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Wang W, Peng D, Baptista RP, Li Y, Kissinger JC, Tarleton RL. Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease. PLoS Pathog 2021; 17:e1009254. [PMID: 33508020 PMCID: PMC7872254 DOI: 10.1371/journal.ppat.1009254] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/09/2021] [Accepted: 12/22/2020] [Indexed: 12/16/2022] Open
Abstract
The protozoan Trypanosoma cruzi almost invariably establishes life-long infections in humans and other mammals, despite the development of potent host immune responses that constrain parasite numbers. The consistent, decades-long persistence of T. cruzi in human hosts arises at least in part from the remarkable level of genetic diversity in multiple families of genes encoding the primary target antigens of anti-parasite immune responses. However, the highly repetitive nature of the genome-largely a result of these same extensive families of genes-have prevented a full understanding of the extent of gene diversity and its maintenance in T. cruzi. In this study, we have combined long-read sequencing and proximity ligation mapping to generate very high-quality assemblies of two T. cruzi strains representing the apparent ancestral lineages of the species. These assemblies reveal not only the full repertoire of the members of large gene families in the two strains, demonstrating extreme diversity within and between isolates, but also provide evidence of the processes that generate and maintain that diversity, including extensive gene amplification, dispersion of copies throughout the genome and diversification via recombination and in situ mutations. Gene amplification events also yield significant copy number variations in a substantial number of genes presumably not required for or involved in immune evasion, thus forming a second level of strain-dependent variation in this species. The extreme genome flexibility evident in T. cruzi also appears to create unique challenges with respect to preserving core genome functions and gene expression that sets this species apart from related kinetoplastids.
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Affiliation(s)
- Wei Wang
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Duo Peng
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Rodrigo P. Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Yiran Li
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Jessica C. Kissinger
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Rick L. Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
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Sereno D, Akhoundi M, Sayehmri K, Mirzaei A, Holzmuller P, Lejon V, Waleckx E. Noninvasive Biological Samples to Detect and Diagnose Infections due to Trypanosomatidae Parasites: A Systematic Review and Meta-Analysis. Int J Mol Sci 2020; 21:E1684. [PMID: 32121441 PMCID: PMC7084391 DOI: 10.3390/ijms21051684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Unicellular eukaryotes of the Trypanosomatidae family include human and animal pathogens that belong to the Trypanosoma and Leishmania genera. Diagnosis of the diseases they cause requires the sampling of body fluids (e.g., blood, lymph, peritoneal fluid, cerebrospinal fluid) or organ biopsies (e.g., bone marrow, spleen), which are mostly obtained through invasive methods. Body fluids or appendages can be alternatives to these invasive biopsies but appropriateness remains poorly studied. To further address this question, we perform a systematic review on clues evidencing the presence of parasites, genetic material, antibodies, and antigens in body secretions, appendages, or the organs or proximal tissues that produce these materials. Paper selection was based on searches in PubMed, Web of Science, WorldWideScience, SciELO, Embase, and Google. The information of each selected article (n = 333) was classified into different sections and data were extracted from 77 papers. The presence of Trypanosomatidae parasites has been tracked in most of organs or proximal tissues that produce body secretions or appendages, in naturally or experimentally infected hosts. The meta-analysis highlights the paucity of studies on human African trypanosomiasis and an absence on animal trypanosomiasis. Among the collected data high heterogeneity in terms of the I2 statistic (100%) is recorded. A high positivity is recorded for antibody and genetic material detection in urine of patients and dogs suffering leishmaniasis, and of antigens for leishmaniasis and Chagas disease. Data on conjunctival swabs can be analyzed with molecular methods solely for dogs suffering canine visceral leishmaniasis. Saliva and hair/bristles showed a pretty good positivity that support their potential to be used for leishmaniasis diagnosis. In conclusion, our study pinpoints significant gaps that need to be filled in order to properly address the interest of body secretion and hair or bristles for the diagnosis of infections caused by Leishmania and by other Trypanosomatidae parasites.
