tRNASec is transcribed by RNA polymerase II in Trypanosoma brucei but not in humans

Nucleic Acids Research

Volumn 38, Issue 17, 2010, Pages 5833-5843

  Aeby, Eric ^a   Ullu, Elisabetta ^b   Yepiskoposyan, Hasmik ^a   Schimanski, Bernd ^a   Roditi, Isabel ^a   Mühlemann, Oliver ^a   Schneider, André ^a  

^a UNIVERSITY OF BERN   (Switzerland)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA AMANITIN; DNA DIRECTED RNA POLYMERASE III; OLIGODEOXYNUCLEOTIDE; RNA POLYMERASE II; SELENOCYSTEINE TRANSFER RNA; SMALL INTERFERING RNA; TRANSFER RNA; UNCLASSIFIED DRUG; TRNA, SELENOCYSTEINE; TRNA, SELENOCYSTEINE-;

ANIMAL CELL; ARTICLE; CISTRON; CONTROLLED STUDY; GENE CLUSTER; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; KINETOPLASTIDA; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYADENYLATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN PROCESSING; RNA INTERFERENCE; RNA TRANSCRIPTION; SPECIES DIFFERENCE; SYNTENY; TRANS SPLICING; TRANSCRIPTION TERMINATION; TRYPANOSOMA BRUCEI; BIOSYNTHESIS; COMPARATIVE STUDY; DRUG ANTAGONISM; DRUG EFFECT; GENETICS; HELA CELL; METABOLISM; MOLECULAR GENETICS;

EUKARYOTA; PROTOZOA; TRYPANOSOMA BRUCEI; TRYPANOSOMATIDAE; VERTEBRATA;

ALPHA-AMANITIN; BASE SEQUENCE; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; RNA INTERFERENCE; RNA POLYMERASE II; RNA, TRANSFER, AMINO ACID-SPECIFIC; TRANSCRIPTION, GENETIC; TRYPANOSOMA BRUCEI BRUCEI;

EID: 77957235945     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq345     Document Type: Article

References (47)

