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Brann T, Beltramini A, Chaparro C, Berriman M, Doyle SR, Protasio AV. Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni. BMC Genomics 2024; 25:217. [PMID: 38413905 PMCID: PMC10900676 DOI: 10.1186/s12864-024-10032-8] [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: 10/03/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The genomic region that lies between the telomere and chromosome body, termed the subtelomere, is heterochromatic, repeat-rich, and frequently undergoes rearrangement. Within this region, large-scale structural changes enable gene diversification, and, as such, large multicopy gene families are often found at the subtelomere. In some parasites, genes associated with proliferation, invasion, and survival are often found in these regions, where they benefit from the subtelomere's highly plastic, rapidly changing nature. The increasing availability of complete (or near complete) parasite genomes provides an opportunity to investigate these typically poorly defined and overlooked genomic regions and potentially reveal relevant gene families necessary for the parasite's lifestyle. RESULTS Using the latest chromosome-scale genome assembly and hallmark repeat richness observed at chromosome termini, we have identified and characterised the subtelomeres of Schistosoma mansoni, a metazoan parasitic flatworm that infects over 250 million people worldwide. Approximately 12% of the S. mansoni genome is classified as subtelomeric, and, in line with other organisms, we find these regions to be gene-poor but rich in transposable elements. We find that S. mansoni subtelomeres have undergone extensive interchromosomal recombination and that these sites disproportionately contribute to the 2.3% of the genome derived from segmental duplications. This recombination has led to the expansion of subtelomeric gene clusters containing 103 genes, including the immunomodulatory annexins and other gene families with unknown roles. The largest of these is a 49-copy plexin domain-containing protein cluster, exclusively expressed in the tegument-the tissue located at the host-parasite physical interface-of intramolluscan life stages. CONCLUSIONS We propose that subtelomeric regions act as a genomic playground for trial-and-error of gene duplication and subsequent divergence. Owing to the importance of subtelomeric genes in other parasites, gene families implicated in this subtelomeric expansion within S. mansoni warrant further characterisation for a potential role in parasitism.
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Affiliation(s)
- T Brann
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK
| | - A Beltramini
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK
| | - C Chaparro
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, F-66860, France
| | - M Berriman
- School of Infection and Immunity, University of Glasgow, Glasgow, G12 8TA, UK
| | - S R Doyle
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - A V Protasio
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK.
- Christ's College, Cambridge, CB2 3BU, UK.
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Hoyos Sanchez MC, Ospina Zapata HS, Suarez BD, Ospina C, Barbosa HJ, Carranza Martinez JC, Vallejo GA, Urrea Montes D, Duitama J. A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families. Sci Rep 2024; 14:2054. [PMID: 38267502 PMCID: PMC10808112 DOI: 10.1038/s41598-024-52449-x] [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: 08/03/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
Chagas is an endemic disease in tropical regions of Latin America, caused by the parasite Trypanosoma cruzi. High intraspecies variability and genome complexity have been challenges to assemble high quality genomes needed for studies in evolution, population genomics, diagnosis and drug development. Here we present a chromosome-level phased assembly of a TcI T. cruzi strain (Dm25). While 29 chromosomes show a large collinearity with the assembly of the Brazil A4 strain, three chromosomes show both large heterozygosity and large divergence, compared to previous assemblies of TcI T. cruzi strains. Nucleotide and protein evolution statistics indicate that T. cruzi Marinkellei separated before the diversification of T. cruzi in the known DTUs. Interchromosomal paralogs of dispersed gene families and histones appeared before but at the same time have a more strict purifying selection, compared to other repeat families. Previously unreported large tandem arrays of protein kinases and histones were identified in this assembly. Over one million variants obtained from Illumina reads aligned to the primary assembly clearly separate the main DTUs. We expect that this new assembly will be a valuable resource for further studies on evolution and functional genomics of Trypanosomatids.
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Affiliation(s)
- Maria Camila Hoyos Sanchez
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, 79106, USA
| | | | - Brayhan Dario Suarez
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | - Carlos Ospina
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | - Hamilton Julian Barbosa
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | | | - Gustavo Adolfo Vallejo
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | - Daniel Urrea Montes
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
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Contreras SM, Zambrano Siri RT, Rivera EM, Cristaldi C, Kamenetzky L, Kim K, Clemente M, Ocampo J, Vanagas L, Angel SO. Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres. EPIGENOMES 2022; 6:29. [PMID: 36135316 PMCID: PMC9498087 DOI: 10.3390/epigenomes6030029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Subtelomeres (ST) are chromosome regions that separate telomeres from euchromatin and play relevant roles in various biological processes of the cell. While their functions are conserved, ST structure and genetic compositions are unique to each species. This study aims to identify and characterize the subtelomeric regions of the 13 Toxoplasma gondii chromosomes of the Me49 strain. Here, STs were defined at chromosome ends based on poor gene density. The length of STs ranges from 8.1 to 232.4 kbp, with a gene density of 0.049 genes/kbp, lower than the Me49 genome (0.15 kbp). Chromatin organization showed that H3K9me3, H2A.X, and H3.3 are highly enriched near telomeres and the 5' end of silenced genes, decaying in intensity towards euchromatin. H3K4me3 and H2A.Z/H2B.Z are shown to be enriched in the 5' end of the ST genes. Satellite DNA was detected in almost all STs, mainly the sat350 family and a novel satellite named sat240. Beyond the STs, only short dispersed fragments of sat240 and sat350 were found. Within STs, there were 12 functional annotated genes, 59 with unknown functions (Hypothetical proteins), 15 from multigene FamB, and 13 from multigene family FamC. Some genes presented low interstrain synteny associated with the presence of satellite DNA. Orthologues of FamB and FamC were also detected in Neospora caninum and Hammondia hammondi. A re-analysis of previous transcriptomic data indicated that ST gene expression is strongly linked to the adaptation to different situations such as extracellular passage (evolve and resequencing study) and changes in metabolism (lack of acetyl-CoA cofactor). In conclusion, the ST region of the T. gondii chromosomes was defined, the STs genes were determined, and it was possible to associate them with high interstrain plasticity and a role in the adaptability of T. gondii to environmental changes.
