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. 1994 Jun 11;22(11):2057–2064. doi: 10.1093/nar/22.11.2057

Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron aI2.

J V Moran 1, K L Mecklenburg 1, P Sass 1, S M Belcher 1, D Mahnke 1, A Lewin 1, P Perlman 1
PMCID: PMC308121  PMID: 8029012

Abstract

Six mutations blocking the function of a seven intron form of the mitochondrial gene encoding subunit I of cytochrome c oxidase (COXI) and mapping upstream of exon 3 were isolated and characterized. A cis-dominant mutant of the group IIA intron 1 defines a helical portion of the C1 substructure of domain 1 as essential for splicing. A trans-recessive mutant confirms that the intron 1 reading frame encodes a maturase function. A cis-dominant mutant in exon 2 was found to have no effect on the splicing of intron 1 or 2. A trans-recessive mutant, located in the group IIA intron 2, demonstrates for the first time that intron 2 encodes a maturase. A genetic dissection of the five missense mutations present in the intron 2 reading frame of that strain demonstrates that the maturase defect results from one or both of the missense mutations in a newly-recognized conserved sequence called domain X.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ahmad I., Finkelstein J. A., Steggles A. W. The analysis of RNA by in situ agarose gel hybridization is more sensitive than the equivalent northern blot analysis. Biotechniques. 1990 Feb;8(2):162–165. [PubMed] [Google Scholar]
  2. Alexander N. J., Periman P. S., Hanson D. K., Mahler H. R. Mosaic organization of a mitochondrial gene: evidence from double mutants in the cytochrome b region of Saccharomyces cerevisiae. Cell. 1980 May;20(1):199–206. doi: 10.1016/0092-8674(80)90247-0. [DOI] [PubMed] [Google Scholar]
  3. Alexander N. J., Vincent R. D., Perlman P. S., Miller D. H., Hanson D. K., Mahler H. R. Regulatory interactions between mitochondrial genes. I. Genetic and biochemical characterization of some mutant types affecting apocytochrome b and cytochrome oxidase. J Biol Chem. 1979 Apr 10;254(7):2471–2479. [PubMed] [Google Scholar]
  4. Anziano P. Q., Butow R. A. Splicing-defective mutants of the yeast mitochondrial COXI gene can be corrected by transformation with a hybrid maturase gene. Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5592–5596. doi: 10.1073/pnas.88.13.5592. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Anziano P. Q., Moran J. V., Gerber D., Perlman P. S. Novel hybrid maturases in unstable pseudorevertants of maturaseless mutants of yeast mitochondrial DNA. Nucleic Acids Res. 1990 Jun 11;18(11):3233–3239. doi: 10.1093/nar/18.11.3233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Arnberg A. C., Van Ommen G. J., Grivell L. A., Van Bruggen E. F., Borst P. Some yeast mitochondrial RNAs are circular. Cell. 1980 Feb;19(2):313–319. doi: 10.1016/0092-8674(80)90505-x. [DOI] [PubMed] [Google Scholar]
  7. Bergantino E., Carignani G. Antibodies against a fused gene product identify the protein encoded by a group II yeast mitochondrial intron. Mol Gen Genet. 1990 Sep;223(2):249–257. doi: 10.1007/BF00265061. [DOI] [PubMed] [Google Scholar]
  8. Bonitz S. G., Coruzzi G., Thalenfeld B. E., Tzagoloff A., Macino G. Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase. J Biol Chem. 1980 Dec 25;255(24):11927–11941. [PubMed] [Google Scholar]
