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W2012023653 abstract "In trypanosomes small nucleolar RNA (snoRNA) genes are clustered, and the clusters encode for either single or multiple RNAs. We previously reported on a genomic locus inLeptomonas collosoma that encodes for multiple C/D snoRNAs whose expression is regulated at the processing level (Xu, Y., Liu, L., Lopez-Estraño, C., and Michaeli, S. (2001) J. Biol. Chem. 276, 14289–14298). In this study we have characterized, in the same genomic locus, the first trypanosome H/ACA RNA, which we termed h1. Having a length of 69 nucleotides, h1 has the potential to guide pseudouridylation on 28 S rRNA. The h1 is processed from a long polycistronic transcript that carries both the C/D and h1 snoRNAs. The h1/rRNA duplex obeys the rules for guiding pseudouridylation. Mapping of the pseudouridine site indicated that the predicted U is indeed modified. However, in contrast to all H/ACA RNAs, h1 consists of a single hairpin structure and is the shortest H/ACA RNA described so far. In trypanosomes small nucleolar RNA (snoRNA) genes are clustered, and the clusters encode for either single or multiple RNAs. We previously reported on a genomic locus inLeptomonas collosoma that encodes for multiple C/D snoRNAs whose expression is regulated at the processing level (Xu, Y., Liu, L., Lopez-Estraño, C., and Michaeli, S. (2001) J. Biol. Chem. 276, 14289–14298). In this study we have characterized, in the same genomic locus, the first trypanosome H/ACA RNA, which we termed h1. Having a length of 69 nucleotides, h1 has the potential to guide pseudouridylation on 28 S rRNA. The h1 is processed from a long polycistronic transcript that carries both the C/D and h1 snoRNAs. The h1/rRNA duplex obeys the rules for guiding pseudouridylation. Mapping of the pseudouridine site indicated that the predicted U is indeed modified. However, in contrast to all H/ACA RNAs, h1 consists of a single hairpin structure and is the shortest H/ACA RNA described so far. pseudouridine nucleotide(s) spliced leader-associated RNA small nucleolar RNA base pair(s) reverse transcription polymerase chain reaction N-cyclohexyl-N′-β-(4-methylmorpholinium)ethylcarbodiimidep-tosylate All RNAs undergo post-transcriptional site-specific modifications. The most common modifications are conversion of uridine to pseudouridine (Ψ)1 and 2′-O-methylation of the backbone ribose. The function of the modified nucleotides is currently unknown. Most ribosomal pseudouridines and 2′-O-methyl groups are dispensable for cell growth. However, both pseudouridines and 2′-O-methyl nucleotides are clustered around the functionally important regions in the RNAs, suggesting their importance. Site-specific pseudouridylation and 2′-O-methylation of rRNA is directed by snoRNAs in the nucleolus (1Kiss-László Z. Henry Y. Bachellerie J.P. Caizergues-Ferrer M. Kiss T. Cell. 1996; 85: 1077-1088Abstract Full Text Full Text PDF PubMed Scopus (652) Google Scholar, 2Ganot P. Bortolin M.L. Kiss T. Cell. 1997; 89: 799-809Abstract Full Text Full Text PDF PubMed Scopus (486) Google Scholar, 3Ni J. Tien A.L. Fournier M.J. Cell. 1997; 89: 565-573Abstract Full Text Full Text PDF PubMed Scopus (419) Google Scholar). The snoRNAs that guide 2′-O-methylation carry two conserved boxes: the C (5′-RUGAUGA-3′), where R represents a purine (A or G), and D (5′-CUGA-3′) boxes, which often form a 5′–3′ terminal stem (1Kiss-László Z. Henry Y. Bachellerie J.P. Caizergues-Ferrer M. Kiss T. Cell. 1996; 85: 1077-1088Abstract Full Text Full Text PDF PubMed Scopus (652) Google Scholar). Fibrillarin shares common motifs with known methyltransferases and is likely to be the enzyme that catalyzes the formation of the 2′-O-methyl nucleotide (4Smith C.M. Steitz J.A. Cell. 1997; 89: 669-672Abstract Full Text Full Text PDF PubMed Scopus (278) Google Scholar, 5Bachellerie J.