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Affiliation(s)
- Susana M. Contreras
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Romina T. Zambrano Siri
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires C1428ADN, Argentina
| | - Elías M. Rivera
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Constanza Cristaldi
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Laura Kamenetzky
- Laboratorio de Genómica y Bioinformática de Patógenos, iB3|Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Marina Clemente
- Laboratorio de Molecular Farming y Vacunas, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires C1428ADN, Argentina
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, Instituto Tecnológico Chascomús (INTECH), Universidad Nacional de General San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Chascomús 7130, Argentina
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de Castro Neto AL, da Silveira JF, Mortara RA. Role of Virulence Factors of Trypanosomatids in the Insect Vector and Putative Genetic Events Involved in Surface Protein Diversity. Front Cell Infect Microbiol 2022; 12:807172. [PMID: 35573777 PMCID: PMC9097677 DOI: 10.3389/fcimb.2022.807172] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Trypanosomatids are flagellate protozoans that can infect several invertebrate and vertebrate hosts, including insects and humans. The three most studied species are the human pathogens Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. which are the causative agents of Human African Trypanosomiasis (HAT), Chagas disease and different clinical forms of leishmaniasis, respectively. These parasites possess complex dixenous life cycles, with zoonotic and anthroponotic stages, and are transmitted by hematophagous insects. To colonize this myriad of hosts, they developed mechanisms, mediated by virulence factors, to infect, propagate and survive in different environments. In insects, surface proteins play roles in parasite attachment and survival in the insect gut, whilst in the mammalian host, the parasites have a whole group of proteins and mechanisms that aid them invading the host cells and evading its immune system components. Many studies have been done on the impact of these molecules in the vertebrate host, however it is also essential to notice the importance of these virulence factors in the insect vector during the parasite life cycle. When inside the insect, the parasites, like in humans, also need to survive defense mechanisms components that can inhibit parasite colonization or survival, e.g., midgut peritrophic membrane barrier, digestive enzymes, evasion of excretion alongside the digested blood meal, anatomic structures and physiological mechanisms of the anterior gut. This protection inside the insect is often implemented by the same group of virulence factors that perform roles of immune evasion in the mammalian host with just a few exceptions, in which a specific protein is expressed specifically for the insect vector form of the parasite. This review aims to discuss the roles of the virulence molecules in the insect vectors, showing the differences and similarities of modes of action of the same group of molecules in insect and humans, exclusive insect molecules and discuss possible genetic events that may have generated this protein diversity.
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Cortez DR, Lima FM, Reis-Cunha JL, Bartholomeu DC, Villacis RAR, Rogatto SR, Costa-Martins AG, Marchiano FS, do Carmo RA, da Silveira JF, Marini MM. Trypanosoma cruzi Genomic Variability: Array Comparative Genomic Hybridization Analysis of Clone and Parental Strain. Front Cell Infect Microbiol 2022; 12:760830. [PMID: 35402315 PMCID: PMC8992781 DOI: 10.3389/fcimb.2022.760830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, exhibits extensive inter- and intrastrain genetic diversity. As we have previously described, there are some genetic differences between the parental G strain and its clone D11, which was isolated by the limiting dilution method and infection of cultured mammalian cells. Electrophoretic karyotyping and Southern blot hybridization of chromosomal bands with specific markers revealed chromosome length polymorphisms of small size with additional chromosomal bands in clone D11 and the maintenance of large syntenic groups. Both G strain and clone D11 belong to the T. cruzi lineage TcI. Here, we designed intraspecific array-based comparative genomic hybridization (aCGH) to identify chromosomal regions harboring copy-number variations between clone D11 and the G strain. DNA losses were more extensive than DNA gains in clone D11. Most alterations were flanked by repeated sequences from multigene families that could be involved in the duplication and deletion events. Several rearrangements were detected by chromoblot hybridization and confirmed by aCGH. We have integrated the information of genomic sequence data obtained by aCGH to the electrophoretic karyotype, allowing the reconstruction of possible recombination events that could have generated the karyotype of clone D11. These rearrangements may be explained by unequal crossing over between sister or homologous chromatids mediated by flanking repeated sequences and unequal homologous recombination via break-induced replication. The genomic changes detected by aCGH suggest the presence of a dynamic genome that responds to environmental stress by varying the number of gene copies and generating segmental aneuploidy.
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Affiliation(s)
- Danielle Rodrigues Cortez
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fabio Mitsuo Lima
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Centro Universitário São Camilo, Biomedicina, São Paulo, Brazil
| | - João Luís Reis-Cunha
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Silvia Regina Rogatto
- Department of Clinical Genetics, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
| | - André Guilherme Costa-Martins
- Department of Clinical and Toxicological Analyses, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda Sycko Marchiano
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rafaela Andrade do Carmo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jose Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- *Correspondence: Marjorie Mendes Marini, ; Jose Franco da Silveira,
| | - Marjorie Mendes Marini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Centro Universitário São Camilo, Biomedicina, São Paulo, Brazil
- *Correspondence: Marjorie Mendes Marini, ; Jose Franco da Silveira,
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6
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Ding H, Zhang N, Cao L, Gong P, Wang X, Li X, Cheng S, Li J, Zhang X. First identification of telomeric DNA sequences in Trichomonas vaginalis. Acta Trop 2022; 225:106196. [PMID: 34687640 DOI: 10.1016/j.actatropica.2021.106196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 11/28/2022]
Abstract
Trichomoniasis is the most common nonviral sexually transmitted disease; it is caused by Trichomonas vaginalis and seriously threatens human reproductive health. Telomeres are specialised DNA-protein complexes at the ends of chromosomes that have a protective function. The aim of the present study was to identify and characterise the telomeric DNA of T. vaginalis-which has not been previously reported-by multiple molecular methods including sequencing, the Bal nuclease (BAL) 31 nuclease assay, fluorescence in situ hybridisation (FISH), and Southern blotting. We found numerous repeated units of TTTTAGGG in T. vaginalis genomic DNA digested with S1 nuclease in combination with XbaI restriction enzyme. The (TTTTAGGG)n tandem repeats were also highly sensitive to BAL 31 exonuclease digestion. We confirmed that the (TTTTAGGG)n repeats were located at the end of T. vaginalis chromosomes by FISH. Restriction enzyme digestion combined with Southern blotting using a digoxigenin-labelled (TTTTAGGG)5 probe showed that the T. vaginalis telomeric DNA length varied from 1.0 to 1.5 kb. This is the first report on the telomeric DNA sequence of T. vaginalis which includes the length and distribution on chromosomes; our findings lay a foundation for further study on telomere maintenance mechanisms in T. vaginalis.
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Affiliation(s)
- He Ding
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Nan Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Lili Cao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China; Department of Parasite, Jilin Academy of Animal Husbandry and Veterinary Medicine, Changchun 130062, China
| | - Pengtao Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiaocen Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xin Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Shuqin Cheng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jianhua Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Xichen Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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Rodríguez-Bejarano OH, Avendaño C, Patarroyo MA. Mechanisms Associated with Trypanosoma cruzi Host Target Cell Adhesion, Recognition and Internalization. Life (Basel) 2021; 11:534. [PMID: 34207491 PMCID: PMC8227291 DOI: 10.3390/life11060534] [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] [Received: 05/13/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Chagas disease is caused by the kinetoplastid parasite Trypanosoma cruzi, which is mainly transmitted by hematophagous insect bites. The parasite's lifecycle has an obligate intracellular phase (amastigotes), while metacyclic and bloodstream-trypomastigotes are its infective forms. Mammalian host cell recognition of the parasite involves the interaction of numerous parasite and host cell plasma membrane molecules and domains (known as lipid rafts), thereby ensuring internalization by activating endocytosis mechanisms triggered by various signaling cascades in both host cells and the parasite. This increases cytoplasmatic Ca2+ and cAMP levels; cytoskeleton remodeling and endosome and lysosome intracellular system association are triggered, leading to parasitophorous vacuole formation. Its membrane becomes modified by containing the parasite's infectious form within it. Once it has become internalized, the parasite seeks parasitophorous vacuole lysis for continuing its intracellular lifecycle, fragmenting such a vacuole's membrane. This review covers the cellular and molecular mechanisms involved in T. cruzi adhesion to, recognition of and internalization in host target cells.
