Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1983;2(1):33–38. doi: 10.1002/j.1460-2075.1983.tb01376.x

Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members.

F Michel 1, B Dujon 1
PMCID: PMC555082  PMID: 11894905

Abstract

Two families of fungal mitochondrial introns that include all known sequences have been recognized. These families are now extended to incorporate a plant mitochondrial intron and several introns in chloroplast- and nuclear-encoded rRNA and tRNA precursors. Members of the same family share distinctive sequence stretches and a number of potential RNA secondary structures that would bring these stretches and the intron-exon junctions into relatively close proximity. Using several of these introns which have been extensively studied by either biochemical or genetic means, an attempt is made to integrate the available data into a common picture.

Full text

PDF

Selected References

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

  1. Allet B., Rochaix J. D. Structure analysis at the ends of the intervening DNA sequences in the chloroplast 23S ribosomal genes of C. reinhardii. Cell. 1979 Sep;18(1):55–60. doi: 10.1016/0092-8674(79)90353-2. [DOI] [PubMed] [Google Scholar]
  2. Bertrand H., Bridge P., Collins R. A., Garriga G., Lambowitz A. M. RNA splicing in Neurospora mitochondria. Characterization of new nuclear mutants with defects in splicing the mitochondrial large rRNA. Cell. 1982 Jun;29(2):517–526. doi: 10.1016/0092-8674(82)90168-4. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. Breathnach R., Benoist C., O'Hare K., Gannon F., Chambon P. Ovalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon-intron boundaries. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4853–4857. doi: 10.1073/pnas.75.10.4853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cech T. R., Zaug A. J., Grabowski P. J. In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell. 1981 Dec;27(3 Pt 2):487–496. doi: 10.1016/0092-8674(81)90390-1. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Dieckmann C. L., Pape L. K., Tzagoloff A. Identification and cloning of a yeast nuclear gene (CBP1) involved in expression of mitochondrial cytochrome b. Proc Natl Acad Sci U S A. 1982 Mar;79(6):1805–1809. doi: 10.1073/pnas.79.6.1805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dujardin G., Jacq C., Slonimski P. P. Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene. Nature. 1982 Aug 12;298(5875):628–632. doi: 10.1038/298628a0. [DOI] [PubMed] [Google Scholar]
  9. Dujon B. Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and rib-1 loci. Cell. 1980 May;20(1):185–197. doi: 10.1016/0092-8674(80)90246-9. [DOI] [PubMed] [Google Scholar]
  10. Faye G., Simon M. Caractérisation d'un gène nucléaire participant à la maturation du pré-messager mitochondrial de la sous-unité l de la cytochrome c oxydase chez la levure. C R Seances Acad Sci III. 1982 Feb 1;294(5):245–248. [PubMed] [Google Scholar]
  11. Fox T. D., Leaver C. J. The Zea mays mitochondrial gene coding cytochrome oxidase subunit II has an intervening sequence and does not contain TGA codons. Cell. 1981 Nov;26(3 Pt 1):315–323. doi: 10.1016/0092-8674(81)90200-2. [DOI] [PubMed] [Google Scholar]
  12. Groudinsky O., Dujardin G., Slonimski P. P. Long range control circuits within mitochondria and between nucleus and mitochondria. II. Genetic and biochemical analyses of suppressors which selectively alleviate the mitochondrial intron mutations. Mol Gen Genet. 1981;184(3):493–503. doi: 10.1007/BF00352529. [DOI] [PubMed] [Google Scholar]
  13. Guillemaut P., Weil J. H. The nucleotide sequence of the maize and spinach chloroplast isoleucine transfer RNA encoded in the 16S to 23S rDNA spacer. Nucleic Acids Res. 1982 Mar 11;10(5):1653–1659. doi: 10.1093/nar/10.5.1653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Jacq C., Lazowska J., Slonimski P. P. Sur un nouveau mécanisme de la régulation de l'expression génétique. C R Seances Acad Sci D. 1980 Jan 14;290(2):89–92. [PubMed] [Google Scholar]