-P. Cavaille J. Qu L.-H. Garrett R.A. Douthwaite S.R. Liljas A. Matheson A.T. Moore P.R. Noller H.F. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions. ASM Press, Washington, D. C.2000: 191-203Google Scholar, 6Tollervey D. Kiss T. Curr. Opin. Cell Biol. 1997; 9: 337-342Crossref PubMed Scopus (375) Google Scholar). Many snoRNAs also carry internal C′ and D′ boxes. The D and/or D′ boxes are preceded by 10–21 nt that are a perfect match to the rRNA sequences. The modified nucleotide is always present 5 nt upstream to the D/D′ box. This is known as the +5 rule (1Kiss-László Z. Henry Y. Bachellerie J.P. Caizergues-Ferrer M. Kiss T. Cell. 1996; 85: 1077-1088Abstract Full Text Full Text PDF PubMed Scopus (652) Google Scholar).More relevant to this study are the snoRNAs that guide pseudouridylation. Structurally these snoRNAs consist of two hairpin domains connected by a single-stranded hinge, the H (ANANNA) domain, and a tail region, the ACA box. Two short rRNA recognition motifs of the snoRNA base pair with rRNA sequences flanking the uridine to be pseudouridylated. The Ψ is always located 14–16 nt upstream to the H or ACA box of the snoRNA (2Ganot P. Bortolin M.L. Kiss T. Cell. 1997; 89: 799-809Abstract Full Text Full Text PDF PubMed Scopus (486) Google Scholar, 3Ni J. Tien A.L. Fournier M.J. Cell. 1997; 89: 565-573Abstract Full Text Full Text PDF PubMed Scopus (419) Google Scholar, 7Bortolin M.L. Ganot P. Kiss T. EMBO J. 1999; 18: 457-469Crossref PubMed Scopus (98) Google Scholar).Although the snoRNAs select the site to be modified on the target RNA, the snoRNP proteins may carry out the actual modification. Four H/ACA binding proteins have been identified: Gar1P, Cb5p (which shows striking structural similarities to pseudouridine synthase), Nhp2p, and Nop10p (5Bachellerie J.-P. Cavaille J. Qu L.-H. Garrett R.A. Douthwaite S.R. Liljas A. Matheson A.T. Moore P.R. Noller H.F. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions. ASM Press, Washington, D. C.2000: 191-203Google Scholar, 8Balakin A.G. Smith L. Fournier M.J. Cell. 1996; 86: 823-834Abstract Full Text Full Text PDF PubMed Scopus (378) Google Scholar, 9Henras A. Henry Y. Bousquet-Antonelli C. Noaillac-Depeyre J. Gélugne J.P. Caizergues-Ferrer M. EMBO J. 1998; 17: 7078-7090Crossref PubMed Scopus (196) Google Scholar, 10Watkins N.J. Gottschalk A. Neubauer G. Kastner B. Fabrizio P. Mann M. Lührmann R. RNA. 1998; 4: 1549-1568Crossref PubMed Scopus (188) Google Scholar). So far none of these proteins were identified in trypanosomes. Interestingly a nucleolar protein was identified inTrypanosoma brucei that may play a role in RNA metabolism in the nucleolus (11Das A. Peterson G.C. Kanner S.B. Frevert U. Parsons M. J. Biol. Chem. 1996; 271: 15675-15681Abstract Full Text Full Text PDF PubMed Scopus (33) Google Scholar).In vertebrates many of the guide snoRNAs are encoded by introns of host genes that encode for proteins involved in ribosome biogenesis and function (6Tollervey D. Kiss T. Curr. Opin. Cell Biol. 1997; 9: 337-342Crossref PubMed Scopus (375) Google Scholar, 12Weinstein L.B. Steitz J.A. Curr. Opin. Cell Biol. 1999; 11: 378-384Crossref PubMed Scopus (249) Google Scholar). In yeast, only a few snoRNAs are encoded by introns, and most of them are independently transcribed (13Lowe T.M. Eddy S.R. Science. 