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Affiliation(s)
- Oscar Hernán Rodríguez-Bejarano
- Health Sciences Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Calle 222#55-37, Bogotá 111166, Colombia;
| | - Catalina Avendaño
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Calle 222#55-37, Bogotá 111166, Colombia;
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Carrera 9#51-11, Bogotá 110231, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
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Lima ARJ, de Araujo CB, Bispo S, Patané J, Silber AM, Elias MC, da Cunha JPC. Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life forms. PLoS Pathog 2021; 17:e1009272. [PMID: 33497423 PMCID: PMC7864430 DOI: 10.1371/journal.ppat.1009272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/05/2021] [Accepted: 01/04/2021] [Indexed: 11/25/2022] Open
Abstract
Trypanosoma cruzi alternates between replicative and nonreplicative life forms, accompanied by a shift in global transcription levels and by changes in the nuclear architecture, the chromatin proteome and histone posttranslational modifications. To gain further insights into the epigenetic regulation that accompanies life form changes, we performed genome-wide high-resolution nucleosome mapping using two T. cruzi life forms (epimastigotes and cellular trypomastigotes). By combining a powerful pipeline that allowed us to faithfully compare nucleosome positioning and occupancy, more than 125 thousand nucleosomes were mapped, and approximately 20% of them differed between replicative and nonreplicative forms. The nonreplicative forms have less dynamic nucleosomes, possibly reflecting their lower global transcription levels and DNA replication arrest. However, dynamic nucleosomes are enriched at nonreplicative regulatory transcription initiation regions and at multigenic family members, which are associated with infective-stage and virulence factors. Strikingly, dynamic nucleosome regions are associated with GO terms related to nuclear division, translation, gene regulation and metabolism and, notably, associated with transcripts with different expression levels among life forms. Finally, the nucleosome landscape reflects the steady-state transcription expression: more abundant genes have a more deeply nucleosome-depleted region at putative 5' splice sites, likely associated with trans-splicing efficiency. Taken together, our results indicate that chromatin architecture, defined primarily by nucleosome positioning and occupancy, reflects the phenotypic differences found among T. cruzi life forms despite the lack of a canonical transcriptional control context.
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Affiliation(s)
- Alex R. J. Lima
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Christiane B. de Araujo
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Saloe Bispo
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - José Patané
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ariel M. Silber
- Laboratory of Biochemistry of Tryps–LaBTryps, Department of Parasitology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - M. Carolina Elias
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
- * E-mail: (MCE); (JPCC)
| | - Julia P. C. da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
- * E-mail: (MCE); (JPCC)
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Herreros-Cabello A, Callejas-Hernández F, Gironès N, Fresno M. Trypanosoma Cruzi Genome: Organization, Multi-Gene Families, Transcription, and Biological Implications. Genes (Basel) 2020; 11:E1196. [PMID: 33066599 PMCID: PMC7602482 DOI: 10.3390/genes11101196] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 01/20/2023] Open
Abstract
Chagas disease caused by the parasite Trypanosoma cruzi affects millions of people. Although its first genome dates from 2005, its complexity hindered a complete assembly and annotation. However, the new sequencing methods have improved genome annotation of some strains elucidating the broad genetic diversity and complexity of this parasite. Here, we reviewed the genomic structure and regulation, the genetic diversity, and the analysis of the principal multi-gene families of the recent genomes for several strains. The telomeric and sub-telomeric regions are sites with high recombination events, the genome displays two different compartments, the core and the disruptive, and the genome plasticity seems to play a key role in the survival and the infection process. Trypanosoma cruzi (T. cruzi) genome is composed mainly of multi-gene families as the trans-sialidases, mucins, and mucin-associated surface proteins. Trans-sialidases are the most abundant genes in the genome and show an important role in the effectiveness of the infection and the parasite survival. Mucins and MASPs are also important glycosylated proteins of the surface of the parasite that play a major biological role in both insect and mammal-dwelling stages. Altogether, these studies confirm the complexity of T. cruzi genome revealing relevant concepts to better understand Chagas disease.
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Affiliation(s)
- Alfonso Herreros-Cabello
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (A.H.-C.); (F.C.-H.)
| | - Francisco Callejas-Hernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (A.H.-C.); (F.C.-H.)
| | - Núria Gironès
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (A.H.-C.); (F.C.-H.)
- Instituto Sanitario de Investigación Princesa, 28006 Madrid, Spain
| | - Manuel Fresno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (A.H.-C.); (F.C.-H.)
- Instituto Sanitario de Investigación Princesa, 28006 Madrid, Spain
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10
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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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11
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Ramirez JL. Trypanosoma cruzi Genome 15 Years Later: What Has Been Accomplished? Trop Med Infect Dis 2020; 5:E129. [PMID: 32781761 PMCID: PMC7559697 DOI: 10.3390/tropicalmed5030129] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022] Open
Abstract
On 15 July 2020 was the 15th anniversary of the Science Magazine issue that reported three trypanosomatid genomes, namely Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. That publication was a milestone for the research community working with trypanosomatids, even more so, when considering that the first draft of the human genome was published only four years earlier after 15 years of research. Although nowadays, genome sequencing has become commonplace, the work done by researchers before that publication represented a huge challenge and a good example of international cooperation. Research in neglected diseases often faces obstacles, not only because of the unique characteristics of each biological model but also due to the lower funds the research projects receive. In the case of Trypanosoma cruzi the etiologic agent of Chagas disease, the first genome draft published in 2005 was not complete, and even after the implementation of more advanced sequencing strategies, to this date no final chromosomal map is available. However, the first genome draft enabled researchers to pick genes a la carte, produce proteins in vitro for immunological studies, and predict drug targets for the treatment of the disease or to be used in PCR diagnostic protocols. Besides, the analysis of the T. cruzi genome is revealing unique features about its organization and dynamics. In this work, I briefly summarize the actions of Latin American researchers that contributed to the first publication of the T. cruzi genome and discuss some features of the genome that may help to understand the parasite's robustness and adaptive capabilities.
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Affiliation(s)
- Jose Luis Ramirez
- Instituto de Estudios Avanzados, Caracas, Venezuela and Universidad Central de Venezuela, Caracas 1080, Venezuela
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12
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Damasceno JD, Reis-Cunha J, Crouch K, Beraldi D, Lapsley C, Tosi LRO, Bartholomeu D, McCulloch R. Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication. PLoS Genet 2020; 16:e1008828. [PMID: 32609721 PMCID: PMC7360064 DOI: 10.1371/journal.pgen.1008828] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 07/14/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Homologous recombination (HR) has an intimate relationship with genome replication, both during repair of DNA lesions that might prevent DNA synthesis and in tackling stalls to the replication fork. Recent studies led us to ask if HR might have a more central role in replicating the genome of Leishmania, a eukaryotic parasite. Conflicting evidence has emerged regarding whether or not HR genes are essential, and genome-wide mapping has provided evidence for an unorthodox organisation of DNA replication initiation sites, termed origins. To answer this question, we have employed a combined CRISPR/Cas9 and DiCre approach to rapidly generate and assess the effect of conditional ablation of RAD51 and three RAD51-related proteins in Leishmania major. Using this approach, we demonstrate that loss of any of these HR factors is not immediately lethal but in each case growth slows with time and leads to DNA damage and accumulation of cells with aberrant DNA content. Despite these similarities, we show that only loss of RAD51 or RAD51-3 impairs DNA synthesis and causes elevated levels of genome-wide mutation. Furthermore, we show that these two HR factors act in distinct ways, since ablation of RAD51, but not RAD51-3, has a profound effect on DNA replication, causing loss of initiation at the major origins and increased DNA synthesis at subtelomeres. Our work clarifies questions regarding the importance of HR to survival of Leishmania and reveals an unanticipated, central role for RAD51 in the programme of genome replication in a microbial eukaryote.
