1
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Eijlers P, Al-Khafaji M, Soto-Martin E, Fasimoye R, Stead D, Wenzel M, Müller B, Pettitt J. A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs. Nucleic Acids Res 2024; 52:7245-7260. [PMID: 38676950 PMCID: PMC11229312 DOI: 10.1093/nar/gkae321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Spliced leader trans-splicing of pre-mRNAs is a critical step in the gene expression of many eukaryotes. How the spliced leader RNA and its target transcripts are brought together to form the trans-spliceosome remains an important unanswered question. Using immunoprecipitation followed by protein analysis via mass spectrometry and RIP-Seq, we show that the nematode-specific proteins, SNA-3 and SUT-1, form a complex with a set of enigmatic non-coding RNAs, the SmY RNAs. Our work redefines the SmY snRNP and shows for the first time that it is essential for nematode viability and is involved in spliced leader trans-splicing. SNA-3 and SUT-1 are associated with the 5' ends of most, if not all, nascent capped RNA polymerase II transcripts, and they also interact with components of the major nematode spliced leader (SL1) snRNP. We show that depletion of SNA-3 impairs the co-immunoprecipitation between one of the SL1 snRNP components, SNA-2, and several core spliceosomal proteins. We thus propose that the SmY snRNP recruits the SL1 snRNP to the 5' ends of nascent pre-mRNAs, an instrumental step in the assembly of the trans-spliceosome.
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Affiliation(s)
- Peter Eijlers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Mohammed Al-Khafaji
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Eva Soto-Martin
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Rotimi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - David Stead
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Rowett Institute, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ Scotland, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
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2
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Pękacz M, Basałaj K, Młocicki D, Kamaszewski M, Carretón E, Morchón R, Wiśniewski M, Zawistowska-Deniziak A. Molecular insights and antibody response to Dr20/22 in dogs naturally infected with Dirofilaria repens. Sci Rep 2024; 14:12979. [PMID: 38839868 PMCID: PMC11153217 DOI: 10.1038/s41598-024-63523-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
Subcutaneous dirofilariasis, caused by the parasitic nematode Dirofilaria repens, is a growing concern in Europe, affecting both dogs and humans. This study focused on D. repens Dr20/22, a protein encoded by an alt (abundant larval transcript) gene family. While well-documented in L3 larvae of other filariae species, this gene family had not been explored in dirofilariasis. The research involved cloning Dr20/22 cDNA, molecular characterization, and evaluating its potential application in the diagnosis of dirofilariasis. Although Real-Time analysis revealed mRNA expression in both adult worms and microfilariae, the native protein remained undetected in lysates from both developmental stages. This suggests the protein's specificity for L3 larvae and may be related to a process called SLTS (spliced leader trans-splicing), contributing to stage-specific gene expression. The specificity of the antigen for invasive larvae positions it as a promising early marker for dirofilariasis. However, ELISA tests using sera from infected and uninfected dogs indicated limited diagnostic utility. While further research is required, our findings contribute to a deeper understanding of the molecular and immunological aspects of host-parasite interactions and could offer insights into the parasite's strategies for evading the immune system.
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Affiliation(s)
- Mateusz Pękacz
- Division of Parasitology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Katarzyna Basałaj
- Museum and Institute of Zoology, Polish Academy of Sciences, 00-818, Warsaw, Poland
| | - Daniel Młocicki
- Department of General Biology and Parasitology, Medical University of Warsaw, 02-004, Warsaw, Poland
| | - Maciej Kamaszewski
- Department of Ichthyology and Biotechnology in Aquaculture, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Elena Carretón
- Internal Medicine, Faculty of Veterinary Medicine, University of Las Palmas de Gran Canaria, Campus Arucas, Arucas, 35413, Las Palmas, Spain
| | - Rodrigo Morchón
- Zoonotic Diseases and One Health Group, Faculty of Pharmacy, University of Salamanca, Campus Miguel Unamuno, 37007, Salamanca, Spain
| | - Marcin Wiśniewski
- Division of Parasitology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Anna Zawistowska-Deniziak
- Department of Immunology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, 02-095, Warsaw, Poland.
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3
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Shaheen F, Stephany-Brassesco I, Kelly BL. Dynamic modulation of Leishmania cytochrome c oxidase subunit IV (LmCOX4) expression in response to mammalian temperature. Mol Biochem Parasitol 2021; 244:111391. [PMID: 34144085 DOI: 10.1016/j.molbiopara.2021.111391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
The Leishmania LACK antigen is a ribosome-associated protein that facilitates expression of mitochondrial cytochrome c oxidase subunit IV (LmCOX4) to support parasite mitochondrial fitness and virulence within the vertebrate host. To further examine the relationship between LACK, its putative ribosome binding motif and LmCOX4, we compared the kinetics of LmCOX4 expression following temperature elevation in wildtype LACK (LACK WT) and LACK-putative ribosome-binding mutant (LACKDDE) L. major. We found that, after initial exposure to mammalian temperature, LmCOX4 levels became undetectable in LACKDDE L. major and also, surprisingly, in wild type (WT) control strains. Upon sustained exposure to mammalian temperature, LmCOX4 expression returned in WT control strains only. The initial loss of LmCOX4 in WT L. major was substantially reversed by treatment with the proteasome inhibitor MG132. Our findings indicate that initial loss of LmCOX4 under mammalian conditions is dependent upon proteasome degradation and LmCOX4 re-expression is dependent upon LACK possessing a WT putative ribosome binding motif.
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Affiliation(s)
- Farhana Shaheen
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Isabel Stephany-Brassesco
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Ben L Kelly
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
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4
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On the Possibility of an Early Evolutionary Origin for the Spliced Leader Trans-Splicing. J Mol Evol 2017; 85:37-45. [DOI: 10.1007/s00239-017-9803-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/17/2017] [Indexed: 01/12/2023]
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5
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Stiles JK, Hicock PI, Shah PH, Meade JC. Genomic organization, transcription, splicing and gene regulation inLeishmania. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 2016. [DOI: 10.1080/00034983.1999.11813485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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6
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Pérez-Valle J, Vilardell J. Intronic features that determine the selection of the 3' splice site. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:707-17. [PMID: 22807288 DOI: 10.1002/wrna.1131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Most eukaryotic primary transcripts include segments, or introns, that will be accurately removed during RNA biogenesis. This process, known as pre-messenger RNA splicing, is catalyzed by the spliceosome, accurately selecting a set of intronic marks from others apparently equivalent. This identification is critical, as incorrectly spliced RNAs can be toxic for the organism. One of these marks, the dinucleotide AG, signals the intronic 3' end, or 3' splice site (ss). In this review we will focus on those intronic features that have an impact on 3' ss selection. These include the location and type of neighboring sequences, and their distance to the 3' end. We will see that their interplay is needed to select the right intronic end, and that this can be modulated by additional intronic elements that contribute to alternative splicing, whereby diverse RNAs can be generated from identical precursors. This complexity, still poorly understood, is fundamental for the accuracy of gene expression. In addition, a clear knowledge of 3' ss selection is needed to fully decipher the coding potential of genomes.
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Affiliation(s)
- Jorge Pérez-Valle
- Department of Molecular Genòmics, Institute of Molecular Biology of Barcelona (IBMB), Barcelona, Spain
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7
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Sierro N, Li S, Suzuki Y, Yamashita R, Nakai K. Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis. Gene 2008; 430:44-9. [PMID: 18996449 DOI: 10.1016/j.gene.2008.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 10/04/2008] [Accepted: 10/08/2008] [Indexed: 11/19/2022]
Abstract
Ciona intestinalis is a useful model organism to analyze chordate development and genetics. However, unlike vertebrates, it shares a unique mechanism called trans-splicing with lower eukaryotes. In the computational analysis of trans-splicing in C. intestinalis we report here, we discovered that although the amount of non-trans-spliced and trans-spliced genes is usually equivalent, the expression ratio between the two groups varies significantly with tissues and developmental stages. Among the seven tissues studied, the observed ratios ranged from 2.53 in "gonad" to 19.53 in "endostyle", and during development they increased from 1.68 at the "egg" stage to 7.55 at the "juvenile" stage. We further hypothesize that this enrichment in trans-spliced mRNAs in early developmental stages might be related to the abundance of trans-spliced mRNAs in "gonad". Our analysis indicates that in C. intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently.