1999; 283: 1168-1171Crossref PubMed Scopus (384) Google Scholar). The maturation of most of the intron-encoded snoRNAs involves debranching of the lariat and exonucleolytic trimming (14Ooi S.L. Samarsky D.A. Fournier M.J. Boeke J.D. RNA. 1998; 4: 1096-1110Crossref PubMed Scopus (90) Google Scholar). The self-transcribed snoRNAs are processed from a precursor by endonucleolytic cleavage and exonucleolytic trimming (15Villa T. Ceradini F. Presutti C. Bozzoni I. Mol. Cell. Biol. 1998; 18: 3376-3383Crossref PubMed Scopus (54) Google Scholar). In yeast, two exonucleases, Rat1 and Xrn1, were shown to carry out 5′ to 3′ trimming (15Villa T. Ceradini F. Presutti C. Bozzoni I. Mol. Cell. Biol. 1998; 18: 3376-3383Crossref PubMed Scopus (54) Google Scholar, 16Petfalski E. Dandekar T. Henry Y. Tollervey D. Mol. Cell. Biol. 1998; 18: 1181-1189Crossref PubMed Scopus (174) Google Scholar, 17Qu L.H. Henras A. Lu Y.J. Zhou H. Zhou W.X. Zhu Y.Q. Zhao J. Henry Y. Caizergues-Ferrer M. Bachellerie J.P. Mol. Cell. Biol. 1999; 19: 1144-1158Crossref PubMed Scopus (137) Google Scholar), and the endonuclease that cleaves the snoRNA precursors carrying either H/ACA or C/D snoRNA is Rnt1, which is the yeast homologue of bacterial RNase III (18Chanfreau G. Legrain P. Jacquier A. J. Mol. Biol. 1998; 284: 975-988Crossref PubMed Scopus (138) Google Scholar, 19Chanfreau G. Rotondo G. Legrain P. Jacquier A. EMBO J. 1998; 17: 3726-3737Crossref PubMed Scopus (140) Google Scholar). A splicing-independent processing pathway that functions in processing clustered snoRNAs carrying both C/D and H/ACA snoRNAs operates in plants (20Leader D.J. Clark G.P. Watters J. Beven A.F. Shaw P.J. Brown J.W. Plant Mol. Biol. 1999; 39: 1091-1100Crossref PubMed Scopus (29) Google Scholar).Trypanosomatids are protozoan parasites that diverged early in the eukaryotic lineage and possess unique RNA processing pathways such astrans-splicing and RNA editing. Trypanosome rRNAs undergo a nonconventional processing pathway that results in cleaving the 28 S rRNA into two large and six small rRNA fragments (21Campbell D.A. Kubo K. Clark C.G. Boothroyd J.C. J. Mol. Biol. 1987; 196: 113-124Crossref PubMed Scopus (97) Google Scholar).Very little is known about ribosome biogenesis and modification in trypanosomatids. However, C/D snoRNAs were characterized in several trypanosomatid species (22Levitan A. Xu Y. Ben-Dov C. Ben-Shlomo H. Zhang Y. Michaeli S. Nucleic Acids Res. 1998; 26: 1775-1783Crossref PubMed Scopus (21) Google Scholar, 23Roberts T.G. Sturm N.R. Yee B.K., Yu, M.C. Hartshorne T. Agabian N. Campbell D.A. Mol. Cell. Biol. 1998; 18: 4409-4417Crossref PubMed Scopus (41) Google Scholar, 24Dunbar D.A. Wormsley S. Lowe T.M. Baserga S.J. J. Biol. Chem. 2000; 275: 14767-14776Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar, 25Dunbar D.A. Chen A.A. Wormsley S. Baserga S.J. Nucleic Acids Res. 2000; 28: 2855-2861Crossref PubMed Google Scholar, 26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). The first study on trypanosome snoRNAs suggested that trypanosomes obey the +5 rule for snoRNA-mediated methylation (22Levitan A. Xu Y. Ben-Dov C. Ben-Shlomo H. Zhang Y. Michaeli S. Nucleic Acids Res. 1998; 26: 1775-1783Crossref PubMed Scopus (21) Google Scholar). However, studies carried out on snoRNAs that are located within the spliced leader-associated (SLA1) RNA loci in several trypanosomatid species suggested that trypanosomes do not obey the general methylation rules and indicated that the methylation site can have an alternate position located 6 or even 1 nt upstream to the D or D′ box (23Roberts T.G. Sturm N.R. Yee B.K., Yu, M.C. Hartshorne T. Agabian N. Campbell D.A. Mol. Cell. Biol. 1998; 18: 4409-4417Crossref PubMed Scopus (41) Google Scholar). Further studies of T. brucei analyzing 17 C/D snoRNAs identified by immunoprecipitation using antibodies raised against the T. brucei fibrillarin protein concluded thatT. brucei obeys the +5 rule (24Dunbar D.A. Wormsley S. Lowe T.M. Baserga S.J. J. Biol. Chem. 2000; 275: 14767-14776Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar). A more recent study performed on snoRNAs present in two clusters in Leptomonas