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Affiliation(s)
- Jeziel D. Damasceno
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
- * E-mail: (JDD); (RM)
| | - João Reis-Cunha
- Laboratório de Imunologia e Genômica de Parasitos, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Kathryn Crouch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
| | - Dario Beraldi
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
| | - Craig Lapsley
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
| | - Luiz R. O. Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo; Ribeirão Preto, SP, Brazil
| | - Daniella Bartholomeu
- Laboratório de Imunologia e Genômica de Parasitos, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
- * E-mail: (JDD); (RM)
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13
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de Araujo CB, da Cunha JPC, Inada DT, Damasceno J, Lima ARJ, Hiraiwa P, Marques C, Gonçalves E, Nishiyama-Junior MY, McCulloch R, Elias MC. Replication origin location might contribute to genetic variability in Trypanosoma cruzi. BMC Genomics 2020; 21:414. [PMID: 32571205 PMCID: PMC7310030 DOI: 10.1186/s12864-020-06803-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/05/2020] [Indexed: 11/29/2022] Open
Abstract
Background DNA replication in trypanosomatids operates in a uniquely challenging environment, since most of their genomes are constitutively transcribed. Trypanosoma cruzi, the etiological agent of Chagas disease, presents high variability in both chromosomes size and copy number among strains, though the underlying mechanisms are unknown. Results Here we have mapped sites of DNA replication initiation across the T. cruzi genome using Marker Frequency Analysis, which has previously only been deployed in two related trypanosomatids. The putative origins identified in T. cruzi show a notable enrichment of GC content, a preferential position at subtelomeric regions, coinciding with genes transcribed towards the telomeres, and a pronounced enrichment within coding DNA sequences, most notably in genes from the Dispersed Gene Family 1 (DGF-1). Conclusions These findings suggest a scenario where collisions between DNA replication and transcription are frequent, leading to increased genetic variability, as seen by the increase SNP levels at chromosome subtelomeres and in DGF-1 genes containing putative origins.
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Affiliation(s)
- Christiane Bezerra de Araujo
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil.,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil. .,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
| | - Davi Toshio Inada
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil.,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Jeziel Damasceno
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Alex Ranieri Jerônimo Lima
- Laboratório de Tecnologia Biomolecular - Bioinformática, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | - Catarina Marques
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Evonnildo Gonçalves
- Laboratório de Tecnologia Biomolecular - Bioinformática, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Milton Yutaka Nishiyama-Junior
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.,Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Maria Carolina Elias
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil. .,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
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14
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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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15
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da Silva MS, Cayres-Silva GR, Vitarelli MO, Marin PA, Hiraiwa PM, Araújo CB, Scholl BB, Ávila AR, McCulloch R, Reis MS, Elias MC. Transcription activity contributes to the firing of non-constitutive origins in African trypanosomes helping to maintain robustness in S-phase duration. Sci Rep 2019; 9:18512. [PMID: 31811174 PMCID: PMC6898680 DOI: 10.1038/s41598-019-54366-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022] Open
Abstract
The co-synthesis of DNA and RNA potentially generates conflicts between replication and transcription, which can lead to genomic instability. In trypanosomatids, eukaryotic parasites that perform polycistronic transcription, this phenomenon and its consequences are still little studied. Here, we showed that the number of constitutive origins mapped in the Trypanosoma brucei genome is less than the minimum required to complete replication within S-phase duration. By the development of a mechanistic model of DNA replication considering replication-transcription conflicts and using immunofluorescence assays and DNA combing approaches, we demonstrated that the activation of non-constitutive (backup) origins are indispensable for replication to be completed within S-phase period. Together, our findings suggest that transcription activity during S phase generates R-loops, which contributes to the emergence of DNA lesions, leading to the firing of backup origins that help maintain robustness in S-phase duration. The usage of this increased pool of origins, contributing to the maintenance of DNA replication, seems to be of paramount importance for the survival of this parasite that affects million people around the world.
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Affiliation(s)
- Marcelo S da Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Gustavo R Cayres-Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Marcela O Vitarelli
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Paula A Marin
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Priscila M Hiraiwa
- Plataforma de citometria de fluxo, Instituto Carlos Chagas, FIOCRUZ, Paraná, Brazil
| | - Christiane B Araújo
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Bruno B Scholl
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Andrea R Ávila
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, FIOCRUZ, Paraná, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Marcelo S Reis
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
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16
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Briggs E, Hamilton G, Crouch K, Lapsley C, McCulloch R. Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome. Nucleic Acids Res 2018; 46:11789-11805. [PMID: 30304482 PMCID: PMC6294496 DOI: 10.1093/nar/gky928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/25/2018] [Accepted: 10/05/2018] [Indexed: 01/09/2023] Open
Abstract
R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere maintenance, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localization was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the regions between coding sequences of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination the most widespread localization of R-loops in T. brucei suggests a novel correlation with pre-mRNA processing. Finally, we find little evidence for correlation between R-loop localization and mapped sites of DNA replication initiation.
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Affiliation(s)
- Emma Briggs
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Rd, Bearsden, G61 1QH, UK
| | - Kathryn Crouch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Craig Lapsley
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
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17
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Callejas-Hernández F, Rastrojo A, Poveda C, Gironès N, Fresno M. Genomic assemblies of newly sequenced Trypanosoma cruzi strains reveal new genomic expansion and greater complexity. Sci Rep 2018; 8:14631. [PMID: 30279473 PMCID: PMC6168536 DOI: 10.1038/s41598-018-32877-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 09/13/2018] [Indexed: 12/19/2022] Open
Abstract
Chagas disease is a complex illness caused by the protozoan Trypanosoma cruzi displaying highly diverse clinical outcomes. In this sense, the genome sequence elucidation and comparison between strains may lead to disease understanding. Here, two new T. cruzi strains, have been sequenced, Y using Illumina and Bug2148 using PacBio, assembled, analyzed and compared with the T. cruzi annotated genomes available to date. The assembly stats from the new sequences show effective improvement of T. cruzi genome over the actual ones. Such as, the largest contig assembled (1.3 Mb in Bug2148) in de novo attempts and the highest mean assembly coverage (71X for Y). Our analysis reveals a new genomic expansion and greater complexity for those multi-copy gene families related to infection process and disease development, such as Trans-sialidases, Mucins and Mucin Associated Surface Proteins, among others. On one side, we demonstrate that multi-copy gene families are located near telomeric regions of the "chromosome-like" 1.3 Mb contig assembled of Bug2148, where they likely suffer high evolutive pressure. On the other hand, we identified several strain-specific single copy genes that might help to understand the differences in infectivity and physiology among strains. In summary, our results indicate that T. cruzi has a complex genomic architecture that may have promoted its evolution.
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Affiliation(s)
- Francisco Callejas-Hernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Cristina Poveda
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Núria Gironès
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
- Instituto Sanitario de Investigación Princesa, Madrid, Spain.
| | - Manuel Fresno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
- Instituto Sanitario de Investigación Princesa, Madrid, Spain.