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Affiliation(s)
- Denis Sereno
- Institut de Recherche pour le Dévelopement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, 34032 Montpellier, France; (V.L.); (E.W.)
- Institut de Recherche pour le Dévelopement, Université de Montpellier, UMR MIVEGEC IRD, CNRS, 34032 Montpellier, France
| | - Mohammad Akhoundi
- Parasitology-Mycology Department, Avicenne Hospital, AP-HP, 93000 Bobigny, France;
| | - Kourosh Sayehmri
- Psychosocial Injuries Research Center, Department of Biostatistics, Ilam University of Medical Sciences, Ilam 6931851147, Iran;
| | - Asad Mirzaei
- Parasitology Department, Paramedical School, Ilam University of Medical Sciences, Ilam 6931851147, Iran;
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam 6931851147, Iran
| | - Philippe Holzmuller
- CIRAD, UMR ASTRE “Animal, Santé, Territoires, Risques et Ecosystèmes”, F-34398 Montpellier, France;
- ASTRE, CIRAD, INRAE, Université de Montpellier (I-MUSE), 34000 Montpellier, France
| | - Veerle Lejon
- Institut de Recherche pour le Dévelopement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, 34032 Montpellier, France; (V.L.); (E.W.)
| | - Etienne Waleckx
- Institut de Recherche pour le Dévelopement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, 34032 Montpellier, France; (V.L.); (E.W.)
- Centro de Investigaciones Regionales «Dr Hideyo Noguchi», Universidad autònoma de yucatán, Merida, Yucatán 97000, Mexico
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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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Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2). PLoS Negl Trop Dis 2018; 12:e0006351. [PMID: 29608573 PMCID: PMC5897034 DOI: 10.1371/journal.pntd.0006351] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 04/12/2018] [Accepted: 02/27/2018] [Indexed: 11/24/2022] Open
Abstract
Background Chagas disease also known as American trypanosomiasis is caused by the protozoan Trypanosoma cruzi. Over the last 30 years, Chagas disease has expanded from a neglected parasitic infection of the rural population to an urbanized chronic disease, becoming a potentially emergent global health problem. T. cruzi strains were assigned to seven genetic groups (TcI-TcVI and TcBat), named discrete typing units (DTUs), which represent a set of isolates that differ in virulence, pathogenicity and immunological features. Indeed, diverse clinical manifestations (from asymptomatic to highly severe disease) have been attempted to be related to T.cruzi genetic variability. Due to that, several DTU typing methods have been introduced. Each method has its own advantages and drawbacks such as high complexity and analysis time and all of them are based on genetic signatures. Recently, a novel method discriminated bacterial strains using a peptide identification-free, genome sequence-independent shotgun proteomics workflow. Here, we aimed to develop a Trypanosoma cruzi Strain Typing Assay using MS/MS peptide spectral libraries, named Tc-STAMS2. Methods/Principal findings The Tc-STAMS2 method uses shotgun proteomics combined with spectral library search to assign and discriminate T. cruzi strains independently on the genome knowledge. The method is based on the construction of a library of MS/MS peptide spectra built using genotyped T. cruzi reference strains. For identification, the MS/MS peptide spectra of unknown T. cruzi cells are identified using the spectral matching algorithm SpectraST. The Tc-STAMS2 method allowed correct identification of all DTUs with high confidence. The method was robust towards different sample preparations, length of chromatographic gradients and fragmentation techniques. Moreover, a pilot inter-laboratory study showed the applicability to different MS platforms. Conclusions and significance This is the first study