collosoma suggested that the methylation-guiding rule of trypanosomatid snoRNA is not unusual; also L. collosomaobeys the +5 rule (26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). As opposed to C/D snoRNAs, nothing is known about trypanosome H/ACA RNA.Cloning and sequencing of trypanosomatid snoRNA genes suggest that the snoRNAs are organized in clusters that carry single or multiple RNAs (22Levitan A. Xu Y. Ben-Dov C. Ben-Shlomo H. Zhang Y. Michaeli S. Nucleic Acids Res. 1998; 26: 1775-1783Crossref PubMed Scopus (21) Google Scholar, 26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). The snoRNA genes analyzed are transcribed as polycistronic RNAs (25Dunbar D.A. Chen A.A. Wormsley S. Baserga S.J. Nucleic Acids Res. 2000; 28: 2855-2861Crossref PubMed Google Scholar, 26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar) that are further processed to generate the mature RNAs. Expression studies on snoRNA-2, which encodes for a single C/D snoRNA, suggest that expression of the gene, when cloned into the pXneo episomal vector, requires at least a 20-bp flanking sequence. However, expression of the tagged gene, although at a lower level, was detected in the absence of an upstream sequence, suggesting the lack of a conventional promoter adjacent to the gene. The expression of the snoRNA genes, however, is dependent on the transcription from the upstream episomal neo gene. Data obtained from transcription in permeable cells suggest that snoRNA genes are transcribed by RNA polymerase II. Interestingly all C/D snoRNAs are flanked by sequences that form a perfect stem structure. The significance of this stem for the processing of the snoRNA is currently unknown (26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar).In this study, we have cloned and sequenced the entire repeat that was recently described (26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). Additional three C/D snoRNAs (B3, B4, and B5) and two copies of the first trypanosome H/ACA RNA, termed h1 RNA, were revealed. h1 is 69 nt long and can be folded into the canonical H/ACA RNA structure but consists of only a single hairpin structure rather than two hairpins connected by a single-stranded hinge and tail regions. However, h1 carries an AGA box at the 3′-end. Two short motifs of h1 in the internal loop base pair with the 28 S rRNA sequence flanking the target uridine. Mapping of the pseudouridines present in this region indicated that U3643 on 28 S rRNA, the predicted site, is indeed pseudouridylated. The h1 is present on the same polycistronic transcript that encodes for the C/D snoRNAs. Like the C/D snoRNAs, h1 is flanked by a stem structure. This is the first report on a trypanosome H/ACA RNA. h1 is the shortest H/ACA RNA described so far. All RNAs undergo post-transcriptional site-specific modifications. The most common modifications are conversion of uridine to pseudouridine (Ψ)1 and 2′-O-methylation of the backbone ribose. The function of the modified nucleotides is currently unknown. Most ribosomal pseudouridines and 2′-O-methyl groups are dispensable for cell growth. However, both pseudouridines and 2′-O-methyl nucleotides are clustered around the functionally important regions in the RNAs, suggesting their importance. Site-specific pseudouridylation and 2′-O-methylation of rRNA is directed by snoRNAs in the nucleolus (1Kiss-László Z. Henry Y. Bachellerie J.P. Caizergues-Ferrer M. Kiss T. Cell. 1996; 85: 1077-1088Abstract Full Text Full Text PDF PubMed Scopus (652) Google Scholar, 2Ganot P. Bortolin M.L. Kiss T. Cell. 1997; 89: 799-809Abstract Full Text Full Text PDF PubMed Scopus (486) Google Scholar, 3Ni J. Tien A.L. Fournier M.J. Cell. 1997; 89: 565-573Abstract Full Text Full Text PDF PubMed Scopus (419) Google Scholar). The