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Kramer S, Meyer-Natus E, Stigloher C, Thoma H, Schnaufer A, Engstler M. Parallel monitoring of RNA abundance, localization and compactness with correlative single molecule FISH on LR White embedded samples. Nucleic Acids Res 2021; 49:e14. [PMID: 33275141 PMCID: PMC7897490 DOI: 10.1093/nar/gkaa1142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/16/2020] [Accepted: 11/17/2020] [Indexed: 01/19/2023] Open
Abstract
Single mRNA molecules are frequently detected by single molecule fluorescence in situ hybridization (smFISH) using branched DNA technology. While providing strong and background-reduced signals, the method is inefficient in detecting mRNAs within dense structures, in monitoring mRNA compactness and in quantifying abundant mRNAs. To overcome these limitations, we have hybridized slices of high pressure frozen, freeze-substituted and LR White embedded cells (LR White smFISH). mRNA detection is physically restricted to the surface of the resin. This enables single molecule detection of RNAs with accuracy comparable to RNA sequencing, irrespective of their abundance, while at the same time providing spatial information on RNA localization that can be complemented with immunofluorescence and electron microscopy, as well as array tomography. Moreover, LR White embedding restricts the number of available probe pair recognition sites for each mRNA to a small subset. As a consequence, differences in signal intensities between RNA populations reflect differences in RNA structures, and we show that the method can be employed to determine mRNA compactness. We apply the method to answer some outstanding questions related to trans-splicing, RNA granules and mitochondrial RNA editing in single-cellular trypanosomes and we show an example of differential gene expression in the metazoan Caenorhabditis elegans.
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Affiliation(s)
- Susanne Kramer
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | | | - Christian Stigloher
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany.,Imaging Core Facility, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Hanna Thoma
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Achim Schnaufer
- Institute for Immunology & Infection Research, University of Edinburgh, Edinburgh, UK
| | - Markus Engstler
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
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Inoue AH, Serpeloni M, Hiraiwa PM, Yamada-Ogatta SF, Muniz JRC, Motta MCM, Vidal NM, Goldenberg S, Ávila AR. Identification of a novel nucleocytoplasmic shuttling RNA helicase of trypanosomes. PLoS One 2014; 9:e109521. [PMID: 25313564 PMCID: PMC4196910 DOI: 10.1371/journal.pone.0109521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression in trypanosomes is controlled mostly by post-transcriptional pathways. Little is known about the components of mRNA nucleocytoplasmic export routes in these parasites. Comparative genomics has shown that the mRNA transport pathway is the least conserved pathway among eukaryotes. Nonetheless, we identified a RNA helicase (Hel45) that is conserved across eukaryotes and similar to shuttling proteins involved in mRNA export. We used in silico analysis to predict the structure of Trypanosoma cruzi Hel45, including the N-terminal domain and the C-terminal domain, and our findings suggest that this RNA helicase can form complexes with mRNA. Hel45 was present in both nucleus and cytoplasm. Electron microscopy showed that Hel45 is clustered close to the cytoplasmic side of nuclear pore complexes, and is also present in the nucleus where it is associated with peripheral compact chromatin. Deletion of a predicted Nuclear Export Signal motif led to the accumulation of Hel45ΔNES in the nucleus, indicating that Hel45 shuttles between the nucleus and the cytoplasm. This transport was dependent on active transcription but did not depend on the exportin Crm1. Knockdown of Mex67 in T. brucei caused the nuclear accumulation of the T. brucei ortholog of Hel45. Indeed, Hel45 is present in mRNA ribonucleoprotein complexes that are not associated with polysomes. It is still necessary to confirm the precise function of Hel45. However, this RNA helicase is associated with mRNA metabolism and its nucleocytoplasmic shuttling is dependent on an mRNA export route involving Mex67 receptor.
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Affiliation(s)
| | - Mariana Serpeloni
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
- Departamento de Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | | | - Maria Cristina Machado Motta
- Departamento de Biologia Celular e Parasitologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Newton Medeiros Vidal
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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SL RNA Biogenesis in Kinetoplastids: A Long and Winding Road. RNA METABOLISM IN TRYPANOSOMES 2012. [DOI: 10.1007/978-3-642-28687-2_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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4
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Gupta SK, Hury A, Ziporen Y, Shi H, Ullu E, Michaeli S. Small nucleolar RNA interference in Trypanosoma brucei: mechanism and utilization for elucidating the function of snoRNAs. Nucleic Acids Res 2010; 38:7236-47. [PMID: 20601683 PMCID: PMC2978370 DOI: 10.1093/nar/gkq599] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Expression of dsRNA complementary to small nucleolar RNAs (snoRNAs) in Trypanosoma brucei results in snoRNA silencing, termed snoRNAi. Here, we demonstrate that snoRNAi requires the nuclear TbDCL2 protein, but not TbDCL1, which is involved in RNA interference (RNAi) in the cytoplasm. snoRNAi depends on Argonaute1 (Slicer), and on TbDCL2, suggesting that snoRNA dicing and slicing takes place in the nucleus, and further suggesting that AGO1 is active in nuclear silencing. snoRNAi was next utilized to elucidate the function of an abundant snoRNA, TB11Cs2C2 (92 nt), present in a cluster together with the spliced leader associated RNA (SLA1) and snR30, which are both H/ACA RNAs with special nuclear functions. Using AMT-UV cross-linking and RNaseH cleavage, we provide evidence for the interaction of TB11Cs2C2 with the small rRNAs, srRNA-2 and srRNA-6, which are part of the large subunit (LSU) rRNA. snoRNAi of TB11Cs2C2 resulted in defects in generating srRNA-2 and LSUβ rRNA. This is the first snoRNA described so far to engage in trypanosome-specific processing events.
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Affiliation(s)
- Sachin Kumar Gupta
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
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5
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Lee MC, Toh LL, Yaw LP, Luo Y. Drosophila octamer elements and Pdm-1 dictate the coordinated transcription of core histone genes. J Biol Chem 2010; 285:9041-53. [PMID: 20097756 DOI: 10.1074/jbc.m109.075358] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We reveal a set of divergent octamer elements in Drosophila melanogaster (dm) core histone gene promoters. These elements recruit transcription factor POU-domain protein in D. melanogaster 1 (Pdm-1), which along with co-activator dmOct-1 coactivator in S-phase (dmOCA-S), activates transcription from at least the Drosophila histone 2B (dmH2B) and 4 (dmH4) promoters in a fashion similar to the transcription of mammalian histone 2B (H2B) gene activated by octamer binding transcription factor 1 (Oct-1) and Oct-1 coactivator in S-phase (OCA-S). The expression of core histone genes in both kingdoms is coordinated; however, although the expression of mammalian histone genes involves subtype-specific transcription factors and/or co-activator(s), the expression of Drosophila core histone genes is regulated by a common module (Pdm-1/dmOCA-S) in a directly coordinated manner. Finally, dmOCA-S is recruited to the Drosophila histone locus bodies in the S-phase, marking S-phase-specific transcription activation of core histone genes.