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18
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Abstract
The terminal regions of eukaryotic chromosomes, composed of telomere repeat sequences and sub-telomeric sequences, represent some of the most variable and rapidly evolving regions of the genome. The sub-telomeric regions are characterized by segmentally duplicated repetitive DNA elements, interstitial telomere repeat sequences and families of variable genes. Sub-telomeric repeat sequence families are shared among multiple chromosome ends, often rendering detailed sequence characterization difficult. These regions are composed of constitutive heterochromatin and are subjected to high levels of meiotic recombination. Dysfunction within telomere repeat arrays, either due to disruption in the chromatin structure or because of telomere shortening, can lead to chromosomal fusion and the generation of large-scale genomic rearrangements across the genome. The dynamic nature of telomeric regions, therefore, provides functionally useful variation to create genetic diversity, but also provides a mechanism for rapid genomic evolution that can lead to reproductive isolation and speciation. This article is part of the theme issue 'Understanding diversity in telomere dynamics'.This article is part of the theme issue 'Understanding diversity in telomere dynamics'.
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Affiliation(s)
- Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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19
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Pech-Canul ÁDLC, Monteón V, Solís-Oviedo RL. A Brief View of the Surface Membrane Proteins from Trypanosoma cruzi. J Parasitol Res 2017; 2017:3751403. [PMID: 28656101 PMCID: PMC5474541 DOI: 10.1155/2017/3751403] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/31/2017] [Accepted: 04/27/2017] [Indexed: 12/22/2022] Open
Abstract
Trypanosoma cruzi is the causal agent of Chagas' disease which affects millions of people around the world mostly in Central and South America. T. cruzi expresses a wide variety of proteins on its surface membrane which has an important role in the biology of these parasites. Surface molecules of the parasites are the result of the environment to which the parasites are exposed during their life cycle. Hence, T. cruzi displays several modifications when they move from one host to another. Due to the complexity of this parasite's cell surface, this review presents some membrane proteins organized as large families, as they are the most abundant and/or relevant throughout the T. cruzi membrane.
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Affiliation(s)
- Ángel de la Cruz Pech-Canul
- Centre for Biomolecular Sciences, The University of Nottingham, University Park, University Blvd, Nottingham NG7 2RD, UK
| | - Victor Monteón
- Investigaciones Biomédicas, Universidad Autónoma de Campeche, Av. Patricio Trueba s/n, Col. Lindavista, 24039 Campeche, CAM, Mexico
| | - Rosa-Lidia Solís-Oviedo
- Centre for Biomolecular Sciences, The University of Nottingham, University Park, University Blvd, Nottingham NG7 2RD, UK
- Investigaciones Biomédicas, Universidad Autónoma de Campeche, Av. Patricio Trueba s/n, Col. Lindavista, 24039 Campeche, CAM, Mexico
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20
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Chiurillo MA, Moraes Barros RR, Souza RT, Marini MM, Antonio CR, Cortez DR, Curto MÁ, Lorenzi HA, Schijman AG, Ramirez JL, da Silveira JF. Subtelomeric I-SceI-Mediated Double-Strand Breaks Are Repaired by Homologous Recombination in Trypanosoma cruzi. Front Microbiol 2016; 7:2041. [PMID: 28066363 PMCID: PMC5177640 DOI: 10.3389/fmicb.2016.02041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/05/2016] [Indexed: 11/21/2022] Open
Abstract
Trypanosoma cruzi chromosome ends are enriched in surface protein genes and pseudogenes (e.g., trans-sialidases) surrounded by repetitive sequences. It has been proposed that the extensive sequence variability among members of these protein families could play a role in parasite infectivity and evasion of host immune response. In previous reports we showed evidence suggesting that sequences located in these regions are subjected to recombination. To support this hypothesis we introduced a double-strand break (DSB) at a specific target site in a T. cruzi subtelomeric region cloned into an artificial chromosome (pTAC). This construct was used to transfect T. cruzi epimastigotes expressing the I-SceI meganuclease. Examination of the repaired sequences showed that DNA repair occurred only through homologous recombination (HR) with endogenous subtelomeric sequences. Our findings suggest that DSBs in subtelomeric repetitive sequences followed by HR between them may contribute to increased variability in T. cruzi multigene families.
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Affiliation(s)
- Miguel A Chiurillo
- Laboratorio de Genética Molecular "Dr. Yunis-Turbay," Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado Barquisimeto, Venezuela
| | - Roberto R Moraes Barros
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville MD, USA
| | - Renata T Souza
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Marjorie M Marini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Cristiane R Antonio
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Danielle R Cortez
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - María Á Curto
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular - Consejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires, Argentina
| | - Hernán A Lorenzi
- Department of Infectious Diseases, J. Craig Venter Institute, Rockville MD, USA
| | - Alejandro G Schijman
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular - Consejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires, Argentina
| | - José L Ramirez
- Centro de Biotecnología, Fundación Instituto de Estudios Avanzados Caracas, Venezuela
| | - José F da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
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Mao P, Liu J, Zhang Z, Zhang H, Liu H, Gao S, Rong YS, Zhao Y. Homologous recombination-dependent repair of telomeric DSBs in proliferating human cells. Nat Commun 2016; 7:12154. [PMID: 27396625 PMCID: PMC4942568 DOI: 10.1038/ncomms12154] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/07/2016] [Indexed: 12/28/2022] Open
Abstract
Telomeres prevent chromosome ends from being recognized as double-stranded breaks (DSBs). Meanwhile, G/C-rich repetitive telomeric DNA is susceptible to attack by DNA-damaging agents. How cells balance the need to protect DNA ends and the need to repair DNA lesions in telomeres is unknown. Here we show that telomeric DSBs are efficiently repaired in proliferating cells, but are irreparable in stress-induced and replicatively senescent cells. Using the CRISPR-Cas9 technique, we specifically induce DSBs at telomeric or subtelomeric regions. We find that DSB repair (DSBR) at subtelomeres occurs in an error-prone manner resulting in small deletions, suggestive of NHEJ. However, DSBR in telomeres involves 'telomere-clustering', 3'-protruding C-rich telomeric ssDNA, and HR between sister-chromatid or interchromosomal telomeres. DSBR in telomeres is suppressed by deletion or inhibition of Rad51. These findings reveal proliferation-dependent DSBR in telomeres and suggest that telomeric HR, which is normally constitutively suppressed, is activated in the context of DSBR.