snoRNAs that guide 2′-O-methylation carry two conserved boxes: the C (5′-RUGAUGA-3′), where R represents a purine (A or G), and D (5′-CUGA-3′) boxes, which often form a 5′–3′ terminal stem (1Kiss-László Z. Henry Y. Bachellerie J.P. Caizergues-Ferrer M. Kiss T. Cell. 1996; 85: 1077-1088Abstract Full Text Full Text PDF PubMed Scopus (652) Google Scholar). Fibrillarin shares common motifs with known methyltransferases and is likely to be the enzyme that catalyzes the formation of the 2′-O-methyl nucleotide (4Smith C.M. Steitz J.A. Cell. 1997; 89: 669-672Abstract Full Text Full Text PDF PubMed Scopus (278) Google Scholar, 5Bachellerie J.-P. Cavaille J. Qu L.-H. Garrett R.A. Douthwaite S.R. Liljas A. Matheson A.T. Moore P.R. Noller H.F. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions. ASM Press, Washington, D. C.2000: 191-203Google Scholar, 6Tollervey D. Kiss T. Curr. Opin. Cell Biol. 1997; 9: 337-342Crossref PubMed Scopus (375) Google Scholar). Many snoRNAs also carry internal C′ and D′ boxes. The D and/or D′ boxes are preceded by 10–21 nt that are a perfect match to the rRNA sequences. The modified nucleotide is always present 5 nt upstream to the D/D′ box. This is known as the +5 rule (1Kiss-László Z. Henry Y. Bachellerie J.P. Caizergues-Ferrer M. Kiss T. Cell. 1996; 85: 1077-1088Abstract Full Text Full Text PDF PubMed Scopus (652) Google Scholar). More relevant to this study are the snoRNAs that guide pseudouridylation. Structurally these snoRNAs consist of two hairpin domains connected by a single-stranded hinge, the H (ANANNA) domain, and a tail region, the ACA box. Two short rRNA recognition motifs of the snoRNA base pair with rRNA sequences flanking the uridine to be pseudouridylated. The Ψ is always located 14–16 nt upstream to the H or ACA box of the snoRNA (2Ganot P. Bortolin M.L. Kiss T. Cell. 1997; 89: 799-809Abstract Full Text Full Text PDF PubMed Scopus (486) Google Scholar, 3Ni J. Tien A.L. Fournier M.J. Cell. 1997; 89: 565-573Abstract Full Text Full Text PDF PubMed Scopus (419) Google Scholar, 7Bortolin M.L. Ganot P. Kiss T. EMBO J. 1999; 18: 457-469Crossref PubMed Scopus (98) Google Scholar). Although the snoRNAs select the site to be modified on the target RNA, the snoRNP proteins may carry out the actual modification. Four H/ACA binding proteins have been identified: Gar1P, Cb5p (which shows striking structural similarities to pseudouridine synthase), Nhp2p, and Nop10p (5Bachellerie J.-P. Cavaille J. Qu L.-H. Garrett R.A. Douthwaite S.R. Liljas A. Matheson A.T. Moore P.R. Noller H.F. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions. ASM Press, Washington, D. C.2000: 191-203Google Scholar, 8Balakin A.G. Smith L. Fournier M.J. Cell. 1996; 86: 823-834Abstract Full Text Full Text PDF PubMed Scopus (378) Google Scholar, 9Henras A. Henry Y. Bousquet-Antonelli C. Noaillac-Depeyre J. Gélugne J.P. Caizergues-Ferrer M. EMBO J. 1998; 17: 7078-7090Crossref PubMed Scopus (196) Google Scholar, 10Watkins N.J. Gottschalk A. Neubauer G. Kastner B. Fabrizio P. Mann M. Lührmann R. RNA. 1998; 4: 1549-1568Crossref PubMed Scopus (188) Google Scholar). So far none of these proteins were identified in trypanosomes. Interestingly a nucleolar protein was identified inTrypanosoma brucei that may play a role in RNA metabolism in the nucleolus (11Das A. Peterson G.C. Kanner S.B. Frevert U. Parsons M. J. Biol. Chem. 1996; 271: 15675-15681Abstract Full Text Full Text PDF PubMed Scopus (33) Google Scholar). In vertebrates many of the guide snoRNAs are encoded by introns of host genes that encode for proteins involved in ribosome biogenesis and function (6Tollervey D. Kiss T. Curr. Opin. Cell Biol. 1997; 9: 337-342Crossref PubMed Scopus (375) Google Scholar, 12Weinstein L.B. Steitz J.A. Curr. Opin. Cell Biol. 1999; 11: 378-384Crossref PubMed Scopus (249) Google Scholar). In yeast, only a few snoRNAs are encoded by introns, and most of them are independently transcribed (13Lowe T.M. Eddy S.R. Science. 