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Affiliation(s)
- Mei-Chin Lee
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore
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Nocua P, Gómez C, Cuervo C, Puerta C. Cl gene cluster encoding several small nucleolar RNAs: a comparison amongst trypanosomatids. Mem Inst Oswaldo Cruz 2009; 104:473-80. [PMID: 19547875 DOI: 10.1590/s0074-02762009000300013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 03/03/2009] [Indexed: 11/22/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are small non-coding RNAs that modify RNA molecules such as rRNA and snRNA by guiding 2'-O-ribose methylation (C/D box snoRNA family) and pseudouridylation reactions (H/ACA snoRNA family). H/ACA snoRNAs are also involved in trans-splicing in trypanosomatids. The aims of this work were to characterise the Cl gene cluster that encodes several snoRNAs in Trypanosoma rangeli and compare it with clusters from Trypanosoma cruzi, Trypanosoma brucei, Leishmania major, Leishmania infantum, Leishmania braziliensis and Leptomonas collosoma. The T. rangeli Cl gene cluster is an 801 base pair (bp) repeat sequence that encodes three C/D (Cl1, Cl2 and Cl4) and three H/ACA (Cl3, Cl5 and Cl6) snoRNAs. In contrast to T. brucei, the Cl3 and Cl5 homologues have not been annotated in the Leishmania or T. cruzi genome projects (http//:www.genedb.org). Of note, snoRNA transcribed regions have a high degree of sequence identity among all species and share gene synteny. Collectively, these findings suggest that the Cl cluster could constitute an interesting target for therapeutic (gene silencing) or diagnostic intervention strategies (PCR-derived tools).
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Affiliation(s)
- Paola Nocua
- Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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Trypanosoma brucei spliced leader RNA maturation by the cap 1 2'-O-ribose methyltransferase and SLA1 H/ACA snoRNA pseudouridine synthase complex. Mol Cell Biol 2008; 29:1202-11. [PMID: 19103757 DOI: 10.1128/mcb.01496-08] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Kinetoplastid flagellates attach a 39-nucleotide spliced leader (SL) upstream of protein-coding regions in polycistronic RNA precursors through trans splicing. SL modifications include cap 2'-O-ribose methylation of the first four nucleotides and pseudouridine (psi) formation at uracil 28. In Trypanosoma brucei, TbMTr1 performs 2'-O-ribose methylation of the first transcribed nucleotide, or cap 1. We report the characterization of an SL RNA processing complex with TbMTr1 and the SLA1 H/ACA small nucleolar ribonucleoprotein (snoRNP) particle that guides SL psi(28) formation. TbMTr1 is in a high-molecular-weight complex containing the four conserved core proteins of H/ACA snoRNPs, a kinetoplastid-specific protein designated methyltransferase-associated protein (TbMTAP), and the SLA1 snoRNA. TbMTAP-null lines are viable but have decreased SL RNA processing efficiency in cap methylation, 3'-end maturation, and psi(28) formation. TbMTAP is required for association between TbMTr1 and the SLA1 snoRNP but does not affect U1 small nuclear RNA methylation. A complex methylation profile in the mRNA population of TbMTAP-null lines indicates an additional effect on cap 4 methylations. The TbMTr1 complex specializes the SLA1 H/ACA snoRNP for efficient processing of multiple modifications on the SL RNA substrate.
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Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S, Unger R. Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes. BMC Bioinformatics 2008; 9:471. [PMID: 18986541 PMCID: PMC2613932 DOI: 10.1186/1471-2105-9-471] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 11/05/2008] [Indexed: 11/12/2022] Open
Abstract
Background Detection of non coding RNA (ncRNA) molecules is a major bioinformatics challenge. This challenge is particularly difficult when attempting to detect H/ACA molecules which are involved in converting uridine to pseudouridine on rRNA in trypanosomes, because these organisms have unique H/ACA molecules (termed H/ACA-like) that lack several of the features that characterize H/ACA molecules in most other organisms. Results We present here a computational tool called Psiscan, which was designed to detect H/ACA-like molecules in trypanosomes. We started by analyzing known H/ACA-like molecules and characterized their crucial elements both computationally and experimentally. Next, we set up constraints based on this analysis and additional phylogenic and functional data to rapidly scan three trypanosome genomes (T. brucei, T. cruzi and L. major) for sequences that observe these constraints and are conserved among the species. In the next step, we used minimal energy calculation to select the molecules that are predicted to fold into a lowest energy structure that is consistent with the constraints. In the final computational step, we used a Support Vector Machine that was trained on known H/ACA-like molecules as positive examples and on negative examples of molecules that were identified by the computational analyses but were shown experimentally not to be H/ACA-like molecules. The leading candidate molecules predicted by the SVM model were then subjected to experimental validation. Conclusion The experimental validation showed 11 molecules to be expressed (4 out of 25 in the intermediate stage and 7 out of 19 in the final validation after the machine learning stage). Five of these 11 molecules were further shown to be bona fide H/ACA-like molecules. As snoRNA in trypanosomes are organized in clusters, the new H/ACA-like molecules could be used as starting points to manually search for additional molecules in their neighbourhood. All together this study increased our repertoire by fourteen H/ACA-like and six C/D snoRNAs molecules from T. brucei and L. Major. In addition the experimental analysis revealed that six ncRNA molecules that are expressed are not downregulated in CBF5 silenced cells, suggesting that they have structural features of H/ACA-like molecules but do not have their standard function. We termed this novel class of molecules AGA-like, and we are exploring their function. This study demonstrates the power of tight collaboration between computational and experimental approaches in a combined effort to reveal the repertoire of ncRNA molecles.
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Affiliation(s)
- Inna Myslyuk
- Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel.
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9
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Hellman K, Prohaska K, Williams N. Trypanosoma brucei RNA binding proteins p34 and p37 mediate NOPP44/46 cellular localization via the exportin 1 nuclear export pathway. EUKARYOTIC CELL 2007; 6:2206-13. [PMID: 17921352 PMCID: PMC2168238 DOI: 10.1128/ec.00176-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 09/21/2007] [Indexed: 11/20/2022]
Abstract
We have previously identified and characterized two novel nuclear RNA binding proteins, p34 and p37, which have been shown to interact with a family of nucleolar phosphoproteins, NOPP44/46, in Trypanosoma brucei. These proteins are nearly identical, the major difference being an 18-amino-acid insert in the N terminus of p37. In order to characterize the interaction between p34 and p37 and NOPP44/46, we have utilized an RNA interference (RNAi) cell line that specifically targets p34 and p37. Within these RNAi cells, we detected a disruption of a higher-molecular-weight complex containing NOPP44/46, as well as a dramatic increase in nuclear NOPP44/46 protein levels. We demonstrated that no change occurred in NOPP44/46 mRNA steady-state levels or stability, nor was there a change in cellular protein levels. These results led us to investigate whether p34 and p37 regulate NOPP44/46 cellular localization. Examination of the p34 and p37 amino acid sequences revealed a leucine-rich nuclear export signal, which interacts with the nuclear export factor exportin 1. Immune capture experiments demonstrated that p34, p37, and NOPP44/46 associate with exportin 1. When these experiments were performed with p34/p37 RNAi cells, NOPP44/46 no longer associated with exportin 1. Sequential immune capture experiments demonstrated that p34, p37, NOPP44/46, and exportin 1 exist in a common complex. Inhibiting exportin 1-mediated nuclear export led to an increase in nuclear NOPP44/46 proteins, indicating that they are exported from the nucleus via this pathway. Together, our results demonstrate that p34 and p37 regulate NOPP44/46 cellular localization by facilitating their association with exportin 1.