1. Archambault,J. and Friesen,J.D. (1993) Genetics of eukaryotic RNA polymerasese I, II and III. Microbiol. Rev., 57, 703-724.
2. Commans,S. and Böck,A. (1999) Selenocysteine inserting tRNAs: an overview. FEMS Microbiol. Rev., 23, 335-351.
3. Hatfield,D.L., Carlson,B.A., Xu,X.M., Mix,H. and Gladyshev,V.N. (2006) Selenocysteine incorporation machinery and the role of selenoproteins in development and health. Prog. Nucleic Acid Res. Mol. Biol., 81, 97-142.
4. Lee,B.J., Kang,S.G. and Hatfield,D. (1989) Transcription of Xenopus selenocysteine tRNA Ser (formerly designated opal suppressor phosphoserine tRNA) gene is directed by multiple 5′-extragenic regulatory elements. J. Biol. Chem., 264, 9696-9702.
5. Myslinski,E., Krol,A. and Carbon,P. (1992) Optimal tRNA(Ser)Sec gene activity requires an upstream SPH motif. Nucleic Acids Res., 20, 203-209.
6. Carbon,P. and Krol,A. (1991) Transcription of the Xenopus laevis selenocysteine tRNA(Ser)Sec gene: a system that combines an internal B box and upstream elements also found in U6 snRNA genes. EMBO J., 10, 599-606.
7. Schuster,C., Myslinski,E., Krol,A. and Carbon,P. (1995) Staf, a novel zinc finger protein that activates the RNA polymerase III promoter of the selenocysteine tRNA gene. EMBO J., 14, 3777-3787.
8. Jawdekar,G.W. and Henry,R.W. (2008) Transcriptional regulation of human small nuclear RNA genes. Biochim. Biophys. Acta, 1779, 295-305.
9. Hernandez,N. (2001) Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J. Biol. Chem., 276, 26733-26736.
10. Lobo,S.M. and Hernandez,N. (1989) A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter. Cell, 58, 55-67.
11. Listerman,I., Bledau,A.S., Grishina,I. and Neugebauer,K.M. (2007) Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PLoS Genet., 3, e212.
12. Raha,D., Wang,Z., Moqtaderi,Z., Wu,L., Zhong,G., Gerstein,M., Struhl,K. and Snyder,M. (2010) Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc. Natl Acad. Sci. USA, 107, 3639-3644.
13. Aeby,E., Palioura,S., Pusnik,M., Marazzi,J., Lieberman,A., Ullu,E., Söll,D. and Schneider,A. (2009) The canonical pathway for selenocysteine insertion is dispensable in Trypanosomes. Proc. Natl Acad. Sci. USA, 106, 5088-5092.
14. Adl,S.M., Simpson,A.G., Farmer,M.A., Andersen,R.A., Anderson,O.R., Barta,J.R., Bowser,S.S., Brugerolle,G., Fensome,R.A., Fredericq,S. et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol., 52, 399-451.
15. Simpson,A.G. and Roger,A.J. (2004) The real 'kingdoms' of eukaryotes. Curr. Biol., 14, R693-R696.
16. Campbell,D.A., Thomas,S. and Sturm,N.R. (2003) Transcription in kinetoplastid protozoa: why be normal? Microbes Infect., 5, 1231-1240.
17. Palenchar,J.B. and Bellofatto,V. (2006) Gene transcription in trypanosomes. Mol. Biochem. Parasitol., 146, 135-141.
18. Tschudi,C. and Ullu,E. (2002) Unconventional rules of small nuclear RNA transcription and cap modification in trypanosomatids. Gene Expr., 10, 3-16.
19. Kelly,S., Wickstead,B. and Gull,K. (2005) An in silico analysis of trypanosomatid RNA polymerases: insights into their unusual transcription. Biochem. Soc. Trans., 33, 1435-1437.
20. Günzl,A., Bruderer,T., Laufer,G., Schimanski,B., Tu,L.C., Chung,H.M., Lee,P.T. and Lee,M.G. (2003) RNA polymerase I transcribes procyclin genes and variant surface glycoprotein gene expression sites in Trypanosoma brucei. Eukaryot. Cell, 2, 542-551.
21. Johnson,P.J., Kooter,J.M. and Borst,P. (1987) Inactivation of transcription by UV irradiation of T. brucei provides evidence for a multicistronic transcription unit including a VSG gene. Cell, 51, 273-281.
22. Sutton,R.E. and Boothroyd,J.C. (1986) Evidence for trans splicing in trypanosomes. Cell, 47, 527-535.
23. Liang,X.H., Haritan,A., Uliel,S. and Michaeli,S. (2003) Trans and cis splicing in trypanosomatids: mechanism, factors, and regulation. Eukaryot. Cell, 2, 830-840.
24. Nakaar,V., Dare,A.O., Hong,D., Ullu,E. and Tschudi,C. (1994) Upstream tRNA genes are essential for expression of small nuclear and cytoplasmic RNA genes in trypanosomes. Mol. Cell. Biol., 14, 6736-6742.
25. Chomczyinski,P. and Sacchi,N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem., 162, 156-159.
26. Paillusson,A., Hirschi,N., Vallan,C., Azzalin,C.M. and Mühlemann,O. (2005) A GFP-based reporter system to monitor nonsense-mediated mRNA decay. Nucleic Acids Res., 33, e54.
27. Ullu,E. and Tschudi,C. (1990) Permeable trypanosome cells as a model system for transcription and trans-splicing. Nucleic Acids Res., 18, 3319.
28. Wirtz,E., Leal,S., Ochatt,C. and Cross,G.A. (1999) A tightly regulated inducible expression system for conditional gene knock-outs and dominant-negative genetics in Trypanosoma brucei. Mol. Biochem. Parasitol., 99, 89-101.
29. Bochud-Allemann,N. and Schneider,A. (2002) Mitochondrial substrate level phosphorylation is essential for growth of procyclic Trypanosoma brucei. J. Biol. Chem., 277, 32849-32854.
30. Devaux,S., Lecordier,L., Uzureau,P., Walgraffe,D., Dierick,J.F., Poelvoorde,P., Pays,E. and Vanhamme,L. (2006) Characterization of RNA polymerase II subunits of Trypanosoma brucei. Mol. Biochem. Parasitol., 148, 60-68.
31. Crausaz-Esseiva,A., Marechal-Drouard,L., Cosset,A. and Schneider,A. (2004) The T-stem determines the cytosolic or mitochondrial localization of trypanosomal methionyl-tRNAs. Mol. Biol. Cell., 15, 2750-2757.
32. Brun,R. and Schönenberger,M. (1979) Cultivation an in vitro cloning of procyclic culture forms of Trypansoma brucei in a semi-defined medium. Acta Tropica, 36, 289-292.
33. Beverley,S.M. and Clayton,C.E. (1993) Transfection of Leishmania and Trypanosoma brucei by electroporation. Methods Mol. Biol., 21, 333-348.
34. Tan,T.H.P., Pach,R., Crausaz,A., Ivens,A. and Schneider,A. (2002) tRNAs in Trypanosoma brucei: genomic organization, expression and mitochondrial import. Mol. Cell. Biol., 22, 3707-3717.
35. Pusnik,M., Small,I., Read,L.K., Fabbro,T. and Schneider,A. (2007) Pentatricopeptide repeat proteins in Trypanosoma brucei function in mitochondrial ribosomes. Mol. Cell Biol., 27, 6876-6888.
36. Domitrovich,A.M. and Kunkel,G.R. (2003) Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies. Nucleic Acids Res., 31, 2344-2352.
37. Padilla-Mejía,N.E., Florencio-Martínez,L.E., Figueroa-Angulo,E.E., Manning-Cela,R.G., Hernández-Rivas,R., Myler,P.J. and Martínez-Calvillo,S. (2009) Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites. BMC Genomics, 10, 232.
38. Berriman,M., Ghedin,E., Hertz-Fowler,C., Blandin,G., Renauld,H., Bartholomeu,D.C., Lennard,N.J., Caler,E., Hamlin,N.E., Haas,B. et al. (2005) The genome of the African trypanosome Trypanosoma brucei. Science, 309, 416-422.
39. Siegel,T.N., Hekstra,D.R., Kemp,L.E., Figueiredo,L.M., Lowell,J.E., Fenyo,D., Wang,X., Dewell,S. and Cross,G.A. (2009) Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. Genes Dev., 23, 1063-1076.
40. Bachellerie,J.P., Cavaillé,J. and Hüttenhofer,A. (2002) The expanding snoRNA world. Biochimie, 84, 775-790.
41. Pusnik,M., Charrière,F., Mäser,P., Waller,R.F., Dagley,M.J., Lithgow,T. and Schneider,A. (2009) The single mitochondrial porin of Trypanosoma brucei is the main metabolite transporter in the outer mitochondrial membrane. Mol. Biol. Evol., 26, 671-680.
42. Galli,G., Hofstetter,H. and Birnstiel,M.L. (1981) Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. Nature, 294, 626-631.
43. Xu,X.M., Carlson,B.A., Mix,H., Zhang,Y., Saira,K., Glass,R.S., Berry,M.J., Gladyshev,V.N. and Hatfield,D.L. (2007) Biosynthesis of selenocysteine on its tRNA in eukaryotes. PLoS Biol., 5, e4.
44. Hertz-Fowler,C., Peacock,C.S., Wood,V., Aslett,M., Kerhornou,A., Mooney,P., Tivey,A., Berriman,M., Hall,N., Rutherford,K. et al. (2004) GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res., 32, D339-D343.
45. Krol,A.R.v.d., Mol,J.N.M. and Stuitje,A.R. (1988) Modulation of eukaryotic gene expression by complementary RNA or DNA sequences. Biotechniques, 6, 958-972.
46. Das,A., Banday,M. and Bellofatto,V. (2008) RNA polymerase transcription machinery in trypanosomes. Eukaryot. Cell, 7, 429-434.
47. Zamboni,M., Scarabino,D. and Tocchini-Valentini,G.P. (2009) Splicing of mRNA mediated by tRNA sequences in mouse cells. RNA, 15, 2122-2128.