Strategies of Kinetoplastid Cryptogene Discovery and Analysis

Methods in Enzymology

Volumn 424, Issue , 2007, Pages 127-139

  Maslov, Dmitri A ^a   Simpson, Larry ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUIDE RNA; MESSENGER RNA; URIDINE; BISBENZIMIDE; COLORING AGENT; ETHIDIUM; INTERCALATING AGENT; KINETOPLAST DNA;

BODO SALTANS; CRYPTOGENE; FLAGELLATE; GENE; GENE EXPRESSION; HEMOFLAGELLATE; NONHUMAN; NUCLEOTIDE DELETION; NUCLEOTIDE INSERTION; PRIORITY JOURNAL; PROTOZOON; REVIEW; RNA EDITING; RNA PROCESSING; RNA SEQUENCE; SEQUENCE ANALYSIS; TRYPANOPLASMA BORRELI; ANIMAL; ARTICLE; BIOCHEMISTRY; GENETIC PROCEDURES; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; TRYPANOSOMA;

KINETOPLASTIDA;

ANIMALS; BIOCHEMISTRY; BISBENZIMIDE; COLORING AGENTS; DNA, KINETOPLAST; ETHIDIUM; GENETIC TECHNIQUES; GENETICS; INTERCALATING AGENTS; KINETOPLASTIDA; RNA EDITING; TRYPANOSOMA;

EID: 34548577769     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)24006-6     Document Type: Chapter

References (51)