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Affiliation(s)
- Kristina Hellman
- Department of Microbiology and Immunology and The Witebsky Center for Microbial Pathogenesis and Immunology, 253 Biomedical Research Building, University at Buffalo, Buffalo, New York 14214, USA
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10
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Elucidating the role of C/D snoRNA in rRNA processing and modification in Trypanosoma brucei. EUKARYOTIC CELL 2007; 7:86-101. [PMID: 17981991 DOI: 10.1128/ec.00215-07] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Most eukaryotic C/D small nucleolar RNAs (snoRNAs) guide 2'-O methylation (Nm) on rRNA and are also involved in rRNA processing. The four core proteins that bind C/D snoRNA in Trypanosoma brucei are fibrillarin (NOP1), NOP56, NOP58, and SNU13. Silencing of NOP1 by RNA interference identified rRNA-processing and modification defects that caused lethality. Systematic mapping of 2'-O-methyls on rRNA revealed the existence of hypermethylation at certain positions of the rRNA in the bloodstream form of the parasites, suggesting that this modification may assist the parasites in coping with the major temperature changes during cycling between their insect and mammalian hosts. The rRNA-processing defects of NOP1-depleted cells suggest the involvement of C/D snoRNA in trypanosome-specific rRNA-processing events to generate the small rRNA fragments. MRP RNA, which is involved in rRNA processing, was identified in this study in one of the snoRNA gene clusters, suggesting that trypanosomes utilize a combination of unique C/D snoRNAs and conserved snoRNAs for rRNA processing.
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11
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Pasternack DA, Sayegh J, Clarke S, Read LK. Evolutionarily divergent type II protein arginine methyltransferase in Trypanosoma brucei. EUKARYOTIC CELL 2007; 6:1665-81. [PMID: 17601874 PMCID: PMC2043365 DOI: 10.1128/ec.00133-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein arginine methylation is a posttranslational modification that impacts cellular functions, such as RNA processing, transcription, DNA repair, and signal transduction. The majority of our knowledge regarding arginine methylation derives from studies of yeast and mammals. Here, we describe a protein arginine N-methyltransferase (PRMT), TbPRMT5, from the early-branching eukaryote Trypanosoma brucei. TbPRMT5 shares the greatest sequence similarity with PRMT5 and Skb1 type II enzymes from humans and Schizosaccharomyces pombe, respectively, although it is significantly divergent at the amino acid level from its mammalian and yeast counterparts. Recombinant TbPRMT5 displays broad substrate specificity in vitro, including methylation of a mitochondrial-gene-regulatory protein, RBP16. TbPRMT5 catalyzes the formation of omega-N(G)-monomethylarginine and symmetric omega-N(G),N(G')-dimethylarginine and does not require trypanosome cofactors for this activity. These data establish that type II PRMTs evolved early in the eukaryotic lineage. In vivo, TbPRMT5 is constitutively expressed in the bloodstream form and procyclic-form (insect host) life stages of the parasite and localizes to the cytoplasm. Genetic disruption via RNA interference in procyclic-form trypanosomes indicates that TbPRMT5 is not essential for growth in this life cycle stage. TbPRMT5-TAP ectopically expressed in procyclic-form trypanosomes is present in high-molecular-weight complexes and associates with an RG domain-containing DEAD box protein related to yeast Ded1 and two kinetoplastid-specific proteins. Thus, TbPRMT5 is likely to be involved in novel methylation-regulated functions in trypanosomes, some of which may include RNA processing and/or translation.
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Affiliation(s)
- Deborah A Pasternack
- Department of Microbiology and Immunology and Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York School of Medicine, Buffalo, New York 14214, USA
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Jäger AV, De Gaudenzi JG, Cassola A, D'Orso I, Frasch AC. mRNA maturation by two-step trans-splicing/polyadenylation processing in trypanosomes. Proc Natl Acad Sci U S A 2007; 104:2035-42. [PMID: 17267594 PMCID: PMC1892994 DOI: 10.1073/pnas.0611125104] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Indexed: 11/18/2022] Open
Abstract
Trypanosomes are unique eukaryotic cells, in that they virtually lack mechanisms to control gene expression at the transcriptional level. These microorganisms mostly control protein synthesis by posttranscriptional regulation processes, like mRNA stabilization and degradation. Transcription in these cells is polycistronic. Tens to hundreds of protein-coding genes of unrelated function are arrayed in long clusters on the same DNA strand. Polycistrons are cotranscriptionally processed by trans-splicing at the 5' end and polyadenylation at the 3' end, generating monocistronic units ready for degradation or translation. In this work, we show that some trans-splicing/polyadenylation sites may be skipped during normal polycistronic processing. As a consequence, dicistronic units or monocistronic transcripts having long 3' UTRs are produced. Interestingly, these unspliced transcripts can be processed into mature mRNAs by the conventional trans-splicing/polyadenylation events leading to translation. To our knowledge, this is a previously undescribed mRNA maturation by trans-splicing uncoupled from transcription. We identified an RNA-recognition motif-type protein, homologous to the mammalian polypyrimidine tract-binding protein, interacting with one of the partially processed RNAs analyzed here that might be involved in exon skipping. We propose that splice-site skipping might be part of a posttranscriptional mechanism to regulate gene expression in trypanosomes, through the generation of premature nontranslatable RNA molecules.
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Affiliation(s)
- Adriana V. Jäger
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
| | - Javier G. De Gaudenzi
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
| | - Alejandro Cassola
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
| | - Iván D'Orso
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
| | - Alberto C. Frasch
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
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Liang XH, Hury A, Hoze E, Uliel S, Myslyuk I, Apatoff A, Unger R, Michaeli S. Genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Leishmania major indicates conservation among trypanosomatids in the repertoire and in their rRNA targets. EUKARYOTIC CELL 2006; 6:361-77. [PMID: 17189491 PMCID: PMC1828925 DOI: 10.1128/ec.00296-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are a large group of noncoding RNAs that exist in eukaryotes and archaea and guide modifications such as 2'-O-ribose methylations and pseudouridylation on rRNAs and snRNAs. Recently, we described a genome-wide screening approach with Trypanosoma brucei that revealed over 90 guide RNAs. In this study, we extended this approach to analyze the repertoire of the closely related human pathogen Leishmania major. We describe 23 clusters that encode 62 C/Ds that can potentially guide 79 methylations and 37 H/ACA-like RNAs that can potentially guide 30 pseudouridylation reactions. Like T. brucei, Leishmania also contains many modifications and guide RNAs relative to its genome size. This study describes 10 H/ACAs and 14 C/Ds that were not found in T. brucei. Mapping of 2'-O-methylations in rRNA regions rich in modifications suggests the existence of trypanosomatid-specific modifications conserved in T. brucei and Leishmania. Structural features of C/D snoRNAs, such as copy number, conservation of boxes, K turns, and intragenic and extragenic base pairing, were examined to elucidate the great variation in snoRNA abundance. This study highlights the power of comparative genomics for determining conserved features of noncoding RNAs.