1999; 283: 1168-1171Crossref PubMed Scopus (384) Google Scholar). The maturation of most of the intron-encoded snoRNAs involves debranching of the lariat and exonucleolytic trimming (14Ooi S.L. Samarsky D.A. Fournier M.J. Boeke J.D. RNA. 1998; 4: 1096-1110Crossref PubMed Scopus (90) Google Scholar). The self-transcribed snoRNAs are processed from a precursor by endonucleolytic cleavage and exonucleolytic trimming (15Villa T. Ceradini F. Presutti C. Bozzoni I. Mol. Cell. Biol. 1998; 18: 3376-3383Crossref PubMed Scopus (54) Google Scholar). In yeast, two exonucleases, Rat1 and Xrn1, were shown to carry out 5′ to 3′ trimming (15Villa T. Ceradini F. Presutti C. Bozzoni I. Mol. Cell. Biol. 1998; 18: 3376-3383Crossref PubMed Scopus (54) Google Scholar, 16Petfalski E. Dandekar T. Henry Y. Tollervey D. Mol. Cell. Biol. 1998; 18: 1181-1189Crossref PubMed Scopus (174) Google Scholar, 17Qu L.H. Henras A. Lu Y.J. Zhou H. Zhou W.X. Zhu Y.Q. Zhao J. Henry Y. Caizergues-Ferrer M. Bachellerie J.P. Mol. Cell. Biol. 1999; 19: 1144-1158Crossref PubMed Scopus (137) Google Scholar), and the endonuclease that cleaves the snoRNA precursors carrying either H/ACA or C/D snoRNA is Rnt1, which is the yeast homologue of bacterial RNase III (18Chanfreau G. Legrain P. Jacquier A. J. Mol. Biol. 1998; 284: 975-988Crossref PubMed Scopus (138) Google Scholar, 19Chanfreau G. Rotondo G. Legrain P. Jacquier A. EMBO J. 1998; 17: 3726-3737Crossref PubMed Scopus (140) Google Scholar). A splicing-independent processing pathway that functions in processing clustered snoRNAs carrying both C/D and H/ACA snoRNAs operates in plants (20Leader D.J. Clark G.P. Watters J. Beven A.F. Shaw P.J. Brown J.W. Plant Mol. Biol. 1999; 39: 1091-1100Crossref PubMed Scopus (29) Google Scholar). Trypanosomatids are protozoan parasites that diverged early in the eukaryotic lineage and possess unique RNA processing pathways such astrans-splicing and RNA editing. Trypanosome rRNAs undergo a nonconventional processing pathway that results in cleaving the 28 S rRNA into two large and six small rRNA fragments (21Campbell D.A. Kubo K. Clark C.G. Boothroyd J.C. J. Mol. Biol. 1987; 196: 113-124Crossref PubMed Scopus (97) Google Scholar). Very little is known about ribosome biogenesis and modification in trypanosomatids. However, C/D snoRNAs were characterized in several trypanosomatid species (22Levitan A. Xu Y. Ben-Dov C. Ben-Shlomo H. Zhang Y. Michaeli S. Nucleic Acids Res. 1998; 26: 1775-1783Crossref PubMed Scopus (21) Google Scholar, 23Roberts T.G. Sturm N.R. Yee B.K., Yu, M.C. Hartshorne T. Agabian N. Campbell D.A. Mol. Cell. Biol. 1998; 18: 4409-4417Crossref PubMed Scopus (41) Google Scholar, 24Dunbar D.A. Wormsley S. Lowe T.M. Baserga S.J. J. Biol. Chem. 2000; 275: 14767-14776Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar, 25Dunbar D.A. Chen A.A. Wormsley S. Baserga S.J. Nucleic Acids Res. 2000; 28: 2855-2861Crossref PubMed Google Scholar, 26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). The first study on trypanosome snoRNAs suggested that trypanosomes obey the +5 rule for snoRNA-mediated methylation (22Levitan A. Xu Y. Ben-Dov C. Ben-Shlomo H. Zhang Y. Michaeli S. Nucleic Acids Res. 1998; 26: 1775-1783Crossref PubMed Scopus (21) Google Scholar). However, studies carried out on snoRNAs that are located within the spliced leader-associated (SLA1) RNA loci in several trypanosomatid species suggested that trypanosomes do not obey the general methylation rules and indicated that the methylation site can have an alternate position located 6 or even 1 nt upstream to the D or D′ box (23Roberts T.G. Sturm