Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1999 Feb 15;18(4):1003–1013. doi: 10.1093/emboj/18.4.1003

In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron.

A Vader 1, H Nielsen 1, S Johansen 1
PMCID: PMC1171192  PMID: 10022842

Abstract

The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual twin-ribozyme organization. One of the ribozymes (DiGIR2) catalyses intron excision and exon ligation. The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open reading frame (ORF) is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1 and IPS2) located at its 3' end. Examination of the in vivo expression of DiSSU1 shows that after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed cleavage upstream of the ORF 5' end, as well as truncation and polyadenylation downstream of the ORF 3' end. A spliceosomal intron, the first to be reported within a group I intron and the rDNA, is removed before the I-DirI mRNA associates with the polysomes. Taken together, our results imply that DiSSU1 uses a unique combination of intron-supplied ribozyme activity and adaptation to the general RNA polymerase II pathway of mRNA expression to allow a protein to be produced from the RNA polymerase I-transcribed rDNA.

Full Text

The Full Text of this article is available as a PDF (468.7 KB).

Selected References

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

  1. Bachellerie J. P., Michot B., Nicoloso M., Balakin A., Ni J., Fournier M. J. Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem Sci. 1995 Jul;20(7):261–264. doi: 10.1016/s0968-0004(00)89039-8. [DOI] [PubMed] [Google Scholar]
  2. Balakin A. G., Smith L., Fournier M. J. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell. 1996 Sep 6;86(5):823–834. doi: 10.1016/s0092-8674(00)80156-7. [DOI] [PubMed] [Google Scholar]
  3. Beagley C. T., Okada N. A., Wolstenholme D. R. Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase. Proc Natl Acad Sci U S A. 1996 May 28;93(11):5619–5623. doi: 10.1073/pnas.93.11.5619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brehm S. L., Cech T. R. Fate of an intervening sequence ribonucleic acid: excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo. Biochemistry. 1983 May 10;22(10):2390–2397. doi: 10.1021/bi00279a014. [DOI] [PubMed] [Google Scholar]
  5. Buchman A. R., Berg P. Comparison of intron-dependent and intron-independent gene expression. Mol Cell Biol. 1988 Oct;8(10):4395–4405. doi: 10.1128/mcb.8.10.4395. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Burke J. M., RajBhandary U. L. Intron within the large rRNA gene of N. crassa mitochondria: a long open reading frame and a consensus sequence possibly important in splicing. Cell. 1982 Dec;31(3 Pt 2):509–520. doi: 10.1016/0092-8674(82)90307-5. [DOI] [PubMed] [Google Scholar]
  7. Collis P., Antoniou M., Grosveld F. Definition of the minimal requirements within the human beta-globin gene and the dominant control region for high level expression. EMBO J. 1990 Jan;9(1):233–240. doi: 10.1002/j.1460-2075.1990.tb08100.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cummings D. J., Domenico J. M., Nelson J., Sogin M. L. DNA sequence, structure, and phylogenetic relationship of the small subunit rRNA coding region of mitochondrial DNA from Podospora anserina. J Mol Evol. 1989 Mar;28(3):232–241. doi: 10.1007/BF02102481. [DOI] [PubMed] [Google Scholar]
  9. Decatur W. A., Einvik C., Johansen S., Vogt V. M. Two group I ribozymes with different functions in a nuclear rDNA intron. EMBO J. 1995 Sep 15;14(18):4558–4568. doi: 10.1002/j.1460-2075.1995.tb00135.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Din N., Engberg J., Kaffenberger W., Eckert W. A. The intervening sequence in the 26S rRNA coding region of T. thermophila is transcribed within the largest stable precursor for rRNA. Cell. 1979 Oct;18(2):525–532. doi: 10.1016/0092-8674(79)90069-2. [DOI] [PubMed] [Google Scholar]