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Affiliation(s)
- Xue-hai Liang
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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14
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Li CH, Irmer H, Gudjonsdottir-Planck D, Freese S, Salm H, Haile S, Estévez AM, Clayton C. Roles of a Trypanosoma brucei 5'->3' exoribonuclease homolog in mRNA degradation. RNA (NEW YORK, N.Y.) 2006; 12:2171-86. [PMID: 17077271 PMCID: PMC1664730 DOI: 10.1261/rna.291506] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Accepted: 09/21/2006] [Indexed: 05/09/2023]
Abstract
The genome of the kinetoplastid parasite Trypanosoma brucei encodes four homologs of the Saccharomyces cerevisiae 5'-->3' exoribonucleases Xrn1p and Xrn2p/Rat1p, XRNA, XRNB, XRNC, and XRND. In S. cerevisiae, Xrn1p is a cytosolic enzyme involved in degradation of mRNA, whereas Xrn2p is involved in RNA processing in the nucleus. Trypanosome XRND was found in the nucleus, XRNB and XRNC were found in the cytoplasm, and XRNA appeared to be in both compartments. XRND and XRNA were essential for parasite growth. Depletion of XRNA increased the abundances of highly unstable developmentally regulated mRNAs, perhaps by delaying a deadenylation-independent decay pathway. Degradation of more stable or unregulated mRNAs was not affected by XRNA depletion although a slight decrease in average poly(A) tail length was observed. We conclude that in trypanosomes 5'-->3' exonuclease activity is important in degradation of highly unstable, regulated mRNAs, but that for other mRNAs another step is more important in determining the decay rate.
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Affiliation(s)
- Chi-Ho Li
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), D-69120 Heidelberg, Germany
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15
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Dumas C, Chow C, Müller M, Papadopoulou B. A novel class of developmentally regulated noncoding RNAs in Leishmania. EUKARYOTIC CELL 2006; 5:2033-46. [PMID: 17071827 PMCID: PMC1694821 DOI: 10.1128/ec.00147-06] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Leishmania is a protozoan parasite that causes serious morbidity and mortality in humans worldwide. The ability of these parasites to survive within the phagolysosomes of mammalian macrophages is dependent on the developmental regulation of a variety of genes. Identifying genomic sequences that are preferentially expressed during the parasite's intracellular growth would provide new insights about the mechanisms controlling stage-specific gene regulation for intracellular development of the parasite. Using a genomic library that differentially hybridized to probes made from total RNA from Leishmania infantum amastigote or promastigote life cycle stages, we identified a new class of noncoding RNAs (ncRNAs) ranging from approximately 300 to 600 nucleotides in size that are expressed specifically in the intracellular amastigote stage. These ncRNAs are transcribed by RNA polymerase II from genomic clusters of tandem head-to-tail repeats, which are mainly located within subtelomeric regions. Remarkably, both the sense and antisense orientations of these ncRNAs are transcribed and are processed by trans splicing and polyadenylation. The levels of antisense transcripts are at least 10-fold lower than those of the sense transcripts and are tightly regulated. The sense and antisense ncRNAs are cytosolic as shown by fluorescence in situ hybridization studies and cosediment with a small ribonucleoprotein complex. Amastigote-specific regulation of these ncRNAs possibly occurs at the level of RNA stability. Interestingly, overexpression of these ncRNAs in promastigotes, as part of an episomal expression vector, failed to produce any transcript, which further highlights the instability of these RNAs in the promastigote stage. This is the first report describing developmentally regulated ncRNAs in protozoan parasites.
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Affiliation(s)
- Carole Dumas
- Infectious Diseases Research Center, CHUL Research Center, CHUQ, Laval University, 2705 Laurier Blvd., Quebec, Canada G1V 4G2
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16
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Barth S, Hury A, Liang XH, Michaeli S. Elucidating the role of H/ACA-like RNAs in trans-splicing and rRNA processing via RNA interference silencing of the Trypanosoma brucei CBF5 pseudouridine synthase. J Biol Chem 2005; 280:34558-68. [PMID: 16107339 DOI: 10.1074/jbc.m503465200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most pseudouridinylation in eukaryotic rRNA and small nuclear RNAs is guided by H/ACA small nucleolar RNAs. In this study, the Trypanosoma brucei pseudouridine synthase, Cbf5p, a snoRNP protein, was identified and silenced by RNAi. Depletion of this protein destabilized all small nucleolar RNAs of the H/ACA-like family. Following silencing, defects in rRNA processing, such as accumulation of precursors and inhibition of cleavages to generate the mature rRNA, were observed. snR30, an H/ACA RNA involved in rRNA maturation, was identified based on prototypical conserved domains characteristic of this RNA in other eukaryotes. The silencing of CBF5 also eliminated the spliced leader-associated (SLA1) RNA that directs pseudouridylation on the spliced leader RNA (SL RNA), which is the substrate for the trans-splicing reaction. Surprisingly, the depletion of Cbf5p not only eliminated the pseudouridine on the SL RNA but also abolished capping at the fourth cap-4 nucleotide. As a result of defects in the SL RNA and decreased modification on the U small nuclear RNA, trans-splicing was inhibited at the first step of the reaction, providing evidence for the essential role of H/ACA RNAs and the modifications they guide on trans-splicing.
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MESH Headings
- Alternative Splicing
- Animals
- Base Sequence
- Blotting, Northern
- Gene Deletion
- Gene Silencing
- Hydro-Lyases/chemistry
- Hydro-Lyases/genetics
- Hydro-Lyases/metabolism
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Models, Genetic
- Molecular Sequence Data
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Phenotype
- Pseudouridine/chemistry
- RNA/metabolism
- RNA Interference
- RNA Splicing
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nucleolar/genetics
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Temperature
- Time Factors
- Transfection
- Trypanosoma/metabolism
- Trypanosoma brucei brucei/enzymology
- Trypanosoma brucei brucei/genetics
- Tubulin/chemistry
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Affiliation(s)
- Sarit Barth
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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17
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Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification. RNA (NEW YORK, N.Y.) 2005; 11:619-45. [PMID: 15840815 PMCID: PMC1370750 DOI: 10.1261/rna.7174805] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2004] [Accepted: 01/17/2005] [Indexed: 05/19/2023]
Abstract
Small nucleolar RNAs (snoRNAs) constitute newly discovered noncoding small RNAs, most of which function in guiding modifications such as 2'-O-ribose methylation and pseudouridylation on rRNAs and snRNAs. To investigate the genome organization of Trypanosoma brucei snoRNAs and the pattern of rRNA modifications, we used a whole-genome approach to identify the repertoire of these guide RNAs. Twenty-one clusters encoding for 57 C/D snoRNAs and 34 H/ACA-like RNAs, which have the potential to direct 84 methylations and 32 pseudouridines, respectively, were identified. The number of 2'-O-methyls (Nms) identified on rRNA represent 80% of the expected modifications. The modifications guided by these RNAs suggest that trypanosomes contain many modifications and guide RNAs relative to their genome size. Interestingly, approximately 40% of the Nms are species-specific modifications that do not exist in yeast, humans, or plants, and 40% of the species-specific predicted modifications are located in unique positions outside the highly conserved domains. Although most of the guide RNAs were found in reiterated clusters, a few single-copy genes were identified. The large repertoire of modifications and guide RNAs in trypanosomes suggests that these modifications possibly play a central role in these parasites.
