Probing novel elements for protein splicing in the yeast Vmal protozyme: A study of replacement mutagenesis and intragenic suppression

Genetics

Volumn 147, Issue 1, 1997, Pages 73-85

  Nogami, Satoru ^a   Satow, Yoshinori ^a   Ohya, Yoshikazu ^a   Anraku, Yasuhiro ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATASE;

AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; ENZYME SUBUNIT; FUNGUS MUTANT; HYDROPHOBICITY; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROCESSING; SACCHAROMYCES CEREVISIAE; YEAST;

AMINO ACID SEQUENCE; ENDODEOXYRIBONUCLEASES; ISOLEUCINE; MUTAGENESIS; PROTEIN SPLICING; PROTON-TRANSLOCATING ATPASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT; SUPPRESSION, GENETIC; TYROSINE; VALINE;

FUNGI; SACCHAROMYCES CEREVISIAE;

EID: 0030982430     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (37)

1. ABRAHAMS, J. P., A. G. W. LESLIE, R. LUTTER and J. E. WALKER, 1994 Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria. Nature 370: 621-628.
2. ANRAKU, Y. and R. HIRATA, 1994 Protozyme: emerging evidence in nature. J. Biochem. 115: 175-178.
3. BULT, C. J., O. WHITE, G. J. OLSEN, L. ZHOU, R. D. FLEISCHMANN et al., 1996 Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058-1073.
4. CADWELL, R. C., and G. F. JOYCE, 1992 Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2: 28-33.
5. CHONG, S., Y. SHAO, H. PAULUS, J. BENNER, F. B. PERLER et al., 1996 Protein splicing involving the Saccharomyces cerevisiae VMA intein. The steps in the splicing pathway, side reactions leading to protein cleavage, and establishment of an in vitro splicing system. J. Biol. Chem. 271: 22159-22168.
6. COOPER, A. A., Y.-J. CHEN, M. A. LINDORFER and T. H. STEVENS, 1993 Protein splicing of the yeast TFP1 intervening protein sequence: a model for self-excision. EMBO J. 12: 2575-2583.
7. DAVIS, E. O., P. J. JENNER, P. C. BROOKS, M. J. COLSTON and S. G. SEDOWICK, 1992 Protein splicing in the maturation of M. tuberculosis RecA protein: a mechanism for tolerating a novel class of intervening sequence. Cell 71: 201-210.
8. DAVIS, E. O., H. S. THANGARAJ, P. C. BROOKS and M. J. COLSTON, 1994 Evidence of selection for protein introns in the RecAs of pathogenic mycobacteria. EMBO J. 13: 699-703.
9. FSIHI, H., V. VINCENT and S. T. COLE, 1996 Homing events in the gyrA gene of some mycobacteria. Proc. Natl. Acad. Sci. USA 93: 3410-3415.
10. GEOURJON, C., and G. DELEAGE, 1995 SOPMA: significant improvements in protein secondary structure prediction by prediction from multiple alignments. Comput. Appl. Biosci. 11: 681-684.
11. GIMBLE, F. S., and J. THORNER, 1992 Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature 357: 301-306.
12. Gu, H. H., J. Xu, M. GALLAGHER and G. E. DEAN, 1993 Peptide splicing in the vacuolar ATPase subunit A from Candida tropicalis. J. Biol. Chem. 268: 7372-7381.
13. +-ATPase, inhibit its processing by protein splicing. Biochem. Biophys. Res. Commun. 188: 40-47.
14. +-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J. Biol. Chem. 265: 6726-6733.
15. Ho, S. N., H. D. HUNT, R. M. HORTON, J. K. PULLEN and L. R. PEASE, 1989 Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51-59.
16. JONES, J. S., and L. PRAKASH, 1990 Yeast Saccharomyces cerevisiae selectable markers in pUC18 polylinkers. Yeast 6: 363-366.
17. KAISER, C., S. MICHAELIS and A. MITCHELL, 1994 Methods in Yeast Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
18. +-adenosine triphosphatase. Science 250: 651-657.
19. KAWASAKI, M., S.-I. MAKINO, H. MATSUZAWA, Y. SATOW, Y. OHYA et al., 1996 Folding-dependent in vitro protein splicing of the Saccharomyces cerevisiae VMA1 protozyme. Biochem. Biophys. Res. Commun. 222: 827-832.
20. KAWASAKI, M., S. NOGAMI, Y. SATOW, Y. OHYA and Y. ANRAKU, 1997 Identification of three core regions essential for protein splicing of the Yeast Vmal protozyme. A random mutagenesis study of the entire VMA1-derived sequence. J. Biol. Chem. 272: 15668-15674.
21. LAMBOWITZ, A. M. and M. BELFORT, 1993 Introns as mobile genetic elements. Annu. Rev. Biochem. 62: 587-622.
22. LIFSON, S., and C. SANDER, 1979 Antiparallel and parallel β strands differ in amino acid residue preferences. Nature 282: 109-111.
23. LIFSON, S., and C. SANDER, 1980 Specific recognition in the tertiary structure of β-sheets of proteins. J. Mol. Biol. 139: 627-639.
24. MUHLRAD, D., R. HUNTER and R. PARKER, 1992 A rapid method for localized mutagenesis of yeast genes. Yeast 8: 79-82.
25. +-ATPase activity. J. Biol. Chem. 266: 13971-13977.
26. PALZKILL, T., and D. BOTSTEIN, 1992 Probing β-lactamase structure and function using random replacement mutagenesis. Proteins 14: 29-44.
27. PERLER, F. B., D. G. COMB, W. E. JACK, L. S. MORAN, B. QIANG et al., 1992 Intervening sequences in an Archaea DNA polymerase gene. Proc. Natl. Acad. Sci. USA 89: 5577-5581.
28. PERLER, F. B., E. O. DAVIS, G. E. DEAN, F. S. GIMBLE, W. E. JACK et al., 1994 Protein splicing elements: inteins and exteins - a definition of terms and recommended nomenclature. Nucleic Acids Res. 22: 1125-1127.
29. PERLER, F. B., G. J. OLSEN and E. ADAM, 1997 Compilation and analysis of intein sequences. Nucleic Acids Res. 25: 1087-1094.
30. 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.
31. PIETROKOVSKI, S., 1996 A new intein in cyanobacteria and its significance for the spread of inteins. Trends Genet. 12: 287-288.
32. SAMBROOK, J., E. F. FRITSCH and T. MANIATIS, 1989 Molecular Cloning. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
33. SHIH, C.K., R. WAGNER, S. FEINSTEIN, C. KANIK-ENNULAT and N. NEFF, 1988 A dominant trifluoperazine resistance gene from Saccharomyces cerevisiae has homology with F0F1 ATP synthase and confers calcium-sensitive growth. Mol. Cell Biol. 8: 3094-3103.
34. SIKORSKI, R. S., and P. HIETER, 1989 A system of shuttle vector and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
35. STORY, R. M., I. T. WEBER and T. A. STEITZ, 1992 The structure of the E. coli recA protein monomer and polymer. Nature 355: 318-325.
36. XU, M.-Q., M. W. SOUTHWORTH, F. B. MERSHA, L. J. HORNSTRA and F. B. PERLER, 1993 In vitro protein splicing of purified precursor and the identification of a branched intermediate. Cell 75: 1371-1377.
37. XU, M.-Q., D. G. COMB, H. PAULUS, C. J. NOREN, Y. SHAO et al., 1994 Protein splicing: an analysis of the branched intermediate and its resolution by succinimide formation. EMBO J. 13: 5517-22.