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Affiliation(s)
- Nicolas Sierro
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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8
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García-Estrada C, Pérez-Pertejo Y, Ordóñez D, Balaña-Fouce R, Reguera RM. Analysis of genetic elements regulating the methionine adenosyltransferase gene in Leishmania infantum. Gene 2007; 389:163-73. [PMID: 17196769 DOI: 10.1016/j.gene.2006.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 09/07/2006] [Accepted: 11/03/2006] [Indexed: 01/16/2023]
Abstract
Methionine adenosyltransferase (MAT) is an important enzyme for metabolic processes, inasmuch as its product, S-adenosylmethionine (AdoMet), plays a key role in trans-methylation, trans-sulphuration and polyamine synthesis. Our prior studies have shown that the Leishmania infantum genome contains two identical copies of the gene encoding MAT (MAT2 gene), arranged in head-to-tail configuration and alternating with another gene, called LORIEN that contains a zinc-finger motif. Both genes are constitutively expressed throughout the promastigote stage of the parasite cell cycle, and their flanking regions were detected by RT-PCR. Luciferase (luc) reporter assays indicated the presence of regulatory elements within the MAT2 3'UTR and intergenic region, and fragments responsible for such regulation were identified by deletional analysis. By site-directed mutagenesis of the wild-type -42 AG recognized in the trans-splicing of the MAT2 gene, the AG slightly downstream (position -36) was observed to be able to generate the same levels of luc expression, thus suggesting that potentially this gene has alternative spliced leader acceptor sites. The stability of MAT2 and LORIEN transcripts was very similar in both logarithmic and stationary phases. However, cycloheximide (CHX) inhibition of protein synthesis increased MAT2 and LORIEN mRNA levels in the logarithmic phase only, an indication that these genes are regulated in promastigotes at the post-transcriptional level by protein factors that targets both transcripts for degradation. However, during the stationary phase, another CHX-independent factor also led to MAT2 and LORIEN mRNAs degradation, indicating the existence of different mechanisms operating on the post-transcriptional regulation of these two genes.
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Affiliation(s)
- Carlos García-Estrada
- Departamento de Farmacología y Toxicología, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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9
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Abstract
Alternative splicing is a powerful means of controlling gene expression and increasing protein diversity. Most genes express a limited number of mRNA isoforms, but there are several examples of genes that use alternative splicing to generate hundreds, thousands and even tens of thousands of isoforms. Collectively such genes are considered to undergo complex alternative splicing. The best example is the Drosophila Down syndrome cell adhesion molecule (Dscam) gene, which can generate 38,016 isoforms by the alternative splicing of 95 variable exons. In this review, we will describe several genes that use complex alternative splicing to generate large repertoires of mRNAs and what is known about the mechanisms by which they do so.
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10
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Dhalia R, Reis CRS, Freire ER, Rocha PO, Katz R, Muniz JRC, Standart N, de Melo Neto OP. Translation initiation in Leishmania major: characterisation of multiple eIF4F subunit homologues. Mol Biochem Parasitol 2005; 140:23-41. [PMID: 15694484 DOI: 10.1016/j.molbiopara.2004.12.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2004] [Revised: 11/25/2004] [Accepted: 12/07/2004] [Indexed: 10/26/2022]
Abstract
In eukaryotes protein synthesis initiates with the binding of the multimeric translation initiation complex eIF4F - eIF4E, eIF4A and eIF4G - to the monomethylated cap present on the 5' end of mRNAs. eIF4E interacts directly with the cap nucleotide, while eIF4A is a highly conserved RNA helicase and eIF4G acts as a scaffold for the complex with binding sites for both eIF4E and eIF4A. eIF4F binding to the mRNA recruits the small ribosomal subunit to its 5' end. Little is known in detail of protein synthesis in the protozoan parasites belonging to the family Trypanosomatidae. However, the presence of the highly modified cap structure, cap4, and the spliced leader sequence on the 5' ends of all mRNAs suggests possible differences in mRNA recruitment by ribosomes. We identified several potential eIF4F homologues by searching Leishmania major databases: four eIF4Es (LmEIF4E1-4), two eIF4As (LmEIF4A1-2) and five eIF4Gs (LmEIF4G1-5). We report the initial characterisation of LmEIF4E1-3, LmEIF4A1-2 and LmEIF4G3. First, the expression of these proteins in L. major promastigotes was quantitated by Western blotting using isoform specific antibodies. LmEIF4A1 and LmEIF4E3 are very abundant, LmEIF4G3 is moderately abundant and LmEIF4E1/LmEIF4E2/LmEIF4A2 are rare or not detected. In cap-binding assays, only LmEIF4E1 bound to the 7-methyl-GTP-Sepharose resin. Molecular modelling confirmed that LmEIF4E1 has all the structural features of a cap-binding protein. Finally, pull-down assays were used to investigate the potential interaction between the eIF4A (LmEIF4A1/LmEIF4A2) and eIF4G (LmEIF4G1-3) homologues. Only LmEIF4G3, via the HEAT domain, bound specifically both to LmEIF4A1 as well as to human eIF4A. Therefore for each factor, one of the L. major forms seems to fulfil, in part at least, the expected characteristics of a translational initiation factor.
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Affiliation(s)
- Rafael Dhalia
- Departamento de Biologia Celular, Universidade de Brasilia, Brasilia 70910-900, D.F., Brazil
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11
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Zaric B, Chami M, Rémigy H, Engel A, Ballmer-Hofer K, Winkler FK, Kambach C. Reconstitution of two recombinant LSm protein complexes reveals aspects of their architecture, assembly, and function. J Biol Chem 2005; 280:16066-75. [PMID: 15711010 DOI: 10.1074/jbc.m414481200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sm and Sm-like (LSm) proteins form complexes engaging in various RNA-processing events. Composition and architecture of the complexes determine their intracellular distribution, RNA targets, and function. We have reconstituted the human LSm1-7 and LSm2-8 complexes from their constituent components in vitro. Based on the assembly pathway of the canonical Sm core domain, we used heterodimeric and heterotrimeric sub-complexes to assemble LSm1-7 and LSm2-8. Isolated sub-complexes form ring-like higher order structures. LSm1-7 is assembled and stable in the absence of RNA. LSm1-7 forms ring-like structures very similar to LSm2-8 at the EM level. Our in vitro reconstitution results illustrate likely features of the LSm complex assembly pathway. We prove the complexes to be functional both in an RNA bandshift and an in vivo cellular transport assay.
