Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1988 Aug;7(8):2509–2514. doi: 10.1002/j.1460-2075.1988.tb03098.x

Transcripts from the frameshifted MURF3 gene from Crithidia fasciculata are edited by U insertion at multiple sites.

H van der Spek 1, J van den Burg 1, A Croiset 1, M van den Broek 1, P Sloof 1, R Benne 1
PMCID: PMC457121  PMID: 2461295

Abstract

In trypanosome mitochondria an RNA editing process is operative, which co- or post-transcriptionally alters the nucleotide sequence of transcripts by insertion and/or deletion of U residues at specific sites. To increase our understanding of the mechanism of this process we have compared the nucleotide sequence of the frameshifted mitochondrial MURF3 gene from Crithidia fasciculata to that of a large number of MURF3 cDNAs. We found cDNAs derived from transcripts edited at two different sites in the protein coding sequence: (i) at the frameshift position five extra U residues connect the two reading frames and (ii) at the 5' terminus 22 inserted Us shift a putative initiator codon out of phase. The collection also contained cDNAs that were derived from non-edited transcripts. Partially edited sequences were not found, except in one cDNA, which contained an edited frameshift site in combination with a non-edited 5' terminus. The analysis further showed that MURF3 transcripts have a 3'-terminal poly(AU) extension, which varies in sequence. The implications of these results are discussed.