that develops a MS-based platform for T. cruzi strain typing. Indeed, the Tc-STAMS2 method allows T. cruzi strain typing using MS/MS spectra as discriminatory features and allows the differentiation of TcI-TcVI DTUs. Similar to genomic-based strategies, the Tc-STAMS2 method allows identification of strains within DTUs. Its robustness towards different experimental and biological variables makes it a valuable complementary strategy to the current T. cruzi genotyping assays. Moreover, this method can be used to identify DTU-specific features correlated with the strain phenotype. Chagas disease is one of the most important neglected diseases with an estimated number of 6–7 million infected individuals, the majority living in Central and South America. The Trypanosoma cruzi (T.cruzi) protozoan parasite is the etiological agent of Chagas disease. T.cruzi is highly genetically diverse and a new nomenclature assigned each strain to seven genetic groups (TcI-TcVI and Tcbat), named Discrete Typing Units (DTUs), based on their biochemical, immunological and phenotypical characteristics. T.cruzi DTUs have been correlated to diverse clinical outcomes highlighting the importance of molecular epidemiological screens. Despite the development of T.cruzi typing methods based on genetic signatures, each method presents its own advantages and challenges. The work presented here shows the application of mass spectrometry for Trypanosoma cruzi Strain Typing Assay using MS2 peptide spectral libraries (Tc-STAMS2). The novelty of the method is based on the use of peptide fragmentation spectra as strain-specific fingerprints to classify and identify DTUs. Initially, a spectra library is generated from characterized T.cruzi strains. The library is subsequently inspected using MS/MS spectra from unknown strains and confidently assigned to a specific strain in an automated and computationally-driven approach. The Tc-STAMS2 method was challenged to test several variables such as sample type and preparation, instrument setup and identification platform. Tc-STAMS2 provided high confidence and robustness in T.cruzi strain typing. The Tc-STAMS2 method represents a proof-of-concept of a complementary strategy to the current DNA-based T. cruzi genotyping methods. Moreover, the method allows the identification of strain-specific features that could be related to the biology of T.cruzi strains and their clinical outcomes.
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Messenger LA, Miles MA, Bern C. Between a bug and a hard place: Trypanosoma cruzi genetic diversity and the clinical outcomes of Chagas disease. Expert Rev Anti Infect Ther 2015; 13:995-1029. [PMID: 26162928 PMCID: PMC4784490 DOI: 10.1586/14787210.2015.1056158] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the last 30 years, concomitant with successful transnational disease control programs across Latin America, Chagas disease has expanded from a neglected, endemic parasitic infection of the rural poor to an urbanized chronic disease, and now a potentially emergent global health problem. Trypanosoma cruzi infection has a highly variable clinical course, ranging from complete absence of symptoms to severe and often fatal cardiovascular and/or gastrointestinal manifestations. To date, few correlates of clinical disease progression have been identified. Elucidating a putative role for T. cruzi strain diversity in Chagas disease pathogenesis is complicated by the scarcity of parasites in clinical specimens and the limitations of our contemporary genotyping techniques. This article systematically reviews the historical literature, given our current understanding of parasite genetic diversity, to evaluate the evidence for any association between T. cruzi genotype and chronic clinical outcome, risk of congenital transmission or reactivation and orally transmitted outbreaks.
