Three Small Nucleolar RNAs Identified from the Spliced Leader-Associated RNA Locus in Kinetoplastid Protozoans

REFERENCES

• Altschul, S. F., W. Gish, W. Miller, E. W. Meyers, and D. J. Lipman 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.
   PubMed Web of Science ®Google Scholar
• Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl 1994. Current protocols in molecular biology, suppl. 19. Greene Publishing Associates and Wiley Interscience, New York, N.Y.
   Google Scholar
• Balakin, A. G., L. Smith, and M. J. Fournier 1996. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86: 823–834.
   PubMed Web of Science ®Google Scholar
• Bechthold, A., and H. G. Floss 1994. Overexpression of the thiostrepton-resistance gene from Streptomyces azureus in Escherichia coli and characterization of recognition sites of the 23S rRNA A1067 2′-methyltransferase in the guanosine triphosphatase center of 23S ribosomal RNA. Eur. J. Biochem. 224: 431–437.
   PubMedGoogle Scholar
• Bienen, E. J., E. Hammadi, and G. C. Hill 1981. Trypanosoma brucei: biochemical and morphological changes during in vitro transformation of bloodstream- to procyclic-trypomastigotes. Exp. Parasitol. 51: 408–417.
   PubMedGoogle Scholar
• Blum, B., N. Bakalara, and L. Simpson 1990. A model for RNA editing in kinetoplastid mitochondria: “guide” RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60: 189–198.
   PubMed Web of Science ®Google Scholar
• Briones, M. R., K. Nelson, S. M. Beverley, H. T. Affonso, E. P. Camargo, and L. M. Floeter-Winter 1992. Leishmania tarentolae taxonomic relatedness inferred from phylogenetic analysis of the small subunit ribosomal RNA gene. Mol. Biochem. Parasitol. 53: 121–127.
   PubMedGoogle Scholar
• Brun, R., and M. Schönenberger 1979. Cultivation and in vitro cloning or procyclic culture forms of Trypanosoma brucei in a semi-defined medium. Acta Trop. 36: 289–292.
   PubMed Web of Science ®Google Scholar
• Campbell, D. A. Unpublished data.
   Google Scholar
• Campbell, D. A., K. Kubo, C. G. Clark, and J. C. Boothroyd 1987. Precise identification of cleavage sites involved in the unusual processing of trypanosome ribosomal RNA. J. Mol. Biol. 196: 113–124.
   PubMed Web of Science ®Google Scholar
• Campbell, D. A., Y. Suyama, and L. Simpson 1989. Genomic organisation of nuclear tRNAGly and tRNALeu genes in Trypanosoma brucei. Mol. Biochem. Parasitol. 37: 257–262.
   PubMedGoogle Scholar
• Campbell, D. A., D. A. Thornton, and J. C. Boothroyd 1984. Apparent discontinuous transcription of Trypanosoma brucei variant surface antigen genes. Nature 311: 350–355.
   PubMedGoogle Scholar
• Cappai, R., A. H. Osborn, and E. Handman 1994. Cloning and sequence of a Leishmania major homologue to the fibrillarin gene. Mol. Biochem. Parasitol. 64: 353–355.
   PubMedGoogle Scholar
• Christensen, M. E., J. Moloo, J. L. Swischuk, and M. E. Schelling 1986. Characterization of the nucleolar protein, B-36, using monoclonal antibodies. Exp. Cell Res. 166: 77–93.
   PubMedGoogle Scholar
• Cordingley, J. S., and M. J. Turner 1980. 6.5S RNA: preliminary characterisation of unusual small RNAs in Trypanosoma brucei. Mol. Biochem. Parasitol. 1: 91–96.
   PubMedGoogle Scholar
• Dams, E., L. Hendriks, Y. Van de Peer, J. M. Neefs, G. Smits, I. Vandenbempt, and R. De Wachter. 1988. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 16(Suppl.): 87–173.
   Google Scholar
• Devereux, J., P. Haeberli, and O. Smithies 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12: 387–395.
   PubMed Web of Science ®Google Scholar
• Dungan, J. M., K. P. Watkins, and N. Agabian 1996. Evidence for the presence of a small U5-like RNA in active trans-spliceosomes of Trypanosoma brucei. EMBO J. 15: 4016–4029.
   PubMed Web of Science ®Google Scholar
• Enright, C. A., E. S. Maxwell, and B. Sollner-Webb 1996. 5′ETS rRNA processing facilitated by four small RNAs: U14, E3, U17, and U3. RNA 2: 1094–1099.
   PubMed Web of Science ®Google Scholar
• Fleischmann, J., and D. A. Campbell 1994. Expression of the Leishmania tarentolae ubiquitin-encoding and mini-exon genes. Gene 144: 45–51.
   PubMed Web of Science ®Google Scholar
• Ganot, P., M. L. Bortolin, and T. Kiss 1997. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89: 799–809.