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Affiliation(s)
- Pingsu Mao
- Key Laboratory of Gene Engineering of the Ministry of Education, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China
| | - Jingfan Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China
- Zhongshan Medical School, Sun Yat-sen University, Guangzhou 510006, China
| | - Zepeng Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hong Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Haiying Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yikang S. Rong
- Key Laboratory of Gene Engineering of the Ministry of Education, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yong Zhao
- Key Laboratory of Gene Engineering of the Ministry of Education, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China
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DNA Recombination Strategies During Antigenic Variation in the African Trypanosome. Microbiol Spectr 2016; 3:MDNA3-0016-2014. [PMID: 26104717 DOI: 10.1128/microbiolspec.mdna3-0016-2014] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Survival of the African trypanosome in its mammalian hosts has led to the evolution of antigenic variation, a process for evasion of adaptive immunity that has independently evolved in many other viral, bacterial and eukaryotic pathogens. The essential features of trypanosome antigenic variation have been understood for many years and comprise a dense, protective Variant Surface Glycoprotein (VSG) coat, which can be changed by recombination-based and transcription-based processes that focus on telomeric VSG gene transcription sites. However, it is only recently that the scale of this process has been truly appreciated. Genome sequencing of Trypanosoma brucei has revealed a massive archive of >1000 VSG genes, the huge majority of which are functionally impaired but are used to generate far greater numbers of VSG coats through segmental gene conversion. This chapter will discuss the implications of such VSG diversity for immune evasion by antigenic variation, and will consider how this expressed diversity can arise, drawing on a growing body of work that has begun to examine the proteins and sequences through which VSG switching is catalyzed. Most studies of trypanosome antigenic variation have focused on T. brucei, the causative agent of human sleeping sickness. Other work has begun to look at antigenic variation in animal-infective trypanosomes, and we will compare the findings that are emerging, as well as consider how antigenic variation relates to the dynamics of host-trypanosome interaction.
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Bouzid M, Elwin K, Nader JL, Chalmers RM, Hunter PR, Tyler KM. Novel real-time PCR assays for the specific detection of human infective Cryptosporidium species. Virulence 2016; 7:395-9. [PMID: 26890369 PMCID: PMC4871645 DOI: 10.1080/21505594.2016.1149670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Maha Bouzid
- a Norwich Medical School, University of East Anglia , Norwich , UK
| | - Kristin Elwin
- b Cryptosporidium Reference Unit, Public Health Wales , Swansea , UK
| | - Johanna L Nader
- a Norwich Medical School, University of East Anglia , Norwich , UK
| | - Rachel M Chalmers
- b Cryptosporidium Reference Unit, Public Health Wales , Swansea , UK
| | - Paul R Hunter
- a Norwich Medical School, University of East Anglia , Norwich , UK
| | - Kevin M Tyler
- a Norwich Medical School, University of East Anglia , Norwich , UK
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Dia N, Lavie L, Faye N, Méténier G, Yeramian E, Duroure C, Toguebaye BS, Frutos R, Niang MN, Vivarès CP, Ben Mamoun C, Cornillot E. Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures. BMC Genomics 2016; 17:34. [PMID: 26744270 PMCID: PMC4704409 DOI: 10.1186/s12864-015-1920-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 09/11/2015] [Indexed: 12/23/2022] Open
Abstract
Background The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the genome identified only 3 of the 22 expected rDNA units. While chromosome end assembly remains a difficult process in most eukaryotic genomes, it is of significant importance for pathogens because these regions encode factors important for virulence and host evasion. Results Here we report the first complete assembly of E. cuniculi chromosome ends, and describe a novel mosaic structure of segmental duplications (EXT repeats) in these regions. EXT repeats range in size between 3.5 and 23.8 kbp and contain four multigene families encoding membrane associated proteins. Twenty-one recombination sites were identified in the sub-terminal region of E. cuniculi chromosomes. Our analysis suggests that these sites contribute to the diversity of chromosome ends organization through Double Strand Break repair mechanisms. The region containing EXT repeats at chromosome extremities can be differentiated based on gene composition, GC content, recombination sites density and chromosome landscape. Conclusion Together this study provides the complete structure of the chromosome ends of E. cuniculi GB-M1, and identifies important factors, which could play a major role in parasite diversity and host-parasite interactions. Comparison with other eukaryotic genomes suggests that terminal regions could be distinguished precisely based on gene content, genetic instability and base composition biais. The diversity of processes assciated with chromosome extremities and their biological consequences, as they are presented in the present study, emphasize the fact that great effort will be necessary in the future to characterize more carefully these regions during whole genome sequencing efforts. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1920-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ndongo Dia
- Unité de Virologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, B.P. 220, Dakar, Sénégal.
| | - Laurence Lavie
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, UMR 6023, CNRS, 63177, Aubière, France.
| | - Ngor Faye
- Laboratoire de Parasitologie Générale, Département de Biologie Animale, Faculté des Sciences et Technologies, Université Cheikh Anta Diop, Dakar, Sénégal.
| | - Guy Méténier
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, UMR 6023, CNRS, 63177, Aubière, France.
| | - Edouard Yeramian
- Unité de Bioinformatique Structurale, UMR 3528 CNRS, Institut Pasteur, 25-28, rue du Dr Roux, 75015, Paris, France.
| | - Christophe Duroure
- Laboratoire de Météorologie Physique, OPGC UMR 6016 CNRS-Université Blaise Pascal, 24 Avenue des Landais, 63177, Aubière Cedex, France.
| | - Bhen S Toguebaye
- Laboratoire de Parasitologie Générale, Département de Biologie Animale, Faculté des Sciences et Technologies, Université Cheikh Anta Diop, Dakar, Sénégal.
| | - Roger Frutos
- CIRAD, UMR 17, Cirad-Ird, TA-A17/G, Campus International de Baillarguet, 34398, Montpellier, France.
| | - Mbayame N Niang
- Unité de Virologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, B.P. 220, Dakar, Sénégal.
| | - Christian P Vivarès
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, UMR 6023, CNRS, 63177, Aubière, France.
| | - Choukri Ben Mamoun
- Section of Infectious Disease and Department of Microbial Pathogenesis, Winchester Building WWW403D, Yale School of Medicine, 15 York St., New Haven, CT, 06520, USA.
| | - Emmanuel Cornillot
- Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U1194 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d'Aurelle, 34298, Montpellier cedex 5, France. .,Institut de Biologie Computationnelle, IBC, Campus Saint Priest, 34090, Montpellier, France.
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Druzhinina IS, Kopchinskiy AG, Kubicek EM, Kubicek CP. A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:75. [PMID: 27030800 PMCID: PMC4812632 DOI: 10.1186/s13068-016-0488-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/15/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Investigations on a few eukaryotic model organisms showed that many genes are non-randomly distributed on chromosomes. In addition, chromosome ends frequently possess genes that are important for the fitness of the organisms. Trichoderma reesei is an industrial producer of enzymes for food, feed and biorefinery production. Its seven chromosomes have recently been assembled, thus making an investigation of its chromosome architecture possible. RESULTS We manually annotated and mapped 9194 ORFs on their respective chromosomes and investigated the clustering of the major gene categories and of genes encoding carbohydrate-active enzymes (CAZymes), and the relationship between clustering and expression. Genes responsible for RNA processing and modification, amino acid metabolism, transcription, translation and ribosomal structure and biogenesis indeed showed loose clustering, but this had no impact on their expression. A third of the genes encoding CAZymes also occurred in loose clusters that also contained a high number of genes encoding small secreted cysteine-rich proteins. Five CAZyme clusters were located less than 50 kb apart from the chromosome ends. These genes exhibited the lowest basal (but not induced) expression level, which correlated with an enrichment of H3K9 methylation in the terminal 50 kb areas indicating gene silencing. No differences were found in the expression of CAZyme genes present in other parts of the chromosomes. The putative subtelomeric areas were also enriched in genes encoding secreted proteases, amino acid permeases, enzyme clusters for polyketide synthases (PKS)-non-ribosomal peptide synthase (NRPS) fusion proteins (PKS-NRPS) and proteins involved in iron scavenging. They were strongly upregulated during conidiation and interaction with other fungi. CONCLUSIONS Our findings suggest that gene clustering on the T. reesei chromosomes occurs but generally has no impact on their expression. CAZyme genes, located in subtelomers, however, exhibited a much lower basal expression level. The gene inventory of the subtelomers suggests a major role of competition for nitrogen and iron supported by antibiosis for the fitness of T. reesei. The availability of fully annotated chromosomes will facilitate the use of genetic crossings in identifying still unknown genes responsible for specific traits of T. reesei.