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Affiliation(s)
- Louisa A Messenger
- Department of Pathogen Molecular Biology, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Michael A Miles
- Department of Pathogen Molecular Biology, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Caryn Bern
- Global Health Sciences, Department of Epidemiology and Biostatistics, School of Medicine, University of California San Francisco, San Francisco, CA, USA
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Lima FM, Souza RT, Santori FR, Santos MF, Cortez DR, Barros RM, Cano MI, Valadares HMS, Macedo AM, Mortara RA, da Silveira JF. Interclonal variations in the molecular karyotype of Trypanosoma cruzi: chromosome rearrangements in a single cell-derived clone of the G strain. PLoS One 2013; 8:e63738. [PMID: 23667668 PMCID: PMC3646811 DOI: 10.1371/journal.pone.0063738] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 04/11/2013] [Indexed: 12/22/2022] Open
Abstract
Trypanosoma cruzi comprises a pool of populations which are genetically diverse in terms of DNA content, growth and infectivity. Inter- and intra-strain karyotype heterogeneities have been reported, suggesting that chromosomal rearrangements occurred during the evolution of this parasite. Clone D11 is a single-cell-derived clone of the T. cruzi G strain selected by the minimal dilution method and by infecting Vero cells with metacyclic trypomastigotes. Here we report that the karyotype of clone D11 differs from that of the G strain in both number and size of chromosomal bands. Large chromosomal rearrangement was observed in the chromosomes carrying the tubulin loci. However, most of the chromosome length polymorphisms were of small amplitude, and the absence of one band in clone D11 in relation to its reference position in the G strain could be correlated to the presence of a novel band migrating above or below this position. Despite the presence of chromosomal polymorphism, large syntenic groups were conserved between the isolates. The appearance of new chromosomal bands in clone D11 could be explained by chromosome fusion followed by a chromosome break or interchromosomal exchange of large DNA segments. Our results also suggest that telomeric regions are involved in this process. The variant represented by clone D11 could have been induced by the stress of the cloning procedure or could, as has been suggested for Leishmania infantum, have emerged from a multiclonal, mosaic parasite population submitted to frequent DNA amplification/deletion events, leading to a 'mosaic' structure with different individuals having differently sized versions of the same chromosomes. If this is the case, the variant represented by clone D11 would be better adapted to survive the stress induced by cloning, which includes intracellular development in the mammalian cell. Karyotype polymorphism could be part of the T. cruzi arsenal for responding to environmental pressure.
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Affiliation(s)
- Fabio Mitsuo Lima
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Renata Torres Souza
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Fábio Rinaldo Santori
- Skirball Institute of Biomolecular Medicine, New York University Cancer Center, New York University School of Medicine, New York, New York, United States of America
| | - Michele Fernandes Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Danielle Rodrigues Cortez
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Roberto Moraes Barros
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Isabel Cano
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Botucatu, São Paulo, Brazil
| | - Helder Magno Silva Valadares
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del-Rey, Divinópolis, Minas Gerais, Brazil
| | - Andréa Mara Macedo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Renato Arruda Mortara
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - José Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
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Franzén O, Talavera-López C, Ochaya S, Butler CE, Messenger LA, Lewis MD, Llewellyn MS, Marinkelle CJ, Tyler KM, Miles MA, Andersson B. Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei. BMC Genomics 2012; 13:531. [PMID: 23035642 PMCID: PMC3507753 DOI: 10.1186/1471-2164-13-531] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 10/01/2012] [Indexed: 02/07/2023] Open
Abstract
Background Trypanosoma cruzi marinkellei is a bat-associated parasite of the subgenus Schizotrypanum and it is regarded as a T. cruzi subspecies. Here we report a draft genome sequence of T. c. marinkellei and comparison with T. c. cruzi. Our aims were to identify unique sequences and genomic features, which may relate to their distinct niches. Results The T. c. marinkellei genome was found to be ~11% smaller than that of the human-derived parasite T. c. cruzi Sylvio X10. The genome size difference was attributed to copy number variation of coding and non-coding sequences. The sequence divergence in coding regions was ~7.5% between T. c. marinkellei and T. c. cruzi Sylvio X10. A unique acetyltransferase gene was identified in T. c. marinkellei, representing an example of a horizontal gene transfer from eukaryote to eukaryote. Six of eight examined gene families were expanded in T. c. cruzi Sylvio X10. The DGF gene family was expanded in T. c. marinkellei. T. c. cruzi Sylvio X10 contained ~1.5 fold more sequences related to VIPER and L1Tc elements. Experimental infections of mammalian cell lines indicated that T. c. marinkellei has the capacity to invade non-bat cells and undergo intracellular replication. Conclusions Several unique sequences were identified in the comparison, including a potential subspecies-specific gene acquisition in T. c. marinkellei. The identified differences reflect the distinct evolutionary trajectories of these parasites and represent targets for functional investigation.