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Affiliation(s)
- Bozidarka Zaric
- Paul Scherrer Institut, Biomolecular Research, CH5232 Villigen, Switzerland
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12
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Schlesinger J, Arama D, Noy H, Dagash M, Belinky P, Gross G. In-cell generation of antibody single-chain Fv transcripts by targeted RNA trans-splicing. J Immunol Methods 2003; 282:175-86. [PMID: 14604551 DOI: 10.1016/j.jim.2003.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The humoral immune response propels the production of a diversified pool of antibodies with high affinity and selectivity for the eliciting antigen. Their isolation entails either B-cell cloning or the linking of authentic pairs of variable region genes encoding them. We hypothesized that targeted RNA trans-splicing (TS) inside the B-cell nucleus could be harnessed as a novel means to link both variable region genes and reconstitute genuine immune B-cell specificities. This could be accomplished by a special targeting gene harboring a peptide linker exon flanked by sequences capable of targeting both heavy (HC) and light chain (LC) transcripts. Following sequential trans-splicing reactions, the resulting RNA in each cell would encode the two variable regions, joined by the peptide linker. In this study, we examined genetic components and configurations required for the separate trans-splicing steps and for the combined two-step reactions. Using a model antibody, we show that in transiently transfected cells, we can target variable region exons through both their acceptor and donor splice sites, precisely joining an exon encoding a synthetic linker and the complementary variable region so as to form a single-chain Fv. We also demonstrate the accurate formation of single-chain Fv transcript as a result of trans-splicing of RNA synthesized from two chromosomal genes expressed by a stably transfected B-cell hybridoma. Our attempts to link the two variable region genes via a synthetic linker exon through sequential trans-splicing events were only successful with regard to both ends of the linker and to the 3' end of the light chain, but repeatedly resulted in a deletion at the 5' end of the joined heavy chain transcript. The implications of our findings on the potential application of trans-splicing for the isolation of useful antibodies are discussed.
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Affiliation(s)
- Jacob Schlesinger
- Department of Immunology, MIGAL-Galilee Technology Center, South Industrial Zone, Kiryat Shmona 11016, Israel
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13
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Li Z, Stuart RO, Eraly SA, Gittes G, Beier DR, Nigam SK. Debt91, a putative zinc finger protein differentially expressed during epithelial morphogenesis. Biochem Biophys Res Commun 2003; 306:623-8. [PMID: 12810064 DOI: 10.1016/s0006-291x(03)00875-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In a differential screen for genes that might be important in the regulation of epithelial morphogenesis, we identified a novel gene, Debt91 (differentially expressed in branching tubulogenesis), which is up-regulated in an in vitro model of renal tubulogenesis and branching. Debt91 appears to encode a 381 amino acid molecule with high Ser and Thr composition and is highly conserved at its N-terminus across species. Sequence analysis suggests that it is a coiled-coil nuclear phosphoprotein with zinc finger motifs at the N-terminal conserved region, which is rich in cysteine and histidine. Debt91 is located on mouse chromosome 6 at a region that has conserved synteny with human chromosome 2p11.2, and appears to express two transcripts in several mouse cell lines and adult tissues. On whole murine embryo blots Debt91 expresses primarily its small transcript and is differentially regulated during development. Analysis of expression in in vitro cell culture models suggests that Debt91 is an immediate early gene up-regulated during growth factor-induced branching tubulogenesis.
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Affiliation(s)
- Zhixing Li
- Renal Division, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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14
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Couvreur B, Bollen A, Le Ray D, Dujardin JC. Reverse transcription-polymerase chain reaction construction of plasmid-based, full-length cDNA libraries from Leishmania infantum for in vitro expression screening. Mem Inst Oswaldo Cruz 2003; 98:477-80. [PMID: 12937757 DOI: 10.1590/s0074-02762003000400008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We describe a streamlined reverse transcription-polymerase chain reaction methodology for constructing full-length cDNA libraries of trypanosomatids on the basis of conserved sequences located at the 5' and 3'ends of trans-spliced mRNAs. The amplified cDNA corresponded to full-length messengers and was amenable to in vitro expression. Fractionated libraries could be rapidly constructed in a plasmid vector by the TA cloning method (Invitrogen). We believe this is useful when there are concerns over the use of restriction enzymes and phage technology as well as in cases where expression of proteins in their native conformation is desired.
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Affiliation(s)
- Bernard Couvreur
- Laboratory of Applied Genetics, IBMM, Free University of Brussels, Gosselies, Belgium
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15
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Liu Y, Kuersten S, Huang T, Larsen A, MacMorris M, Blumenthal T. An uncapped RNA suggests a model for Caenorhabditis elegans polycistronic pre-mRNA processing. RNA (NEW YORK, N.Y.) 2003; 9:677-87. [PMID: 12756326 PMCID: PMC1370435 DOI: 10.1261/rna.2128903] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2002] [Accepted: 02/27/2003] [Indexed: 05/24/2023]
Abstract
Polycistronic pre-mRNAs from Caenohabditis elegans operons are processed by internal cleavage and polyadenylation to create 3' ends of mature mRNAs. This is accompanied by trans-splicing with SL2 approximately 100 nucleotides downstream of the 3' end formation sites to create the 5' ends of downstream mRNAs. SL2 trans-splicing depends on a U-rich element (Ur), located approximately 70 nucleotides upstream of the trans-splice site in the intercistronic region (ICR), as well as a functional 3' end formation signal. Here we report the existence of a novel gene-length RNA, the Ur-RNA, starting just upstream of the Ur element. The expression of Ur-RNA is dependent on 3' end formation as well as on the presence of the Ur element, but does not require a trans-splice site. The Ur-RNA is not capped, and alteration of the location of the Ur element in either the 5' or 3' direction alters the location of the 5' end of the Ur-RNA. We propose that a 5' to 3' exonuclease degrades the precursor RNA following cleavage at the poly(A) site, stopping when it reaches the Ur element, presumably attributable to a bound protein. Part of the function of this protein can be performed by the MS2 coat protein. Recruitment of coat protein to the ICR in the absence of the Ur element results in accumulation of an RNA equivalent to Ur-RNA, and restores trans-splicing. Only SL1, however, is used. Therefore, coat protein is sufficient for blocking the exonuclease and thereby allowing formation of a substrate for trans-splicing, but it lacks the ability to recruit the SL2 snRNP. Our results also demonstrate that MS2 coat protein can be used as an in vivo block to an exonuclease, which should have utility in mRNA stability studies.
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Affiliation(s)
- Yingmiao Liu
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, Colorado 80262, USA
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16
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Zhang C, Xie Y, Martignetti JA, Yeo TT, Massa SM, Longo FM. A candidate chimeric mammalian mRNA transcript is derived from distinct chromosomes and is associated with nonconsensus splice junction motifs. DNA Cell Biol 2003; 22:303-15. [PMID: 12941158 DOI: 10.1089/104454903322216653] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The process of creating chimeric mRNA transcripts derived from separately transcribed genes via known spliceosome mechanisms is termed trans-splicing, and has been primarily described in lower eukaryotes. Isolation of cDNA clones containing sequences from distinct genes has raised the possibility of trans-splicing across distinct genes in mammalian systems; however, the possibility of cloning artifacts or splicing via nonspliceosome mechanisms has been difficult to rule out. In most cases, the absence of corresponding genomic clones has limited assessment of splice donor and acceptance sites and associated intronic elements that would be expected to participate in spliceosome-based reactions. We have previously reported a cDNA clone encoding the rat Leukocyte Common Antigen-Related (LAR) tyrosine phosphatase receptor that contains an alternative 3' UTR. In the present study Northern, RT-PCR and RNase protection assays verified the existence of developmentally regulated 3' UTR alternative splicing of LAR transcripts in vivo. FISH and radiation hybrid mapping demonstrated that loci encoding LAR and its alternative 3' UTR are present on distinct chromosomes, raising the possibility that alternatively spliced transcripts resulted from trans-splicing. Exon/intron analysis of corresponding genomic clones revealed nonconsensus splice junctions along with elements known to promote both cis- and trans-splicing. Verification in a mammalian in vivo system of chimeric transcripts derived from distinct genes along with identification of atypical nonconsensus-associated genomic elements points to the novel possibilities of atypical spliceosome-based trans-splicing or nonconventional, nonspliceosome-based mechanisms leading to chimeric transcripts.
