Evolution of the U-insertion/deletion RNA editing in mitochondria of kinetoplastid protozoa

Annals of the New York Academy of Sciences

Volumn 870, Issue , 1999, Pages 190-205

  Simpson, Larry ^a   Maslov, Dmitri A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFERENCE PAPER; EVOLUTION; GENE DELETION; GENE INSERTION; LEISHMANIA; MITOCHONDRION; NONHUMAN; RNA EDITING; TRYPANOSOMA BRUCEI;

PROTOZOA; TRYPANOSOMA; TRYPANOSOMA BRUCEI;

EID: 0032768953     PISSN: 00778923     EISSN: None     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.1999.tb08879.x     Document Type: Conference Paper

References (65)

1. SIMPSON, L. & R.B. EMESON. 1996. RNA editing. Annu. Rev. Neurosci. 19: 27-52.
2. BENNE, R., J. VAN DEN BURG, J. BRAKENHOFF, P. SLOOF, J. VAN BOOM & M. TROMP. 1986. Major transcript of the frameshifted coxΠ gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46: 819-826.
3. SIMPSON, L. & J. SHAW. 1989. RNA editing and the mitochondrial cryptogenes of kinetoplastid protozoa. Cell 57: 355-366.
4. ARTS, G.J. & R. BENNE. 1996. Mechanism and evolution of RNA editing in Kinetoplastida. Biochim. Biophys. Acta Gene Struct. Expression 1307: 39-54.
5. STUART, K., T.E. ALLEN, S. HEIDMANN & S.D. SEIWERT. 1997. RNA editing in kinetoplastid protozoa. Microbiol. Rev. 61: 105-120.
6. ADLER, B.K. & S.L. HAJDUK. 1994. Mechanisms and origins of RNA editing. Curr. Opin. Genet. Dev. 4: 316-322.
7. SIMPSON, L. 1987. The mitochondrial genome of kinetoplastid protozoa: Genomic organization, transcription, replication and evolution. Ann. Rev. Microbiol. 41: 363-382.
8. SIMPSON, L. 1986. Kinetoplast DNA in trypanosomid flagellates. Int. Rev. Cytol. 99: 119-179.
9. SIMPSON, L. 1972. The kinetoplast of the hemoflagellates. Int. Rev. Cytol. 32: 139-207.
10. STURM, N.R. & L. SIMPSON. 1990. Kinetoplast DNA minicircles encode guide RNAs for editing of cytochrome oxidase subunit III mRNA. Cell 61: 879-884.
11. ALFONZO, J.D., O. THIEMANN & L. SIMPSON. 1997. The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria. Nucleic Acids Res. 25: 3751-3759.
12. BLUM, B., N. BAKALARA & L. SIMPSON. 1990. A model for RNA editing in kinetoplastid mitochondria: "Guide" RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60: 189-198.
13. PILLER, K.J., L.N. RUSCHE, J. CRUZ-REYES & B. SOLLNER-WEBB. 1997. Resolution of the RNA editing gRNA-directed endonuclease from two other endonucleases of Trypanosoma brucei mitochondria. RNA 3: 279-290.
14. CRUZ-REYES, J., L. RUSCHE, K.J. PILLER & B. SOLLNER-WEBB. 1998. T. brucei RNA editing: Adenosine nucleotides inversely affect U-deletion and U-insertion reactions at mRNA cleavage. Mol. Cell 1: 401-409.
15. ALFONZO, J.D., O.H. THIEMANN & L. SIMPSON. 1998. Purification and characterization of MAR1: A mitochondrial-associated ribonuclease from Leishmania tarentolae. J. Biol. Chem. 273: 30003-30011.
16. BAKALARA, N., A.M. SIMPSON & L. SIMPSON. 1989. The Leishmania kinetoplast-mitochondrion contains terminal uridylyltransferase and RNA ligase activities. J. Biol. Chem. 264: 18679-18686.
17. KABLE, M.L., S.D. SEIWERT, S. HEIDMANN & K. STUART. 1996. RNA editing: A mechanism for gRNA-specified uridylate insertion into precursor mRNA [see comments]. Science 273: 1189-1195.
18. SEIWERT, S.D., S. HEIDMANN & K. STUART. 1996. Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing. Cell 84: 831-841.
19. BYRNE, E.M., G.J. CONNELL & L. SIMPSON. 1996. Guide RNA-directed uridine insertion RNA editing in vitro. EMBO J. 15: 6758-6765.
20. SABATINI, R. & S.L. HAJDUK. 1995. RNA ligase and its involvement in guide RNA/mRNA chimera formation. J. Biol. Chem. 270: 7233-7240.
21. PERIS, M., G.C. FRECH, A.M. SIMPSON, F. BRINGAUD, E. BYRNE, A. BAKKER & L. SIMPSON. 1994. Characterization of two classes of ribonucleoprotein complexes possibly involved in RNA editing from Leishmania tarentolae mitochondria. EMBO J. 13: 1664-1672.
22. ABRAHAM, J., J. FEAGIN & K. STUART. 1988. Characterization of cytochrome c oxidase III transcripts that are edited only in the 3′ region. Cell 55: 267-272.
23. MASLOV, D.A. & L. SIMPSON. 1992. The polarity of editing within a multiple gRNA-mediated domain is due to formation of anchors for upstream gRNAs by downstream editing. Cell 70: 459-467.
24. MISSEL, A., G. NORSKAU, H.H. SHU & H.U. GORINGER. 1995. A putative RNA helicase of the DEAD box family from Trypanosoma brucei. Mol. Biochem. Parasitol. 75: 123-126.
25. MISSEL, A., A.E. SOUZA, G. NORSKAU & H.U. GORINGER. 1997. Disruption of a gene encoding a novel mitochondrial DEAD-box protein in Trypanosoma brucei affects edited mRNAs. Mol. Cell Biol. 17: 4895-4903.
26. CORELL, R.A., L.K. READ, G.R. RILEY, J.K. NELLISSERY, T.E. ALLEN, M.L. KABLE, M.D. WACHAL, S.D. SEIWERT, P.J. MYLER & K.D. STUART. 1996. Complexes from Trypanosoma brucei that exhibit deletion editing and other editing-associated properties. Mol. Cell. Biol. 16: 1410-1418.
27. BLUM, B., N.R. STURM, A.M. SIMPSON & L. SIMPSON. 1991. Chimeric gRNA-mRNA molecules with oligo(U) tails covalently linked at sites of RNA editing suggest that U addition occurs by transesterification. Cell 65: 543-550.
28. CECH, T.R. 1991. RNA editing: World's smallest introns. Cell 64: 667-669.
29. SIMPSON, L., N. NECKELMANN, V. DE LA CRUZ, A. SIMPSON, J. FEAGIN, D. JASMER & K. STUART. 1987. Comparison of the maxicircle (mitochondrial) genomes of Leishmania tarentolae and Trypanosoma brucei at the level of nucleotide sequence. J. Biol. Chem. 262: 6182-6196.
30. FEAGIN, J.E., J. ABRAHAM & K. STUART. 1988. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei. Cell 53: 413-422.
31. SHAW, J., J.E. FEAGIN, K. STUART & L. SIMPSON. 1988. Editing of mitochondrial mRNAs by uridine addition and deletion generates conserved amino acid sequences and AUG initiation codons. Cell 53: 401-411.
32. FERNANDES, A.P., K. NELSON & S.M. BEVERLEY. 1993. Evolution of nuclear ribosomal RNAs in kinetoplastid protozoa: Perspectives on the age and origins of parasitism. Proc. Natl. Acad. Sci. USA 90: 11608-11612.
33. MASLOV, D.A., H.A. AVILA, J.A. LAKE & L. SIMPSON. 1994. Evolution of RNA editing in kinetoplastid protozoa. Nature 365: 345-348.
34. LANDWEBER, L.F. & W. GILBERT. 1994. Phylogenetic analysis of RNA editing: A primitive genetic phenomenon. Proc. Natl. Acad. Sci. USA 91: 918-921.
35. MASLOV, D.A., J. LUKEŠ, M. JIRKU & L. SIMPSON. 1996. 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. 75: 197-205.
36. LUKEŠ, J., M. JIRKU, D. DOLEZEL, I. KRAL'OVA, L. HOLLAR & D.A. MASLOV. 1997. Analysis of ribosomal RNA genes suggests that trypanosomes are monophyletic. J. Mol. Evol. 44: 521-527.
37. ALVAREZ, F., M.N. CORTINAS & H. MUSTO. 1996. The analysis of protein coding genes suggests monophyly of Trypanosoma. Mol. Phylogenet. Evol. 5: 333-343.
38. HAAG, J., C. O'HUIGIN & P. OVERATH. 1998. The molecular phylogeny of trypanosomes: Evidence for an early divergence of the Salivaria. Mol. Biochem. Parasitol. 91: 37-49.
39. BERCHTOLD, M., H. PHILIPPE, A. BREUNIG, G. BRUGEROLLE & H. KOENIG. 1995. The phylogenetic position of Dimastigella trypaniformis within the parasitic kinetoplastids. Parasitol. Res. 80: 672-679.
40. MARCHE, S., C. ROTH, H. PHILIPPE, M. DOLLET & T. BALTZ. 1995. Characterization and detection of plant trypanosomatids by sequence analysis of the small subunit ribosomal RNA gene. Mol. Biochem. Parasitol. 71: 15-26.
41. HOLLAR, L., J. LUKES & D.A. MASLOV. 1998. Monophyly of endosymbiont containing trypanosomatids: Phylogeny versus taxonomy. J. Eukaryot. Microbiol. 45: 293-297.
42. HOLLAR, L. & D.A. MASLOV. 1997. A phylogenetic view on the genus Phytomonas. Mol. Biochem. Parasitol. 89: 295-299.
43. BLOM, D., A. DE HAAN, M. VAN DEN BERG, P. SLOOF, M. JIRKU, J. LUKEŠ & R. BENNE. 1998. RNA editing in the free-living bodonid Bodo saltans. Nucleic Acids Res. 26: 1205-1213.
44. Maslov, D.A. & L. Simpson, 1995. Evolution of parasitism in kinetoplastid protozoa. Parasitol. Today 11: 30-32.
45. YASUHIRA, S. & L. SIMPSON. 1997. Phylogenetic affinity of mitochondria of Euglena gracilis and kinetoplastids using cytochrome oxidase I and hsp60. J. Mol. Evol. 44: 341-347.
46. TESSIER, L.H., H. VAN DER SPECK, J.M. GUALBERTO & J.M. GRIENENBERGER. 1997. The cox1 gene from Euglena gracilis: A protist mitochondrial gene without introns and genetic code modifications. Curr. Genet. 31: 208-213.
47. LANG, B.F., G. BURGER, C.J. O'KELLY, R. CEDERGREN, G.B. GOLDING, C. LEMIEUX, D. SANKOFF, M. TURMEL & M.W. GRAY. 1997. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387: 493-497.
48. YASUHIRA, S. & L. SIMPSON. 1996. Guide RNAs and guide RNA genes in the cryptobiid kinetoplastid protzoan, Trypanoplasma borreli. RNA 2: 1153-1160.
49. MASLOV, D.A. & L. SIMPSON. 1994. RNA editing and mitochondrial genomic organization in the cryptobiid kinetoplastid protozoan, Trypanoplasma borreli. Mol. Cell. Biol. 14: 8174-8182.
50. SIMPSON, L. & D.A. MASLOV. 1994. RNA editing and the evolution of parasites. Science 264: 1870-1871.
51. LANDWEBER, L.F. 1992. The evolution of RNA editing in kinetoplastid protozoa. BioSystems 28: 41-45.
52. GONZÁLEZ, C.I., M.C. THOMAS, F. MARTIN, J. ALCAMI, C. ALONSO & M.C. LÓPEZ. 1997. Reverse transcriptase-like activity in Trypanosoma cruzi. Acta Tropica 63: 117-126.
53. GABRIEL, A. & J.D. BOEKE. 1991. Reverse transcriptase encoded by a retrotransposon from the trypanosomatid Crithidia fasciculata. Proc. Natl. Acad. Sci. USA 88: 9794-9798.
54. THIEMANN, O.H., D.A. MASLOW & L. SIMPSON. 1994. Disruption of RNA editing in Leishmania tarentolae by the loss of minicircle-encoded guide RNA genes. EMBO J. 13: 5689-5700.
55. MASLOV, D.A., O. THIEMANN & L. SIMPSON. 1994. Editing and misediting of transcripts of the kinetoplast maxicircle G5 (ND3) cryptogene in an old laboratory strain of Leishmania tarentolae. Mol. Biochem. Parasitol. 68: 155-159.
56. CAVALIER-SMITH, T. 1997. Cell and genome coevolution: Facultative anaerobiosis, glycosomes and kinetoplastan RNA editing. Trends Genet. 13: 6-9.
57. COVELLO, P.S. & M.W. GRAY. 1993. On the evolution of RNA editing. Trends Genet. 9: 265-268.
58. VON HAESELER, A., B. BLUM, L. SIMPSON, N. STURM & M.S. WATERMAN. 1992. Computer methods for locating kinetoplastid cryptogenes. Nucleic Acids Res. 20: 2717-2724.
59. FEAGIN, J., D. JASMER & K. STUART. 1987. Developmentally regulated addition of nucleotides within apocytochrome b transcripts in Trypanosoma brucei. Cell 49: 337-345.
60. FEAGIN, J. & K. STUART. 1988. Developmental aspects of uridine addition within mitochondrial transcripts of Trypanosoma brucei. Mol. Cell Biol. 8: 1259-1265.
61. KOSLOWSKY, D.J., G.J. BHAT, A.L. PERROLLAZ, J.E. FEAGIN, & K. STUART. 1990. The MURF3 gene of T. brucei contains multiple domains of extensive editing and is homologous to a subunit of NADH dehydrogenase. Cell 62: 901-911.
62. SOUZA, A.E., P.J. MYLER & K. STUART. 1992. Maxicircle CR1 transcripts of Trypanosoma brucei are edited, developmentally regulated, and encode a putative iron-sulfur protein homologous to an NADH dehydrogenase subunit. Mol. Cell. Biol. 12: 2100-2107.
63. READ, L.K., MYLER, P.J. & STUART, K. 1992. Extensive editing of both processed and preprocessed maxicircle CR6 transcripts in Trypanosoma brucei. J. Biol. Chem. 267: 1123-1128.
64. LUKEŠ, J., M. JIRKU, N. AVLIYAKULOV & O. BENADA. 1998. Pankinetoplast DNA structure in a primitive bodonid flagellate, Cryptobia helicis. EMBO J. 17: 838-846.
65. BORST, P. 1991. Why kinetoplast DNA networks? Trends. Genet. 7: 139-141.