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Affiliation(s)
- Xue-Hai Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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18
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Liang XH, Haritan A, Uliel S, Michaeli S. trans and cis splicing in trypanosomatids: mechanism, factors, and regulation. EUKARYOTIC CELL 2004; 2:830-40. [PMID: 14555465 PMCID: PMC219355 DOI: 10.1128/ec.2.5.830-840.2003] [Citation(s) in RCA: 246] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Xue-hai Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900 Israel
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19
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Uliel S, Liang XH, Unger R, Michaeli S. Small nucleolar RNAs that guide modification in trypanosomatids: repertoire, targets, genome organisation, and unique functions. Int J Parasitol 2004; 34:445-54. [PMID: 15013734 DOI: 10.1016/j.ijpara.2003.10.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Revised: 10/14/2003] [Accepted: 10/15/2003] [Indexed: 11/27/2022]
Abstract
Small nucleolar RNAs constitute a family of newly discovered non-coding small RNAs, most of which function in guiding RNA modifications. Two prevalent types of modifications are 2'-O-methylation and pseudouridylation. The modification is directed by the formation of a canonical small nucleolar RNA-target duplex. Initially, RNA-guided modification was shown to take place on rRNA, but recent studies suggest that small nuclear RNA, mRNA, tRNA, and the trypanosome spliced leader RNA also undergo guided modifications. Trypanosomes contain more modifications and potentially more small nucleolar RNAs than yeast, and the increased number of modifications may help to preserve ribosome function under adverse environmental conditions during the cycling between the insect and mammalian host. The genome organisation in clusters carrying the two types of small nucleolar RNAs, C/D and H/ACA-like RNAs, resembles that in plants. However, the trypanosomatid H/ACA RNAs are similar to those found in Archaea and are composed of a single hairpin that may represent the primordial H/ACA RNA. In this review we summarise this new field of trypanosome small nucleolar RNAs, emphasising the open questions regarding the number of small nucleolar RNAs, the repertoire, genome organisation, and the unique function of guided modifications in these protozoan parasites.
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Affiliation(s)
- Shai Uliel
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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20
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Liang XH, Ochaion A, Xu YX, Liu Q, Michaeli S. Small nucleolar RNA clusters in trypanosomatid Leptomonas collosoma. Genome organization, expression studies, and the potential role of sequences present upstream from the first repeated cluster. J Biol Chem 2003; 279:5100-9. [PMID: 14645367 DOI: 10.1074/jbc.m308264200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosomatid small nucleolar RNA (snoRNA) genes are clustered in the genome. snoRNAs are transcribed polycistronically and processed into mature RNAs. In this study, we characterized four snoRNA clusters in Leptomonas collosoma. All of the clusters analyzed carry both C/D and H/ACA RNAs. The H/ACA RNAs are composed of a single hairpin, a structure typical to trypanosome and archaea guide RNAs. Using deletion and mutational analysis of a tagged C/D snoRNA situated within the snoRNA cluster, we identified 10-nucleotide flanking sequences that are essential for processing snoRNA from its precursor. Chromosome walk was performed on a snoRNA cluster, and a sequence of 700 bp was identified between the first repeat and the upstream open reading frame. Cloning of this sequence in an episome vector enhanced the expression of a tagged snoRNA gene in an orientation-dependent manner. However, continuous transcript spanning of this region was detected in steady-state RNA, suggesting that snoRNA transcription also originates from an upstream-long polycistronic transcriptional unit. The 700-bp fragment may therefore represent an example of many more elements to be discovered that enhance transcription along the chromosome, especially when transcription from the upstream gene is reduced or when enhanced transcription is needed.
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Affiliation(s)
- Xue-hai Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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21
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Zeiner GM, Sturm NR, Campbell DA. Exportin 1 mediates nuclear export of the kinetoplastid spliced leader RNA. EUKARYOTIC CELL 2003; 2:222-30. [PMID: 12684371 PMCID: PMC154853 DOI: 10.1128/ec.2.2.222-230.2003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2002] [Accepted: 01/28/2003] [Indexed: 01/06/2023]
Abstract
The kinetoplastid protozoan spliced leader (SL) RNA is the common substrate pre-mRNA utilized in all trans-splicing reactions. Here we show by fluorescence in situ hybridization that the SL RNA is present in the cytoplasm of Leishmania tarentolae and Trypanosoma brucei. Treatment with the karyopherin-specific inhibitor leptomycin B was toxic to T. brucei and eliminated the cytoplasmic SL RNA, suggesting that cytoplasmic SL RNA was dependent on the nuclear exporter exportin 1 (XPO1). Ectopic expression of xpo1 with a C506S mutation in T. brucei conferred resistance to leptomycin B. A reduction in SL RNA 3' extension removal and 5' methylation of nucleotide U(4) was observed in wild-type T. brucei treated with leptomycin B, suggesting that the cytoplasmic stage is necessary for SL RNA biogenesis. This study demonstrates spatial and mechanistic similarities between the posttranscriptional trafficking of the kinetoplastid protozoan SL RNA and the metazoan cis-spliceosomal small nuclear RNAs.
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MESH Headings
- Active Transport, Cell Nucleus/drug effects
- Active Transport, Cell Nucleus/physiology
- Animals
- Cytoplasm/genetics
- Cytoplasm/metabolism
- DNA, Kinetoplast/genetics
- DNA, Kinetoplast/metabolism
- Drug Resistance/genetics
- Fatty Acids, Unsaturated/pharmacology
- Karyopherins/genetics
- Karyopherins/metabolism
- Leishmania/drug effects
- Leishmania/genetics
- Leishmania/metabolism
- Methylation/drug effects
- Mutation/genetics
- RNA Processing, Post-Transcriptional/drug effects
- RNA Processing, Post-Transcriptional/genetics
- RNA, Spliced Leader/genetics
- RNA, Spliced Leader/metabolism
- Receptors, Cytoplasmic and Nuclear
- Trans-Splicing/drug effects
- Trans-Splicing/physiology
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/metabolism
- Exportin 1 Protein
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Affiliation(s)
- Gusti M Zeiner
- Department of Microbiology, University of California at Los Angeles, Los Angeles, California 90095-1489, USA
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22
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Sturm NR, Vargas NS, Westenberger SJ, Zingales B, Campbell DA. Evidence for multiple hybrid groups in Trypanosoma cruzi. Int J Parasitol 2003; 33:269-79. [PMID: 12670512 DOI: 10.1016/s0020-7519(02)00264-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A role for parasite genetic variability in the spectrum of Chagas disease is emerging but not yet evident, in part due to an incomplete understanding of the population structure of Trypanosoma cruzi. To investigate further the observed genotypic variation at the sequence and chromosomal levels in strains of standard and field-isolated T. cruzi we have undertaken a comparative analysis of 10 regions of the genome from two isolates representing T. cruzi I (Dm28c and Silvio X10) and two from T. cruzi II (CL Brener and Esmeraldo). Amplified regions contained intergenic (non-coding) sequences from tandemly repeated genes. Multiple nucleotide polymorphisms correlated with the T. cruzi I/T. cruzi II classification. Two intergenic regions had useful polymorphisms for the design of classification probes to test on genomic DNA from other known isolates. Two adjacent nucleotide polymorphisms in HSP 60 correlated with the T. cruzi I and T. cruzi II distinction. 1F8 nucleotide polymorphisms revealed multiple subdivisions of T. cruzi II: subgroups IIa and IIc displayed the T. cruzi I pattern; subgroups IId and IIe possessed both the I and II patterns. Furthermore, isolates from subgroups IId and IIe contained the 1F8 polymorphic markers on different chromosome bands supporting a genetic exchange event that resulted in chromosomes V and IX of T. cruzi strain CL Brener. Based on these analyses, T. cruzi I and subgroup IIb appear to be pure lines, while subgroups IIa/IIc and IId/IIe are hybrid lines. These data demonstrate for the first time that IIa/IIc are hybrid, consistent with the hypothesis that genetic recombination has occurred more than once within the T. cruzi lines.