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MESH Headings
- 3' Untranslated Regions/genetics
- Alternative Splicing
- Animals
- Base Sequence
- Blotting, Northern
- Chimera
- Chromosomes/genetics
- Conserved Sequence
- DNA Primers
- DNA, Complementary
- Exons
- Gene Expression Regulation, Developmental
- Genome
- Introns
- Molecular Sequence Data
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Protein Tyrosine Phosphatases/genetics
- Protein Tyrosine Phosphatases/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Radiation Hybrid Mapping
- Rats
- Rats, Sprague-Dawley
- Receptor-Like Protein Tyrosine Phosphatases, Class 2
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonuclease, Pancreatic/metabolism
- Trans-Splicing
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Affiliation(s)
- Cheng Zhang
- Department of Neurology, University of California at San Francisco, San Francisco, California, USA
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17
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Motta MCM, de Souza W, Thiry M. Immunocytochemical detection of DNA and RNA in endosymbiont-bearing trypanosomatids. FEMS Microbiol Lett 2003; 221:17-23. [PMID: 12694905 DOI: 10.1016/s0378-1097(03)00087-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Research about the kinetoplast of trypanosomatids has yielded valuable information about the organization of extranuclear structure. However, the ultrastructural localization of nucleic acids within these protozoa remains uncertain. We have applied cytochemical and immunocytochemical approaches to precisely identify DNA and RNA in lower endosymbiont-bearing trypanosomatids. Using the Terminal deoxynucleotidyl Transferase (TdT) immunogold technique, we showed that nuclear DNA is seen associated with the nuclear envelope during the trypanosomatid cell cycle. By combining the TdT technique with the acetylation method, which improves the contrast between structures containing fibrils and granules, we have demonstrated that the nucleolus of endosymbiont-bearing trypanosomatids is composed of two constituents: a granular component and a DNA-positive fibrillar zone. Moreover, we revealed that DNA of endosymbiotic bacteria consisted of electron-dense filaments which are usually in close contact with the prokaryote envelope. Using a Lowicryl post-embedding immunogold labeling procedure with anti-RNA antibodies, we showed the presence of RNA not only over the cytoplasm, the interchromatin spaces and the nucleolus, but also over the kinetoplast and virus-like particles present in Crithidia desouzai.
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Affiliation(s)
- Maria Cristina M Motta
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, CCS, Bloco G, Ilha do Fundão, 21940-900 Rio de Janeiro, RJ, Brazil.
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18
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Requena JM, Quijada L, Soto M, Alonso C. Conserved nucleotides surrounding the trans-splicing acceptor site and the translation initiation codon in Leishmania genes. Exp Parasitol 2003; 103:78-81. [PMID: 12810050 DOI: 10.1016/s0014-4894(03)00061-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jose M Requena
- Centro de Biología Molecular Severo Ochoa, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, E-28049, Madrid, Spain.
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19
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Hirzmann J, Hintz M, Kasper M, Shresta TR, Taubert A, Conraths FJ, Geyer R, Stirm S, Zahner H, Hobom G. Cloning and expression analysis of two mucin-like genes encoding microfilarial sheath surface proteins of the parasitic nematodes Brugia and Litomosoides. J Biol Chem 2002; 277:47603-12. [PMID: 12356773 DOI: 10.1074/jbc.m205770200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In several filarial genera the first stage larvae (microfilariae) are enclosed by an eggshell-derived sheath that provides a major interface between the parasite and the host immune system. Analysis of the polypeptide constituents of the microfilarial sheath from the cotton rat filaria Litomosoides sigmodontis identified two abundant surface glycoproteins: Shp3a and Shp3. The corresponding genes and the orthologues of the human parasite Brugia malayi and the rodent filaria Brugia pahangi were cloned and sequenced. They encode secreted, mucin-like proteins with N-terminal Ser/Thr-rich repeats and a C-terminal anchor domain rich in aromatic amino acids. About 75% of the protein molecular masses result from post-translational modifications. The Ser/Thr-rich motifs are supposed to serve as targets for dimethylaminoethanol-phosphate substitutions. These modifications were detected only on the sheaths of the late developmental stage of stretched microfilariae, corresponding with the expression of the proteins in the epithelium of the distal part of the uterus and the specific transcription of shp3 and shp3a in the anterior female worm segment. Genomic analysis of all three species demonstrated a conserved linkage of the two genes. Their transcripts undergo cis- and trans-splicing. The transcription start sites of the primary transcripts were determined for the L. sigmodontis genes. The core promoter regions are remarkably conserved between the paralogue genes Ls-shp3a and Ls-shp3 and their orthologues in Brugia, implicating conserved regulatory elements.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Brugia malayi/metabolism
- Brugia pahangi/metabolism
- Carbohydrates/chemistry
- Chromatography, Gas
- Cloning, Molecular
- DNA, Complementary/metabolism
- Female
- Filarioidea/metabolism
- Male
- Models, Genetic
- Molecular Sequence Data
- Monosaccharides/chemistry
- Mucins/chemistry
- Mucins/genetics
- Mucins/metabolism
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- RNA/metabolism
- Rats
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Transcription, Genetic
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20
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Iñiguez AM, Vicente ACP, Araújo A, Ferreira LF, Reinhard KJ. Enterobius vermicularis: specific detection by amplification of an internal region of 5S ribosomal RNA intergenic spacer and trans-splicing leader RNA analysis. E. vermicularis: specific detection by PCR and SL1 RNA analysis. Exp Parasitol 2002; 102:218-22. [PMID: 12856320 DOI: 10.1016/s0014-4894(03)00059-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
MESH Headings
- Animals
- Base Sequence
- DNA, Helminth/chemistry
- DNA, Helminth/isolation & purification
- Enterobiasis/diagnosis
- Enterobiasis/parasitology
- Enterobius/genetics
- Enterobius/isolation & purification
- Feces/parasitology
- Humans
- Molecular Sequence Data
- Polymerase Chain Reaction
- RNA, Helminth/chemistry
- RNA, Helminth/genetics
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Spliced Leader/chemistry
- RNA, Spliced Leader/genetics
- Trans-Splicing/genetics
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Affiliation(s)
- Alena M Iñiguez
- Departamento de Genética, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21045-900, Brazil.
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21
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Brehm K, Hubert K, Sciutto E, Garate T, Frosch M. Characterization of a spliced leader gene and of trans-spliced mRNAs from Taenia solium. Mol Biochem Parasitol 2002; 122:105-10. [PMID: 12076776 DOI: 10.1016/s0166-6851(02)00074-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Klaus Brehm
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany.
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22
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Affiliation(s)
- D L Redmond
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Penicuik, Midlothian EH26 0PZ, UK
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23
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Collins BM, Harrop SJ, Kornfeld GD, Dawes IW, Curmi PM, Mabbutt BC. Crystal structure of a heptameric Sm-like protein complex from archaea: implications for the structure and evolution of snRNPs. J Mol Biol 2001; 309:915-23. [PMID: 11399068 DOI: 10.1006/jmbi.2001.4693] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The Sm/Lsm proteins associate with small nuclear RNA to form the core of small nuclear ribonucleoproteins, required for processes as diverse as pre-mRNA splicing, mRNA degradation and telomere formation. The Lsm proteins from archaea are likely to represent the ancestral Sm/Lsm domain. Here, we present the crystal structure of the Lsm alpha protein from the thermophilic archaeon Methanobacterium thermoautotrophicum at 2.0 A resolution. The Lsm alpha protein crystallizes as a heptameric ring comprised of seven identical subunits interacting via beta-strand pairing and hydrophobic interactions. The heptamer can be viewed as a propeller-like structure in which each blade consists of a seven-stranded antiparallel beta-sheet formed from neighbouring subunits. There are seven slots on the inner surface of the heptamer ring, each of which is lined by Asp, Asn and Arg residues that are highly conserved in the Sm/Lsm sequences. These conserved slots are likely to form the RNA-binding site. In archaea, the gene encoding Lsm alpha is located next to the L37e ribosomal protein gene in a putative operon, suggesting a role for the Lsm alpha complex in ribosome function or biogenesis.