  11. Einvik C., Nielsen H., Westhof E., Michel F., Johansen S. Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites. RNA. 1998 May;4(5):530–541. doi: 10.1017/s1355838298971758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Elde M., Haugen P., Willassen N. P., Johansen S. I-NjaI, a nuclear intron-encoded homing endonuclease from Naegleria, generates a pentanucleotide 3' cleavage-overhang within a 19 base-pair partially symmetric DNA recognition site. Eur J Biochem. 1999 Jan;259(1-2):281–288. doi: 10.1046/j.1432-1327.1999.00035.x. [DOI] [PubMed] [Google Scholar]
  13. Fleischer S., Grummt I. Expression of an mRNA coding gene under the control of an RNA polymerase I promoter. EMBO J. 1983;2(12):2319–2322. doi: 10.1002/j.1460-2075.1983.tb01740.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gott J. M., Zeeh A., Bell-Pedersen D., Ehrenman K., Belfort M., Shub D. A. Genes within genes: independent expression of phage T4 intron open reading frames and the genes in which they reside. Genes Dev. 1988 Dec;2(12B):1791–1799. doi: 10.1101/gad.2.12b.1791. [DOI] [PubMed] [Google Scholar]
  15. Grummt I., Skinner J. A. Efficient transcription of a protein-coding gene from the RNA polymerase I promoter in transfected cells. Proc Natl Acad Sci U S A. 1985 Feb;82(3):722–726. doi: 10.1073/pnas.82.3.722. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gunnery S., Mathews M. B. Functional mRNA can be generated by RNA polymerase III. Mol Cell Biol. 1995 Jul;15(7):3597–3607. doi: 10.1128/mcb.15.7.3597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hirose Y., Manley J. L. RNA polymerase II is an essential mRNA polyadenylation factor. Nature. 1998 Sep 3;395(6697):93–96. doi: 10.1038/25786. [DOI] [PubMed] [Google Scholar]
  18. Iizuka N., Najita L., Franzusoff A., Sarnow P. Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae. Mol Cell Biol. 1994 Nov;14(11):7322–7330. doi: 10.1128/mcb.14.11.7322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Johansen S., Elde M., Vader A., Haugen P., Haugli K., Haugli F. In vivo mobility of a group I twintron in nuclear ribosomal DNA of the myxomycete Didymium iridis. Mol Microbiol. 1997 May;24(4):737–745. doi: 10.1046/j.1365-2958.1997.3921743.x. [DOI] [PubMed] [Google Scholar]
  20. Johansen S., Vogt V. M. An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group I ribozyme and a novel ribozyme that cooperate in self-splicing. Cell. 1994 Feb 25;76(4):725–734. doi: 10.1016/0092-8674(94)90511-8. [DOI] [PubMed] [Google Scholar]
  21. Johansen T., Johansen S., Haugli F. B. Nucleotide sequence of the Physarum polycephalum small subunit ribosomal RNA as inferred from the gene sequence: secondary structure and evolutionary implications. Curr Genet. 1988 Sep;14(3):265–273. doi: 10.1007/BF00376747. [DOI] [PubMed] [Google Scholar]
  22. Kreivi J. P., Lamond A. I. RNA splicing: unexpected spliceosome diversity. Curr Biol. 1996 Jul 1;6(7):802–805. doi: 10.1016/s0960-9822(02)00599-7. [DOI] [PubMed] [Google Scholar]
  23. Lee M. G., Van der Ploeg L. H. Transcription of protein-coding genes in trypanosomes by RNA polymerase I. Annu Rev Microbiol. 1997;51:463–489. doi: 10.1146/annurev.micro.51.1.463. [DOI] [PubMed] [Google Scholar]
  24. Lewis J. D., Gunderson S. I., Mattaj I. W. The influence of 5' and 3' end structures on pre-mRNA metabolism. J Cell Sci Suppl. 1995;19:13–19. doi: 10.1242/jcs.1995.supplement_19.2. [DOI] [PubMed] [Google Scholar]
  25. Lin J., Vogt V. M. I-PpoI, the endonuclease encoded by the group I intron PpLSU3, is expressed from an RNA polymerase I transcript. Mol Cell Biol. 1998 Oct;18(10):5809–5817. doi: 10.1128/mcb.18.10.5809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Lo H. J., Huang H. K., Donahue T. F. RNA polymerase I-promoted HIS4 expression yields uncapped, polyadenylated mRNA that is unstable and inefficiently translated in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Feb;18(2):665–675. doi: 10.1128/mcb.18.2.665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lodes M. J., Merlin G., deVos T., Ghosh A., Madhubala R., Myler P. J., Stuart K. Increased expression of LD1 genes transcribed by RNA polymerase I in Leishmania donovani as a result of duplication into the rRNA gene locus. Mol Cell Biol. 1995 Dec;15(12):6845–6853. doi: 10.1128/mcb.15.12.6845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lopata M. A., Cleveland D. W., Sollner-Webb B. RNA polymerase specificity of mRNA production and enhancer action. Proc Natl Acad Sci U S A. 1986 Sep;83(18):6677–6681. doi: 10.1073/pnas.83.18.6677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. McCracken S., Fong N., Yankulov K., Ballantyne S., Pan G., Greenblatt J., Patterson S. D., Wickens M., Bentley D. L. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature. 1997 Jan 23;385(6614):357–361. doi: 10.1038/385357a0. [DOI] [PubMed] [Google Scholar]
