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Kostygov AY, Skýpalová K, Kraeva N, Kalita E, McLeod C, Yurchenko V, Field MC, Lukeš J, Butenko A. Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote. BMC Biol 2024; 22:281. [PMID: 39627879 PMCID: PMC11613528 DOI: 10.1186/s12915-024-02080-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Accepted: 11/26/2024] [Indexed: 12/08/2024] Open
Abstract
BACKGROUND In trypanosomatids, a group of unicellular eukaryotes that includes numerous important human parasites, cis-splicing has been previously reported for only two genes: a poly(A) polymerase and an RNA helicase. Conversely, trans-splicing, which involves the attachment of a spliced leader sequence, is observed for nearly every protein-coding transcript. So far, our understanding of splicing in this protistan group has stemmed from the analysis of only a few medically relevant species. In this study, we used an extensive dataset encompassing all described trypanosomatid genera to investigate the distribution of intron-containing genes and the evolution of splice sites. RESULTS We identified a new conserved intron-containing gene encoding an RNA-binding protein that is universally present in Kinetoplastea. We show that Perkinsela sp., a kinetoplastid endosymbiont of Amoebozoa, represents the first eukaryote completely devoid of cis-splicing, yet still preserving trans-splicing. We also provided evidence for reverse transcriptase-mediated intron loss in Kinetoplastea, extensive conservation of 5' splice sites, and the presence of non-coding RNAs within a subset of retained trypanosomatid introns. CONCLUSIONS All three intron-containing genes identified in Kinetoplastea encode RNA-interacting proteins, with a potential to fine-tune the expression of multiple genes, thus challenging the perception of cis-splicing in these protists as a mere evolutionary relic. We suggest that there is a selective pressure to retain cis-splicing in trypanosomatids and that this is likely associated with overall control of mRNA processing. Our study provides new insights into the evolution of introns and, consequently, the regulation of gene expression in eukaryotes.
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Affiliation(s)
- Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, 199034, Russia
| | - Karolína Skýpalová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Natalia Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Elora Kalita
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Cameron McLeod
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic.
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
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Arendt CS. Crithidia fasciculata adenosine transporter 1 (CfAT1), a novel high-affinity equilibrative nucleoside transporter specific for adenosine. Mol Biochem Parasitol 2013; 191:75-9. [PMID: 24120444 DOI: 10.1016/j.molbiopara.2013.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 09/26/2013] [Accepted: 09/29/2013] [Indexed: 11/26/2022]
Abstract
Most eukaryotic organisms including protozoans like Crithidia, Leishmania, and Plasmodium encode a repertoire of equilibrative nucleoside transporters (ENTs). Using genomic sequencing data from Crithidia fasciculata, we discovered that this organism contains multiple ENT genes of highly similar sequence to the previously cloned and characterized adenosine transporter CfNT1: CfAT1 and CfNT3, and an allele of CfAT1, named CfAT1.2. Characterization of CfAT1 shows that it is an adenosine-only transporter, 87% identical to CfNT1 in protein sequence, with a 50-fold lower Km for adenosine. Site directed mutation of a key residue in transmembrane domain 4 (TM4) in both CfNT1 and CfAT1 shows that lysine at this position results in a high affinity phenotype, while threonine decreases adenosine affinity in both transporters. These results show that C. fasciculata has at least two adenosine transporters, and that as in other protozoan ENTs, a lysine residue in TM4 plays a key role in ligand affinity.
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Affiliation(s)
- Cassandra S Arendt
- Pacific University School of Pharmacy, 222 SE 8th Avenue, Suite 451, Hillsboro, OR 97123, USA.
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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: 251] [Impact Index Per Article: 12.0] [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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Palfi Z, Lane WS, Bindereif A. Biochemical and functional characterization of the cis-spliceosomal U1 small nuclear RNP from Trypanosoma brucei. Mol Biochem Parasitol 2002; 121:233-43. [PMID: 12034457 DOI: 10.1016/s0166-6851(02)00044-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent studies in the trypanosome system have revealed that in addition to trans splicing of a short spliced leader (SL) exon, there is also cis splicing of internal introns. It has been suggested that cis splicing requires base-pairing of U1 small nuclear RNA (snRNA) and the 5' splice site. We have cloned the gene for U1 snRNA from Trypanosoma brucei and characterized the U1 snRNP. Based on immunoprecipitation and direct mass-spectrometric protein analysis the U1 snRNP contains the common Sm core found also in the known trans-spliceosomal snRNPs U2, U4/U6, and U5. The 5' end of U1 snRNA in the U1 snRNP is accessible for and functional in specific recognition of the 5' splice site of the poly(A) polymerase intron.