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Affiliation(s)
- Oscar Franzén
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, Stockholm SE 17177, Sweden.
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Souza RT, Lima FM, Barros RM, Cortez DR, Santos MF, Cordero EM, Ruiz JC, Goldenberg S, Teixeira MMG, da Silveira JF. Genome size, karyotype polymorphism and chromosomal evolution in Trypanosoma cruzi. PLoS One 2011; 6:e23042. [PMID: 21857989 PMCID: PMC3155523 DOI: 10.1371/journal.pone.0023042] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/04/2011] [Indexed: 01/07/2023] Open
Abstract
Background The Trypanosoma cruzi genome was sequenced from a hybrid strain (CL Brener). However, high allelic variation and the repetitive nature of the genome have prevented the complete linear sequence of chromosomes being determined. Determining the full complement of chromosomes and establishing syntenic groups will be important in defining the structure of T. cruzi chromosomes. A large amount of information is now available for T. cruzi and Trypanosoma brucei, providing the opportunity to compare and describe the overall patterns of chromosomal evolution in these parasites. Methodology/Principal Findings The genome sizes, repetitive DNA contents, and the numbers and sizes of chromosomes of nine strains of T. cruzi from four lineages (TcI, TcII, TcV and TcVI) were determined. The genome of the TcI group was statistically smaller than other lineages, with the exception of the TcI isolate Tc1161 (José-IMT). Satellite DNA content was correlated with genome size for all isolates, but this was not accompanied by simultaneous amplification of retrotransposons. Regardless of chromosomal polymorphism, large syntenic groups are conserved among T. cruzi lineages. Duplicated chromosome-sized regions were identified and could be retained as paralogous loci, increasing the dosage of several genes. By comparing T. cruzi and T. brucei chromosomes, homologous chromosomal regions in T. brucei were identified. Chromosomes Tb9 and Tb11 of T. brucei share regions of syntenic homology with three and six T. cruzi chromosomal bands, respectively. Conclusions Despite genome size variation and karyotype polymorphism, T. cruzi lineages exhibit conservation of chromosome structure. Several syntenic groups are conserved among all isolates analyzed in this study. The syntenic regions are larger than expected if rearrangements occur randomly, suggesting that they are conserved owing to positive selection. Mapping of the syntenic regions on T. cruzi chromosomal bands provides evidence for the occurrence of fusion and split events involving T. brucei and T. cruzi chromosomes.
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Affiliation(s)
- Renata T. Souza
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fábio M. Lima
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Roberto Moraes Barros
- 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
| | - Michele F. Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Esteban M. Cordero
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | | | - Marta M. G. Teixeira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - José Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- * E-mail:
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9
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Macedo AM, Pena SD. Genetic Variability of Trypanosoma cruzi:Implications for the Pathogenesis of Chagas Disease. ACTA ACUST UNITED AC 2011; 14:119-24. [PMID: 17040719 DOI: 10.1016/s0169-4758(97)01179-4] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Chagas disease, caused by the protozoan Trypanosoma cruzi, has a variable clinical course, ranging from symptomless infection to severe chronic disease with cardiovascular or gastrointestinal involvement or even overwhelming acute episodes. The factors influencing this clinical variability have not been elucidated, but genetic variation of both the host and parasite is likely to be important. Here, Andréa M. Macedo and Sérgio D.J. Pena review the evidence showing a role for the genetic constitution of T. cruzi in determining the clinical characteristics of Chagas disease, and propose a ;clonal-histotropic model' for the pathogenesis of this disease.