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Affiliation(s)
- Irina S. Druzhinina
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
| | - Alexey G. Kopchinskiy
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
| | - Eva M. Kubicek
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
- />Steinschötelgasse 7, 1100 Vienna, Austria
| | - Christian P. Kubicek
- />Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria
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Sinkovics JG. The cell survival pathways of the primordial RNA-DNA complex remain conserved in the extant genomes and may function as proto-oncogenes. Eur J Microbiol Immunol (Bp) 2015; 5:25-43. [PMID: 25883792 PMCID: PMC4397846 DOI: 10.1556/eujmi-d-14-00034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/22/2014] [Indexed: 01/09/2023] Open
Abstract
Malignantly transformed (cancer) cells of multicellular hosts, including human cells, operate activated biochemical pathways that recognizably derived from unicellular ancestors. The descendant heat shock proteins of thermophile archaea now chaperon oncoproteins. The ABC cassettes of toxin-producer zooxantella Symbiodinia algae pump out the cytoplasmic toxin molecules; malignantly transformed cells utilize the derivatives of these cassettes to get rid of chemotherapeuticals. High mobility group helix-loop-helix proteins, protein arginine methyltransferases, proliferating cell nuclear antigens, and Ki-67 nuclear proteins, that protect and repair DNA in unicellular life forms, support oncogenes in transformed cells. The cell survival pathways of Wnt-β-catenin, Hedgehog, PI3K, MAPK-ERK, STAT, Ets, JAK, Pak, Myb, achaete scute, circadian rhythms, Bruton kinase and others, which are physiological in uni- and early multicellular eukaryotic life forms, are constitutively encoded in complex oncogenic pathways in selected single cells of advanced multicellular eukaryotic hosts. Oncogenes and oncoproteins in advanced multicellular hosts recreate selected independently living and immortalized unicellular life forms, which are similar to extinct and extant protists. These unicellular life forms are recognized at the clinics as autologous "cancer cells".
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Affiliation(s)
- J G Sinkovics
- St. Joseph's Hospital Cancer Institute Affiliated with the H. L. Moffitt Comprehensive Cancer Center, Morsani College of Medicine, Department of Molecular Medicine, The University of South Florida Tampa, FL USA
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Trofimova I, Popova D, Vasilevskaya E, Krasikova A. Non-coding RNA derived from a conservative subtelomeric tandem repeat in chicken and Japanese quail somatic cells. Mol Cytogenet 2014; 7:102. [PMID: 25610495 PMCID: PMC4301066 DOI: 10.1186/s13039-014-0102-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/12/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Subtelomeres are located close to the ends of chromosomes and organized by tandemly repetitive sequences, duplicated copies of genes, pseudogenes and retrotransposons. Transcriptional activity of tandemly organized DNA at terminal chromosomal regions and the distribution of subtelomere-derived non-coding RNAs are poorly investigated. Here we aimed to analyze transcriptional activity of subtelomeric tandem repeat in somatic tissues and cultured cells of birds. We focused on tissue-specific differences of subtelomeric repeats transcription, structure of the resulting transcripts and the behavior of subtelomere-derived RNA during mitosis. RESULTS Transcriptional activity of short subtelomeric PO41 ("pattern of 41 bp") tandem repeat in the somatic and cultured cells of chicken (Gallus gallus domesticus) and Japanese quail (Coturnix coturnix japonica) was examined using RNA fluorescence in situ hybridization approach. We discovered transcripts from both strands of the PO41 repeat in chicken MDCC-MSB1 cells as well as in chicken and Japanese quail somatic tissues, such as tissues of cerebellum, telencephalon, muscles, oviduct, small and large intestine. Normal somatic and transformed cells demonstrate similar distribution of PO41 repeat transcripts in interphase nuclei. We revealed one or two major foci of PO41 repeat transcripts associated with RNA polymerase II, representing nascent RNA, and dispersed PO41 repeat transcripts localized in euchromatin or interchromatin space, representing released RNA. During mitosis PO41 non-coding RNA distribute between condensed chromosomes till anaphase, when they concentrate at the cleavage plane. At telophase, clusters of PO41 RNA surround terminal regions of chromosomes. Treatments with RNases of different substrate specificity indicate that PO41 repeat transcripts are single-stranded RNAs with short double-stranded regions due to appearance of inverted repeats. CONCLUSION Transcription of a subtelomeric tandem repeat in avian somatic cells is reported here for the first time. PO41 repeat transcription is conserved among Galliformes and has similar pattern in somatic tissues. We demonstrated redistribution of non-coding PO41 RNA occurring during the cell cycle. Potential regulatory role of the PO41 repeat transcripts in RNA-dependent process of subtelomere heterochromatin maintenance is discussed.
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Affiliation(s)
- Irina Trofimova
- Department of Cytology and Histology, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, 198504 Saint-Petersburg, Russia
| | - Darya Popova
- Department of Cytology and Histology, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, 198504 Saint-Petersburg, Russia
| | - Elena Vasilevskaya
- Department of Cytology and Histology, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, 198504 Saint-Petersburg, Russia
| | - Alla Krasikova
- Department of Cytology and Histology, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, 198504 Saint-Petersburg, Russia
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Stoco PH, Wagner G, Talavera-Lopez C, Gerber A, Zaha A, Thompson CE, Bartholomeu DC, Lückemeyer DD, Bahia D, Loreto E, Prestes EB, Lima FM, Rodrigues-Luiz G, Vallejo GA, Filho JFDS, Schenkman S, Monteiro KM, Tyler KM, de Almeida LGP, Ortiz MF, Chiurillo MA, de Moraes MH, Cunha ODL, Mendonça-Neto R, Silva R, Teixeira SMR, Murta SMF, Sincero TCM, Mendes TADO, Urmenyi TP, Silva VG, DaRocha WD, Andersson B, Romanha ÁJ, Steindel M, de Vasconcelos ATR, Grisard EC. Genome of the avirulent human-infective trypanosome--Trypanosoma rangeli. PLoS Negl Trop Dis 2014; 8:e3176. [PMID: 25233456 PMCID: PMC4169256 DOI: 10.1371/journal.pntd.0003176] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 08/08/2014] [Indexed: 11/25/2022] Open
Abstract
Background Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts. Methodology/Principal Findings The T. rangeli haploid genome is ∼24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heat-shock proteins. Conclusions/Significance Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets. Comparative genomics is a powerful tool that affords detailed study of the genetic and evolutionary basis for aspects of lifecycles and pathologies caused by phylogenetically related pathogens. The reference genome sequences of three trypanosomatids, T. brucei, T. cruzi and L. major, and subsequent addition of multiple Leishmania and Trypanosoma genomes has provided data upon which large-scale investigations delineating the complex systems biology of these human parasites has been built. Here, we compare the annotated genome sequence of T. rangeli strain SC-58 to available genomic sequence and annotation data from related species. We provide analysis of gene content, genome architecture and key characteristics associated with the biology of this non-pathogenic trypanosome. Moreover, we report striking new genomic features of T. rangeli compared with its closest relative, T. cruzi, such as (1) considerably less amplification on the gene copy number within multigene virulence factor families such as MASPs, trans-sialidases and mucins; (2) a reduced repertoire of genes encoding anti-oxidant defense enzymes; and (3) the presence of vestigial orthologs of the RNAi machinery, which are insufficient to constitute a functional pathway. Overall, the genome of T. rangeli provides for a much better understanding of the identity, evolution, regulation and function of trypanosome virulence determinants for both mammalian host and insect vector.
