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Hakim JMC, Gutierrez Guarnizo SA, Málaga Machaca E, Gilman RH, Mugnier MR. Whole-genome assembly of a hybrid Trypanosoma cruzi strain assembled with Nanopore sequencing alone. G3 (BETHESDA, MD.) 2024; 14:jkae076. [PMID: 38592968 PMCID: PMC11152063 DOI: 10.1093/g3journal/jkae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/12/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, which causes 10,000 deaths per year. Despite the high mortality associated with Chagas, relatively few parasite genomes have been assembled to date, with genome assemblies unavailable even for some commonly used laboratory strains. This is at least partially due to T. cruzi's highly complex and highly repetitive genome, which defies investigation using traditional short-read sequencing methods. In this study, we have generated a high-quality whole-genome assembly of the hybrid Tulahuen strain, a commercially available type VI strain, using long-read Nanopore sequencing without short-read scaffolding. The assembled genome contains 25% repeat regions, 17% variable multigene family members, and 27% transposable elements (TEs) and is of comparable quality with T. cruzi genome assemblies that utilized both long- and short-read data. Notably, we find that regions with TEs are significantly enriched for multicopy surface proteins, and that surface proteins are, on average, closer to TEs than to other coding regions. This finding suggests that mobile genetic elements such as transposons may drive recombination within surface protein gene families. This work demonstrates the feasibility of Nanopore sequencing to resolve complex regions of T. cruzi genomes, and with these resolved regions, provides support for a possible mechanism for genomic diversification.
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Affiliation(s)
- Jill M C Hakim
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Edith Málaga Machaca
- Asociación Benéfica PRISMA, Lima 15102, Peru
- Infectious Diseases Research Laboratory, Department of Cellular and Molecular Sciences, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Robert H Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Monica R Mugnier
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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Hakim JMC, Guarnizo SAG, Machaca EM, Gilman RH, Mugnier MR. Whole Genome Assembly of a Hybrid Trypanosoma cruzi Strain Assembled with Nanopore Sequencing Alone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550875. [PMID: 37546813 PMCID: PMC10402163 DOI: 10.1101/2023.07.27.550875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, which causes 10,000 deaths per year. Despite the high mortality caused by the pathogen, relatively few parasite genomes have been assembled to date; even some commonly used laboratory strains do not have publicly available genome assemblies. This is at least partially due to T. cruzi's highly complex and highly repetitive genome: while describing the variation in genome content and structure is critical to better understanding T. cruzi biology and the mechanisms that underlie Chagas disease, the complexity of the genome defies investigation using traditional short read sequencing methods. Here, we have generated a high-quality whole genome assembly of the hybrid Tulahuen strain, a commercially available Type VI strain, using long read Nanopore sequencing without short read scaffolding. Using automated tools and manual curation for annotation, we report a genome with 25% repeat regions, 17% variable multigene family members, and 27% transposable elements. Notably, we find that regions with transposable elements are significantly enriched for surface proteins, and that on average surface proteins are closer to transposable elements compared to other coding regions. This finding supports a possible mechanism for diversification of surface proteins in which mobile genetic elements such as transposons facilitate recombination within the gene family. This work demonstrates the feasibility of nanopore sequencing to resolve complex regions of T. cruzi genomes, and with these resolved regions, provides support for a possible mechanism for genomic diversification.
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Olzog VJ, Gärtner C, Stadler PF, Fallmann J, Weinberg CE. cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3' cyclic phosphates and 5' hydroxyl ends. RNA Biol 2021; 18:818-831. [PMID: 34906034 PMCID: PMC8782182 DOI: 10.1080/15476286.2021.1999105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Self-cleaving ribozymes are catalytically active RNAs that cleave themselves into a 5′-fragment with a 2′,3′-cyclic phosphate and a 3′-fragment with a 5′-hydroxyl. They are widely applied for the construction of synthetic RNA devices and RNA-based therapeutics. However, the targeted discovery of self-cleaving ribozymes remains a major challenge. We developed a transcriptome-wide method, called cyPhyRNA-seq, to screen for ribozyme cleavage fragments in total RNA extract. This approach employs the specific ligation-based capture of ribozyme 5′-fragments using a variant of the Arabidopsis thaliana tRNA ligase we engineered. To capture ribozyme 3′-fragments, they are enriched from total RNA by enzymatic treatments. We optimized and enhanced the individual steps of cyPhyRNA-seq in vitro and in spike-in experiments. Then, we applied cyPhyRNA-seq to total RNA isolated from the bacterium Desulfovibrio vulgaris and detected self-cleavage of the three predicted type II hammerhead ribozymes, whose activity had not been examined to date. cyPhyRNA-seq can be used for the global analysis of active self-cleaving ribozymes with the advantage to capture both ribozyme cleavage fragments from total RNA. Especially in organisms harbouring many self-cleaving RNAs, cyPhyRNA-seq facilitates the investigation of cleavage activity. Moreover, this method has the potential to be used to discover novel self-cleaving ribozymes in different organisms.