1. Arts G.J., Van der Spek H., Speijer D., Van den Burg J., Van Steeg H., Sloof P., and Benne R. Implications of novel guide RNA features for the mechanism of RNA editing in Crithidia fasciculata. EMBO J. 12 (1993) 1523-1532
2. Avila H.A., and Simpson L. Organization and complexity of minicircle-encoded guide RNAs in Trypanosoma cruzi. RNA 1 (1995) 939-947
3. Benne R., Van den Burg J., Brakenhoff J., Sloof P., Van Boom J., and Tromp M. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46 (1986) 819-826
4. Blom D., De Haan A., Van den Berg M., Sloof P., Jirků M., Lukeš J., and Benne R. RNA editing in the free-living bodonid Bodo saltans. Nucl. Acids Res. 26 (1998) 1205-1213
5. Blom D., De Haan A., Van den Burg J., Van den Berg M., Sloof P., Jirků M., Lukeš J., and Benne R. Mitochondrial minicircles in the free-living bodonid Bodo saltans contain two gRNA gene cassettes and are not found in large networks. RNA 6 (2000) 121-135
6. Blum B., Bakalara N., and Simpson L. A model for RNA editing in kinetoplastid mitochondria: "Guide" RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60 (1990) 189-198
7. Campbell D.A., Thomas S., and Sturm N.R. Transcription in kinetoplastid protozoa: Why be normal?. Microbes Infect. 5 (2003) 1231-1240
8. Corell R.A., Myler P., and Stuart K. Trypanosoma brucei mitochondrial CR4 gene encodes an extensively edited mRNA with completely edited sequence only in bloodstream forms. Mol. Biochem. Parasitol. 64 (1994) 65-74
9. Decker C.J., and Sollner-Webb B. RNA editing involves indiscriminate U changes throughout precisely defined editing domains. Cell 61 (1990) 1001-1011
10. Feagin J.E., Abraham J., and Stuart K. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei. Cell 53 (1988) 413-422
11. Feagin J.E., Shaw J.M., Simpson L., and Stuart K. Creation of AUG initiation codons by addition of uridines within cytochrome b transcripts of kinetoplastids. Proc. Natl. Acad. Sci. USA 85 (1988) 539-543
12. Gao G.G., Kapushoc S.T., Simpson A.M., Thiemann O.H., and Simpson L. Guide RNAs of the recently isolated LEM125 strain of Leishmania tarentolae: An unexpected complexity. RNA 7 (2001) 1335-1347
13. Hong M., and Simpson L. Genomic organization of Trypanosoma brucei kinetoplast DNA minicircles. Protist 154 (2003) 265-279
14. Koslowsky D.J., Bhat G.J., Read L.K., and Stuart K. Cycles of progressive realignment of gRNA with mRNA in RNA editing. Cell 67 (1991) 537-546
15. Lukeš J., Arts G.J., Van den Burg J., De Haan A., Opperdoes F., Sloof P., and Benne R. Novel pattern of editing regions in mitochondrial transcripts of the cryptobiid Trypanoplasma borreli. EMBO J. 13 (1994) 5086-5098
16. Lukeš J., Jirků M., Avliyakulov N., and Benada O. Pankinetoplast DNA structure in a primitive bodonid flagellate, Cryptobia helicis. EMBO J. 17 (1998) 838-846
17. Lukeš J., Guilbride D.L., Votýpka J., Zíková A., Benne R., and Englund P.T. Kinetoplast DNA network: Evolution of an improbable structure. Eukaryot. Cell 1 (2002) 495-502
18. Lukeš J., Hashimi H., and Zíková A. Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr. Genet. 48 (2005) 277-299
19. Maslov D.A., and 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 70 (1992) 459-467
20. Maslov D.A., and Simpson L. RNA editing and mitochondrial genomic organization in the cryptobiid kinetoplastid protozoan, Trypanoplasma borreli. Mol. Cell. Biol. 14 (1994) 8174-8182
21. Maslov D.A., Sturm N.R., Niner B.M., Gruszynski E.S., Peris M., and 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. 12 (1992) 56-67
22. Maslov D.A., Elgort M.G., Wong S., Pecková H., Lom J., Simpson L., and Campbell D.A. Organization of mini-exon and 5S rRNA genes in the kinetoplastid Trypanoplasma borreli. Mol. Biochem. Parasitol. 61 (1993) 127-136
23. Maslov D.A., Avila H.A., Lake J.A., and Simpson L. Evolution of RNA editing in kinetoplastid protozoa. Nature 365 (1994) 345-348
24. Nawathean P., and Maslov D.A. The absence of genes for cytochrome c oxidase and reductase subunits in maxicircle kinetoplast DNA of the respiration-deficient plant trypanosomatid Phytomonas serpens. Curr. Genet. 38 (2000) 95-103
25. Panigrahi A.K., Ernst N.L., Domingo G.J., Fleck M., Salavati R., and Stuart K.D. Compositionally and functionally distinct editosomes in Trypanosoma brucei. RNA 12 (2006) 1038-1049
26. Pollard V.W., Rohrer S.P., Michelotti E.F., Hancock K., and Hajduk S.L. Organization of minicircle genes for guide RNAs in Trypanosoma brucei. Cell 63 (1990) 783-790