   PubMed Web of Science ®Google Scholar
• Ganot, P., F. M. Caizergues, and T. Kiss 1997. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 11: 941–956.
   PubMed Web of Science ®Google Scholar
• Gray, M. W. 1979. The ribosomal RNA of the trypanosomatid protozoan Crithidia fasciculata: physical characteristics and methylated sequences. Can. J. Biochem. 57: 914–926.
   PubMedGoogle Scholar
• Greenwood, S. J., M. N. Schnare, and M. W. Gray 1996. Molecular characterization of U3 small nucleolar RNA from the early diverging protist, Euglena gracilis. Curr. Genet. 30: 338–346.
   PubMedGoogle Scholar
• Gu, J., J. R. Patton, S. Shimba, and R. Reddy 1996. Localization of modified nucleotides in Schizosaccharomyces pombe spliceosomal small nuclear RNAs: modified nucleotides are clustered in functionally important regions. RNA 2: 909–918.
   PubMed Web of Science ®Google Scholar
• Hanke, J., D. O. Sanchez, J. Henriksson, L. Aslund, U. Pettersson, A. C. Frasch, and J. D. Hoheisel 1996. Mapping the Trypanosoma cruzi genome: analyses of representative cosmid libraries. BioTechniques 21: 686–688, 690–693.
   PubMedGoogle Scholar
• Hartshorne, T., and N. Agabian 1993. RNA B is the major nucleolar trimethylguanosine-capped small nuclear RNA associated with fibrillarin and pre-rRNAs in Trypanosoma brucei. Mol. Cell. Biol. 13: 144–154.
   PubMed Web of Science ®Google Scholar
• Hasan, G., M. J. Turner, and J. S. Cordingley 1984. Ribosomal RNA genes of Trypanosoma brucei: mapping the regions specifying the six small ribosomal RNAs. Gene 27: 75–86.
   PubMedGoogle Scholar
• Kiss-László, Z., Y. Henry, J. P. Bachellerie, F. M. Caizergues, and T. Kiss 1996. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85: 1077–1088.
   PubMed Web of Science ®Google Scholar
• Kooter, J. M., L. T. De, and P. Borst 1984. Discontinuous synthesis of mRNA in trypanosomes. EMBO J. 3: 2387–2392.
   PubMedGoogle Scholar
• Lafontaine, D., and D. Tollervey 1995. Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing. Biochem. Cell Biol. 73: 803–812.
   PubMedGoogle Scholar
• Leader, D. J., J. F. Sanders, R. Waugh, P. Shaw, and J. W. Brown 1994. Molecular characterisation of plant U14 small nucleolar RNA genes: closely linked genes are transcribed as polycistronic U14 transcripts. Nucleic Acids Res. 22: 5196–5203.
   PubMed Web of Science ®Google Scholar
• Maden, B. E. 1986. Identification of the locations of the methyl groups in 18S ribosomal RNA from Xenopus laevis and man. J. Mol. Biol. 189: 681–699.
   PubMedGoogle Scholar
• Maden, B. E. 1990. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 39: 241–303.
   PubMedGoogle Scholar
• Maden, B. E., M. E. Corbett, P. A. Heeney, K. Pugh, and P. M. Ajuh 1995. Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie 77: 22–29.
   PubMed Web of Science ®Google Scholar
• Maxwell, E. S., and M. J. Fournier 1995. The small nucleolar RNAs. Annu. Rev. Biochem. 64: 897–934.
   PubMed Web of Science ®Google Scholar
• Michaeli, S., D. Podell, N. Agabian, and E. Ullu 1992. The 7SL RNA homologue of Trypanosoma brucei is closely related to mammalian 7SL RNA. Mol. Biochem. Parasitol. 51: 55–64.
   PubMedGoogle Scholar
• Milhausen, M., R. G. Nelson, S. Sather, M. Selkirk, and N. Agabian 1984. Identification of a small RNA containing the trypanosome spliced leader: a donor of shared 5′ sequences of trypanosomatid mRNAs? Cell 38: 721–729.
   PubMedGoogle Scholar
• Mottram, J., K. L. Perry, P. M. Lizardi, R. Luhrmann, N. Agabian, and R. G. Nelson 1989. Isolation and sequence of four small nuclear U RNA genes of Trypanosoma brucei subsp. brucei: identification of the U2, U4, and U6 RNA analogs. Mol. Cell. Biol. 9: 1212–1223.
   PubMedGoogle Scholar
• Mottram, J. C., Y. Shafi, and J. D. Barry 1991. Sequence of a tRNA gene cluster in Trypanosoma brucei. Nucleic Acids Res. 19: 3995.
   PubMedGoogle Scholar
• Nakaar, V., A. O. Dare, D. Hong, E. Ullu, and C. Tschudi 1994. Upstream tRNA genes are essential for expression of small nuclear and cytoplasmic RNA genes in trypanosomes. Mol. Cell. Biol. 14: 6736–6742.