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Affiliation(s)
- V Janett Olzog
- Department of Life Science, Institute for Biochemistry, Leipzig, Germany
| | - Christiane Gärtner
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Theoretical Chemistry, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, University of Vienna, Santa Fe, New Mexico, USA
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
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Macías F, Afonso-Lehmann R, Carreira PE, Thomas MC. TBP and SNAP50 transcription factors bind specifically to the Pr77 promoter sequence from trypanosomatid non-LTR retrotransposons. Parasit Vectors 2021; 14:313. [PMID: 34108018 PMCID: PMC8190864 DOI: 10.1186/s13071-021-04803-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Background Trypanosomatid genomes are colonized by active and inactive mobile DNA elements, such as LINE, SINE-like, SIDER and DIRE retrotransposons. These elements all share a 77-nucleotide-long sequence at their 5′ ends, known as Pr77, which activates transcription, thereby generating abundant unspliced and translatable transcripts. However, transcription factors that mediates this process have still not been reported. Methods TATA-binding protein (TBP) and small nuclear RNA-activating protein 50 kDa (SNAP50) recombinant proteins and specific antibodies raised against them were generated. Protein capture assay, electrophoretic mobility-shift assays (EMSA) and EMSA competition assays carried out using these proteins and nuclear proteins of the parasite together to specific DNA sequences used as probes allowed detecting direct interaction of these transcription factors to Pr77 sequence. Results This study identified TBP and SNAP50 as part of the DNA-protein complex formed by the Pr77 promoter sequence and nuclear proteins of Trypanosoma cruzi. TBP establishes direct and specific contact with the Pr77 sequence, where the DPE and DPE downstream regions are docking sites with preferential binding. TBP binds cooperatively (Hill coefficient = 1.67) to Pr77 and to both strands of the Pr77 sequence, while the conformation of this highly structured sequence is not involved in TBP binding. Direct binding of SNAP50 to the Pr77 sequence is weak and may be mediated by protein–protein interactions through other trypanosomatid nuclear proteins. Conclusions Identification of the transcription factors that mediate Pr77 transcription may help to elucidate how these retrotransposons are mobilized within the trypanosomatid genomes and their roles in gene regulation processes in this human parasite. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04803-5.
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Affiliation(s)
- Francisco Macías
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, 18016, Granada, Spain
| | - Raquel Afonso-Lehmann
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, 18016, Granada, Spain
| | - Patricia E Carreira
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, 18016, Granada, Spain.,Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia
| | - M Carmen Thomas
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina "López Neyra", Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, 18016, Granada, Spain.
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Genomic Organization and Generation of Genetic Variability in the RHS (Retrotransposon Hot Spot) Protein Multigene Family in Trypanosoma cruzi. Genes (Basel) 2020; 11:genes11091085. [PMID: 32957642 PMCID: PMC7563717 DOI: 10.3390/genes11091085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Retrotransposon Hot Spot (RHS) is the most abundant gene family in Trypanosoma cruzi, with unknown function in this parasite. The aim of this work was to shed light on the organization and expression of RHS in T. cruzi. The diversity of the RHS protein family in T. cruzi was demonstrated by phylogenetic and recombination analyses. Transcribed sequences carrying the RHS domain were classified into ten distinct groups of monophyletic origin. We identified numerous recombination events among the RHS and traced the origins of the donors and target sequences. The transcribed RHS genes have a mosaic structure that may contain fragments of different RHS inserted in the target sequence. About 30% of RHS sequences are located in the subtelomere, a region very susceptible to recombination. The evolution of the RHS family has been marked by many events, including gene duplication by unequal mitotic crossing-over, homologous, as well as ectopic recombination, and gene conversion. The expression of RHS was analyzed by immunofluorescence and immunoblotting using anti-RHS antibodies. RHS proteins are evenly distributed in the nuclear region of T. cruzi replicative forms (amastigote and epimastigote), suggesting that they could be involved in the control of the chromatin structure and gene expression, as has been proposed for T. brucei.
