Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 May 25;20(10):2553–2557. doi: 10.1093/nar/20.10.2553

Analysis of nonuniformity in intron phase distribution.

A Fedorov 1, G Suboch 1, M Bujakov 1, L Fedorova 1
PMCID: PMC312392  PMID: 1598214

Abstract

The distribution of different intron groups with respect to phases has been analyzed. It has been established that group II introns and nuclear introns have a minimum frequency of phase 2 introns. Since the phase of introns is an extremely conservative measure the observed minimum reflects evolutionary processes. A sample of all known, group I introns was too small to provide a valid characteristic of their phase distribution. The findings observed for the unequal distribution of phases cannot be explained solely on the basis of the mobile properties of introns. One of the most likely explanations for this nonuniformity in the intron phase distribution is the process of exon shuffling. It is proposed that group II introns originated at the early stages of evolution and were involved in the process of exon shuffling.

Full text

PDF

Selected References

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

  1. Cech T. R. Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review. Gene. 1988 Dec 20;73(2):259–271. doi: 10.1016/0378-1119(88)90492-1. [DOI] [PubMed] [Google Scholar]
  2. Christopher D. A., Hallick R. B. Euglena gracilis chloroplast ribosomal protein operon: a new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III. Nucleic Acids Res. 1989 Oct 11;17(19):7591–7608. doi: 10.1093/nar/17.19.7591. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chu F. K., Maley G. F., Maley F., Belfort M. Intervening sequence in the thymidylate synthase gene of bacteriophage T4. Proc Natl Acad Sci U S A. 1984 May;81(10):3049–3053. doi: 10.1073/pnas.81.10.3049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Craik C. S., Sprang S., Fletterick R., Rutter W. J. Intron-exon splice junctions map at protein surfaces. Nature. 1982 Sep 9;299(5879):180–182. doi: 10.1038/299180a0. [DOI] [PubMed] [Google Scholar]
  5. Csank C., Taylor F. M., Martindale D. W. Nuclear pre-mRNA introns: analysis and comparison of intron sequences from Tetrahymena thermophila and other eukaryotes. Nucleic Acids Res. 1990 Sep 11;18(17):5133–5141. doi: 10.1093/nar/18.17.5133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Davies R. W., Waring R. B., Ray J. A., Brown T. A., Scazzocchio C. Making ends meet: a model for RNA splicing in fungal mitochondria. Nature. 1982 Dec 23;300(5894):719–724. doi: 10.1038/300719a0. [DOI] [PubMed] [Google Scholar]
  7. Dorit R. L., Schoenbach L., Gilbert W. How big is the universe of exons? Science. 1990 Dec 7;250(4986):1377–1382. doi: 10.1126/science.2255907. [DOI] [PubMed] [Google Scholar]
  8. Edman J. C., Kovacs J. A., Masur H., Santi D. V., Elwood H. J., Sogin M. L. Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi. Nature. 1988 Aug 11;334(6182):519–522. doi: 10.1038/334519a0. [DOI] [PubMed] [Google Scholar]
  9. Gilbert W. Why genes in pieces? Nature. 1978 Feb 9;271(5645):501–501. doi: 10.1038/271501a0. [DOI] [PubMed] [Google Scholar]
  10. Go M. Correlation of DNA exonic regions with protein structural units in haemoglobin. Nature. 1981 May 7;291(5810):90–92. doi: 10.1038/291090a0. [DOI] [PubMed] [Google Scholar]
  11. Goodrich-Blair H., Scarlato V., Gott J. M., Xu M. Q., Shub D. A. A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1. Cell. 1990 Oct 19;63(2):417–424. doi: 10.1016/0092-8674(90)90174-d. [DOI] [PubMed] [Google Scholar]
  12. Gott J. M., Shub D. A., Belfort M. Multiple self-splicing introns in bacteriophage T4: evidence from autocatalytic GTP labeling of RNA in vitro. Cell. 1986 Oct 10;47(1):81–87. doi: 10.1016/0092-8674(86)90368-5. [DOI] [PubMed] [Google Scholar]
  13. Hickey D. A., Benkel B. F., Abukashawa S. M. A general model for the evolution of nuclear pre-mRNA introns. J Theor Biol. 1989 Mar 7;137(1):41–53. doi: 10.1016/s0022-5193(89)80148-1. [DOI] [PubMed] [Google Scholar]
  14. Kjems J., Jensen J., Olesen T., Garrett R. A. Comparison of transfer RNA and ribosomal RNA intron splicing in the extreme thermophile and archaebacterium Desulfurococcus mobilis. Can J Microbiol. 1989 Jan;35(1):210–214. doi: 10.1139/m89-033. [DOI] [PubMed] [Google Scholar]
