Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1998 Jan 1;26(1):170–176. doi: 10.1093/nar/26.1.170

U-insertion/deletion Edited Sequence Database.

L Simpson 1, S H Wang 1, O H Thiemann 1, J D Alfonzo 1, D A Maslov 1, H A Avila 1
PMCID: PMC147258  PMID: 9399827

Abstract

Uridine insertion/deletion RNA editing is a post-transcriptional RNA modification occurring in the mitochondria of kinetoplastid protozoa. The U-insertion/deletion Edited Sequence Database is a compilation of mitochondrial genes and edited mRNAs from five kinetoplastid species. It contains separate files with the DNA, mRNA (both unedited and edited) and predicted protein sequences, as well as alignments of the Leishmania tarentolae and Trypanosoma brucei protein sequences from edited and unedited genes. The sequence files are in GCG format. A 'map' sequence file showing the location of U-deletions, U-insertions and the translated amino acid sequences is also provided for each gene. Genomic maps for each species are also provided with clickable genes, including maxicircle-encoded gRNAs. Sets of aligned nuclear rRNA sequences from kinetoplastid protozoa are also provided, which were used for phylogenetic reconstructions in an analysis of the origin of RNA editing. The database is available through the World Wide Web as an HTML document at the URLhttp://www.lifesci.ucla.edu/RNA/trypanosome/ database.html

Full Text

The Full Text of this article is available as a PDF (590.3 KB).

Selected References

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

  1. Alfonzo J. D., Thiemann O., Simpson L. The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria. Nucleic Acids Res. 1997 Oct 1;25(19):3751–3759. doi: 10.1093/nar/25.19.3751. [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. 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]
  4. Corell R. A., Myler P., Stuart K. Trypanosoma brucei mitochondrial CR4 gene encodes an extensively edited mRNA with completely edited sequence only in bloodstream forms. Mol Biochem Parasitol. 1994 Mar;64(1):65–74. doi: 10.1016/0166-6851(94)90135-x. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Kable M. L., Heidmann S., Stuart K. D. RNA editing: getting U into RNA. Trends Biochem Sci. 1997 May;22(5):162–166. doi: 10.1016/s0968-0004(97)01041-4. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Lukes J., Arts G. J., van den Burg J., de Haan A., Opperdoes F., Sloof P., Benne R. Novel pattern of editing regions in mitochondrial transcripts of the cryptobiid Trypanoplasma borreli. EMBO J. 1994 Nov 1;13(21):5086–5098. doi: 10.1002/j.1460-2075.1994.tb06838.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lukes J., Jirkû M., Dolezel D., Kral'ová I., Hollar L., Maslov D. A. Analysis of ribosomal RNA genes suggests that trypanosomes are monophyletic. J Mol Evol. 1997 May;44(5):521–527. doi: 10.1007/pl00006176. [DOI] [PubMed] [Google Scholar]
  10. Maslov D. A., Avila H. A., Lake J. A., Simpson L. Evolution of RNA editing in kinetoplastid protozoa. Nature. 1994 Mar 24;368(6469):345–348. doi: 10.1038/368345a0. [DOI] [PubMed] [Google Scholar]
  11. Maslov D. A., Lukes J., Jirku M., Simpson L. Phylogeny of trypanosomes as inferred from the small and large subunit rRNAs: implications for the evolution of parasitism in the trypanosomatid protozoa. Mol Biochem Parasitol. 1996 Jan;75(2):197–205. doi: 10.1016/0166-6851(95)02526-x. [DOI] [PubMed] [Google Scholar]
  12. Maslov D. A., Simpson L. RNA editing and mitochondrial genomic organization in the cryptobiid kinetoplastid protozoan Trypanoplasma borreli. Mol Cell Biol. 1994 Dec;14(12):8174–8182. doi: 10.1128/mcb.14.12.8174. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. 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]
  15. 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]
  16. Read L. K., Wilson K. D., Myler P. J., Stuart K. Editing of Trypanosoma brucei maxicircle CR5 mRNA generates variable carboxy terminal predicted protein sequences. Nucleic Acids Res. 1994 Apr 25;22(8):1489–1495. doi: 10.1093/nar/22.8.1489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Simpson L., Shaw J. RNA editing and the mitochondrial cryptogenes of kinetoplastid protozoa. Cell. 1989 May 5;57(3):355–366. doi: 10.1016/0092-8674(89)90911-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Simpson L. The genomic organization of guide RNA genes in kinetoplastid protozoa: several conundrums and their solutions. Mol Biochem Parasitol. 1997 Jun;86(2):133–141. doi: 10.1016/s0166-6851(97)00037-6. [DOI] [PubMed] [Google Scholar]
  20. Simpson L., Thiemann O. H. Sense from nonsense: RNA editing in mitochondria of kinetoplastid protozoa and slime molds. Cell. 1995 Jun 16;81(6):837–840. doi: 10.1016/0092-8674(95)90003-9. [DOI] [PubMed] [Google Scholar]
  21. Sloof P., Benne R. RNA editing in kinetoplastid parasites: what to do with U. Trends Microbiol. 1997 May;5(5):189–195. doi: 10.1016/S0966-842X(97)01034-2. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. 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]
  24. Sturm N. R., Simpson L. Partially edited mRNAs for cytochrome b and subunit III of cytochrome oxidase from Leishmania tarentolae mitochondria: RNA editing intermediates. Cell. 1990 Jun 1;61(5):871–878. doi: 10.1016/0092-8674(90)90197-m. [DOI] [PubMed] [Google Scholar]
  25. Yasuhira S., Simpson L. Guide RNAs and guide RNA genes in the cryptobiid kinetoplastid protozoan, Trypanoplasma borreli. RNA. 1996 Nov;2(11):1153–1160. [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES