Minimal pre-mRNA substrates with natural and converted sites for full-round U insertion and U deletion RNA editing in trypanosomes

Nucleic Acids Research

Volumn 33, Issue 20, 2005, Pages 6610-6620

  Cifuentes Rojas, Catherine ^a   Halbig, Kari ^a   Sacharidou, Anastasia ^a   De Nova Ocampo, Monica ^a,b   Cruz Reyes, Jorge ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSIDAD AUTÓNOMA DEL ESTADO DE HIDALGO   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA PRECURSOR; PROTOZOAL RNA;

ARTICLE; DNA TEMPLATE; GENE DELETION; GENE INSERTION SEQUENCE; MOLECULAR INTERACTION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; RNA EDITING; TRYPANOSOMA;

ADENOSINE TRIPHOSPHATASES; ANIMALS; BASE SEQUENCE; CYTOCHROMES B; MITOCHONDRIAL PROTEINS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; RIBOSOMAL PROTEINS; RNA EDITING; RNA PRECURSORS; RNA, MESSENGER; TRYPANOSOMA BRUCEI BRUCEI; URACIL NUCLEOTIDES;

TRYPANOSOMA;

EID: 29144533269     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki943     Document Type: Article

References (31)

1. Madison-Antenucci,S., Grams,J. and Hajduk,S.L. (2002) Editing machines: the complexities of trypanosome RNA editing. Cell, 108, 435-438.
2. Stuart,K.D., Schnaufer,A., Ernst,N.L. and Panigrahi,A.K. (2005) Complex management: RNA editing in trypanosomes. Trends Biochem. Sci., 30, 97-105.
3. Simpson,L., Aphasizhev,R., Gao,G. and Kang,X. (2004) Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U-insertion/deletion RNA editing. RNA, 10, 159-170.
4. Blum,B., Bakalara,N. and Simpson,L. (1990) A model for RNA editing in kinetoplastid mitochondria: "guide"; RNA molecules transcribed from maxicircle DNA provide the edited information. Cell, 60, 189-198.
5. Seiwert,S.D., Heidmann,S. and Stuart,K. (1996) Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing. Cell, 84, 831-841.
6. Cruz-Reyes,J. and Sollner-Webb,B. (1996) Trypanosome U-deletional RNA editing involves guide RNA-directed endonuclease cleavage, terminal U exonuclease, and RNA ligase activities. Proc. Natl Acad. Sci. USA, 93, 8901-8906.
7. Kable,M.L., Seiwert,S.D., Heidmann,S. and Stuart,K. (1996) RNA editing: a mechanism for gRNA-specified uridylate insertion into precursor mRNA. Science, 273, 1189-1195.
8. Blom,D., Burg,Jv., Breek,C.K., Speijer,D., Muijsers,A.O. and Benne,R. (2001) Cloning and characterization of two guide RNA-binding proteins from mitochondria of Crithidia fasciculata: gBP27, a novel protein, and gBP29, the orthologue of Trypanosoma brucei gBP21. Nucleic Acids Res., 29, 2950-2962.
9. Muller,U.F., Lambert,L. and Goringer,H.U. (2001) Annealing of RNA editing substrates facilitated by guide RNA-binding protein gBP21. EMBO J., 20, 1394-1404.
10. Cruz-Reyes,J., Rusche,L.N., Piller,K.J. and Sollner-Webb,B. (2001) Trypanosome RNA editing: simple guide RNA features enhance U deletion 100-fold. Mol. Cell Biol., 21, 884-892.
11. Igo,R.P.Jr, Lawson,S.D. and Stuart,K. (2002) RNA sequence and base pairing effects on insertion editing in Trypanosoma brucei. Mol. Cell Biol., 22, 1567-1576.
12. Lawson,S.D., Igo,R.P. Jr, Salavati,R. and Stuart,K.D. (2001) The specificity of nucleotide removal during RNA editing in Trypanosoma brucei. RNA, 7, 1793-1802.
13. Leung,S.S. and Koslowsky,D.J. (1999) Mapping contacts between gRNA and mRNA in trypanosome RNA editing. Nucleic Acids Res., 27, 778-787.
14. Leung,S.S. and Koslowsky,D.J. (2001) RNA editing in Trypanosoma brucei: characterization of gRNA U-tail interactions with partially edited mRNA substrates. Nucleic Acids Res., 29, 703-709.
15. Igo,R.P.Jr, Palazzo,S.S., Burgess,M.L., Panigrahi,A.K. and Stuart,K. (2000) Uridylate addition and RNA ligation contribute to the specificity of kinetoplastid insertion RNA editing. Mol. Cell Biol., 20, 8447-8457.
16. Kapushoc,S.T. and Simpson,L. (1999) In vitro uridine insertion RNA editing mediated by cis-acting guide RNAs. RNA, 5, 656-669.
17. Kabb,A.L., Oppegard,L.M., McKenzie,B.A. and Connell,G.J. (2001) A mRNA determinant of gRNA-directed kinetoplastid editing. Nucleic Acids Res., 29, 2575-2580.
18. Seiwert,S.D. and Stuart,K. (1994) RNA editing: transfer of genetic information from gRNA to precursor mRNA in vitro. Science, 266, 114-117.
19. Cruz-Reyes,J., Rusche,L.N., Piller,K.J. and Sollner-Webb,B. (1998) T.brucei RNA editing: adenosine nucleotides inversely affect U-deletion and U-insertion reactions at mRNA cleavage. Mol. Cell, 1, 401-409.
20. Cruz-Reyes,J., Rusche,L.N. and Sollner-Webb,B. (1998) Trypanosoma brucei U insertion and U deletion activities co-purify with an enzymatic editing complex but are differentially optimized. Nucleic Acids Res., 26, 3634-3639.
21. Cruz-Reyes,J., Zhelonkina,A.G., Huang,C.E. and Sollner-Webb,B. (2002) Distinct functions of two RNA ligases in active Trypanosoma brucei RNA editing complexes. Mol. Cell Biol., 22, 4652-4660.
22. Huang,C.E., Cruz-Reyes,J., Zhelonkina,A.G., O'Hearn,S., Wirtz,E. and Sollner-Webb,B. (2001) Roles for ligases in the RNA editing complex of Trypanosoma brucei: band IV is needed for U-deletion and RNA repair. EMBO J., 20, 4694-4703.
23. Schnaufer,A., Ernst,N.L., Palazzo,S.S., O'Rear,J., Salavati,R. and Stuart,K. (2003) Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex. Mol. Cell, 12, 307-319.
24. Igo,R.P.Jr, Weston,D.S., Ernst,N.L., Panigrahi,A.K., Salavati,R. and Stuart,K. (2002) Role of uridylate-specific exoribonuclease activity in Trypanosoma brucei RNA editing. Eukaryot Cell, 1, 112-118.
25. Milligan,J.F., Groebe,D.R., Witherell,G.W. and Uhlenbeck,O.C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res., 15, 8783-8798.
26. Sollner-Webb,B., Rusche,L.N. and Cruz-Reyes,J. (2001) Ribonuclease activities of trypanosome RNA editing complex directed to cleave specifically at a chosen site. Methods Enzymol., 341, 154-174.
27. Harris,M.E. and Hajduk,S.L. (1992) Kinetoplastid RNA editing: in vitro formation of cytochrome b gRNA-mRNA chimeras from synthetic substrate RNAs. Cell, 68, 1091-1099.
28. Rusche,L.N., Cruz-Reyes,J., Piller,K.J. and Sollner-Webb,B. (1997) Purification of a functional enzymatic editing complex from Trypanosoma brucei mitochondria. EMBO J., 16, 4069-4081.
29. Pai,R.D., Oppegard,L.M. and Connell,G.J. (2003) Sequence and structural requirements for optimal guide RNA-directed insertional editing within Leishmania tarentolae. RNA, 9, 469-483.
30. Oppegard,L.M., Kabb,A.L. and Connell,G.J. (2000) Activation of guide RNA-directed editing of a cytochrome b mRNA. J. Biol. Chem., 275, 33911-33919.
31. Sturm,N.R., Maslov,D.A., Blum,B. and Simpson,L. (1992) Generation of unexpected editing patterns in Leishmania tarentolae mitochondrial mRNAs: misediting produced by misguiding. Cell, 70, 469-476.