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Affiliation(s)
- Nancy R Sturm
- Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, 609 Charles E. Young Drive East, Los Angeles, CA 90095-1489, USA
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23
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Fragoso SP, Plazanet-Menut C, Carreira MAC, Motta MC, Dallagiovana B, Krieger MA, Goldenberg S. Cloning and characterization of a gene encoding a putative protein associated with U3 small nucleolar ribonucleoprotein in Trypanosoma cruzi. Mol Biochem Parasitol 2003; 126:113-7. [PMID: 12554092 DOI: 10.1016/s0166-6851(02)00247-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Stenio P Fragoso
- Instituto de Biologia Molecular do Paraná, Rua Professor Algacyr Munhoz Mader 3775, Curitiba 81350-010, PR, Brazil
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24
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Morales L, Romero I, Diez H, Del Portillo P, Montilla M, Nicholls S, Puerta C. Characterization of a candidate Trypanosoma rangeli small nucleolar RNA gene and its application in a PCR-based parasite detection. Exp Parasitol 2002; 102:72-80. [PMID: 12706742 DOI: 10.1016/s0014-4894(03)00027-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, we report the isolation and characterization of a candidate Trypanosoma rangeli small nucleolar RNA (snoRNA) gene, and the development of a PCR assay for detection of the parasite based on its nucleotide sequence. This gene, isolated from a T. rangeli genomic sub-library, was named snoRNA-cl1 and is encoded by a multi-copy gene of 801bp in length. Computer sequence analysis of snoRNA-cl1 showed the presence of two sequence motifs, box C and box D, as well as of two long stretches that perfectly complement the universal core region of the mature rRNA 28S, suggesting that cl1 encodes for a Box C/D snoRNA from the parasite. Hybridization analysis using cl1 as probe, showed a weak hybridization signal with Trypanosoma cruzi DNA, demonstrating the existence of differences in this locus between these two species. Two oligonucleotide primers from this gene, which specifically amplified a 620-bp fragment in KP1 (+) and KP1 (-) strains of T. rangeli, were used in a PCR assay. The amplification allowed the detection of 1pg of DNA in the presence of heterologous DNA and no amplification was observed with different T. cruzi strains (groups I and II). In addition, the PCR assay reported here is able to detect T. rangeli in the presence of T. cruzi DNA, and is useful for detection of the parasite in samples from infected vectors.
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Affiliation(s)
- Liliana Morales
- Laboratorio de Parasitología Molecular, Departamento de Microbiología, Facultad Ciencias, Universidad Javeriana, Carrera 7 No 43-82, Lab. 113, Bogotá, Colombia
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25
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Liang XH, Xu YX, Michaeli S. The spliced leader-associated RNA is a trypanosome-specific sn(o) RNA that has the potential to guide pseudouridine formation on the SL RNA. RNA (NEW YORK, N.Y.) 2002; 8:237-46. [PMID: 11911368 PMCID: PMC1370245 DOI: 10.1017/s1355838202018290] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The spliced leader-associated (SLA1) RNA is a trypanosome-specific small RNA with unknown function. SLA1 carries a Sm-like site, and is associated with core Sm proteins. Here we found that SLA1 belongs to a family of hairpin-containing RNAs that are implicated in directing pseudouridylation. A potential for base-pair interaction between SLA1 and spliced leader (SL) RNA agrees with the canonical rules for guiding pseudouridylation on SL RNA. Direct RNA analysis showed that this uridine is indeed pseudouridylated in the SL RNA of Leptomonas collosoma, Leishmania major, and Trypanosoma brucei. This position is conserved in all trypanosomatid SL RNAs. Mutations introduced in the SL RNA to disrupt the interaction domain of SLA1/SL RNA abolished the formation of the pseudouridine. SLA1 is localized both to the nucleolus and nucleoplasm. This study solves a long-standing question regarding the function of this novel RNA and describes the first H/ACA RNA, which, unlike all other pseudouridine guides, is also a bona fide snRNA.
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Affiliation(s)
- Xue-Hai Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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26
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Pitula J, Ruyechan WT, Williams N. Two novel RNA binding proteins from Trypanosoma brucei are associated with 5S rRNA. Biochem Biophys Res Commun 2002; 290:569-76. [PMID: 11779210 DOI: 10.1006/bbrc.2001.6226] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have previously reported the identification of two closely related RNA binding proteins from Trypanosoma brucei which we have termed p34 and p37. The predicted primary structures of the two proteins are highly homologous with one major difference, an 18-amino-acid insert in the N-terminal region of p37. These two proteins have been localized to the nucleus based on immunofluorescence microscopy. To gain insight into their function, we have utilized UV crosslinking, coimmunoprecipitation, and sucrose density gradients to identify T. brucei RNA species that associate with p34 and p37. These experiments have demonstrated a specific interaction of both p34 and p37 with the 5S ribosomal RNA and indicate that other RNA species are unlikely to be specifically bound. This suggests a role for p34 and p37 in the import and/or assembly pathway of T. brucei 5S rRNA in ribosome biogenesis.
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Affiliation(s)
- Joseph Pitula
- Department of Microbiology, State University of New York at Buffalo, Buffalo, NY 14214, USA
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27
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Liang XH, Liu L, Michaeli S. Identification of the first trypanosome H/ACA RNA that guides pseudouridine formation on rRNA. J Biol Chem 2001; 276:40313-8. [PMID: 11483606 DOI: 10.1074/jbc.m104488200] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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 in Leptomonas 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.
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MESH Headings
- Animals
- Base Sequence
- Genes, Protozoan
- Molecular Sequence Data
- Multigene Family
- Nucleic Acid Conformation
- Pseudouridine/biosynthesis
- RNA Editing
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Transcription, Genetic
- Trypanosomatina/genetics
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Affiliation(s)
- X H Liang
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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28
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Cavaillé J, Vitali P, Basyuk E, Hüttenhofer A, Bachellerie JP. A novel brain-specific box C/D small nucleolar RNA processed from tandemly repeated introns of a noncoding RNA gene in rats. J Biol Chem 2001; 276:26374-83. [PMID: 11346658 DOI: 10.1074/jbc.m103544200] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antisense box C/D small nucleolar RNAs (snoRNAs) guide the 2'-O-ribose methylations of eukaryotic rRNAs and small nuclear RNAs (snRNAs) through formation of a specific base pairing at each RNA methylation site. By analysis of a box C/D snoRNA cDNA library constructed from rat brain RNAs, we have identified a novel box C/D snoRNA, RBII-36, which is devoid of complementarity to rRNA or an snRNA and exhibits a brain-specific expression pattern. It is uniformly expressed in all major areas of adult rat brain (except for choroid plexus) and throughout rat brain ontogeny but exclusively detected in neurons in which it exhibits a nucleolar localization. In vertebrates, known methylation guide snoRNAs are intron-encoded and processed from transcripts of housekeeping genes. In contrast, RBII-36 snoRNA is intron-encoded in a gene preferentially expressed in the rat central nervous system and not in proliferating cells. Remarkably, this host gene, which encodes a previously reported noncoding RNA, Bsr, spans tandemly repeated 0.9-kilobase units including the snoRNA-containing intron. The novel brain-specific snoRNA appears to result not only from processing of the debranched lariat but also from endonucleolytic cleavages of unspliced Bsr RNA (i.e. an alternative splicing-independent pathway unreported so far for mammalian intronic snoRNAs). Sequences homologous to RBII-36 snoRNA were exclusively detected in the Rattus genus of rodents, suggesting a very recent origin of this brain-specific snoRNA.