N.R. Yee B.K., Yu, M.C. Hartshorne T. Agabian N. Campbell D.A. Mol. Cell. Biol. 1998; 18: 4409-4417Crossref PubMed Scopus (41) Google Scholar). Further studies of T. brucei analyzing 17 C/D snoRNAs identified by immunoprecipitation using antibodies raised against the T. brucei fibrillarin protein concluded thatT. brucei obeys the +5 rule (24Dunbar D.A. Wormsley S. Lowe T.M. Baserga S.J. J. Biol. Chem. 2000; 275: 14767-14776Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar). A more recent study performed on snoRNAs present in two clusters in Leptomonas collosoma suggested that the methylation-guiding rule of trypanosomatid snoRNA is not unusual; also L. collosomaobeys the +5 rule (26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). As opposed to C/D snoRNAs, nothing is known about trypanosome H/ACA RNA. Cloning and sequencing of trypanosomatid snoRNA genes suggest that the snoRNAs are organized in clusters that carry single or multiple RNAs (22Levitan A. Xu Y. Ben-Dov C. Ben-Shlomo H. Zhang Y. Michaeli S. Nucleic Acids Res. 1998; 26: 1775-1783Crossref PubMed Scopus (21) Google Scholar, 26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). The snoRNA genes analyzed are transcribed as polycistronic RNAs (25Dunbar D.A. Chen A.A. Wormsley S. Baserga S.J. Nucleic Acids Res. 2000; 28: 2855-2861Crossref PubMed Google Scholar, 26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar) that are further processed to generate the mature RNAs. Expression studies on snoRNA-2, which encodes for a single C/D snoRNA, suggest that expression of the gene, when cloned into the pXneo episomal vector, requires at least a 20-bp flanking sequence. However, expression of the tagged gene, although at a lower level, was detected in the absence of an upstream sequence, suggesting the lack of a conventional promoter adjacent to the gene. The expression of the snoRNA genes, however, is dependent on the transcription from the upstream episomal neo gene. Data obtained from transcription in permeable cells suggest that snoRNA genes are transcribed by RNA polymerase II. Interestingly all C/D snoRNAs are flanked by sequences that form a perfect stem structure. The significance of this stem for the processing of the snoRNA is currently unknown (26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). In this study, we have cloned and sequenced the entire repeat that was recently described (26Xu Y. Liu L. Lopez-Estraño C. Michaeli S. J. Biol. Chem. 2001; 276: 14289-14298Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). Additional three C/D snoRNAs (B3, B4, and B5) and two copies of the first trypanosome H/ACA RNA, termed h1 RNA, were revealed. h1 is 69 nt long and can be folded into the canonical H/ACA RNA structure but consists of only a single hairpin structure rather than two hairpins connected by a single-stranded hinge and tail regions. However, h1 carries an AGA box at the 3′-end. Two short motifs of h1 in the internal loop base pair with the 28 S rRNA sequence flanking the target uridine. Mapping of the pseudouridines present in this region indicated that U3643 on 28 S rRNA, the predicted site, is indeed pseudouridylated. The h1 is present on the same polycistronic transcript that encodes for the C/D snoRNAs. Like the C/D snoRNAs, h1 is flanked by a stem structure. This is the first report on a trypanosome H/ACA RNA. h1 is the shortest H/ACA RNA described so far. We thank Yu-xin Xu from many helpful discussions." @default.
W2012023653 created "2016-06-24" @default.
W2012023653 creator A5035551086 @default.
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W2012023653 title "Identification of the First Trypanosome H/ACA RNA That Guides Pseudouridine Formation on rRNA" @default.
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