  9. Carignani G., Groudinsky O., Frezza D., Schiavon E., Bergantino E., Slonimski P. P. An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae. Cell. 1983 Dec;35(3 Pt 2):733–742. doi: 10.1016/0092-8674(83)90106-x. [DOI] [PubMed] [Google Scholar]
  10. Carignani G., Netter P., Bergantino E., Robineau S. Expression of the mitochondrial split gene coding for cytochrome oxidase subunit I in S. cerevisiae: RNA splicing pathway. Curr Genet. 1986;11(1):55–63. doi: 10.1007/BF00389426. [DOI] [PubMed] [Google Scholar]
  11. Chomczynski P., Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr;162(1):156–159. doi: 10.1006/abio.1987.9999. [DOI] [PubMed] [Google Scholar]
  12. Cleveland D. W., Fischer S. G., Kirschner M. W., Laemmli U. K. Peptide mapping by limited proteolysis in sodium dodecyl sulfate and analysis by gel electrophoresis. J Biol Chem. 1977 Feb 10;252(3):1102–1106. [PubMed] [Google Scholar]
  13. Conde J., Fink G. R. A mutant of Saccharomyces cerevisiae defective for nuclear fusion. Proc Natl Acad Sci U S A. 1976 Oct;73(10):3651–3655. doi: 10.1073/pnas.73.10.3651. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. De La Salle H., Jacq C., Slonimski P. P. Critical sequences within mitochondrial introns: pleiotropic mRNA maturase and cis-dominant signals of the box intron controlling reductase and oxidase. Cell. 1982 Apr;28(4):721–732. doi: 10.1016/0092-8674(82)90051-4. [DOI] [PubMed] [Google Scholar]
  15. Doolittle R. F., Feng D. F., Johnson M. S., McClure M. A. Origins and evolutionary relationships of retroviruses. Q Rev Biol. 1989 Mar;64(1):1–30. doi: 10.1086/416128. [DOI] [PubMed] [Google Scholar]
  16. Haid A., Schweyen R. J., Bechmann H., Kaudewitz F., Solioz M., Schatz G. The mitochondrial COB region in yeast codes for apocytochrome b and is mosaic. Eur J Biochem. 1979 Mar;94(2):451–464. doi: 10.1111/j.1432-1033.1979.tb12913.x. [DOI] [PubMed] [Google Scholar]
  17. Halbreich A., Pajot P., Foucher M., Grandchamp C., Slonimski P. A pathway of cytochrome b mRNA processing in yeast mitochondria: specific splicing steps and an intron-derived circular DNA. Cell. 1980 Feb;19(2):321–329. doi: 10.1016/0092-8674(80)90506-1. [DOI] [PubMed] [Google Scholar]
  18. Hanson D. K., Lamb M. R., Mahler H. R., Perlman P. S. Evidence for translated intervening sequences in the mitochondrial genome of Saccharomyces cerevisiae. J Biol Chem. 1982 Mar 25;257(6):3218–3224. [PubMed] [Google Scholar]
  19. Hanson D. K., Miller D. H., Mahler H. R., Alexander N. J., Perlman P. S. Regulatory interaction between mitochondrial genes. II. Detailed characterization of novel mutants mapping within one cluster in the cob2 region. J Biol Chem. 1979 Apr 10;254(7):2480–2490. [PubMed] [Google Scholar]
  20. Hensgens L. A., Arnberg A. C., Roosendaal E., van der Horst G., van der Veen R., van Ommen G. J., Grivell L. A. Variation, transcription and circular RNAs of the mitochondrial gene for subunit I of cytochrome c oxidase. J Mol Biol. 1983 Feb 15;164(1):35–58. doi: 10.1016/0022-2836(83)90086-4. [DOI] [PubMed] [Google Scholar]
  21. Jacquier A., Michel F. Base-pairing interactions involving the 5' and 3'-terminal nucleotides of group II self-splicing introns. J Mol Biol. 1990 Jun 5;213(3):437–447. doi: 10.1016/S0022-2836(05)80206-2. [DOI] [PubMed] [Google Scholar]