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Affiliation(s)
- J Cavaillé
- UMR5099, Laboratoire de Biologie Moléculaire Eucaryote du Centre National de la Recherche Scientifique, Université Paul-Sabatier, 118 route de Narbonne, Toulouse 31062, France.
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29
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Xu Y, Liu L, Lopez-Estraño C, Michaeli S. Expression studies on clustered trypanosomatid box C/D small nucleolar RNAs. J Biol Chem 2001; 276:14289-98. [PMID: 11278327 DOI: 10.1074/jbc.m007007200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We analyzed three chromosomal loci of the trypanosomatid Leptomonas collosoma encoding box C/D small nucleolar RNAs (snoRNAs). All the snoRNAs that were analyzed here carry two sequences complementary to rRNA target sites and obey the +5 rule for guide methylation. Studies on transgenic parasites carrying the snoRNA-2 gene in the episomal expression vector (pX-neo) indicated that no promoter activity was found immediately adjacent to this gene. Deleting the flanking sequences of snoRNA-2 affected the expression; in the absence of the 3'-flanking (but not 5'-flanking) sequence, the expression was almost completely abolished. The snoRNA genes are transcribed as polycistronic RNA. All snoRNAs can be folded into a common stem-loop structure, which may play a role in processing the polycistronic transcript. snoRNA B2, a member of a snoRNA cluster, was expressed when cloned into the episomal vector, suggesting that each gene within a cluster is individually processed. Studies with permeable cells indicated that snoRNA gene transcription was relatively sensitive to alpha-amanitin, thus supporting transcription by RNA polymerase II. We propose that snoRNA gene expression, similar to protein-coding genes in this family, is regulated at the processing level.
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MESH Headings
- Amanitins/pharmacology
- Amino Acid Sequence
- Animals
- Animals, Genetically Modified
- Base Sequence
- Blotting, Northern
- Cloning, Molecular
- DNA Methylation
- DNA-Directed RNA Polymerases/metabolism
- Dose-Response Relationship, Drug
- Electrophoresis, Polyacrylamide Gel
- Gene Deletion
- Genetic Vectors
- Models, Genetic
- Molecular Sequence Data
- Multigene Family
- Nucleic Acid Conformation
- Nucleic Acid Synthesis Inhibitors/pharmacology
- Oligonucleotides/metabolism
- Plasmids/metabolism
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA, Messenger/metabolism
- RNA, Small Nucleolar/ultrastructure
- Reverse Transcriptase Polymerase Chain Reaction
- Ribose/metabolism
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
- Trypanosoma/genetics
- Trypanosoma/metabolism
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Affiliation(s)
- Y Xu
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Xu P, Wen L, Benegal G, Wang X, Buck GA. Identification of a spliced leader RNA binding protein from Trypanosoma cruzi. Mol Biochem Parasitol 2001; 112:39-49. [PMID: 11166385 DOI: 10.1016/s0166-6851(00)00341-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nuclear mRNAs in trypanosomatids are generated by trans-splicing. Although trans-splicing resembles cis-splicing in many ways and most of the U RNA participants have been characterized, relatively few involved proteins have been identified. Herein, we employed a yeast three-hybrid system to identify a protein, XB1, which binds to the Trypanosoma cruzi SL RNA. XB1 is a approximately 45 kDa protein which is homologous to the essential pre-mRNA-splicing factor PRP31p from Saccharomyces cerevisiae. Gel shift assays and UV cross-linking experiments with recombinant XB1 confirmed that this T. cruzi protein binds the SL RNA in vitro. The binding site of XB1 on the SL RNA was mapped to stem-loop II by deletion of the SL RNA 'bait' in the three-hybrid system. Finally, UV cross-linking SL RNA with S100 extract indicated native XB1 protein and SL RNA interaction in T. cruzi extract.
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Affiliation(s)
- P Xu
- Department of Microbiology and Immunology, Medical College of Virginia Campus, Box 980678, Virginia Commonwealth University, 1101 East Marshall, Rm. 5036 Sanger Hall, Richmond, VA 23298-0678, USA
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Kapushoc ST, Alfonzo JD, Rubio MA, Simpson L. End processing precedes mitochondrial importation and editing of tRNAs in Leishmania tarentolae. J Biol Chem 2000; 275:37907-14. [PMID: 10993905 DOI: 10.1074/jbc.m007838200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All mitochondrial tRNAs in Leishmania tarentolae are encoded in the nuclear genome and imported into the mitochondrion from the cytosol. One imported tRNA (tRNA(Trp)) is edited by a C to U modification at the first position of the anticodon. To determine the in vivo substrates for mitochondrial tRNA importation as well as tRNA editing, we examined the subcellular localization and extent of 5'- and 3'-end maturation of tRNA(Trp)(CCA), tRNA(Ile)(UAU), tRNA(Gln)(CUG), tRNA(Lys)(UUU), and tRNA(Val)(CAC). Nuclear, cytosolic, and mitochondrial fractions were obtained with little cross-contamination, as determined by Northern analysis of specific marker RNAs. tRNA(Gln) was mainly cytosolic in localization; tRNA(Ile) and tRNA(Lys) were mainly mitochondrial; and tRNA(Trp) and tRNA(Val) were shared between the two compartments. 5'- and 3'-extended precursors of all five tRNAs were present only in the nuclear fraction, suggesting that the mature tRNAs represent the in vivo substrates for importation into the mitochondrion. Consistent with this model, T7-transcribed mature tRNA(Ile) underwent importation in vitro into isolated mitochondria more efficiently than 5'-extended precursor tRNA(Ile). 5'-Extended precursor tRNA(Trp) was found to be unedited, which is consistent with a mitochondrial localization of this editing reaction. T7-transcribed unedited tRNA(Trp) was imported in vitro more efficiently than edited tRNA(Trp), suggesting the presence of importation determinants in the anticodon.