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Ramirez JL. An Evolutionary View of Trypanosoma Cruzi Telomeres. Front Cell Infect Microbiol 2020; 9:439. [PMID: 31998659 PMCID: PMC6967402 DOI: 10.3389/fcimb.2019.00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 11/21/2022] Open
Abstract
Like in most eukaryotes, the linear chromosomes of Trypanosoma cruzi end in a nucleoprotein structure called the telomere, which is preceded by regions of variable length called subtelomeres. Together telomeres and subtelomeres are dynamic sites where DNA sequence rearrangements can occur without compromising essential interstitial genes or chromosomal synteny. Good examples of subtelomeres involvement are the expansion of human olfactory receptors genes, variant surface antigens in Trypanosoma brucei, and Saccharomyces cerevisiae mating types. T. cruzi telomeres are made of long stretches of the hexameric repeat 5′-TTAGGG-OH-3′, and its subtelomeres are enriched in genes and pseudogenes from the large gene families RHS, TS and DGF1, DEAD/H-RNA helicase and N-acetyltransferase, intermingled with sequences of retrotransposons elements. In particular, members of the Trans-sialidase type II family appear to have played a role in shaping the current T. cruzi telomere structure. Although the structure and function of T. cruzi telomeric and subtelomeric regions have been documented, recent experiments are providing new insights into T. cruzi's telomere-subtelomere dynamics. In this review, I discuss the co-evolution of telomere, subtelomeres and the TS gene family, and the role that these regions may have played in shaping T. cruzi's genome.
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Affiliation(s)
- Jose Luis Ramirez
- Fundación Instituto de Estudios Avanzados and United Nations University UNU-BIOLAC, Caracas, Venezuela
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Weinberg CE, Weinberg Z, Hammann C. Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function. Nucleic Acids Res 2019; 47:9480-9494. [PMID: 31504786 PMCID: PMC6765202 DOI: 10.1093/nar/gkz737] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 08/08/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.
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Affiliation(s)
- Christina E Weinberg
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16–18, 04107 Leipzig, Germany
| | - Christian Hammann
- Ribogenetics & Biochemistry, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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Nishiyama E, Ohshima K. Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons. Genome Biol Evol 2018; 10:1471-1483. [PMID: 29850801 PMCID: PMC6007223 DOI: 10.1093/gbe/evy098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2018] [Indexed: 12/15/2022] Open
Abstract
In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3'-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3'-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3'-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.
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Affiliation(s)
- Eri Nishiyama
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Kazuhiko Ohshima
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
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Macías F, Afonso-Lehmann R, López MC, Gómez I, Thomas MC. Biology of Trypanosoma cruzi Retrotransposons: From an Enzymatic to a Structural Point of View. Curr Genomics 2018; 19:110-118. [PMID: 29491739 PMCID: PMC5814959 DOI: 10.2174/1389202918666170815150738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/13/2017] [Accepted: 04/16/2017] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION An important portion of the Trypanosoma cruzi genome is composed of mobile genetic elements, which are interspersed with genes on all chromosomes. The L1Tc non-LTR retrotransposon and its truncated version NARTc are the most highly represented and best studied of these elements. L1Tc is actively transcribed in all three forms of the Trypanosoma parasite and encodes the proteins that enable it to autonomously mobilize. This mini review discusses the enzymatic properties of L1Tc that enable its mobilization and possibly the mobilization of other non-autonomous retrotransposons in Trypanosoma. We also briefly review the Hepatitis Delta Virus-like autocatalytic and 2A self-cleaving viral-like sequences contained in L1Tc that regulate post-transcriptional properties such as relative protein abundance and mRNA stability. Special emphasis is placed on the Pr77 dual system, which is based on the RNA pol II-dependent internal promoter of L1Tc and NARTc and the HDV-like ribozyme activity encoded by the first 77 nucleotides of the element's DNA and RNA. The high degree of conservation of the Pr77 sequence, referred to as the "Pr77-hallmark", among different trypanosomatid retroelements suggests that these mobile elements are responsible for the distribution of regulatory sequences within the genome they inhabit. CONCLUSION We also discuss how the involvement of L1Tc and NARTc in the gene regulatory processes of these parasites could justify their domestication and long-term coexistence in these ancient organisms.