  22. Kennell J. C., Moran J. V., Perlman P. S., Butow R. A., Lambowitz A. M. Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria. Cell. 1993 Apr 9;73(1):133–146. doi: 10.1016/0092-8674(93)90166-n. [DOI] [PubMed] [Google Scholar]
  23. Kreike J., Bechmann H., Van Hemert F. J., Schweyen R. J., Boer P. H., Kaudewitz F., Groot G. S. The identification of apocytochrome b as a mitochondrial gene product and immunological evidence for altered apocytochrome b in yeast strains having mutations in the COB region of mitochondrial DNA. Eur J Biochem. 1979 Nov;101(2):607–617. doi: 10.1111/j.1432-1033.1979.tb19755.x. [DOI] [PubMed] [Google Scholar]
  24. Lamb M. R., Anziano P. Q., Glaus K. R., Hanson D. K., Klapper H. J., Perlman P. S., Mahler H. R. Functional domains in introns. RNA processing intermediates in cis- and trans-acting mutants in the penultimate intron of the mitochondrial gene for cytochrome b. J Biol Chem. 1983 Feb 10;258(3):1991–1999. [PubMed] [Google Scholar]
  25. Lambowitz A. M., Belfort M. Introns as mobile genetic elements. Annu Rev Biochem. 1993;62:587–622. doi: 10.1146/annurev.bi.62.070193.003103. [DOI] [PubMed] [Google Scholar]
  26. Lancashire W. E., Mattoon J. R. Genetics of oxidative phosphorylation: mitochondrial loci determining ossamycin-, venturicidin- and oligomycin-resistance in yeast. Mol Gen Genet. 1979 Oct 3;176(2):255–264. doi: 10.1007/BF00273220. [DOI] [PubMed] [Google Scholar]
  27. Lazowska J., Jacq C., Slonimski P. P. Sequence of introns and flanking exons in wild-type and box3 mutants of cytochrome b reveals an interlaced splicing protein coded by an intron. Cell. 1980 Nov;22(2 Pt 2):333–348. doi: 10.1016/0092-8674(80)90344-x. [DOI] [PubMed] [Google Scholar]
  28. Lazowska J., Szczepanek T., Macadre C., Dokova M. Two homologous mitochondrial introns from closely related Saccharomyces species differ by only a few amino acid replacements in their Open Reading Frames: one is mobile, the other is not. C R Acad Sci III. 1992;315(2):37–41. [PubMed] [Google Scholar]
  29. Levra-Juillet E., Boulet A., Séraphin B., Simon M., Faye G. Mitochondrial introns aI1 and/or aI2 are needed for the in vivo deletion of intervening sequences. Mol Gen Genet. 1989 May;217(1):168–171. doi: 10.1007/BF00330957. [DOI] [PubMed] [Google Scholar]
  30. Macino G., Tzagoloff A. Assembly of the mitochondrial membrane system: sequence analysis of a yeast mitochondrial ATPase gene containing the oli-2 and oli-4 loci. Cell. 1980 Jun;20(2):507–517. doi: 10.1016/0092-8674(80)90637-6. [DOI] [PubMed] [Google Scholar]
  31. McClure M. A. Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol Biol Evol. 1991 Nov;8(6):835–856. doi: 10.1093/oxfordjournals.molbev.a040686. [DOI] [PubMed] [Google Scholar]
  32. Michel F., Lang B. F. Mitochondrial class II introns encode proteins related to the reverse transcriptases of retroviruses. Nature. 1985 Aug 15;316(6029):641–643. doi: 10.1038/316641a0. [DOI] [PubMed] [Google Scholar]
  33. Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns--a review. Gene. 1989 Oct 15;82(1):5–30. doi: 10.1016/0378-1119(89)90026-7. [DOI] [PubMed] [Google Scholar]
