 28: 137-139.
44. THOMPSON, A. J., and D. L. HERRIN, 1991 In vitro self-splicing reactions of the chloroplast group I intron Cr.LSU from Chlamydomonas reinhardtii and in vivo manipulation via gene replacement. Nucleic Acids Res. 19: 6611-6618.
45. THOMPSON, A. J., X. YUAN, W. KUDLICKI and D. L. HERRIN, 1992 Cleavage and recognition pattern of a double-strand-specific endonuclease (I-CreI) encoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii. Gene 119: 247-251.
46. TURMEL, M., C. OTIS, V. CÔTÉ and C. LEMIEUX, 1997 Evolutionarily conserved and functionally important residues in the I-CeuI homing endonuclease. Nucleic Acids Res. 25: 2610-2619.
47. VILEJO, A. N., R. J. POGULIS and L.R. PEASE, 1995 Mutagenesis and synthesis of novel recombinant genes using PCR, pp. 603-612 in PCR Primer: A Laboratory Manual, Ed. 1, edited by C. W. DIEFFENBACH and G. S. DVEKSLER. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
48. WARING, R. B., R. W. DAVIES, C. SCAZZOCCHIO and T. A. BROWN, 1982 Internal structure of a mitochondrial intron of Aspergillus nidulans. Proc. Natl. Acad. Sci. USA 79: 6332-6336.