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Affiliation(s)
- Patrícia Hermes Stoco
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail: (PHS); (ECG)
| | - Glauber Wagner
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Universidade do Oeste de Santa Catarina, Joaçaba, Santa Catarina, Brazil
| | - Carlos Talavera-Lopez
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Alexandra Gerber
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Arnaldo Zaha
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | | | - Diana Bahia
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Universidade Federal de São Paulo - Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
| | - Elgion Loreto
- Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | | | - Fábio Mitsuo Lima
- Universidade Federal de São Paulo - Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
| | | | | | | | - Sérgio Schenkman
- Universidade Federal de São Paulo - Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
| | | | - Kevin Morris Tyler
- Biomedical Research Centre, School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, United Kingdom
| | | | - Mauro Freitas Ortiz
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Miguel Angel Chiurillo
- Universidade Federal de São Paulo - Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
- Universidad Centroccidental Lisandro Alvarado, Barquisimeto, Venezuela
| | | | | | | | - Rosane Silva
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | - Turán Peter Urmenyi
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Björn Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Álvaro José Romanha
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Mário Steindel
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | | | - Edmundo Carlos Grisard
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail: (PHS); (ECG)
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Abstract
A decade of genome sequencing has transformed our understanding of how
trypanosomatid parasites have evolved and provided fresh impetus to explaining
the origins of parasitism in the Kinetoplastida. In this review, I will consider
the many ways in which genome sequences have influenced our view of genomic
reduction in trypanosomatids; how species-specific genes, and the genomic
domains they occupy, have illuminated the innovations in trypanosomatid genomes;
and how comparative genomics has exposed the molecular mechanisms responsible
for innovation and adaptation to a parasitic lifestyle.
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30
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Cloning and expression of transgenes using linear vectors in Trypanosoma cruzi. Int J Parasitol 2014; 44:447-56. [DOI: 10.1016/j.ijpara.2014.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/13/2014] [Accepted: 03/02/2014] [Indexed: 11/15/2022]
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Oliveira IA, Freire-de-Lima L, Penha LL, Dias WB, Todeschini AR. Trypanosoma cruzi Trans-sialidase: structural features and biological implications. Subcell Biochem 2014; 74:181-201. [PMID: 24264246 DOI: 10.1007/978-94-007-7305-9_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Trypanosoma cruzi trans-sialidase (TcTS) has intrigued researchers all over the world since it was shown that T. cruzi incorporates sialic acid through a mechanism independent of sialyltransferases. The enzyme has being involved in a vast myriad of functions in the biology of the parasite and in the pathology of Chagas' disease. At the structural level experiments trapping the intermediate with fluorosugars followed by peptide mapping, X-ray crystallography, molecular modeling and magnetic nuclear resonance have opened up a three-dimensional understanding of the way this enzyme works. Herein we review the multiple biological roles of TcTS and the structural studies that are slowly revealing the secrets underlining an efficient sugar transfer activity rather than simple hydrolysis by TcTS.
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Affiliation(s)
- Isadora A Oliveira
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Centro de Ciências da Saúde-Bloco D-3, 21941-902, Cidade Universitária, Rio de Janeiro, Brazil
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Mattos EC, Tonelli RR, Colli W, Alves MJM. The Gp85 surface glycoproteins from Trypanosoma cruzi. Subcell Biochem 2014; 74:151-180. [PMID: 24264245 DOI: 10.1007/978-94-007-7305-9_7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Trypanosoma cruzi strains show distinctive characteristics as genetic polymorphism and infectivity. Large repertoires of molecules, such as the Gp85 glycoproteins, members of the Gp85/Trans-sialidase superfamily, as well as multiple signaling pathways, are associated with invasion of mammalian cells by the parasite. Due to the large number of expressed members, encoded by more than 700 genes, the research focused on this superfamily conserved sequences is discussed. Binding sites to laminin have been identified at the N-terminus of the Gp85 molecules. Interestingly, the T. cruzi protein phosphorylation profile is changed upon parasite binding to laminin (or fibronectin), particularly the cytoskeletal proteins such as those from the paraflagellar rod and the tubulins, which are both markedly dephosphorylated. Detailed analysis of the signaling cascades triggered upon T. cruzi binding to extracellular matrix (ECM) proteins revealed the involvement of the MAPK/ERK pathway in this event. At the C-terminus, the conserved FLY sequence is a cytokeratin-binding domain and is involved in augmented host cell invasion in vitro and high levels of parasitemia in vivo. FLY, which is associated to tissue tropism and preferentially binds to the heart vasculature may somehow be correlated with the severe cardiac form, an important clinical manifestation of chronic Chagas' disease.
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Affiliation(s)
- Eliciane C Mattos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900, Cidade Universitária, São Paulo, Brazil
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Correa PRC, Cordero EM, Gentil LG, Bayer-Santos E, da Silveira JF. Genetic structure and expression of the surface glycoprotein GP82, the main adhesin of Trypanosoma cruzi metacyclic trypomastigotes. ScientificWorldJournal 2013; 2013:156734. [PMID: 23431251 PMCID: PMC3575623 DOI: 10.1155/2013/156734] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 12/30/2012] [Indexed: 01/10/2023] Open
Abstract
T. cruzi improves the likelihood of invading or adapting to the host through its capacity to present a large repertoire of surface molecules. The metacyclic stage-specific surface glycoprotein GP82 has been implicated in host cell invasion. GP82 is encoded by multiple genes from the trans-sialidase superfamily. GP82 shows a modular organization, with some variation of N-terminal region flanking a conserved central core where the binding sites to the mammalian cell and gastric mucin are located. The function of GP82 as adhesin in host cell invasion process could expose the protein to an intense conservative and selective pressure. GP82 is a GPI-anchored surface protein, synthesized as a 70 kDa precursor devoid of N-linked sugars. GPI-minus variants accumulate in the ER indicating that GPI anchor acts as a forward transport signal for progressing along the secretory pathway as suggested for T. cruzi mucins. It has been demonstrated that the expression of GP82 is constitutive and may be regulated at post-transcriptional level, for instance, at translational level and/or mRNA stabilization. GP82 mRNAs are mobilized to polysomes and consequently translated, but only in metacyclic trypomastigotes. Analysis of transgenic parasites indicates that the mechanism regulating GP82 expression involves multiple elements in the 3'UTR.
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Affiliation(s)
- Paulo Roberto Ceridorio Correa
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, 04023-062 São Paulo, SP, Brazil
| | - Esteban Mauricio Cordero
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, 04023-062 São Paulo, SP, Brazil
| | - Luciana Girotto Gentil
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, 04023-062 São Paulo, SP, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, 04023-062 São Paulo, SP, Brazil
| | - José Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, 04023-062 São Paulo, SP, Brazil
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