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Affiliation(s)
- B M Collins
- Department of Chemistry, Macquarie University, NSW 2109, Australia
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24
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Chaudhuri M. Cloning and characterization of a novel serine/threonine protein phosphatase type 5 from Trypanosoma brucei. Gene 2001; 266:1-13. [PMID: 11290414 DOI: 10.1016/s0378-1119(01)00367-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Reversible protein phosphorylation is essential for the regulation of numerous cellular functions and differentiation. The haemo-flagellated parasitic protozoan Trypanosoma brucei, the causative agent for African trypanosomiasis undergoes various stages of cellular differentiation during its digenetic life cycle. A complete cDNA of a unique serine/threonine phosphatase type five (TbPP5) was cloned and characterized from T. brucei. TbPP5 contains an open reading frame of 1416 bp that encodes a protein of about 53 kDa and exists as a single copy gene in the T. brucei genome. The deduced amino acid sequence showed 45-48% overall identity and 60-65% similarity with protein phosphatase 5's (PP5) from different species. Analysis of the primary sequence revealed that TbPP5 contains three TPR motifs at the N-terminal region (amino acid residues 7-107) while the phosphatase catalytic domain occurs in the C-terminal region (amino acid residues 210-410). A TbPP5 cDNA hybridized with a transcript of 2.5 kb which is present at similar levels in the procyclic and the bloodstream forms. However, the level of expression of the TbPP5 protein (52 kDa) detected by an antibody developed against a recombinant protein produced in E. coli was about 2-fold higher in the procyclic than the bloodstream form. The TbPP5 transcript level gradually decreased in cells grown in the logarithmic phase to the stationary phase in culture. Moreover, 18 h serum starvation of the procyclic forms decreased the level of the specific transcript about 3-fold suggesting that this protein may play a role during the active growth phase of the organism. The recombinant protein showed phosphatase activity which was stimulated about 2.6-fold by arachidonic acid with half-maximal activity at 75 microM. Indirect immuno-fluorescence of permeabilized cells revealed that the protein is localized in the cytosol and the nucleus This is the first report for the identification of a type 5 serine/threonine protein phosphatase in an ancient eukaryote such as T. brucei.
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MESH Headings
- Amino Acid Sequence
- Animals
- Arachidonic Acid/pharmacology
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Cloning, Molecular
- Culture Media, Serum-Free/pharmacology
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Protozoan/genetics
- Dose-Response Relationship, Drug
- Enzyme Activation/drug effects
- Gene Dosage
- Gene Expression Regulation/drug effects
- Molecular Sequence Data
- Nuclear Proteins/genetics
- Phosphates/metabolism
- Phosphoprotein Phosphatases/genetics
- RNA, Protozoan/drug effects
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Trypanosoma brucei brucei/drug effects
- Trypanosoma brucei brucei/enzymology
- Trypanosoma brucei brucei/genetics
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Affiliation(s)
- M Chaudhuri
- Department of Microbiology, Meharry Medical College, Nashville, TN 37208, USA.
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25
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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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26
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Brehm K, Jensen K, Frosch M. mRNA trans-splicing in the human parasitic cestode Echinococcus multilocularis. J Biol Chem 2000; 275:38311-8. [PMID: 10973970 DOI: 10.1074/jbc.m006091200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An identical 36-nucleotide exon was identified at the 5' termini of different mRNAs from the cestode Echinococcus multilocularis. We provide evidence that this exon constitutes a new spliced leader (SL) that is obviously trans-spliced to echinococcal pre-mRNAs, donated by a non-polyadenylated, trimethylguanosine-capped SL-RNA of 104 nucleotides. Sequence comparisons indicated that cestode and trematode SLs are likely to be derived from a common ancestor gene. No conservation was, however, observed concerning the spectrum of mRNAs that is trans-spliced in cestodes and trematodes, indicating that trans-splicing of a particular flatworm mRNA is not correlated with the function of the encoded protein. We also show that the echinococcal gene elp, encoding a member of the ezrin/radixin/moesin protein family, is expressed via two alternative transcripts, spliced either cis or trans at an identical splice acceptor site. This was accompanied by the formation of different elp primary transcripts, harboring a complete or a truncated upstream intron, which supports the hypothesis that alternative cis/trans-splicing depends on the presence or absence of an upstream splice donor site. A putative SL gene was also identified on chromosomal DNA of Echinococcus granulosus, indicating widespread utilization of trans-splicing in the genus.
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Affiliation(s)
- K Brehm
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
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27
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Agüero F, Verdún RE, Frasch AC, Sánchez DO. A random sequencing approach for the analysis of the Trypanosoma cruzi genome: general structure, large gene and repetitive DNA families, and gene discovery. Genome Res 2000; 10:1996-2005. [PMID: 11116094 PMCID: PMC313047 DOI: 10.1101/gr.gr-1463r] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2000] [Accepted: 09/20/2000] [Indexed: 11/24/2022]
Abstract
A random sequence survey of the genome of Trypanosoma cruzi, the agent of Chagas disease, was performed and 11,459 genomic sequences were obtained, resulting in approximately 4.3 Mb of readable sequences or approximately 10% of the parasite haploid genome. The estimated total GC content was 50.9%, with a high representation of A and T di- and trinucleotide repeats. Out of the estimated 5000 parasite genes, 947 putative new genes were identified. Another 1723 sequences corresponded to genes detected previously in T. cruzi through expression sequence tag analysis. 7735 sequences had no matches in the database, but the presence of open reading frames that passed Fickett's test suggests that some might contain coding DNA. The survey was highly redundant, with approximately 35% of the sequences included in a few large sequence families. Some of them code for protein families present in dozens of copies, including proteins essential for parasite survival and retrotransposons. Other sequence families include repetitive DNA present in thousands of copies per haploid genome. Some families in the latter group are new, parasite-specific, repetitive DNAs. These results suggest that T. cruzi could constitute an interesting model to analyze gene and genome evolution due to its plasticity in terms of sequence amplification and divergence. Additional information can be found at http://www.iib.unsam.edu.ar/tcruzi.gss. html.
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Affiliation(s)
- F Agüero
- Instituto de Investigaciones Biotecnológicas, Instituto Tecnológico de Chascomús, Universidad Nacional de General San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, San Martín, Provincia de Buenos Aires, Argentina
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28
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Agüero F, Verdún RE, Frasch ACC, Sánchez DO. A Random Sequencing Approach for the Analysis of the Trypanosoma cruzi Genome: General Structure, Large Gene and Repetitive DNA Families, and Gene Discovery. Genome Res 2000. [DOI: 10.1101/gr.146300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A random sequence survey of the genome of Trypanosoma cruzi, the agent of Chagas disease, was performed and 11,459 genomic sequences were obtained, resulting in ∼4.3 Mb of readable sequences or ∼10% of the parasite haploid genome. The estimated total GC content was 50.9%, with a high representation of A and T di- and trinucleotide repeats. Out of the estimated 5000 parasite genes, 947 putative new genes were identified. Another 1723 sequences corresponded to genes detected previously in T. cruzi through expression sequence tag analysis. 7735 sequences had no matches in the database, but the presence of open reading frames that passed Fickett's test suggests that some might contain coding DNA. The survey was highly redundant, with ∼35% of the sequences included in a few large sequence families. Some of them code for protein families present in dozens of copies, including proteins essential for parasite survival and retrotransposons. Other sequence families include repetitive DNA present in thousands of copies per haploid genome. Some families in the latter group are new, parasite-specific, repetitive DNAs. These results suggest that T. cruzi could constitute an interesting model to analyze gene and genome evolution due to its plasticity in terms of sequence amplification and divergence. Additional information can be found at http://www.iib.unsam.edu.ar/tcruzi.gss.html.[The sequence data described in this paper have been submitted to the dbGSS database under the following GenBank accession nos.:AQ443439–AQ443513, AQ443743–AQ445667, AQ902981–AQ911366,AZ049857–AZ051184, and AZ302116–AZ302563.]