  34. Moran J. V., Wernette C. M., Mecklenburg K. L., Butow R. A., Perlman P. S. Intron 5 alpha of the COXI gene of yeast mitochondrial DNA is a mobile group I intron. Nucleic Acids Res. 1992 Aug 11;20(15):4069–4076. doi: 10.1093/nar/20.15.4069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Nagley P., Linnane A. W. Expression of mitochondrial DNA in Saccharomyces cerevisiae: the construction of sets of isonuclear haploid strains containing different specified mitochondrial genomes. Biochem Biophys Res Commun. 1978 Nov 29;85(2):585–592. doi: 10.1016/0006-291x(78)91203-2. [DOI] [PubMed] [Google Scholar]
  36. Netter P., Robineau S., Sirand-Pugnet P., Fauvarque M. O. The unusual reversion properties of a mitochondrial mutation in the structural gene of subunit I of cytochrome oxidase of Saccharomyces cerevisiae reveal a probable histidine ligand of the redox center. Curr Genet. 1992 Feb;21(2):147–151. doi: 10.1007/BF00318474. [DOI] [PubMed] [Google Scholar]
  37. Peebles C. L., Belcher S. M., Zhang M., Dietrich R. C., Perlman P. S. Mutation of the conserved first nucleotide of a group II intron from yeast mitochondrial DNA reduces the rate but allows accurate splicing. J Biol Chem. 1993 Jun 5;268(16):11929–11938. [PubMed] [Google Scholar]
  38. Perlman P. S., Butow R. A. Mobile introns and intron-encoded proteins. Science. 1989 Dec 1;246(4934):1106–1109. doi: 10.1126/science.2479980. [DOI] [PubMed] [Google Scholar]
  39. Perlman P. S. Genetic analysis of RNA splicing in yeast mitochondria. Methods Enzymol. 1990;181:539–558. doi: 10.1016/0076-6879(90)81150-s. [DOI] [PubMed] [Google Scholar]
  40. Perlman P. S., Mahler H. R. Genetics and biogenesis of cytochrome b. Methods Enzymol. 1983;97:374–395. doi: 10.1016/0076-6879(83)97150-1. [DOI] [PubMed] [Google Scholar]
  41. Saldanha R., Mohr G., Belfort M., Lambowitz A. M. Group I and group II introns. FASEB J. 1993 Jan;7(1):15–24. doi: 10.1096/fasebj.7.1.8422962. [DOI] [PubMed] [Google Scholar]
  42. Schmelzer C., Haid A., Grosch G., Schweyen R. J., Kaudewitz F. Pathways of transcript splicing in yeast mitochondria. Mutations in intervening sequences of the split gene COB reveal a requirement for intervening sequence-encoded products. J Biol Chem. 1981 Jul 25;256(14):7610–7619. [PubMed] [Google Scholar]
  43. Schmitt M. E., Brown T. A., Trumpower B. L. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 1990 May 25;18(10):3091–3092. doi: 10.1093/nar/18.10.3091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Skelly P. J., Hardy C. M., Clark-Walker G. D. A mobile group II intron of a naturally occurring rearranged mitochondrial genome in Kluyveromyces lactis. Curr Genet. 1991 Jul;20(1-2):115–120. doi: 10.1007/BF00312773. [DOI] [PubMed] [Google Scholar]
  45. Séraphin B., Simon M., Boulet A., Faye G. Mitochondrial splicing requires a protein from a novel helicase family. Nature. 1989 Jan 5;337(6202):84–87. doi: 10.1038/337084a0. [DOI] [PubMed] [Google Scholar]
  46. Wiesenberger G., Waldherr M., Schweyen R. J. The nuclear gene MRS2 is essential for the excision of group II introns from yeast mitochondrial transcripts in vivo. J Biol Chem. 1992 Apr 5;267(10):6963–6969. [PubMed] [Google Scholar]
  47. Xiong Y., Eickbush T. H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990 Oct;9(10):3353–3362. doi: 10.1002/j.1460-2075.1990.tb07536.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Xiong Y., Eickbush T. H. Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol. 1988 Nov;5(6):675–690. doi: 10.1093/oxfordjournals.molbev.a040521. [DOI] [PubMed] [Google Scholar]

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