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Affiliation(s)
- S T Kapushoc
- Departments of Molecular, Cell, and Developmental Biology and Microbiology, Immunology, and Molecular Genetics and the Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, USA
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Dunbar DA, Chen AA, Wormsley S, Baserga SJ. The genes for small nucleolar RNAs in Trypanosoma brucei are organized in clusters and are transcribed as a polycistronic RNA. Nucleic Acids Res 2000; 28:2855-61. [PMID: 10908346 PMCID: PMC102681 DOI: 10.1093/nar/28.15.2855] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2000] [Accepted: 06/13/2000] [Indexed: 11/14/2022] Open
Abstract
Because the organization of snoRNA genes in vertebrates, plants and yeast is diverse, we investigated the organization of snoRNA genes in a distantly related organism, Trypanosoma brucei. We have characterized the second example of a snoRNA gene cluster that is tandemly repeated in the T.BRUCEI: genome. The genes encoding the box C/D snoRNAs TBR12, TBR6, TBR4 and TBR2 make up the cluster. In a genomic organization unique to trypanosomes, there are at least four clusters of these four snoRNA genes tandemly repeated in the T. BRUCEI: genome. We show for the first time that the genes encoding snoRNAs in both this cluster and the SLA cluster are transcribed in an unusual way as a polycistronic RNA.
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Affiliation(s)
- D A Dunbar
- Department of Therapeutic Radiology and Department of Genetics, Yale School of Medicine, 333 Cedar Street, PO Box 208040, New Haven, CT 06520-8040, USA
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Dunbar DA, Wormsley S, Lowe TM, Baserga SJ. Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei. Sequence conservation and implications for 2'-O-ribose methylation of rRNA. J Biol Chem 2000; 275:14767-76. [PMID: 10747997 DOI: 10.1074/jbc.m001180200] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the identification of 17 box C/D fibrillarin-associated small nucleolar RNAs (snoRNAs) from the ancient eukaryote, Trypanosoma brucei. To systematically isolate and characterize these snoRNAs, the T. brucei cDNA for the box C/D snoRNA common protein, fibrillarin, was cloned and polyclonal antibodies to the recombinant fibrillarin protein were generated in rabbits. Immunoprecipitations from T. brucei extracts with the anti-fibrillarin antibodies indicated that this trypanosomatid has at least 30 fibrillarin-associated snoRNAs. We have sequenced seventeen of them and designated them TBR for T. brucei RNA 1-17. All of them bear conserved box C, D, C', and D' elements, a hallmark of fibrillarin-associated snoRNAs in eukaryotes. Fourteen of them are novel T. brucei snoRNAs. Fifteen bear potential guide regions to mature rRNAs suggesting that they are involved in 2'-O-ribose methylation. Indeed, eight ribose methylations have been mapped in the rRNA at sites predicted by the snoRNA sequences. Comparative genomics indicates that six of the seventeen are the first trypanosome homologs of known yeast and vertebrate methylation guide snoRNAs. Our results indicate that T. brucei has many fibrillarin-associated box C/D snoRNAs with roles in 2'-O-ribose methylation of rRNA and that the mechanism for targeting the nucleotide to be methylated at the fifth nucleotide upstream of box D or D' originated in early eukaryotes.
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Affiliation(s)
- D A Dunbar
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut 06520-8040, USA
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Schnare MN, Gray MW. Spliced leader-associated RNA from Crithidia fasciculata contains a structure resembling stem/loop II of U1 snRNA. FEBS Lett 1999; 459:215-7. [PMID: 10518021 DOI: 10.1016/s0014-5793(99)01235-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In contrast to earlier proposals, recent evidence suggests that trans-spliceosomes in trypanosomatid protozoa may contain a homolog of U1 small nuclear (sn) RNA (Schnare, M.N. and Gray, M.W. (1999) J. Biol. Chem. 274, 23,691-23,694). However, the candidate trypanosomatid U1 snRNA is unconventional because it lacks the highly conserved stem/loop II present in all other U1 snRNAs. Trypanosomatids also possess a unique spliced leader-associated (SLA) RNA of unknown function. We present the complete sequence of the SLA RNA from Crithidia fasciculata and propose that it may contribute a U1 snRNA-like stem/loop II to the trans-spliceosome.
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Affiliation(s)
- M N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, N.S., Canada
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Sturm NR, Campbell DA. The role of intron structures in trans-splicing and cap 4 formation for the Leishmania spliced leader RNA. J Biol Chem 1999; 274:19361-7. [PMID: 10383448 DOI: 10.1074/jbc.274.27.19361] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A 39-nucleotide leader is trans-spliced onto all trypanosome nuclear mRNAs. The precursor spliced leader RNA was tested for trans-splicing function in vivo by mutating the intron. We report that in Leishmania tarentolae spliced leader RNA 5' modification is influenced by the primary sequence of stem-loop II, the Sm-binding site, and the secondary structure of stem-loop III. The sequence of stem-loop II was found to be important for cap 4 formation and splicing. As in Ascaris, mutagenesis of the bulge nucleotide in stem-loop II was detrimental to trans-splicing. Because restoration of the L. tarentolae stem-loop II structure was not sufficient to restore splicing, this result contrasts the findings in the kinetoplastid Leptomonas, where mutations that restored stem-loop II structure supported splicing. Methylation of the cap 4 structure and splicing was also dependent on both the Sm-binding site and the structure of stem-loop III and was inhibited by incomplete 3' end processing. The critical nature of the L. tarentolae Sm-binding site is consistent with its essential role in the Ascaris spliced leader RNA, whereas in Leptomonas mutation of the Sm-binding site and deletion of stem-loop III did not affect trans-splicing. A pathway for Leishmania spliced leader RNA processing and maturation is proposed.
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Affiliation(s)
- N R Sturm
- Department of Microbiology and Immunology, UCLA School of Medicine, Los Angeles, California 90095-1747, USA
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Sturm NR, Yu MC, Campbell DA. Transcription termination and 3'-End processing of the spliced leader RNA in kinetoplastids. Mol Cell Biol 1999; 19:1595-604. [PMID: 9891092 PMCID: PMC116087 DOI: 10.1128/mcb.19.2.1595] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/1998] [Accepted: 11/06/1998] [Indexed: 12/18/2022] Open
Abstract
Addition of a 39-nucleotide (nt) spliced leader (SL) by trans splicing is a basic requirement for all trypanosome nuclear mRNAs. The SL RNA in Leishmania tarentolae is a 96-nt precursor transcript synthesized by a polymerase that resembles polymerase II most closely. To analyze SL RNA genesis, we mutated SL RNA intron structures and sequence elements: stem-loops II and III, the Sm-binding site, and the downstream T tract. Using an exon-tagged SL RNA gene, we examined the phenotypes produced by a second-site 10-bp linker scan mutagenic series and directed mutagenesis. Here we report that transcription is terminated by the T tract, which is common to the 3' end of all kinetoplastid SL RNA genes, and that more than six T's are required for efficient termination in vivo. We describe mutants whose SL RNAs end in the T tract or appear to lack efficient termination but can generate wild-type 3' ends. Transcriptionally active nuclear extracts show staggered products in the T tract, directed by eight or more T's. The in vivo and in vitro data suggest that SL RNA transcription termination is staggered in the T tract and is followed by nucleolytic processing to generate the mature 3' end. We show that the Sm-binding site and stem-loop III structures are necessary for correct 3'-end formation. Thus, we have defined the transcription termination element for the SL RNA gene. The termination mechanism differs from that of vertebrate small nuclear RNA genes and the SL RNA homologue in Ascaris.
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Affiliation(s)
- N R Sturm
- Department of Microbiology and Immunology, University of California Los Angeles School of Medicine, Los Angeles, California 90095-1747, USA
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