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29
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Wilson JE, Powell MJ, Hoover SE, Sarnow P. Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 2000; 20:4990-9. [PMID: 10866656 PMCID: PMC85949 DOI: 10.1128/mcb.20.14.4990-4999.2000] [Citation(s) in RCA: 259] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cricket paralysis virus is a member of a group of insect picorna-like viruses. Cloning and sequencing of the single plus-strand RNA genome revealed the presence of two nonoverlapping open reading frames, ORF1 and ORF2, that encode the nonstructural and structural proteins, respectively. We show that each ORF is preceded by one internal ribosome entry site (IRES). The intergenic IRES is located 6,024 nucleotides from the 5' end of the viral RNA and is more active than the IRES located at the 5' end of the RNA, providing a mechanistic explanation for the increased abundance of structural proteins relative to nonstructural proteins in infected cells. Mutational analysis of this intergenic-region IRES revealed that ORF2 begins with a noncognate CCU triplet. Complementarity of this CCU triplet with sequences in the IRES is important for IRES function, pointing to an involvement of RNA-RNA interactions in translation initiation. Thus, the cricket paralysis virus genome is an example of a naturally occurring, functionally dicistronic eukaryotic mRNA whose translation is controlled by two IRES elements located at the 5' end and in the middle of the mRNA. This finding argues that eukaryotic mRNAs can express multiple proteins not only by polyprotein processing, reinitiation and frameshifting but also by using multiple IRES elements.
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Affiliation(s)
- J E Wilson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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30
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Di Noia JM, D'Orso I, Sánchez DO, Frasch AC. AU-rich elements in the 3'-untranslated region of a new mucin-type gene family of Trypanosoma cruzi confers mRNA instability and modulates translation efficiency. J Biol Chem 2000; 275:10218-27. [PMID: 10744707 DOI: 10.1074/jbc.275.14.10218] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma cruzi has a complex mucin gene family of 500 members with hypervariable regions expressed preferentially in vertebrate associated stages of the parasite. In this work, a novel mucin-type gene family is reported, composed of two groups of genes organized in independent tandems and having very short open reading frames. The structures of deduced proteins share the N and C termini but differ in central regions. One group has repeats with the consensus Lys-Asn-Thr(7)-Ser-Thr(3)-Ser(Ser/Lys)-Ala-Pro and the other a Thr-rich sequence of the type Asp-Gln-Thr(17-20)-Asn-Ala-Pro-Ala-Lys-Asp-Thr(5-7)-Asn-Ala-Pro-Ala-L ys. In both cases, expected mature core proteins are around 7 kDa. Both groups, named L and S, respectively, differ in the structure of genomic loci and mRNA, with differential blocks in the 3'-untranslated region. The highest mRNA level for S and L groups are in the epimastigote stage but they show distinct developmentally regulated patterns. Transcripts are short lived and their steady-state abundance is regulated post-transcriptionally with increased mRNA stability in insect stage epimastigote. AU-rich sequences, similar to ARE motives known to cause mRNA instability in higher eukaryotes, are present in the 3'-untranslated region of the transcripts. In transfection experiments this sequence is shown to be functional for the L group destabilizing its mRNA in a stage-specific manner. Furthermore, an effect of this AU-rich region on translation efficiency is shown. To our knowledge, this is the first time that a functional ARE sequence-dependent post-transcriptional regulation mechanism is reported in a lower eukaryote.
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Affiliation(s)
- J M Di Noia
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de General San Martín, C.C. 30, 1650 San Martín, Pcia. de Buenos Aires, Argentina
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31
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Ismaïli N, Pérez-Morga D, Walsh P, Cadogan M, Pays A, Tebabi P, Pays E. Characterization of a Trypanosoma brucei SR domain-containing protein bearing homology to cis-spliceosomal U1 70 kDa proteins. Mol Biochem Parasitol 2000; 106:109-20. [PMID: 10743615 DOI: 10.1016/s0166-6851(99)00205-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The protozoan parasite Trypanosoma brucei relies on trans-splicing of a common spliced leader (SL) RNA to maturate mRNAs. Using the yeast two-hybrid system a protein (TSR1IP) was identified that interacts with the T. brucei serine-arginine (SR) protein termed TSR1. TSR1IP shows homology to U1 70 kDa proteins, and contains an SR rich domain as well as an acidic/arginine domain homologous to the U1 70 kDa poly(A) polymerase inhibiting domain. This protein is localized in the nucleoplasm and excluded from the nucleolus in trypanosomal bloodstream and procyclic forms. Based on structural modelling predictions and on the identification of a RNA recognition motif (RRM), it was possible to demonstrate by the yeast three-hybrid system that TSR1IP interacts with the 5' splice region of the SL RNA. All the above characteristics suggest that TSR1IP could be involved in trans-splicing.
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Affiliation(s)
- N Ismaïli
- Laboratoire de Parasitologie Moléculaire, IBMM-ULB, Gosselies, Belgium
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32
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Wiesgigl M, Clos J. Uniform distribution of transcription complexes over the entire Leishmania donovani clpB (hsp 100) gene locus. Protist 1999; 150:369-73. [PMID: 10714771 DOI: 10.1016/s1434-4610(99)70038-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have analyzed the RNA polymerase density on the Leishmania donovani clpB gene locus. Our results show an even distribution of RNA polymerase over the clpB locus indicating an undiscriminative transcription. We conclude that, unlike the hsp70 genes, the clpB gene is not transcribed individually, but rather as part of a larger, polycistronic transcription unit.
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Affiliation(s)
- M Wiesgigl
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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33
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Pogonka T, Oberländer U, Marti T, Lucius R. Acanthocheilonema viteae: characterization of a molt-associated excretory/secretory 18-kDa protein. Exp Parasitol 1999; 93:73-81. [PMID: 10502469 DOI: 10.1006/expr.1999.4445] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Post-invasive third-stage larvae (pL3) of Acanthocheilonema viteae were labeled with [(35)S]-methionine in vivo, and proteins released into the culture supernatant before and during the third molt were analyzed. The molting supernatant (MSN) contained abundant proteins of 14, 18, 29, and 36 kDa. The 14- and 29-kDa proteins were exclusively found in the MSN, while the 18- and 36-kDa proteins were also produced by nonmolting pL3, albeit in much lower quantities. The cDNA for the most abundant protein in the MSN, an 18-kDa protein (Av18), was isolated by polymerase chain reaction (PCR) with reverse transcribed (RT) RNA of pL3, using information of the protein sequence. The Av18 full-length cDNA of 583 base pairs contained the 5' spliced leader sequence of nematodes, an open reading frame of 427 base pairs, and a poly(A) tail in typical distance to a polyadenylation signal. The deduced amino acid sequence encodes for a protein with a calculated size of 15.8 kDa. The N-terminus starts with a hydrophobic signal sequence and a predicted cleavage site after amino acid 20. The Av18 protein showed homologies to the deduced amino acid sequence of the larval transcripts Bm-alt-1 and alt-2 of Brugia malayi and to the Dirofilaria immitis proteins Di20/22 as well as to the Onchocerca volvulus proteins Ov-alt-1 and Ov-alt-2. Av18 is present in all parasite stages within the mammalian host, as determined by immunoblot with sera against the Escherichia coli-expressed protein and RT-PCR experiments. However, it was released into culture medium only by L3 and adult female worms. In female worms Av18 was localized in the cuticular region as demonstrated by immunofluorescent antibody tests using cryosections.