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Affiliation(s)
- Francisco Macías
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra-CSIC, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC). PTS-Granada. Avda. del Conocimiento S/N, 18016-Granada, Spain
| | - Raquel Afonso-Lehmann
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra-CSIC, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC). PTS-Granada. Avda. del Conocimiento S/N, 18016-Granada, Spain
| | - Manuel C. López
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra-CSIC, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC). PTS-Granada. Avda. del Conocimiento S/N, 18016-Granada, Spain
| | - Inmaculada Gómez
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra-CSIC, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC). PTS-Granada. Avda. del Conocimiento S/N, 18016-Granada, Spain
| | - M. Carmen Thomas
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra-CSIC, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC). PTS-Granada. Avda. del Conocimiento S/N, 18016-Granada, Spain
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Bringaud F, Rogers M, Ghedin E. Identification and analysis of ingi-related retroposons in the trypanosomatid genomes. Methods Mol Biol 2015; 1201:109-22. [PMID: 25388110 DOI: 10.1007/978-1-4939-1438-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Transposable elements (TE), defined as discrete pieces of DNA that can move from one site to another site in genomes, represent significant components of eukaryotic genomes, including trypanosomatids. Up to 5% of the trypanosomatid genome content is composed of retroposons of the ingi clade, further divided into subclades and subfamilies ranging from short extinct truncated elements (SIDER) to long active elements (ingi). Important differences in ingi-related retroposon content have been reported between trypanosomatid species. For instance, Leishmania spp. have expanded and recycled a whole SIDER family to fulfill an important biological pathway, i.e., regulation of gene expression, while trypanosome genomes are primarily composed of active elements. Here, we present an overview of the computational methods used to identify, annotate, and analyze ingi-related retroposons for providing a comprehensive picture of all these TE families in newly available trypanosomatid genome sequences.
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Affiliation(s)
- Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR 5536 CNRS, Université de Bordeaux, 146, rue Léo Saignat, 33076, Bordeaux, France,
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Sánchez-Luque F, López MC, Macias F, Alonso C, Thomas MC. Pr77 and L1TcRz: A dual system within the 5'-end of L1Tc retrotransposon, internal promoter and HDV-like ribozyme. Mob Genet Elements 2014; 2:1-7. [PMID: 22754746 PMCID: PMC3383444 DOI: 10.4161/mge.19233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The sequence corresponding to the first 77 nucleotides of the L1Tc and NARTc non-LTR retrotransposons from Trypanosoma cruzi is an internal promoter (Pr77) that generates abundant, although poorly translatable, un-spliced transcripts. It has been recently described that L1TcRz, an HDV-like ribozyme, resides within the 5'-end of the RNA from the L1Tc and NARTc retrotransposons. Remarkably, the same first 77 nucleotides of L1Tc/NARTc elements comprise both the Pr77 internal promoter and the HDV-like L1TcRz. The L1TcRz cleaves on the 5'-side of the +1 nucleotide of the L1Tc element insuring that the promoter and the ribozyme functions travel with the transposon during retrotransposition. The ribozyme activity would prevent the mobilization of upstream sequences and insure the individuality of the L1Tc/NARTc copies transcribed from associated tandems. The Pr77/L1TcRz sequence is also found in other trypanosomatid's non-LTR retrotransposons and degenerated retroposons. The possible conservation of the ribozyme activity in a widely degenerated retrotransposon, as the Leishmania SIDERs, could indicate that the presence of this element and the catalytic activity could play some favorable genetic regulation. The functional implications of the Pr77/L1TcRz dual system in the regulation of the L1Tc/NARTc retrotransposons and in the gene expression of trypanosomatids are also discussed in this paper.
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Porcel BM, Denoeud F, Opperdoes F, Noel B, Madoui MA, Hammarton TC, Field MC, Da Silva C, Couloux A, Poulain J, Katinka M, Jabbari K, Aury JM, Campbell DA, Cintron R, Dickens NJ, Docampo R, Sturm NR, Koumandou VL, Fabre S, Flegontov P, Lukeš J, Michaeli S, Mottram JC, Szöőr B, Zilberstein D, Bringaud F, Wincker P, Dollet M. The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants. PLoS Genet 2014; 10:e1004007. [PMID: 24516393 PMCID: PMC3916237 DOI: 10.1371/journal.pgen.1004007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022] Open
Abstract
Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease. Some plant trypanosomes, single-celled organisms living in phloem sap, are responsible for important palm diseases, inducing frequent expensive and toxic insecticide treatments against their insect vectors. Other trypanosomes multiply in latex tubes without detriment to their host. Despite the wide range of behaviors and impacts, these trypanosomes have been rather unceremoniously lumped into a single genus: Phytomonas. A battery of molecular probes has been used for their characterization but no clear phylogeny or classification has been established. We have sequenced the genomes of a pathogenic phloem-specific Phytomonas from a diseased South American coconut palm and a latex-specific isolate collected from an apparently healthy wild euphorb in the south of France. Upon comparison with each other and with human pathogenic trypanosomes, both Phytomonas revealed distinctive compact genomes, consisting essentially of single-copy genes, with the vast majority of genes shared by both isolates irrespective of their effect on the host. A strong cohort of enzymes in the sugar metabolism pathways was consistent with the nutritional environments found in plants. The genetic nuances may reveal the basis for the behavioral differences between these two unique plant parasites, and indicate the direction of our future studies in search of effective treatment of the crop disease parasites.
