Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1994 Apr 25;22(8):1489–1495. doi: 10.1093/nar/22.8.1489

Editing of Trypanosoma brucei maxicircle CR5 mRNA generates variable carboxy terminal predicted protein sequences.

L K Read 1, K D Wilson 1, P J Myler 1, K Stuart 1
PMCID: PMC308010  PMID: 7514788

Abstract

RNA editing post-transcriptionally modifies several mRNAs from the maxicircle of kinetoplastid parasites by addition and removal of uridine residues. We report here that maxicircle CR5 transcripts of Trypanosoma brucei are edited in two domains separated by an eight nucleotide sequence that remains unedited. The large 5' domain is edited to a consensus sequence while the smaller 3' domain is edited to multiple final sequences. In all, 205-217 Us are inserted and 13-16 encoded uridines are deleted from the CR5 mRNA, producing a mature transcript 75-80% larger than the unedited transcript. The edited RNAs predict small, highly hydrophobic proteins. The carboxy terminal 15-30% of these predicted proteins have multiple different amino acid sequences as a result of the variable edited 3' mRNA sequence, but these fall into two families of sequence. Limited amino acid sequence and hydrophobicity profile similarities suggest that the protein encoded by edited CR5 mRNA may be a subunit of NADH dehydrogenase.

Full text

PDF

Images in this article

1493Image
on p.1493

Selected References

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

  1. Abraham J. M., Feagin J. E., Stuart K. Characterization of cytochrome c oxidase III transcripts that are edited only in the 3' region. Cell. 1988 Oct 21;55(2):267–272. doi: 10.1016/0092-8674(88)90049-9. [DOI] [PubMed] [Google Scholar]
  2. Barrois M., Riou G., Galibert F. Complete nucleotide sequence of minicircle kinetoplast DNA from Trypanosoma equiperdum. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3323–3327. doi: 10.1073/pnas.78.6.3323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bhat G. J., Koslowsky D. J., Feagin J. E., Smiley B. L., Stuart K. An extensively edited mitochondrial transcript in kinetoplastids encodes a protein homologous to ATPase subunit 6. Cell. 1990 Jun 1;61(5):885–894. doi: 10.1016/0092-8674(90)90199-o. [DOI] [PubMed] [Google Scholar]
  4. Bienen E. J., Saric M., Pollakis G., Grady R. W., Clarkson A. B., Jr Mitochondrial development in Trypanosoma brucei brucei transitional bloodstream forms. Mol Biochem Parasitol. 1991 Apr;45(2):185–192. doi: 10.1016/0166-6851(91)90085-k. [DOI] [PubMed] [Google Scholar]
  5. Blum B., Bakalara N., Simpson L. A model for RNA editing in kinetoplastid mitochondria: "guide" RNA molecules transcribed from maxicircle DNA provide the edited information. Cell. 1990 Jan 26;60(2):189–198. doi: 10.1016/0092-8674(90)90735-w. [DOI] [PubMed] [Google Scholar]
  6. Cabot E. L., Beckenbach A. T. Simultaneous editing of multiple nucleic acid and protein sequences with ESEE. Comput Appl Biosci. 1989 Jul;5(3):233–234. doi: 10.1093/bioinformatics/5.3.233. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Corell R. A., Feagin J. E., Riley G. R., Strickland T., Guderian J. A., Myler P. J., Stuart K. Trypanosoma brucei minicircles encode multiple guide RNAs which can direct editing of extensively overlapping sequences. Nucleic Acids Res. 1993 Sep 11;21(18):4313–4320. doi: 10.1093/nar/21.18.4313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. Fearnley I. M., Walker J. E. Conservation of sequences of subunits of mitochondrial complex I and their relationships with other proteins. Biochim Biophys Acta. 1992 Dec 7;1140(2):105–134. doi: 10.1016/0005-2728(92)90001-i. [DOI] [PubMed] [Google Scholar]
  12. Gadaleta G., Pepe G., De Candia G., Quagliariello C., Sbisà E., Saccone C. The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. J Mol Evol. 1989 Jun;28(6):497–516. doi: 10.1007/BF02602930. [DOI] [PubMed] [Google Scholar]
  13. Gribskov M., McLachlan A. D., Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355–4358. doi: 10.1073/pnas.84.13.4355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hajduk S. L., Harris M. E., Pollard V. W. RNA editing in kinetoplastid mitochondria. FASEB J. 1993 Jan;7(1):54–63. doi: 10.1096/fasebj.7.1.8422975. [DOI] [PubMed] [Google Scholar]
  15. Harris M. E., Moore D. R., Hajduk S. L. Addition of uridines to edited RNAs in trypanosome mitochondria occurs independently of transcription. J Biol Chem. 1990 Jul 5;265(19):11368–11376. [PubMed] [Google Scholar]
  16. Higgins D. G., Bleasby A. J., Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189–191. doi: 10.1093/bioinformatics/8.2.189. [DOI] [PubMed] [Google Scholar]
  17. Jasmer D. P., Stuart K. Sequence organization in African trypanosome minicircles is defined by 18 base pair inverted repeats. Mol Biochem Parasitol. 1986 Mar;18(3):321–331. doi: 10.1016/0166-6851(86)90089-7. [DOI] [PubMed] [Google Scholar]