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Affiliation(s)
- Zsofia Palfi
- Institut für Biochemie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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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: 0.5] [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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Xu Y, Liu L, Michaeli S. Functional analyses of positions across the 5' splice site of the trypanosomatid spliced leader RNA. Implications for base-pair interaction with U5 and U6 snRNAs. J Biol Chem 2000; 275:27883-92. [PMID: 10875928 DOI: 10.1074/jbc.m000639200] [Citation(s) in RCA: 16] [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
In this study, we have used a genetic compensatory approach to examine the functional significance of the previously proposed interaction of spliced leader (SL) RNA with U5 small nuclear RNA (snRNA) (Dungan, J. D., Watkins, K. P., and Agabian, N. (1996) EMBO J. 15, 4016-4029; Xu, Y.-X., Ben Shlomo, H., and Michaeli, S. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 8473-8478) and the interaction of the SL RNA intron with U6 snRNA analogous to cis-splicing. Mutations were introduced at positions -4, -1, +1, +4, +5, and +7/+8 relative to the SL RNA 5' splice site that were proposed to interact with U5 and U6 snRNAs. All mutants exhibited altered splicing phenotypes compared with the parental strain, showing the importance of these intron and exon positions for trans-splicing. Surprisingly, mutation at invariant +1 position did not abolish splicing completely, unlike cis-splicing, but position +2 had the most severe effect on trans-splicing. Compensatory mutations were introduced in U5 and U6 snRNAs to examine whether the defects resulted from failure to interact with these snRNAs by base pairing. Suppression was observed only for positions +5 and +7/+8 with U5 compensatory mutations and for position +5 with a U6 compensatory mutation, supporting the existence of a base pair interaction of U5 and U6 with the SL RNA intron region. The failure to suppress the other SL RNA mutants by the U5 compensatory mutations suggests that another factor(s) interacts with these key SL RNA positions.
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Affiliation(s)
- Y Xu
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel and the Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Bell M, Wöhner R, Bindereif A. U4 small nuclear RNA genes of trypanosomes: cloning of the Leptomonas seymouri gene and mutational analysis of core snRNP assembly. Gene 2000; 247:77-86. [PMID: 10773446 DOI: 10.1016/s0378-1119(00)00118-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trans mRNA splicing in trypanosomatids requires as cofactors small nuclear RNAs (snRNAs) U2, U4, U5, and U6, in addition to the spliced leader (SL) RNA. To allow a phylogenetic comparison and functional analysis of trypanosomatid U4 snRNAs, we have cloned the single-copy gene for the Leptomonas seymouri U4 snRNA. In addition, a putative U4 snRNA gene from Leishmania tarentolae was identified by database searching. Using an episomal expression system, we introduced mutations into the conserved Sm region of the L. seymouri U4, which is the putative binding site for the common proteins that are present in each of the trans-spliceosomal snRNPs. As demonstrated by CsCl density gradient centrifugation, Sm mutant U4 snRNAs are non-functional in core RNP assembly. Furthermore, we present evidence by cell fractionation that U4 snRNAs with Sm mutations are partially defective in nuclear-cytoplasmic translocation. Taken together this indicates that the Sm site of U4 snRNA is responsible for stable core RNP assembly and nuclear localization.
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Affiliation(s)
- M Bell
- Institut für Biochemie, Fachbereich Biologie, Chemie und Geowissenschaften, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, D-35392, Giessen, Germany
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Schnare MN, Gray MW. Structural conservation and variation among U5 small nuclear RNAs from trypanosomatid protozoa. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1490:362-6. [PMID: 10684982 DOI: 10.1016/s0167-4781(00)00009-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
U5 snRNAs in trypanosomatid protozoa do not contain the trimethylguanosine cap structures that are often targeted in snRNA isolation procedures. As a result, the trypanosomatids are not well represented in the database of available U5 snRNA sequences. We have isolated and determined the sequence of the U5 snRNA from Crithidia fasciculata. Comparison with previously published trypanosomatid U5 snRNA sequences allows us to deduce the pattern of structural conservation and variation among these very divergent snRNA molecules.
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Affiliation(s)
- M N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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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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