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Affiliation(s)
- Betina M. Porcel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Université d'Evry, UMR 8030, Evry, France
- Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, France
- * E-mail: (BMP); (MD)
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Université d'Evry, UMR 8030, Evry, France
- Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, France
| | - Fred Opperdoes
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Mohammed-Amine Madoui
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Tansy C. Hammarton
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mark C. Field
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Michael Katinka
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Kamel Jabbari
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Université d'Evry, UMR 8030, Evry, France
- Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - David A. Campbell
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Roxana Cintron
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Nicholas J. Dickens
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Nancy R. Sturm
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States of America
| | | | - Sandrine Fabre
- CIRAD, TA A-98/F, Campus International de Baillarguet, Montpellier, France
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Shulamit Michaeli
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jeremy C. Mottram
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Balázs Szöőr
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Dan Zilberstein
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques, Université Bordeaux Segalen, CNRS UMR-5536, Bordeaux, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Université d'Evry, UMR 8030, Evry, France
- Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, France
| | - Michel Dollet
- CIRAD, TA A-98/F, Campus International de Baillarguet, Montpellier, France
- * E-mail: (BMP); (MD)
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13
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Sánchez-Luque FJ, López MC, Macias F, Alonso C, Thomas MC. Identification of an hepatitis delta virus-like ribozyme at the mRNA 5'-end of the L1Tc retrotransposon from Trypanosoma cruzi. Nucleic Acids Res 2011; 39:8065-77. [PMID: 21724615 PMCID: PMC3185411 DOI: 10.1093/nar/gkr478] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
L1Tc is a non-LTR LINE element from Trypanosoma cruzi that encodes its transposition machinery and bears an internal promoter. Herewith, we report the identification of an in vitro active hepatitis delta virus-like ribozyme located in the first 77 nt at the 5′-end of the L1Tc mRNA (L1TcRz). The data presented show that L1TcRz has a co-transcriptional function. Using gel-purified uncleaved RNA transcripts, the data presented indicate that the kinetics of the self-cleaving, in a magnesium-dependent reaction, fits to a two-phase decay curve. The cleavage point identified by primer extension takes place at +1 position of the element. The hydroxyl nature of the 5′-end of the 3′-fragment generated by the cleavage activity of L1TcRz was confirmed. Since we have previously described that the 77-nt long fragment located at the 5′-end of L1Tc has promoter activity, the existence of a ribozyme in L1Tc makes this element to be the first described non-LTR retroelement that has an internal promoter–ribozyme dual function. The L1Tc nucleotides located downstream of the ribozyme catalytic motif appear to inhibit its activity. This inhibition may be influenced by the existence of a specific L1Tc RNA conformation that is recognized by RNase P.
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Affiliation(s)
- Francisco J Sánchez-Luque
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra-CSIC, Parque Tecnológico de Ciencias de Salud, Granada
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14
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Bringaud F, Berriman M, Hertz-Fowler C. TSIDER1, a short and non-autonomous Salivarian trypanosome-specific retroposon related to the ingi6 subclade. Mol Biochem Parasitol 2011; 179:30-6. [PMID: 21664383 PMCID: PMC3820030 DOI: 10.1016/j.molbiopara.2011.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/23/2011] [Accepted: 05/25/2011] [Indexed: 12/15/2022]
Abstract
Retroposons of the ingi clade are the most abundant transposable elements identified in the trypanosomatid genomes. Some are long autonomous elements (ingi, L1Tc) while others, such as RIME and NARTc, are short non-coding elements that parasitize the retrotransposition machinery of the active autonomous ones for their own mobilization. Here, we identified a new family of short non-autonomous retroposons of the ingi clade, called TSIDER1, which are present in the genome of Salivarian (African) trypanosomes, Trypanosoma brucei, T. congolense and T. vivax, but absent in the T. cruzi and Leishmania spp. genomes and, as such, TSIDER1 is the only retroposon subfamily conserved at the nucleotide level between African trypanosome species. We identified three TvSIDER1 families within the genome of T. vivax and the high level of sequence conservation within the TvSIDER1a and TvSIDER1b groups suggests that they are still active. We propose that TvSIDER1a/b elements are using the Tvingi retrotransposition machinery, as they are preceded by the same conserved pattern characteristic of the ingi6 subclade, which corresponds to the retroposon-encoded endonuclease binding site. In contrast, TcoSIDER1, TbSIDER1 and TvSIDER1c are too divergent to be considered as active retroposons. The relatively low number of SIDER elements identified in the T. congolense (70 copies), T. vivax (32 copies) and T. brucei (22 copies) genomes confirms that trypanosomes have not expanded short transposable elements, which is in contrast to Leishmania spp. (∼2000 copies), where SIDER play a role in the regulation of gene expression.