  15. Kan N. C., Gall J. G. The intervening sequence of the ribosomal RNA gene is highly conserved between two Tetrahymena species. Nucleic Acids Res. 1982 May 11;10(9):2809–2822. doi: 10.1093/nar/10.9.2809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Koch W., Edwards K., Kössel H. Sequencing of the 16S-23S spacer in a ribosomal RNA operon of Zea mays chloroplast DNA reveals two split tRNA genes. Cell. 1981 Jul;25(1):203–213. doi: 10.1016/0092-8674(81)90245-2. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Lazowska J., Jacq C., Slonimski P. P. Splice points of the third intron in the yeast mitochondrial cytochrome b gene. Cell. 1981 Nov;27(1 Pt 2):12–14. doi: 10.1016/0092-8674(81)90355-x. [DOI] [PubMed] [Google Scholar]
  19. Michel F., Jacquier A., Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 1982 Oct;64(10):867–881. doi: 10.1016/s0300-9084(82)80349-0. [DOI] [PubMed] [Google Scholar]
  20. Netter P., Jacq C., Carignani G., Slonimski P. P. Critical sequences within mitochondrial introns: cis-dominant mutations of the "cytochrome-b-like" intron of the oxidase gene. Cell. 1982 Apr;28(4):733–738. doi: 10.1016/0092-8674(82)90052-6. [DOI] [PubMed] [Google Scholar]
  21. Netzker R., Köchel H. G., Basak N., Küntzel H. Nucleotide sequence of Aspergillus nidulans mitochondrial genes coding for ATPase subunit 6, cytochrome oxidase subunit 3, seven unidentified proteins, four tRNAs and L-rRNA. Nucleic Acids Res. 1982 Aug 11;10(15):4783–4794. doi: 10.1093/nar/10.15.4783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Nobrega F. G., Tzagoloff A. Assembly of the mitochondrial membrane system. DNA sequence and organization of the cytochrome b gene in Saccharomyces cerevisiae D273-10B. J Biol Chem. 1980 Oct 25;255(20):9828–9837. [PubMed] [Google Scholar]
  23. Noller H. F., Kop J., Wheaton V., Brosius J., Gutell R. R., Kopylov A. M., Dohme F., Herr W., Stahl D. A., Gupta R. Secondary structure model for 23S ribosomal RNA. Nucleic Acids Res. 1981 Nov 25;9(22):6167–6189. doi: 10.1093/nar/9.22.6167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Nomiyama H., Kuhara S., Kukita T., Otsuka T., Sakaki Y. Nucleotide sequence of the ribosomal RNA gene of Physarum polycephalum: intron 2 and its flanking regions of the 26S rRNA gene. Nucleic Acids Res. 1981 Nov 11;9(21):5507–5520. doi: 10.1093/nar/9.21.5507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Nomiyama H., Sakaki Y., Takagi Y. Nucleotide sequence of a ribosomal RNA gene intron from slime mold Physarum polycephalum. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1376–1380. doi: 10.1073/pnas.78.3.1376. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sprinzl M., Gauss D. H. Compilation of sequences of tRNA genes. Nucleic Acids Res. 1982 Jan 22;10(2):r57–r81. [PMC free article] [PubMed] [Google Scholar]
  27. Steinmetz A., Gubbins E. J., Bogorad L. The anticodon of the maize chloroplast gene for tRNA Leu UAA is split by a large intron. Nucleic Acids Res. 1982 May 25;10(10):3027–3037. doi: 10.1093/nar/10.10.3027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Waring R. B., Davies R. W., Lee S., Grisi E., Berks M. M., Scazzocchio C. The mosaic organization of the apocytochrome b gene of Aspergillus nidulans revealed by DNA sequencing. Cell. 1981 Nov;27(1 Pt 2):4–11. doi: 10.1016/0092-8674(81)90354-8. [DOI] [PubMed] [Google Scholar]
  29. Weiss-Brummer B., Rödel G., Schweyen R. J., Kaudewitz F. Expression of the split gene cob in yeast: evidence for a precursor of a "maturase" protein translated from intron 4 and preceding exons. Cell. 1982 Jun;29(2):527–536. doi: 10.1016/0092-8674(82)90169-6. [DOI] [PubMed] [Google Scholar]
  30. Wild M. A., Sommer R. Sequence of a ribosomal RNA gene intron from Tetrahymena. Nature. 1980 Feb 14;283(5748):693–694. doi: 10.1038/283693a0. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES