Sequence and structural requirements for optimal guide RNA-directed insertional editing within Leishmania tarentolae

RNA

Volumn 9, Issue 4, 2003, Pages 469-483

  Pai, Raj D ^a,c   Oppegard, Lisa M ^a   Connell, Gregory J ^a,b  

^a UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

RNA editing; Selection amplification; SELEX; Trypanosome; Uridylate

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; MITOCHONDRIAL RNA; PHOSPHORUS 32; RNA; URIDINE PHOSPHATE;

ARTICLE; LEISHMANIA; LEISHMANIA TARENTOLAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTOZOON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EDITING; RNA PROCESSING; RNA SEQUENCE; RNA STRUCTURE; THIN LAYER CHROMATOGRAPHY; TRYPANOSOMA;

ANIMALS; BASE PAIRING; LEISHMANIA; RNA EDITING; RNA, GUIDE; RNA, MESSENGER; URIDINE;

INSERTION SEQUENCES; LEISHMANIA TARENTOLAE; PROTOZOA; TRYPANOSOMA; TRYPANOSOMA BRUCEI;

EID: 0037377351     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2175703     Document Type: Article

References (44)

1. Alfonzo, J.D., Thiemann, O., and Simpson L. 1997. The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria. Nucleic Acids Res 25: 3751-3759.
2. Aphasizhev, R., Sbicego, S., Peris, M., Jang, S.H., Aphasizheva, I., Simpson, A.M., Rivlin, A., and Simpson, L. 2002. Trypanosome mitochondrial 3′ terminal uridylyl transferase (TUTase): The key enzyme in U insertion/deletion RNA editing. Cell 108: 637-648.
3. Benne, R. 1992. RNA editing in trypanosomes. The us(e) of guide RNAs. Mol. Biol. Rep. 16: 217-227.
4. Benne, R., Van den Burg, J., Brakenhoff, J.P., Sloof, P., Van Boom, J.H., and Tromp, M.C. 1986. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46: 819-826.
5. 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.
6. Brown, L.M., Burbach, B.J., McKenzie, B.A., and Connell, G.J. 1999. A cis-acting A-U sequence element induces kinetoplastid U-insertions. J. Biol. Chem. 274: 6295-6304.
7. Burgess, M.L.K. and Stuart, K. 2000. Sequence bias in edited kinetoplastid RNAs. RNA 6:1492-1497.
8. Byrne, E.M., Connell, G.J., and Simpson, L. 1996. Guide RNA-directed uridine insertion RNA editing in vitro. EMBO J. 15: 6758-6765.
9. Ciesiolka, J., Illangasekare, M., Majerfeld, I., Nickles, T., Welch, M., Yarus, M., and Zinnen, S. 1996. Affinity selection-amplification from randomized ribooligonucleotide pools. Methods Enzymol. 267: 315-335.
10. Connell, G.J., Byrne, E., and Simpson, L. 1997. Guide RNA-independent and guide RNA-dependent uridine-insertion into cytochrome b mRNA in a mitochondrial lysate from Leishmania tarentolae. J. Biol. Chem. 272: 4212-4218.
11. Corell, R.A., Read, L.K., Riley, G.R., Nellissery, J.K., Allen, T.E., Kable, M.L., Wachal, M.D., Seiwert, S.D., Myler, P.J., and Stuart, K.D. 1996. Complexes from Trypanosoma brucei that exhibit deletion editing and other editing-associated properties. Mol. Cell. Biol. 16: 1410-1418.
12. 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. 93: 8901-8906.
13. 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.
14. Cruz-Reyes, J., Zhelonkina, A., Rusche, L., and Sollner-Webb, B. 2001. Trypanosome RNA editing: Simple guide RNA features enhance U deletion 100-fold. Mol. Cell. Biol. 21: 884-892.
15. Drozdz, M., Palazzo, S.S., Salavati, R., O'Rear, J., Clayton, C., and Stuart, K. 2002. TbMP81 is required for RNA editing in Trypanosoma brucei. EMBO J. 21: 1791-1799.
16. Ellington, A.D. and Szostak, J.W. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
17. Estevez, A.M. and Simpson, L. 1999. Uridine insertion/deletion RNA editing in trypanosome mitochondria: A review. Gene 240: 247-260.
18. Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T., and Turner, D.H. 1986. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. 83: 9373-9377.
19. Huang, C.E., O'Hearn, S.F., and Sollner-Webb, B. 2002. Assembly and function of the RNA editing complex in Trypanosoma brucei requires band III protein. Mol. Cell. Biol. 22: 3194-3203.
20. Igo, R.P., Palazzo, S.S., Burgess, M.L.K., 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.
21. Igo, R.P., 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.
22. 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.
23. 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.
24. Kapushoc, S.T. and Simpson, L. 1999. In vitro uridine insertion RNA editing mediated by cis-acting guide RNAs. RNA 5: 656-669.
25. Krol, A. and Carbon, P. 1989. A guide for probing native small nuclear RNA and ribonucleoprotein structures. Methods Enzymol. 180: 212-227.
26. Madison-Antenucci, S., Grams, J., and Hajduk, S.L. 2002. Editing machines: The complexities of trypanosome RNA editing. Cell 108: 435-438.
27. Maslov, D.A. and Simpson, L. 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.
28. McManus, M.T., Shimamura, M., Grams, J., and Hajduk, S.L. 2001. Identification of candidate mitochondrial RNA editing ligases from Trypanosoma brucei. RNA 7: 167-175.
29. Milligan, J.F. and Uhlenbeck, O.C. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180: 51-62.
30. Oppegard, L.M. and Connell, G.J. 2002. Direct visualization of RNA editing within a Leishmania mitochondrial extract. Int. J. Parasitol. 32: 859-866.
31. 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.
32. Panigrahi, A.K., Gygi, S.P., Ernst, N.L., Igo, R.P., Palazzo, S.S., Schnaufer, A., Weston, D.S., Carmean, N., Salavati, R., Aebersold, R., et al. 2001a. Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex. Mol. Cell. Biol. 21: 380-389.
33. Panigrahi, A.K., Schnaufer, A., Carmean, N., Igo, R.P., Gygi, S.P., Ernst, N.L., Palazzo, S.S., Weston, D.S., Abersold, R., Salavati, R., et al. 2001b. Four related proteins of the Trypanosoma brucei RNA editing complex. Mol. Cell. Biol. 21: 6833-6840.
34. Pollard, V.W., Harris, M.E., and Hajduk, S.L. 1992. Native mRNA editing complexes from Trypanosoma brucei mitochondria. EMBO J. 11: 4429-4438.
35. 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.
36. Rusche, L.N., Huang, C.E., Piller, K.J., Hemann, M., Wirtz, E., and Sollner-Webb, B. 2001. 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. 21: 979-989.
37. Schmid, B., Riley, G.R., Stuart, K., and Goringer, H.U. 1995. The secondary structure of guide RNA molecules from Trypanosoma brucei. Nucleic Acids Res. 23: 3093-3102.
38. Schmid, B., Read, L.K., Stuart, K., and Goringer, H.U. 1996. Experimental verification of the secondary structures of guide RNA-pre-mRNA chimaeric molecules in Trypanosoma brucei. Eur. J. Biochem. 240: 721-731.
39. Schnaufer, A., Panigrahi, A.K., Panicucci, B., Igo, R.P., Wirtz, E., Salavati, R., Stuart K. 2001. An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei. Science 291: 2159-2162.
40. 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.
41. Stuart, K. and Panigrahi, A.K. 2002. RNA editing: Complexity and complications. Mol. Microbiol. 45: 591-596.
42. Thiemann, O.H., Maslov, D.A., and Simpson, L. 1994. Disruption of RNA editing in Leishmania tarentolae by the loss of minicircle-encoded guide RNA genes. EMBO J. 13:5689-5700.
43. Tuerk, C. and Gold, L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
44. Zweig, G. and Sherma, J. 1972. CRC handbook of chromatography. CRC Press, Cleveland, OH.