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Affiliation(s)
- Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR 5536, Université Bordeaux Segalen, CNRS, 146 rue Léo Saignat, 33076 Bordeaux, France.
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15
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Thomas MC, Macias F, Alonso C, López MC. The biology and evolution of transposable elements in parasites. Trends Parasitol 2010; 26:350-62. [PMID: 20444649 DOI: 10.1016/j.pt.2010.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 03/30/2010] [Accepted: 04/01/2010] [Indexed: 12/19/2022]
Abstract
Transposable elements (TEs) are dynamic elements that can reshape host genomes by generating rearrangements with the potential to create or disrupt genes, to shuffle existing genes, and to modulate their patterns of expression. In the genomes of parasites that infect mammals several TEs have been identified that probably have been maintained throughout evolution due to their contribution to gene function and regulation of gene expression. This review addresses how TEs are organized, how they colonize the genomes of mammalian parasites, the functional role these elements play in parasite biology, and the interactions between these elements and the parasite genome.
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Affiliation(s)
- M Carmen Thomas
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra - CSIC, Parque Tecnológico de Ciencias de la Salud, 18100 Granada, Spain
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16
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Trypanosomatid genomes contain several subfamilies of ingi-related retroposons. EUKARYOTIC CELL 2009; 8:1532-42. [PMID: 19666780 DOI: 10.1128/ec.00183-09] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Retroposons are ubiquitous transposable elements found in the genomes of most eukaryotes, including trypanosomatids. The African and American trypanosomes (Trypanosoma brucei and Trypanosoma cruzi) contain long autonomous retroposons of the ingi clade (Tbingi and L1Tc, respectively) and short nonautonomous truncated versions (TbRIME and NARTc, respectively), as well as degenerate ingi-related retroposons devoid of coding capacity (DIREs). In contrast, Leishmania major contains only remnants of extinct retroposons (LmDIREs) and of short nonautonomous heterogeneous elements (LmSIDERs). We extend this comparative and evolutionary analysis of retroposons to the genomes of two other African trypanosomes (Trypanosoma congolense and Trypanosoma vivax) and another Leishmania sp. (Leishmania braziliensis). Three new potentially functional retroposons of the ingi clade have been identified: Tvingi in T. vivax and Tcoingi and L1Tco in T. congolense. T. congolense is the first trypanosomatid containing two classes of potentially active retroposons of the ingi clade. We analyzed sequences located upstream of these new long autonomous ingi-related elements, which code for the recognition site of the retroposon-encoded endonuclease. The closely related Tcoingi and Tvingi elements show the same conserved pattern, indicating that the Tcoingi- and Tvingi-encoded endonucleases share site specificity. Similarly, the conserved pattern previously identified upstream of L1Tc has also been detected at the same relative position upstream of L1Tco elements. A phylogenetic analysis of all ingi-related retroposons identified so far, including DIREs, clearly shows that several distinct subfamilies have emerged and coexisted, though in the course of trypanosomatid evolution, only a few have been maintained as active elements in modern trypanosomatid (sub)species.
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17
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Smith M, Bringaud F, Papadopoulou B. Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome. BMC Genomics 2009; 10:240. [PMID: 19463167 PMCID: PMC2689281 DOI: 10.1186/1471-2164-10-240] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 05/22/2009] [Indexed: 12/17/2022] Open
Abstract
Background We have recently identified two large families of extinct transposable elements termed Short Interspersed DEgenerated Retroposons (SIDERs) in the parasitic protozoan Leishmania major. The characterization of SIDER elements was limited to the SIDER2 subfamily, although members of both subfamilies have been shown to play a role in the regulation of gene expression at the post-transcriptional level. Apparent functional domestication of SIDERs prompted further investigation of their characterization, dissemination and evolution throughout the Leishmania genus, with particular attention to the disregarded SIDER1 subfamily. Results Using optimized statistical profiles of both SIDER1 and SIDER2 subgroups, we report the first automated and highly sensitive annotation of SIDERs in the genomes of L. infantum, L. braziliensis and L. major. SIDER annotations were combined to in-silico mRNA extremity predictions to generate a detailed distribution map of the repeat family, hence uncovering an enrichment of antisense-oriented SIDER repeats between the polyadenylation and trans-splicing sites of intergenic regions, in contrast to the exclusive sense orientation of SIDER elements within 3'UTRs. Our data indicate that SIDER elements are quite uniformly dispersed throughout all three genomes and that their distribution is generally syntenic. However, only 47.4% of orthologous genes harbor a SIDER element in all three species. There is evidence for species-specific enrichment of SIDERs and for their preferential association, especially for SIDER2s, with different metabolic functions. Investigation of the sequence attributes and evolutionary relationship of SIDERs to other trypanosomatid retroposons reveals that SIDER1 is a truncated version of extinct autonomous ingi-like retroposons (DIREs), which were functional in the ancestral Leishmania genome. Conclusion A detailed characterization of the sequence traits for both SIDER subfamilies unveils major differences. The SIDER1 subfamily is more heterogeneous and shows an evolutionary link with vestigial DIRE retroposons as previously observed for the ingi/RIME and L1Tc/NARTc couples identified in the T. brucei and T. cruzi genomes, whereas no identified DIREs are related to SIDER2 sequences. Although SIDER1s and SIDER2s display equivalent genomic distribution globally, the varying degrees of sequence conservation, preferential genomic disposition, and differential association to orthologous genes allude to an intricate web of SIDER assimilation in these parasitic organisms.