  30. Muscarella D. E., Vogt V. M. A mobile group I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of saccharomyces cerevisiae. Mol Cell Biol. 1993 Feb;13(2):1023–1033. doi: 10.1128/mcb.13.2.1023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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]
  32. Nishida H., Tajiri Y., Sugiyama J. Multiple origins of fungal group I introns located in the same position of nuclear SSU rRNA gene. J Mol Evol. 1998 Apr;46(4):442–448. doi: 10.1007/pl00006324. [DOI] [PubMed] [Google Scholar]
  33. Palmer T. D., Miller A. D., Reeder R. H., McStay B. Efficient expression of a protein coding gene under the control of an RNA polymerase I promoter. Nucleic Acids Res. 1993 Jul 25;21(15):3451–3457. doi: 10.1093/nar/21.15.3451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Preiss T., Hentze M. W. Dual function of the messenger RNA cap structure in poly(A)-tail-promoted translation in yeast. Nature. 1998 Apr 2;392(6675):516–520. doi: 10.1038/33192. [DOI] [PubMed] [Google Scholar]
  35. Rocheleau G. A., Woodson S. A. Enhanced self-splicing of Physarum polycephalum intron 3 by a second group I intron. RNA. 1995 Apr;1(2):183–193. [PMC free article] [PubMed] [Google Scholar]
  36. Rudenko G., Chung H. M., Pham V. P., Van der Ploeg L. H. RNA polymerase I can mediate expression of CAT and neo protein-coding genes in Trypanosoma brucei. EMBO J. 1991 Nov;10(11):3387–3397. doi: 10.1002/j.1460-2075.1991.tb04903.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ruoff B., Johansen S., Vogt V. M. Characterization of the self-splicing products of a mobile intron from the nuclear rDNA of Physarum polycephalum. Nucleic Acids Res. 1992 Nov 25;20(22):5899–5906. doi: 10.1093/nar/20.22.5899. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Sachs A. B., Sarnow P., Hentze M. W. Starting at the beginning, middle, and end: translation initiation in eukaryotes. Cell. 1997 Jun 13;89(6):831–838. doi: 10.1016/s0092-8674(00)80268-8. [DOI] [PubMed] [Google Scholar]
  39. Sellem C. H., Belcour L. The in vivo use of alternate 3'-splice sites in group I introns. Nucleic Acids Res. 1994 Apr 11;22(7):1135–1137. doi: 10.1093/nar/22.7.1135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Tarun S. Z., Jr, Sachs A. B. A common function for mRNA 5' and 3' ends in translation initiation in yeast. Genes Dev. 1995 Dec 1;9(23):2997–3007. doi: 10.1101/gad.9.23.2997. [DOI] [PubMed] [Google Scholar]
  41. Yamamoto H., Naruse A., Ohsaki T., Sekiguchi J. Nucleotide sequence and characterization of the large mitochondrial rRNA gene of Penicillium urticae, and its comparison with those of other filamentous fungi. J Biochem. 1995 Apr;117(4):888–896. doi: 10.1093/oxfordjournals.jbchem.a124792. [DOI] [PubMed] [Google Scholar]
  42. Zaug A. J., Cech T. R. In vitro splicing of the ribosomal RNA precursor in nuclei of Tetrahymena. Cell. 1980 Feb;19(2):331–338. doi: 10.1016/0092-8674(80)90507-3. [DOI] [PubMed] [Google Scholar]
  43. Zhu H., Macreadie I. G., Butow R. A. RNA processing and expression of an intron-encoded protein in yeast mitochondria: role of a conserved dodecamer sequence. Mol Cell Biol. 1987 Jul;7(7):2530–2537. doi: 10.1128/mcb.7.7.2530. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Zomerdijk J. C., Kieft R., Borst P. Efficient production of functional mRNA mediated by RNA polymerase I in Trypanosoma brucei. Nature. 1991 Oct 24;353(6346):772–775. doi: 10.1038/353772a0. [DOI] [PubMed] [Google Scholar]

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

RESOURCES