Full text

PDF
2509

Images in this article

Selected References

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

  1. Benne R., De Vries B. F., Van den Burg J., Klaver B. The nucleotide sequence of a segment of Trypanosoma brucei mitochondrial maxi-circle DNA that contains the gene for apocytochrome b and some unusual unassigned reading frames. Nucleic Acids Res. 1983 Oct 25;11(20):6925–6941. doi: 10.1093/nar/11.20.6925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Benne R., Van den Burg J., Brakenhoff J. P., Sloof P., Van Boom J. H., Tromp M. C. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell. 1986 Sep 12;46(6):819–826. doi: 10.1016/0092-8674(86)90063-2. [DOI] [PubMed] [Google Scholar]
  3. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Borst P., Fase-Fowler F. The maxi-circle of Trypanosoma brucei kinetoplast DNA. Biochim Biophys Acta. 1979 Nov 22;565(1):1–12. doi: 10.1016/0005-2787(79)90078-9. [DOI] [PubMed] [Google Scholar]
  5. Borst P., Hoeijmakers J. H. Kinetoplast DNA. Plasmid. 1979 Jan;2(1):20–40. doi: 10.1016/0147-619x(79)90003-9. [DOI] [PubMed] [Google Scholar]
  6. Feagin J. E., Abraham J. M., Stuart K. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei. Cell. 1988 May 6;53(3):413–422. doi: 10.1016/0092-8674(88)90161-4. [DOI] [PubMed] [Google Scholar]
  7. Feagin J. E., Jasmer D. P., Stuart K. Developmentally regulated addition of nucleotides within apocytochrome b transcripts in Trypanosoma brucei. Cell. 1987 May 8;49(3):337–345. doi: 10.1016/0092-8674(87)90286-8. [DOI] [PubMed] [Google Scholar]
  8. Feagin J. E., Shaw J. M., Simpson L., Stuart K. Creation of AUG initiation codons by addition of uridines within cytochrome b transcripts of kinetoplastids. Proc Natl Acad Sci U S A. 1988 Jan;85(2):539–543. doi: 10.1073/pnas.85.2.539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Feagin J. E., Stuart K. Developmental aspects of uridine addition within mitochondrial transcripts of Trypanosoma brucei. Mol Cell Biol. 1988 Mar;8(3):1259–1265. doi: 10.1128/mcb.8.3.1259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gubler U., Hoffman B. J. A simple and very efficient method for generating cDNA libraries. Gene. 1983 Nov;25(2-3):263–269. doi: 10.1016/0378-1119(83)90230-5. [DOI] [PubMed] [Google Scholar]
  11. Hensgens L. A., Brakenhoff J., De Vries B. F., Sloof P., Tromp M. C., Van Boom J. H., Benne R. The sequence of the gene for cytochrome c oxidase subunit I, a frameshift containing gene for cytochrome c oxidase subunit II and seven unassigned reading frames in Trypanosoma brucei mitochondrial maxi-circle DNA. Nucleic Acids Res. 1984 Oct 11;12(19):7327–7344. doi: 10.1093/nar/12.19.7327. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hoeijmakers J. H., Snijders A., Janssen J. W., Borst P. Transcription of kinetoplast DNA in Trypanosoma brucei bloodstream and culture forms. Plasmid. 1981 May;5(3):329–350. doi: 10.1016/0147-619x(81)90009-3. [DOI] [PubMed] [Google Scholar]
  13. Kleisen C. M., Borst P., Weijers P. J. The structure of kinetoplast DNA. I. Properties of the intact multi-circular complex from Crithidia luciliae. Biochim Biophys Acta. 1975 May 1;390(2):155–167. [PubMed] [Google Scholar]
  14. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Shaw J. M., Feagin J. E., Stuart K., Simpson L. Editing of kinetoplastid mitochondrial mRNAs by uridine addition and deletion generates conserved amino acid sequences and AUG initiation codons. Cell. 1988 May 6;53(3):401–411. doi: 10.1016/0092-8674(88)90160-2. [DOI] [PubMed] [Google Scholar]
  16. Simpson L. Kinetoplast DNA in trypanosomid flagellates. Int Rev Cytol. 1986;99:119–179. doi: 10.1016/s0074-7696(08)61426-6. [DOI] [PubMed] [Google Scholar]
  17. Simpson L., Neckelmann N., de la Cruz V. F., Simpson A. M., Feagin J. E., Jasmer D. P., Stuart K. Comparison of the maxicircle (mitochondrial) genomes of Leishmania tarentolae and Trypanosoma brucei at the level of nucleotide sequence. J Biol Chem. 1987 May 5;262(13):6182–6196. [PubMed] [Google Scholar]
  18. Sloof P., Van den Burg J., Voogd A., Benne R., Agostinelli M., Borst P., Gutell R., Noller H. Further characterization of the extremely small mitochondrial ribosomal RNAs from trypanosomes: a detailed comparison of the 9S and 12S RNAs from Crithidia fasciculata and Trypanosoma brucei with rRNAs from other organisms. Nucleic Acids Res. 1985 Jun 11;13(11):4171–4190. doi: 10.1093/nar/13.11.4171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sloof P., van den Burg J., Voogd A., Benne R. The nucleotide sequence of a 3.2 kb segment of mitochondrial maxicircle DNA from Crithidia fasciculata containing the gene for cytochrome oxidase subunit III, the N-terminal part of the apocytochrome b gene and a possible frameshift gene; further evidence for the use of unusual initiator triplets in trypanosome mitochondria. Nucleic Acids Res. 1987 Jan 12;15(1):51–65. doi: 10.1093/nar/15.1.51. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Stuart K. Kinetoplast DNA, mitochondrial DNA with a difference. Mol Biochem Parasitol. 1983 Oct;9(2):93–104. doi: 10.1016/0166-6851(83)90103-2. [DOI] [PubMed] [Google Scholar]
  21. Tabak H. F., Van der Horst G., Osinga K. A., Arnberg A. C. Splicing of large ribosomal precursor RNA and processing of intron RNA in yeast mitochondria. Cell. 1984 Dec;39(3 Pt 2):623–629. doi: 10.1016/0092-8674(84)90469-0. [DOI] [PubMed] [Google Scholar]
  22. Winter G., Fersht A. R., Wilkinson A. J., Zoller M., Smith M. Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding. Nature. 1982 Oct 21;299(5885):756–758. doi: 10.1038/299756a0. [DOI] [PubMed] [Google Scholar]
  23. Zhang H., Scholl R., Browse J., Somerville C. Double stranded DNA sequencing as a choice for DNA sequencing. Nucleic Acids Res. 1988 Feb 11;16(3):1220–1220. doi: 10.1093/nar/16.3.1220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. de Vries B. F., Mulder E., Brakenhoff J. P., Sloof P., Benne R. The variable region of the Trypanosoma brucei kinetoplast maxicircle: sequence and transcript analysis of a repetitive and a non-repetitive fragment. Mol Biochem Parasitol. 1988 Jan 1;27(1):71–82. doi: 10.1016/0166-6851(88)90026-6. [DOI] [PubMed] [Google Scholar]

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

RESOURCES