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Affiliation(s)
- Martin Smith
- Research Centre in Infectious Diseases, CHUL Research Centre, RC-709, 2705 Laurier Blvd, Quebec (QC), G1V4G2 Canada.
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18
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Bartholomeu DC, Cerqueira GC, Leão ACA, daRocha WD, Pais FS, Macedo C, Djikeng A, Teixeira SMR, El-Sayed NM. Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi. Nucleic Acids Res 2009; 37:3407-17. [PMID: 19336417 PMCID: PMC2691823 DOI: 10.1093/nar/gkp172] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A novel large multigene family was recently identified in the human pathogen Trypanosoma cruzi, causative agent of Chagas disease, and corresponds to ∼6% of the parasite diploid genome. The predicted gene products, mucin-associated surface proteins (MASPs), are characterized by highly conserved N- and C-terminal domains and a strikingly variable and repetitive central region. We report here an analysis of the genomic organization and expression profile of masp genes. Masps are not randomly distributed throughout the genome but instead are clustered with genes encoding mucin and other surface protein families. Masp transcripts vary in size, are preferentially expressed during the trypomastigote stage and contain highly conserved 5′ and 3′ untranslated regions. A sequence analysis of a trypomastigote cDNA library reveals the expression of multiple masp variants with a bias towards a particular masp subgroup. Immunofluorescence assays using antibodies generated against a MASP peptide reveals that the expression of particular MASPs at the cell membrane is limited to subsets of the parasite population. Western blots of phosphatidylinositol-specific phospholipase C (PI-PLC)-treated parasites suggest that MASP may be GPI-anchored and shed into the medium culture, thus contributing to the large repertoire of parasite polypeptides that are exposed to the host immune system.
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Affiliation(s)
- Daniella C Bartholomeu
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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Gilbert C, Pace JK, Waters PD. Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome. Gene 2008; 425:1-8. [PMID: 18796327 DOI: 10.1016/j.gene.2008.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 08/18/2008] [Accepted: 08/18/2008] [Indexed: 10/21/2022]
Abstract
SINEs retrotranspose using their partner LINE's enzymatic machinery. It has recently been proposed that AfroSINEs ending with GGTTT 3' tandem repeats were mobilized by RTE elements ending with CAA 3' tandem repeats in the Afrotherian genome. Using sequences from the elephant genome, we show that AfroSINEs derive from RTE ending with GGTTT-like 3' tandem repeats, a subgroup of RTE1_LA that only reached low copy number, and confirm that they were most likely mobilized by RTE ending with CAA(n) tandem repeats (RTE1_LA-CAA(n)). This partnership is supported by sequence similarity between two regions of the elements, overlap in the timing of their activity, common features of their target site consensus that are not shared by other members of the RTE family, and their high copy number. Detailed analyses of pre-insertion loci reveal that like many other apurinic/apyrimidinic endonuclease encoding elements, RTE1_LA-CAA(n) shows loose target site specificity. In addition, the RTE1_LA-CAA(n) target site consensus shares several structural and primary sequence features with that of LINE1, suggesting that these two elements share close functional similarity in the target primed reverse transcription (TPRT) reaction. Interestingly, although globally similar, the target site consensus of AfroSINE(Anc) and RTE1_LA-CAA(n) differ in several aspects. These differences, not observed among all SINE/LINE pairs so far examined, are most likely due to the fact that AfroSINEs and RTE1_LA-CAA(n) are terminated by a different tandem repeat motif. We propose that these differences reflect constraints imposed by base pairing interactions between the mRNA 3' terminal tandem repeats and the target DNA at the onset of TPRT. So in addition to the endonuclease nicking preference, the mRNA of these elements appears to play an important role in integration site choice through a passive, post-nicking, selective process.