   PubMedGoogle Scholar
• Ni, J., A. L. Tien, and M. J. Fournier 1997. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89: 565–573.
   PubMed Web of Science ®Google Scholar
• Nicoloso, M., L. H. Qu, B. Michot, and J. P. Bachellerie 1996. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2′-O-ribose methylation of rRNAs. J. Mol. Biol. 260: 178–195.
   PubMed Web of Science ®Google Scholar
• Palfi, Z., G. L. Xu, and A. Bindereif 1994. Spliced leader-associated RNA of trypanosomes: sequence conservation and association with protein components common to trans-spliceosomal ribonucleoproteins. J. Biol. Chem. 269: 30620–30625.
   PubMed Web of Science ®Google Scholar
• Pays, E., L. Vanhamme, and M. Berberof 1994. Genetic controls for the expression of surface antigens in African trypanosomes. Annu. Rev. Microbiol. 48: 25–52.
   PubMedGoogle Scholar
• Roberts, T. G., J. M. Dungan, K. P. Watkins, and N. Agabian 1996. The SLA RNA gene of Trypanosoma brucei is organized in a tandem array which encodes several small RNAs. Mol. Biochem. Parasitol. 83: 163–174.
   PubMedGoogle Scholar
• Saito, R. M., M. G. Elgort, and D. A. Campbell 1994. A conserved upstream element is essential for transcription of the Leishmania tarentolae mini-exon gene. EMBO J. 13: 5460–5469.
   PubMedGoogle Scholar
• Schnare, M. N., S. H. Damberger, M. W. Gray, and R. R. Gutell 1996. Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA. J. Mol. Biol. 256: 701–719.
   PubMed Web of Science ®Google Scholar
• Sturm, N. R., and L. Simpson 1990. Kinetoplast DNA minicircles encode guide RNAs for editing of cytochrome oxidase subunit III mRNA. Cell 61: 879–884.
   PubMedGoogle Scholar
• Tollervey, D., and T. Kiss 1997. Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell Biol. 9: 337–342.
   PubMed Web of Science ®Google Scholar
• Tschudi, C., A. R. Krainer, and E. Ullu 1988. The U6 small nuclear RNA from Trypanosoma brucei. Nucleic Acids Res. 16: 11375.
   PubMedGoogle Scholar
• Tschudi, C., F. F. Richards, and E. Ullu 1986. The U2 RNA analogue of Trypanosoma brucei gambiense: implications for a splicing mechanism in trypanosomes. Nucleic Acids Res. 14: 8893–8903.
   PubMedGoogle Scholar
• Tyc, K., and J. A. Steitz 1989. U3, U8, and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. EMBO J. 8: 3113–3119.
   PubMed Web of Science ®Google Scholar
• Tycowski, K. T., M. D. Shu, and J. A. Steitz 1996. A mammalian gene with introns instead of exons generating stable RNA products. Nature 379: 464–466.
   PubMedGoogle Scholar
• Tycowski, K. T., C. M. Smith, M. D. Shu, and J. A. Steitz 1996. A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. Proc. Natl. Acad. Sci. USA 93: 14480–14485.
   PubMedGoogle Scholar
• Ullu, E., and C. Tschudi 1995. Accurate modification of the trypanosome spliced leader cap structure in a homologous cell-free system. J. Biol. Chem. 270: 20365–20369.
   PubMedGoogle Scholar
• Vanhamme, L., and E. Pays 1995. Control of gene expression in trypanosomes. Microbiol. Rev. 59: 223–240.
   PubMedGoogle Scholar
• Watkins, K. P., J. M. Dungan, and N. Agabian 1994. Identification of a small RNA that interacts with the 5′ splice site of the Trypanosoma brucei spliced leader RNA in vivo. Cell T6: 171–182.
   Google Scholar
• White, T. C., G. Rudenko, and P. Borst 1986. Three small RNAs within the 10 kb trypanosome rRNA transcription unit are analogous to domain VII of other eukaryotic 28S rRNAs. Nucleic Acids Res. 14: 9471–9489.
   PubMed Web of Science ®Google Scholar
• Xu, Y., H. Ben-Shlomo, and S. Michaeli 1997. The U5 RNA of trypanosomes deviates from the canonical U5 RNA: the Leptomonas collosoma U5 RNA and its coding gene. Proc. Natl. Acad. Sci. USA 94: 8473–8478.
   PubMedGoogle Scholar
• Zhong, P., S. D. Pratt, R. P. Edalji, K. A. Walter, T. F. Holzman, A. G. Shivakumar, and L. Katz 1995. Substrate requirements for ErmC′ methyltransferase activity. J. Bacteriol. 177: 4327–4332.
   PubMedGoogle Scholar