27. Read L.K., Myler P.J., and Stuart K. Extensive editing of both processed and preprocessed maxicircle CR6 transcripts in Trypanosoma brucei. J. Biol. Chem. 267 (1992) 1123-1128
28. Shaw J., Feagin J.E., Stuart K., and Simpson L. Editing of mitochondrial mRNAs by uridine addition and deletion generates conserved amino acid sequences and AUG initiation codons. Cell 53 (1988) 401-411
29. Shaw J., Campbell D., and Simpson L. Internal frameshifts within the mitochondrial genes for cytochrome oxidase subunit II and maxicircle unidentified reading frame 3 in Leishmania tarentolae are corrected by RNA editing: Evidence for translation of the edited cytochrome oxidase subunit II mRNA. Proc. Natl. Acad. Sci. USA 86 (1989) 6220-6224
30. Simpson L. The kinetoplast of the hemoflagellates. Int. Rev. Cytol. 32 (1972) 139-207
31. Simpson L. Isolation of maxicircle component of kinetoplast DNA from hemoflagellate protozoa. Proc. Natl. Acad. Sci. USA 76 (1979) 1585-1588
32. Simpson L. The genomic organization of guide RNA genes in kinetoplastid protozoa: Several conundrums and their solutions. Mol. Biochem. Parasitol. 86 (1997) 133-141
33. Simpson L., and da Silva A.M. Isolation and characterization of kinetoplast DNA from Leishmania tarentolae. J. Mol. Biol. 56 (1971) 443-473
34. Simpson L., and Maslov D.A. RNA editing and the evolution of parasites. Science 264 (1994) 1870-1871
35. Simpson L., and Shaw J. RNA editing and the mitochondrial cryptogenes of kinetoplastid protozoa. Cell 57 (1989) 355-366
36. Simpson L., Neckelmann N., de la Cruz V., Simpson A., Feagin J., Jasmer D., and Stuart K. Comparison of the maxicircle (mitochondrial) genomes of Leishmania tarentolae and Trypanosoma brucei at the level of nucleotide sequence. J. Biol. Chem. 262 (1987) 6182-6196
37. Simpson L., Simpson A.M., and Blum B. RNA editing in mitochondria. In: Higgins S.J., and Hames B.D. (Eds). "RNA Processing" Vol. II (1994), IRL Press, Oxford 69-105
38. Simpson L., Frech G.C., and Maslov D.A. RNA editing in trypanosomatid mitochondria. Methods Enzymol. 264 (1996) 99-121
39. Simpson L., Wang S.H., Thiemann O.H., Alfonzo J.D., Maslov D.A., and Avila H.A. U-insertion/deletion Edited Sequence Database. Nucleic Acids Res. 26 (1998) 170-176
40. Simpson L., Aphasizhev R., Gao G., and Kang X. Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U-insertion/deletion RNA editing. RNA 10 (2004) 159-170
41. Souza A.E., Shu H.-H., Read L.K., Myler P.J., and 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. 13 (1993) 6832-6840
42. Štolba P., Jirků M., and Lukeš J. Polykinetoplast DNA structure in Dimastigella tryaniformis and Dimastigella mimosa (Kinetoplastida). Mol. Biochem. Parasitol. 113 (2001) 323-326
43. Stuart K.D., Schnaufer A., Ernst N.L., and Panigrahi A.K. Complex management: RNA editing in trypanosomes. Trends Biochem. Sci. 30 (2005) 97-105
44. Sturm N.R., and Simpson L. Partially edited mRNAs for cytochrome b and subunits III of cytochrome oxidase from Leishmania tarentolae mitochondria: RNA editing intermediates. Cell 61 (1990) 871-878
45. Sturm N.R., and Simpson L. Kinetoplast DNA minicircles encode guide RNAs for editing of cytochrome oxidase subunit III mRNA. Cell 61 (1990) 879-884
46. Sturm N.R., and Simpson L. Leishmania tarentolae minicircles of different sequence classes encode single guide RNAs located in the variable region approximately 150 bp from the conserved region. Nucleic Acids Res. 19 (1991) 6277-6281
47. Sturm N.R., Maslov D.A., Blum B., and Simpson L. Generation of unexpected editing patterns in Leishmania tarentolae mitochondrial mRNAs: Misediting produced by misguiding. Cell 70 (1992) 469-476
48. Thiemann O.H., Maslov D.A., and Simpson L. Disruption of RNA editing in Leishmania tarentolae by the loss of minicircle-encoded guide RNA genes. EMBO J. 13 (1994) 5689-5700
49. Vickerman K. The diversity of the kinetoplastid flagellates. In: Lumsden W.H.R., and Evans D.A. (Eds). "Biology of the Kinetoplastida" (1976), Academic Press, London 1-34
50. Von Haeseler A., Blum B., Simpson L., Sturm N., and Waterman M.S. Computer methods for locating kinetoplastid cryptogenes. Nucleic Acids Res. 20 (1992) 2717-2724
51. Yasuhira S., and Simpson L. Guide RNAs and guide RNA genes in the cryptobiid kinetoplastid protozoan, Trypanoplasma borreli. RNA 2 (1996) 1153-1160