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Affiliation(s)
- Clément Gilbert
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa.
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20
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Role of transposable elements in trypanosomatids. Microbes Infect 2008; 10:575-81. [PMID: 18467144 DOI: 10.1016/j.micinf.2008.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 02/08/2008] [Indexed: 11/20/2022]
Abstract
Transposable elements constitute 2-5% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.
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21
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Bringaud F, Müller M, Cerqueira GC, Smith M, Rochette A, El-Sayed NMA, Papadopoulou B, Ghedin E. Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania. PLoS Pathog 2007; 3:1291-307. [PMID: 17907803 PMCID: PMC2323293 DOI: 10.1371/journal.ppat.0030136] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 07/27/2007] [Indexed: 01/29/2023] Open
Abstract
Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements--LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)--that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3'-untranslated regions (3'UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3'UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.
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Affiliation(s)
- Frédéric Bringaud
- Laboratoire de Génomique Fonctionnelle des Trypanosomatides, Université Victor Segalen Bordeaux 2, Bordeaux, France
- UMR-5234 CNRS, Bordeaux, France
| | - Michaela Müller
- Infectious Diseases Research Center, Centre Hospitalier de l'Université Laval Research Center, Quebec, Canada
- Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Gustavo Coutinho Cerqueira
- The Institute for Genomic Research, Rockville, Maryland, United States of America
- Departamento de Bioquimica e Imunologica, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Martin Smith
- Infectious Diseases Research Center, Centre Hospitalier de l'Université Laval Research Center, Quebec, Canada
- Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Annie Rochette
- Infectious Diseases Research Center, Centre Hospitalier de l'Université Laval Research Center, Quebec, Canada
- Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Najib M. A El-Sayed
- The Institute for Genomic Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, The University of Maryland, College Park, Maryland, United States of America
| | - Barbara Papadopoulou
- Infectious Diseases Research Center, Centre Hospitalier de l'Université Laval Research Center, Quebec, Canada
- Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Elodie Ghedin
- The Institute for Genomic Research, Rockville, Maryland, United States of America
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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22
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Souza RT, Santos MRM, Lima FM, El-Sayed NM, Myler PJ, Ruiz JC, da Silveira JF. New Trypanosoma cruzi repeated element that shows site specificity for insertion. EUKARYOTIC CELL 2007; 6:1228-38. [PMID: 17526721 PMCID: PMC1951114 DOI: 10.1128/ec.00036-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A new family of site-specific repeated elements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5' end of the element and a sequence domain of approximately 500 bp without a well-defined borderline at the 3' end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of approximately 0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be approximately 173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.
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Affiliation(s)
- Renata T Souza
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, UNIFESP, Rua Botucatu, São Paulo, Brazil
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23
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Heras SR, López MC, Olivares M, Thomas MC. The L1Tc non-LTR retrotransposon of Trypanosoma cruzi contains an internal RNA-pol II-dependent promoter that strongly activates gene transcription and generates unspliced transcripts. Nucleic Acids Res 2007; 35:2199-214. [PMID: 17369274 PMCID: PMC1874656 DOI: 10.1093/nar/gkl1137] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
L1Tc is the best represented autonomous LINE of the Trypanosoma cruzi genome, throughout which several functional copies may exist. In this study, we show that the first 77 bp of L1Tc (Pr77) (also present in the T. cruzi non-autonomous retrotransposon NARTc, in the Trypanosoma brucei RIME/ingi elements, and in the T. cruzi, T. brucei and Leishmania major degenerate L1Tc/ingi-related elements [DIREs]) behave as a promoter element that activates gene transcription. The transcription rate promoted by Pr77 is 10–14-fold higher than that mediated by sequences located upstream from the T. cruzi tandemly repeated genes KMP11 and the GAPDH. The Pr77 promoter-derived mRNAs initiate at nucleotide +1 of L1Tc, are unspliced and translated. L1Tc transcripts show a moderate half life and are RNA pol II dependent. The presence of an internal promoter at the 5′ end of L1Tc favors the production of full-length L1Tc RNAs and reinforces the hypothesis that this mobile element may be naturally autonomous in its transposition.
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Affiliation(s)
| | - Manuel C. López
- *To whom correspondence should be addressed. +34 958 181 662+34 958 181 632 Correspondence may also be addressed to M. Carmen Thomas. +34 958 181 662+34 958 181
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