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Affiliation(s)
- T Pogonka
- Department of Molecular Parasitology (Institute of Biology), Humboldt University Berlin, Philippstrasse 13, Berlin, 10115, USA
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34
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Abstract
We have identified 52 novel human cadherin-like genes organized into three closely linked clusters. Comparison of the genomic DNA sequences with those of representative cDNAs reveals a striking genomic organization similar to that of immunoglobulin and T cell receptor gene clusters. The N-terminal extracellular and transmembrane domains of each cadherin protein are encoded by a distinct and unusually large exon. These exons are organized in a tandem array. By contrast, the C-terminal cytoplasmic domain of each protein is identical and is encoded by three small exons located downstream from the cluster of N-terminal exons. This unusual organization has interesting implications regarding the molecular code required to establish complex networks of neuronal connections in the brain and the mechanisms of cell-specific cadherin-like gene expression.
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Affiliation(s)
- Q Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Cremona ML, Campetella O, Sánchez DO, Frasch AC. Enzymically inactive members of the trans-sialidase family from Trypanosoma cruzi display beta-galactose binding activity. Glycobiology 1999; 9:581-7. [PMID: 10336990 DOI: 10.1093/glycob/9.6.581] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
trans-sialidase is a unique sialidase in that, instead of hydrolizing sialic acid, it preferentially transfers the monosaccharide to a terminal beta-galactose in glycoproteins and glycolipids. This enzyme, originally identified in Trypanosoma cruzi, belongs to a large family of proteins. Some members of the family lack the enzymatic activity. No function has been yet assigned to them. In this work, the gene copy number and the possible function of inactive members of the trans -sialidase family was studied. It is shown that genes encoding inactive members are not a few, but rather, are present in the same copy number (60-80 per haploid genome) as those encoding active trans -sialidases. Recombinant inactive proteins were purified and assayed for sialic acid and galactose binding activity in agglutination tests. The enzymatically inactive trans -sialidases were found to agglutinate de-sialylated erythrocytes but not untreated red blood cells. Assays made with mouse and rabbit red blood cells suggest that inactive trans -sialidases bind to beta, rather than alpha, terminal galactoses, the same specificity required by active trans -sialidases. A recombinant molecule that was made enzymatically inactive through a mutation in a single amino acid also retained the galactose binding activity. The binding was competed by lactose and was dependent on conservation of the protein native conformation. Therefore, at least some molecules in the trans -sialidase family that have lost their enzymatic function still retain their Gal-binding properties and might have a function as lectins in the parasite-host interaction.
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Affiliation(s)
- M L Cremona
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de General San Martín, Casilla de correo 30, 1650 San Martín, Provincia de Buenos Aires, Argentina
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36
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Frantz SA, Thiara AS, Lodwick D, Ng LL, Eperon IC, Samani NJ. Exon repetition in mRNA. Proc Natl Acad Sci U S A 1999; 96:5400-5. [PMID: 10318895 PMCID: PMC21871 DOI: 10.1073/pnas.96.10.5400] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The production of different transcripts (transcript heterogeneity) is a feature of many genes that may result in phenotypic variation. Several mechanisms, that occur at both the DNA and RNA level have been shown to contribute to this transcript heterogeneity in mammals, all of which involve either the rearrangement of sequences within a genome or the use of alternative signals in linear, contiguous DNA or RNA. Here we describe tissue-specific repetition of selective exons in transcripts of a rat gene (SA) with a normal exon-intron organization. We conclude that nonlinear mRNA processing can generate tissue-specific transcripts.
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Affiliation(s)
- S A Frantz
- Department of Cardiology, University of Leicester, Leicester LE3 9QP, United Kingdom
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37
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Ferguson KC, Rothman JH. Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. Mol Cell Biol 1999; 19:1892-900. [PMID: 10022876 PMCID: PMC83982 DOI: 10.1128/mcb.19.3.1892] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Approximately 70% of mRNAs in Caenorhabditis elegans are trans spliced to conserved 21- to 23-nucleotide leader RNAs. While the function of SL1, the major C. elegans trans-spliced leader, is unknown, SL1 RNA, which contains this leader, is essential for embryogenesis. Efforts to characterize in vivo requirements of the SL1 leader sequence have been severely constrained by the essential role of the corresponding DNA sequences in SL1 RNA transcription. We devised a heterologous expression system that circumvents this problem, making it possible to probe the length and sequence requirements of the SL1 leader without interfering with its transcription. We report that expression of SL1 from a U2 snRNA promoter rescues mutants lacking the SL1-encoding genes and that the essential embryonic function of SL1 is retained when approximately one-third of the leader sequence and/or the length of the leader is significantly altered. In contrast, although all mutant SL1 RNAs were well expressed, more severe alterations eliminate this essential embryonic function. The one non-rescuing mutant leader tested was never detected on messages, demonstrating that part of the leader sequence is essential for trans splicing in vivo. Thus, in spite of the high degree of SL1 sequence conservation, its length, primary sequence, and composition are not critical parameters of its essential embryonic function. However, particular nucleotides in the leader are essential for the in vivo function of the SL1 RNA, perhaps for its assembly into a functional snRNP or for the trans-splicing reaction.
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Affiliation(s)
- K C Ferguson
- Department of Molecular, Cellular, and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, California 93106, USA
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Wilson K, Uyetake L, Boothroyd J. Trypanosoma brucei: cis-acting sequences involved in the developmental regulation of PARP expression. Exp Parasitol 1999; 91:222-30. [PMID: 10072324 DOI: 10.1006/expr.1998.4366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The procyclic acidic repetitive protein (PARP or procyclin) of the parasitic protozoan Trypanosoma brucei is a developmentally regulated protein that shows extreme differences in its level of expression in different stages of the parasite's life cycle. Specifically, it is the major surface protein in the procyclic (insect) stage and, although the PARP gene is being actively transcribed in the mammalian bloodstream stage, there is no detectable PARP mRNA or protein in these cells. The 3'-untranslated region (UTR) of PARP, as well as other trypanosome genes, has the ability to confer the appropriate developmental regulation pattern onto chimeric reporter genes. To understand the mechanism of posttranscriptional regulation, selective replacement mutagenesis of the PARP mRNA 3'UTR was done to identify the cis-acting sequences involved in the down-regulation of this mRNA in bloodstream-form T. brucei. Transient transformation of constructs containing the PARP promoter and 5'UTR, the beta-glucuronidase coding region, and the selectively mutagenized or unaltered PARP 3'UTR were performed in procyclic and bloodstream T. brucei. The results of the reporter gene assays on the transformed cells indicate that there are at least two elements in the PARP 3'UTR which in bloodstream cells are involved in regulation of PARP expression and which appear to function as negative elements. In procyclic cells, there are two regions in which mutagenesis indicates positive cis-regulatory sequences, one of which has been previously defined (A. Hehl et al., 1994, Proc. Natl. Acad. Sci. USA 91, 370-374). These results indicate that multiple cis-acting elements within the PARP 3'UTR are involved in the developmental regulation of PARP expression and that regulation is controlled in a complex manner, presumably involving several cellular trans-acting factors.