  15. Kuhsel M. G., Strickland R., Palmer J. D. An ancient group I intron shared by eubacteria and chloroplasts. Science. 1990 Dec 14;250(4987):1570–1573. doi: 10.1126/science.2125748. [DOI] [PubMed] [Google Scholar]
  16. Lambowitz A. M. Infectious introns. Cell. 1989 Feb 10;56(3):323–326. doi: 10.1016/0092-8674(89)90232-8. [DOI] [PubMed] [Google Scholar]
  17. Lonberg N., Gilbert W. Intron/exon structure of the chicken pyruvate kinase gene. Cell. 1985 Jan;40(1):81–90. doi: 10.1016/0092-8674(85)90311-3. [DOI] [PubMed] [Google Scholar]
  18. Marchionni M., Gilbert W. The triosephosphate isomerase gene from maize: introns antedate the plant-animal divergence. Cell. 1986 Jul 4;46(1):133–141. doi: 10.1016/0092-8674(86)90867-6. [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. 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]
  21. Muscarella D. E., Vogt V. M. A mobile group I intron in the nuclear rDNA of Physarum polycephalum. Cell. 1989 Feb 10;56(3):443–454. doi: 10.1016/0092-8674(89)90247-x. [DOI] [PubMed] [Google Scholar]
  22. Ohshima Y., Gotoh Y. Signals for the selection of a splice site in pre-mRNA. Computer analysis of splice junction sequences and like sequences. J Mol Biol. 1987 May 20;195(2):247–259. doi: 10.1016/0022-2836(87)90647-4. [DOI] [PubMed] [Google Scholar]
  23. Quigley F., Martin W. F., Cerff R. Intron conservation across the prokaryote-eukaryote boundary: structure of the nuclear gene for chloroplast glyceraldehyde-3-phosphate dehydrogenase from maize. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2672–2676. doi: 10.1073/pnas.85.8.2672. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Rogers J. H. The role of introns in evolution. FEBS Lett. 1990 Aug 1;268(2):339–343. doi: 10.1016/0014-5793(90)81282-s. [DOI] [PubMed] [Google Scholar]
  25. Senapathy P. Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications. Proc Natl Acad Sci U S A. 1986 Apr;83(7):2133–2137. doi: 10.1073/pnas.83.7.2133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sharp P. A. Speculations on RNA splicing. Cell. 1981 Mar;23(3):643–646. doi: 10.1016/0092-8674(81)90425-6. [DOI] [PubMed] [Google Scholar]
  27. Shih M. C., Heinrich P., Goodman H. M. Intron existence predated the divergence of eukaryotes and prokaryotes. Science. 1988 Nov 25;242(4882):1164–1166. doi: 10.1126/science.3055302. [DOI] [PubMed] [Google Scholar]
  28. Shub D. A., Gott J. M., Xu M. Q., Lang B. F., Michel F., Tomaschewski J., Pedersen-Lane J., Belfort M. Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes. Proc Natl Acad Sci U S A. 1988 Feb;85(4):1151–1155. doi: 10.1073/pnas.85.4.1151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Stone E. M., Rothblum K. N., Schwartz R. J. Intron-dependent evolution of chicken glyceraldehyde phosphate dehydrogenase gene. Nature. 1985 Feb 7;313(6002):498–500. doi: 10.1038/313498a0. [DOI] [PubMed] [Google Scholar]
  30. Südhof T. C., Goldstein J. L., Brown M. S., Russell D. W. The LDL receptor gene: a mosaic of exons shared with different proteins. Science. 1985 May 17;228(4701):815–822. doi: 10.1126/science.2988123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Welch H. M., Darby J. K., Pilz A. J., Ko C. M., Carritt B. Transposition, amplification, and divergence in the origin of the DNF15 loci, a polymorphic repetitive sequence family on chromosomes 1 and 3. Genomics. 1989 Oct;5(3):423–430. doi: 10.1016/0888-7543(89)90005-0. [DOI] [PubMed] [Google Scholar]
  32. Wild M. A., Gall J. G. An intervening sequence in the gene coding for 25S ribosomal RNA of Tetrahymena pigmentosa. Cell. 1979 Mar;16(3):565–573. doi: 10.1016/0092-8674(79)90030-8. [DOI] [PubMed] [Google Scholar]
  33. Wong Z., Royle N. J., Jeffreys A. J. A novel human DNA polymorphism resulting from transfer of DNA from chromosome 6 to chromosome 16. Genomics. 1990 Jun;7(2):222–234. doi: 10.1016/0888-7543(90)90544-5. [DOI] [PubMed] [Google Scholar]
  34. Xu M. Q., Kathe S. D., Goodrich-Blair H., Nierzwicki-Bauer S. A., Shub D. A. Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science. 1990 Dec 14;250(4987):1566–1570. doi: 10.1126/science.2125747. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES