Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes

Current Opinion in Microbiology

Volumn 5, Issue 6, 2002, Pages 620-626

  Horton, Tamara ^a   Landweber, Laura ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE; CYTOCHROME C OXIDASE; GUIDE RNA; LIGASE; URIDINE;

DNA MODIFICATION; DNA TEMPLATE; ENZYME ACTIVITY; FLAGELLATE; GENE DELETION; GENE INSERTION; GENETIC TRANSCRIPTION; MITOCHONDRIAL GENETICS; MYXOMYCETES; NONHUMAN; PHYLOGENY; PHYSARUM POLYCEPHALUM; PROTEIN ANALYSIS; REVIEW; RNA EDITING; TRYPANOSOMA BRUCEI;

CHONDROMYCES; EUKARYOTA; KINETOPLASTIDA; MASTIGOPHORA (FLAGELLATES); MYXOGASTRIA; PHYSARUM POLYCEPHALUM; PROTISTA; TRYPANOSOMA; TRYPANOSOMA BRUCEI;

EID: 0036900559     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(02)00379-X     Document Type: Review

References (64)

1. Landweber LF, Gilbert W: RNA editing as a source of genetic variation. Nature 1993, 363:179-182.
2. Hospattankar A, Higuchi K, Law SW, Meglin N, Brewer HB Jr: Identification of a novel in-frame translational stop codon in human intestine apoB mRNA. Biochem Biophys Res Comm 1987, 148:279-285.
3. Chen S, Habib G, Yang CY, Gu ZW, Lee BR, Weng SA, Silberman SR, Cai SJ, Deslypere JP, Rosseneu M et al.: Apolipoprotein B-48 is the product of messenger RNA with an organ-specific in-frame stop codon. Science 1987, 238:363-366.
4. Powell L, Wallis SC, Pease RJ, Edwards YH, Knott TJ, Scott J: A novel form of tissue-specific RNA processing produces apolipoprotein-B-48 in the intestine. Cell 1987, 50:831-840.
5. Benne R, Van den Burg J, Brakenhoff JP, Sloof P, Van Boom JH, Tromp MC: Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 1986, 46:819-826.
6. Simpson L, Shaw J: RNA editing and the mitochondrial cryptogenes of kinetoplastid protozoa. Cell 1989, 57:355-366.
7. Landweber LF, Gilbert W: Phylogenetic analysis of RNA editing: A primitive genetic phenomenon. Proc Natl Acad Sci USA 1994, 91:918-921.
8. Maslov DA, Avila HA, Lake JA, Simpson L: Evolution of RNA editing in kinetoplastid protozoa [Erratum: Nature 1994, 368:694]. Nature 1994, 368:345-348.
9. Cavalier-Smith T: Cell and genome coevolution: Facultative anaerobiosis, glycosomes and kinetoplastan RNA editing. Trends Genet 1997, 13:6-9.
10. Kable ML, Seiwert SD, Heidmann S, Stuart K: RNA editing: A mechanism for gRNA-specified uridylate insertion into precursor mRNA. Science 1996, 273:1189-1195.
11. Maslov DA, 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, 70:459-467.
12. Muller UF, Lambert L, Goringer HU: Annealing of RNA editing substrates facilitated by guide RNA-binding protein gB P21. EMBO J 2001, 20:1394-1404.
13. Burgess ML, Heidmann S, Stuart K: Kinetoplastid RNA editing does not require the terminal 3′ hydroxyl of guide RNA, but modifications to the guide RNA terminus can inhibit in vitro U insertion. RNA 1999, 5:883-892.
14. Kapushoc ST, Simpson L: In vitro uridine insertion RNA editing mediated by cis-acting guide RNAs. RNA 1999, 5:656-669.
15. Leung SS, Koslowsky DJ: Mapping contacts between gRNA and mRNA in trypanosome RNA editing. Nucleic Acids Res 1999, 27:778-787.
16. McManus MT, Adler BK, Pollard VW, Hajduk SL: Trypanosoma brucei guide RNA poly(U) tail formation is stabilized by cognate mRNA. Mol Cell Biol 2000, 20:883-891.
17. Vickerman K: The evolutionary expansion of the trypanosomatid flagellates. Int J Parasitol 1994, 24:1317-1331.
18. Blom D, de Haan A, van den Berg M, Sloof P, Jirku M, Lukes J, Benne R: RNA editing in the free-living bodonid Bodo saltans. Nucleic Acids Res 1998, 26:1205-1213.
19. Maslov DA, Simpson L: RNA editing and mitochondrial genomic organization in the cryptobiid kinetoplastid protozoan Trypanoplasma borreli. Mol Cell Biol 1994, 14:8174-8182.
20. Lunt D, Hyman B: Animal mitochondrial recombination. Nature 1997, 387:247.
21. Rusche LN, Huang CE, Piller KJ, Hemann M, Wirtz E, Sollner-Webb B: The two RNA ligases of the Trypanosoma brucei RNA editing complex: Cloning the essential band IV gene and identifying the band V gene. Mol Cell Biol 2001, 21:979-989. See annotation Schnaufer et al. (2001) [24•].
22. Panigrahi AK, Gygi SP, Ernst NL, Igo RP Jr, Palazzo SS, Schnaufer A, Weston DS, Carmean N, Salavati R, Aebersold R, Stuart KD: Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex. Mol Cell Biol 2001, 21:380-389. See annotation Schnaufer et al. (2001) [24•].
23. McManus MT, Shimamura M, Grams J, Hajduk SL: Identification of candidate mitochondrial RNA editing ligases from Trypanosoma brucei. RNA 2001, 7:167-175. See annotation Schnaufer et al. (2001) [24•].
24. Schnaufer A, Panigrahi AK, Panicucci B, Igo RP Jr, Wirtz E, Salavati R, Stuart K: An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei. Science 2001, 291:2159-2162. In these four papers [21•-24•], three laboratories independently clone and characterize the same two protein components of the editosome. Both are ligases; one is shown to be essential for growth and RNA editing in the procyclic and bloodstream stage.
25. Huang CE, Cruz-Reyes J, Zhelonkina AG, O'Hearn S, Wirtz E, Sollner-Webb B: Roles for ligases in the RNA editing complex of Trypanosoma brucei: Band IV is needed for U-deletion and RNA repair. EMBO J 2001, 20:4694-4703.
26. Cruz-Reyes J, Zhelonkina AG, Huang CE, Sollner-Webb B: Distinct functions of two RNA ligases in active Trypanosoma brucei RNA editing complexes. Mol Cell Biol 2002, 22:4652-4660. Two ligases, the first protein components of the editosome to be cloned and characterized, are further found to have specialized function in editing. One ligase participates in the U insertion process, while one functions in U deletion. This specialization is intriguingly supportive of a previously suspected separation of these two processes.
27. Huang CE, O'Hearn SF, Sollner-Webb B: Assembly and function of the RNA editing complex in Trypanosoma brucei requires band III protein. Mol Cell Biol 2002, 22:3194-3203.
28. Panigrahi AK, Schnaufer A, Carmean N, Igo RP Jr, Gygi SP, Ernst NL, Palazzo SS, Weston DS, Aebersold R, Salavati R, Stuart KD: Four related proteins of the Trypanosoma brucei RNA editing complex. Mol Cell Biol 2001, 21:6833-6840.
29. Stuart K, Panigrahi AK, Schnaufer A, Drozdz M, Clayton C, Salavati R: Composition of the editing complex of Trypanosoma brucei. Philos Trans R Soc Lond B Biol Sci 2002, 357:71-79.
30. Alfonzo JD, Blanc V, Estevez AM, Rubio MA, Simpson L: C to U editing of the anticodon of imported mitochondrial tRNA(Trp) allows decoding of the UGA stop codon in Leishmania tarentolae. EMBO J 1999, 18:7056-7062.
31. Trp maturation and mitochondrial import preceding mitochondrial RNA editing of the anticodon. The edited tRNA TRNA is used to decode a mitochondrial-specific codon.
32. Ben-Shlomo H, Levitan A, Shay NE, Goncharov I, Michaeli S: RNA editing associated with the generation of two distinct conformations of the trypanosomatid Leptomonas collosoma 7SL RNA. J Biol Chem 1999, 274:25642-25650.
33. Gott JM, Visomirski LM, Hunter JL: Substitutional and insertional RNA editing of the cytochrome c oxidase subunit 1 mRNA of Physarum polycephalum. J Biol Chem 1993, 268:25483-25486.
34. Miller D, Mahendran R, Spottswood M, Costandy H, Wang S, Ling ML, Yang N: Insertional editing in mitochondria of Physarum. Semin Cell Biol 1993, 4:261-266.
35. Rundquist BA, Gott JM: RNA editing of the col mRNA throughout the life cycle of Physarum polycephalum. Mol Gen Genet 1995, 247:306-311.
36. Visomirski-Robic LM, Gott JM: Insertional editing of nascent mitochondrial RNAs in Physarum. Proc Natl Acad Sci USA 1997, 94:4324-4329.
37. Visomirski-Robic LM, Gott JM: Insertional editing in isolated Physarum mitochondria is linked to RNA synthesis. RNA 1997, 3:821-837.
38. Cheng YW, Gott JM: Transcription and RNA editing in a soluble in vitro system from Physarum mitochondria. Nucleic Acids Res 2000, 28:3695-3701. An in vitro system that performs run-on transcription and insertional RNA editing activity was further purified from Physarum mitochondrial lysates. This system should allow greater flexibility in biochemical analysis of editing than the previously utilized system of isolated mitochondria.
39. Cheng YW, Visomirski-Robic LM, Gott JM: Non-templated addition of nucleotides to the 3′ end of nascent RNA during RNA editing in Physarum. EMBO J 2001, 20:1405-1414. In this paper they utilize a recently improved in vitro system developed by two of the authors and provide convincing evidence of co-transcriptional RNA editing in Physarum.
40. Horton TL, Landweber LF: Evolution of four types of RNA editing in myxomycetes. RNA 2000, 6:1339-1346. The first broad phylogenetic analysis of editing in the myxomycetes indicates that all four types of editing described in Physarum polycephalum have separate evolutionary histories. Insertional editing in myxomycetes shows a progression toward an expanded repertoire of editing mechanisms and increased numbers of edited sites over time.
41. Visomirski-Robic LM, Gott JM: Accurate and efficient insertional RNA editing in isolated Physarum mitochondria. RNA 1995, 1:681-691.
42. Wang SS, Mahendran R, Miller DL: Editing of cytochrome b mRNA in Physarum mitochondria. J Biol Chem 1999, 274:2725-2731.
43. Schuster W, Hiesel R, Brennicke A: RNA editing in plant mitochondria. Semin Cell Biol 1993, 4:279-284.
44. Mahendran R, Spottswood MR, Miller DL: RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature 1991, 349:434-438.
45. Barth C, Greferath U, Kotsifas M, Fisher PR: Polycistronic transcription and editing of the mitochondrial small subunit (SSU) ribosomal RNA in Dictyostelium discoideum. Curr Genet 1999, 36:55-61.
46. Covello PS, Gray MW: RNA editing in plant mitochondria. [Erratum: Nature 1989, 342:460] Nature 1989, 341:662-666.
47. Gualberto JM, Lamattina L, Bonnard G, Weil JH, Grienenberger JM: RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature 1989, 341:660-662.
48. Heisel R, Wissinger B, Schuster W, Brennicke A: RNA editing in plant mitochondria. Science 1989, 246:1632-1643.
49. Hoch B, Maier RM, Appel K, Igloi GL, Kossel H: Editing of a chloroplast mRNA by creation of an initiation codon. Nature 1991, 353: 178-180.
50. Sommer B, Kohler M, Sprengel R, Seeburg PH: RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell 1991, 67:11-19.
51. Chang HM, Wu YM, Chang YC, Hsu YC, Hsu HY, Chen YC, Chow WY: Molecular and electrophysiological characterizations of fGluR3 alpha, an ionotropic glutamate receptor subunit of a teleost fish. Brain Res Mol Brain Res 1998, 57:211-220.
52. Sharma PM, Bowman M, Madden SL, Rauscher FJ 3rd, Sukumar S: RNA editing in the Wilms' tumor susceptibility gene, WT1. Genes Dev 1994, 8:720-731.
53. Novo FJ, Kruszewski A, MacDermot KD, Goldspink G, Gorecki DC: Editing of human alpha-galactosidase RNA resulting in a pyrimidine to purine conversion. Nucleic Acids Res 1995, 23:2636-2640.
54. Petschek JP, Mermer MJ, Scheckelhoff MR, Simone AA, Vaughn JC: RNA editing in Drosophila 4f-rnp gene nuclear transcripts by multiple A-to-G conversions. J Mol Biol 1996, 259:885-890.
55. Janke A, Feldmaier-Fuchs G, Thomas WK, von Haeseler A, Paabo S: The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 1994, 137:243-256.
56. Yokobori SI, Pääbo S: tRNA editing in metazoans. [letter] Nature 1995, 377:490.
57. Yokobori S, Pääbo S: Transfer RNA editing in land snail mitochondria. Proc Natl Acad Sci USA 1995, 92:10432-10435.
58. Tomita K, Ueda T, Watanabe K: RNA editing in the acceptor stem of squid mitochondrial tRNA(Tyr). Nucleic Acids Res 1996, 24:4987-4991.
59. Yokobori S, Pääbo S: Polyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNA(Tyr). J Mol Biol 1997, 265:95-99.
60. Lonergan KM, Gray MW: Editing of transfer RNAs in Acanthamoeba castellanii mitochondria. Science 1993, 259:812-816.
61. Laforest MJ, Roewer I, Lang BF: Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG 'stop' codons recognized as leucine. Nucleic Acids Res 1997, 25:626-632.
62. Casey JL, Bergmann KF, Brown TL, Gerin JL: Structural requirements for RNA editing in hepatitis delta virus: Evidence for a uridine-to-cytidine editing mechanism. Proc Natl Acad Sci USA 1992, 89:7149-7153.
63. Thomas S, Lamb R, Paterson R: Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5. Cell 1988, 54:891-902.
64. Volchkov VE, Becker S, Volchkova VA, Ternovoj VA, Kotov AN, Netesov SV, Klenk HD: GP mRNA of Ebola virus is edited by the Ebola virus polymerase and by T7 and vaccinia virus polymerases. Virology 1995, 214:421-430.