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Affiliation(s)
- K Wilson
- Department of Microbiology and Immunology, Stanford University, Stanford, California, 94305, USA
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Ngô H, Tschudi C, Gull K, Ullu E. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc Natl Acad Sci U S A 1998; 95:14687-92. [PMID: 9843950 PMCID: PMC24510 DOI: 10.1073/pnas.95.25.14687] [Citation(s) in RCA: 502] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/1998] [Accepted: 10/16/1998] [Indexed: 11/18/2022] Open
Abstract
Double-stranded RNA (dsRNA) recently has been shown to give rise to genetic interference in Caenorhabditis elegans and also is likely to be the basis for phenotypic cosuppression in plants in certain instances. While constructing a plasmid vector for transfection of trypanosome cells, we serendipitously discovered that in vivo expression of dsRNA of the alpha-tubulin mRNA 5' untranslated region (5' UTR) led to multinucleated cells with striking morphological alterations and a specific block of cytokinesis. Transfection of synthetic alpha-tubulin 5' UTR dsRNA, but not of either strand individually, caused the same phenotype. On dsRNA transfection, tubulin mRNA, but not the corresponding pre-mRNA, was rapidly and specifically degraded, leading to a deficit of alpha-tubulin synthesis. The transfected cells were no longer capable of carrying out cytokinesis and eventually died. Analysis of cytoskeletal structures from these trypanosomes revealed defects in the microtubules of the flagellar axoneme and of the flagellar attachment zone, a complex cortical structure that we propose is essential for establishing the path of the cleavage furrow at cytokinesis. Last, dsRNA-mediated mRNA degradation is not restricted to alpha-tubulin mRNA but can be applied to other cellular mRNAs, thus establishing a powerful tool to genetically manipulate these important protozoan parasites.
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Affiliation(s)
- H Ngô
- Department of Internal Medicine, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8022, USA
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41
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Abstract
Does the intron/exon structure of eukaryotic genes belie their ancient assembly by exon-shuffling or have introns been inserted into preformed genes during eukaryotic evolution? These are the central questions in the ongoing 'introns-early' versus 'introns-late' controversy. The phylogenetic distribution of spliceosomal introns continues to strongly favor the intronslate theory. The introns-early theory, however, has claimed support from intron phase and protein structure correlations.
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Affiliation(s)
- J M Logsdon
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia,B3H 4H7, Canada.
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Chaves I, Zomerdijk J, Dirks-Mulder A, Dirks RW, Raap AK, Borst P. Subnuclear localization of the active variant surface glycoprotein gene expression site in Trypanosoma brucei. Proc Natl Acad Sci U S A 1998; 95:12328-33. [PMID: 9770486 PMCID: PMC22831 DOI: 10.1073/pnas.95.21.12328] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Trypanosoma brucei, transcription by RNA polymerase II and 5' capping of messenger RNA are uncoupled: a capped spliced leader is trans spliced to every RNA. This decoupling makes it possible to have protein-coding gene transcription driven by RNA polymerase I. Indeed, indirect evidence suggests that the genes for the major surface glycoproteins, variant surface glycoproteins (VSGs) in bloodstream-form trypanosomes, are transcribed by RNA polymerase I. In a single trypanosome, only one VSG expression site is maximally transcribed at any one time, and it has been speculated that transcription takes place at a unique site within the nucleus, perhaps in the nucleolus. We tested this by using fluorescence in situ hybridization. With probes that cover about 50 kb of the active 221 expression site, we detected nuclear transcripts of this site in a single fluorescent spot, which did not colocalize with the nucleolus. Analysis of marker gene-tagged active expression site DNA by fluorescent DNA in situ hybridization confirmed the absence of association with the nucleolus. Even an active expression site in which the promoter had been replaced by an rDNA promoter did not colocalize with the nulceolus. As expected, marker genes inserted in the rDNA array predominantly colocalize with the nucleolus, whereas the tubulin gene arrays do not. We conclude that transcription of the active VSG expression site does not take place in the nucleolus.
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Affiliation(s)
- I Chaves
- Division of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Tzfati Y, Shlomai J. Genomic organization and expression of the gene encoding the universal minicircle sequence binding protein. Mol Biochem Parasitol 1998; 94:137-41. [PMID: 9719518 DOI: 10.1016/s0166-6851(98)00052-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Y Tzfati
- Department of Microbiology and Immunology, University of California, San Francisco 94143-0414, USA
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44
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Fast NM, Roger AJ, Richardson CA, Doolittle WF. U2 and U6 snRNA genes in the microsporidian Nosema locustae: evidence for a functional spliceosome. Nucleic Acids Res 1998; 26:3202-7. [PMID: 9628919 PMCID: PMC147691 DOI: 10.1093/nar/26.13.3202] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The removal of introns from pre-messenger RNA is mediated by the spliceosome, a large complex composed of many proteins and five small nuclear RNAs (snRNAs). Of the snRNAs, the U6 and U2 snRNAs are the most conserved in sequence, as they interact extensively with each other and also with the intron, in several base pairings that are necessary for splicing. We have isolated and sequenced the genes encoding both U6 and U2 snRNAs from the intracellularly parasitic microsporidian Nosema locustae . Both genes are expressed. Both RNAs can be folded into secondary structures typical of other known U6 and U2 snRNAs. In addition, the N.locustae U6 and U2 snRNAs have the potential to base pair in the functional intermolecular interactions that have been characterized by extensive analyses in yeast and mammalian systems. These results indicate that the N.locustae U6 and U2 snRNAs may be functional components of an active spliceosome, even though introns have not yet been found in microsporidian genes.
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Affiliation(s)
- N M Fast
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada.
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45
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Lattemann CT, Apfel H. PCR-based amplification of total cDNA with high fidelity and high yield from minute amounts of parasite RNA. Int J Parasitol 1997; 27:955-8. [PMID: 9292312 DOI: 10.1016/s0020-7519(97)00062-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
cDNA, synthesised from total RNA from Acanthocheilonema viteae, was amplified by PCR with a primer derived from the spliced leader 1 sequence of nematodes and oligo-dT. Due to the great number of side products observed in the reaction, a biotinylated oligo-dT primer was used for cDNA-synthesis and the first cycles of PCR. After binding of the PCR products to streptavidin/paramagnetic particles, the (+)strands of the cDNAs were recovered and reamplified. Analysis of the PCR products obtained revealed the presence of full-length cDNAs of at least 1.7 kbp in size in amplified total cDNA from microfilariae, postinfective L3, and adult worms. The total cDNA, from only 20 ex vivo recovered postinfective L3, was efficiently amplified.
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Affiliation(s)
- C T Lattemann
- Max-Planck-Institut für Biologie, Abteilung Infektionsbiologie, Tübingen, Germany
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46
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Abstract
Proteins have been implicated in an expanding variety of functions during pre-mRNA splicing. Molecular cloning has identified genes encoding spliceosomal proteins that potentially act as novel RNA helicases, GTPases, or protein isomerases. Novel protein-protein and protein-RNA interactions that are required for functional spliceosome formation have also been described. Finally, growing evidence suggests that proteins may contribute directly to the spliceosome's active sites.
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Affiliation(s)
- C L Will
- Institut für Molekularbiologie und Tumorforschung, Philipps Universität Marburg, Emil Mannkopff Strasse 2, 35037, Marburg, Germany.
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47
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Malek O, Brennicke A, Knoop V. Evolution of trans-splicing plant mitochondrial introns in pre-Permian times. Proc Natl Acad Sci U S A 1997; 94:553-8. [PMID: 9012822 PMCID: PMC19551 DOI: 10.1073/pnas.94.2.553] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Trans-splicing in angiosperm plant mitochondria connects exons from independent RNA molecules by means of group II intron fragments. Homologues of trans-splicing introns in the angiosperm mitochondrial nad2 and nad5 genes are now identified as uninterrupted group II introns in the ferns Asplenium nidus and Marsilea drummondii. These fern introns are correctly spliced from the pre-mRNA at the sites predicted from their well-conserved secondary structures. The flanking exon sequences of the nad2 and nad5 genes in the ferns require RNA editing, including the removal of in-frame stop codons by U-to-C changes for correct expression of the genetic information. We conclude that cis-splicing introns like the ones now identified in ferns are the ancestors of trans-splicing introns in angiosperm mitochondria. Intron disruption is apparently due to a size increase of the structurally variable group II intron domain IV followed by DNA recombination in the plant mitochondrial genome.
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Affiliation(s)
- O Malek
- Allgemeine Botanik, Universität Ulm, Germany
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48
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