  18. Koslowsky D. J., Bhat G. J., Perrollaz A. L., Feagin J. E., Stuart K. The MURF3 gene of T. brucei contains multiple domains of extensive editing and is homologous to a subunit of NADH dehydrogenase. Cell. 1990 Sep 7;62(5):901–911. doi: 10.1016/0092-8674(90)90265-g. [DOI] [PubMed] [Google Scholar]
  19. Koslowsky D. J., Riley G. R., Feagin J. E., Stuart K. Guide RNAs for transcripts with developmentally regulated RNA editing are present in both life cycle stages of Trypanosoma brucei. Mol Cell Biol. 1992 May;12(5):2043–2049. doi: 10.1128/mcb.12.5.2043. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. doi: 10.1016/0022-2836(82)90515-0. [DOI] [PubMed] [Google Scholar]
  21. Maslov D. A., Simpson L. The polarity of editing within a multiple gRNA-mediated domain is due to formation of anchors for upstream gRNAs by downstream editing. Cell. 1992 Aug 7;70(3):459–467. doi: 10.1016/0092-8674(92)90170-h. [DOI] [PubMed] [Google Scholar]
  22. Maslov D. A., Sturm N. R., Niner B. M., Gruszynski E. S., Peris M., Simpson L. An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12. Mol Cell Biol. 1992 Jan;12(1):56–67. doi: 10.1128/mcb.12.1.56. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Pollard V. W., Rohrer S. P., Michelotti E. F., Hancock K., Hajduk S. L. Organization of minicircle genes for guide RNAs in Trypanosoma brucei. Cell. 1990 Nov 16;63(4):783–790. doi: 10.1016/0092-8674(90)90144-4. [DOI] [PubMed] [Google Scholar]
  25. Read L. K., Corell R. A., Stuart K. Chimeric and truncated RNAs in Trypanosoma brucei suggest transesterifications at non-consecutive sites during RNA editing. Nucleic Acids Res. 1992 May 11;20(9):2341–2347. doi: 10.1093/nar/20.9.2341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Read L. K., Fish W. R., Muthiani A. M., Stuart K. Maxicircle DNA and edited mRNA sequences of closely related trypanosome species: implications of kRNA editing for evolution of maxicircle genomes. Nucleic Acids Res. 1993 Aug 25;21(17):4073–4078. doi: 10.1093/nar/21.17.4073. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Read L. K., Myler P. J., Stuart K. Extensive editing of both processed and preprocessed maxicircle CR6 transcripts in Trypanosoma brucei. J Biol Chem. 1992 Jan 15;267(2):1123–1128. [PubMed] [Google Scholar]
  28. 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]
  29. Simpson L., Braly P. Synchronization of Leishmania tarentolae by hydroxyurea. J Protozool. 1970 Nov;17(4):511–517. doi: 10.1111/j.1550-7408.1970.tb04719.x. [DOI] [PubMed] [Google Scholar]
  30. Souza A. E., Myler P. J., Stuart K. Maxicircle CR1 transcripts of Trypanosoma brucei are edited and developmentally regulated and encode a putative iron-sulfur protein homologous to an NADH dehydrogenase subunit. Mol Cell Biol. 1992 May;12(5):2100–2107. doi: 10.1128/mcb.12.5.2100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Souza A. E., Shu H. H., Read L. K., Myler P. J., Stuart K. D. Extensive editing of CR2 maxicircle transcripts of Trypanosoma brucei predicts a protein with homology to a subunit of NADH dehydrogenase. Mol Cell Biol. 1993 Nov;13(11):6832–6840. doi: 10.1128/mcb.13.11.6832. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Stormo G. D., Schneider T. D., Gold L. M. Characterization of translational initiation sites in E. coli. Nucleic Acids Res. 1982 May 11;10(9):2971–2996. doi: 10.1093/nar/10.9.2971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Stuart K. D., Gelvin S. B. Localization of kinetoplast DNA maxicircle transcripts in bloodstream and procyclic form Trypanosoma brucei. Mol Cell Biol. 1982 Jul;2(7):845–852. doi: 10.1128/mcb.2.7.845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Stuart K., Feagin J. E. Mitochondrial DNA of kinetoplastids. Int Rev Cytol. 1992;141:65–88. doi: 10.1016/s0074-7696(08)62063-x. [DOI] [PubMed] [Google Scholar]
  35. Stuart K., Gobright E., Jenni L., Milhausen M., Thomashow L., Agabian N. The IsTaR 1 serodeme of Trypanosoma brucei: development of a new serodeme. J Parasitol. 1984 Oct;70(5):747–754. [PubMed] [Google Scholar]
  36. Stuart K. RNA editing in mitochondrial mRNA of trypanosomatids. Trends Biochem Sci. 1991 Feb;16(2):68–72. doi: 10.1016/0968-0004(91)90027-s. [DOI] [PubMed] [Google Scholar]
  37. Stuart K. RNA editing in trypanosomatid mitochondria. Annu Rev Microbiol. 1991;45:327–344. doi: 10.1146/annurev.mi.45.100191.001551. [DOI] [PubMed] [Google Scholar]
  38. Young I. G., Rogers B. L., Campbell H. D., Jaworowski A., Shaw D. C. Nucleotide sequence coding for the respiratory NADH dehydrogenase of Escherichia coli. UUG initiation codon. Eur J Biochem. 1981 May;116(1):165–170. doi: 10.1111/j.1432-1033.1981.tb05314.x. [DOI] [PubMed] [Google Scholar]

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

RESOURCES