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Matsunaga S, Endo T, Yagita K, Hirukawa Y, Tomino S, Matsugo S, Tsuruhara T. Chromosome size polymorphisms in the genus acanthamoeba electrokaryotype by pulsed-field gel electrophoresis. Protist 2009. [PMID: 23194715 DOI: 10.1016/s1434-4610(98)70039-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Twenty-eight strains from 12 species from the genus Acanthamoeba, including five isolates from amoebic keratitis patients, were subjected to molecular karyotyping by pulsed-field gel electrophoresis. 9 to 21 chromosome-sized DNA bands ranging from 200 kb to 3 Mb in size were detected. Molecular karyotypes also showed a wide multifariousness, i.e. there existed inter- and intraspecific heterogeneity. The five isolates from amoebic keratitis patients did not exhibit characteristic molecular karyotypes distinguishable from environmental isolates. Although karyotypic heterogeneity was observed within group I amoeba, they are distinguishable from those of group II and III. Strains having identical restriction fragment length polymorphism profiles of mtDNA did not have an identical molecular karyotype, i.e. weak correlation was found between molecular karyotypes and mtDNA restriction fragment length polymorphism profiles.
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Affiliation(s)
- S Matsunaga
- Department of Biology, Tokyo Gakugei University, Koganei-shi, Tokyo 184-8501, Japan
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Weatherly DB, Boehlke C, Tarleton RL. Chromosome level assembly of the hybrid Trypanosoma cruzi genome. BMC Genomics 2009; 10:255. [PMID: 19486522 PMCID: PMC2698008 DOI: 10.1186/1471-2164-10-255] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 06/01/2009] [Indexed: 11/10/2022] Open
Abstract
Background In contrast to the essentially fully assembled genome sequences of the kinetoplastid pathogens Leishmania major and Trypanosoma brucei the assembly of the Trypanosoma cruzi genome has been hindered by its repetitive nature and the fact that the reference strain (CL Brener) is a hybrid of two distinct lineages. In this work, the majority of the contigs and scaffolds were assembled into pairs of homologous chromosomes based on predicted parental haplotype, inference from TriTryp synteny maps and the use of end sequences from T. cruzi BAC libraries. Results Ultimately, 41 pairs of chromosomes were assembled using this approach, a number in agreement with the predicted number of T. cruzi chromosomes based upon pulse field gel analysis, with over 90% (21133 of 23216) of the genes annotated in the genome represented. The approach was substantiated through the use of Southern blot analysis to confirm the mapping of BAC clones using as probes the genes they are predicted to contain, and each chromosome construction was visually validated to ensure sufficient evidence was present to support the organization. While many members of large gene families are incorporated into the chromosome assemblies, the majority of genes excluded from the chromosomes belong to gene families, as these genes are frequently impossible to accurately position. Conclusion Now assembled, these chromosomes bring T. cruzi to the same level of organization as its kinetoplastid relatives and have been used as the basis for the T. cruzi genome in TriTrypDB, a trypanosome database of EuPathDB. In addition, they will provide the foundation for analyses such as reverse genetics, where the location of genes and their alleles and/or paralogues is necessary and comparative genome hybridization analyses (CGH), where a chromosome-level view of the genome is ideal.
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Affiliation(s)
- D Brent Weatherly
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.
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12
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Vallejo G, Guhl F, Schaub G. Triatominae-Trypanosoma cruzi/T. rangeli: Vector-parasite interactions. Acta Trop 2009; 110:137-47. [PMID: 18992212 DOI: 10.1016/j.actatropica.2008.10.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 10/01/2008] [Accepted: 10/01/2008] [Indexed: 01/12/2023]
Abstract
Of the currently known 140 species in the family Reduviidae, subfamily Triatominae, those which are most important as vectors of the aetiologic agent of Chagas disease, Trypanosoma cruzi, belong to the tribes Triatomini and Rhodniini. The latter not only transmit T. cruzi but also Trypanosoma rangeli, which is considered apathogenic for the mammalian host but can be pathogenic for the vectors. Using different molecular methods, two main lineages of T. cruzi have been classified, T. cruzi I and T. cruzi II. Within T. cruzi II, five subdivisions are recognized, T. cruzi IIa-IIe, according to the variability of the ribosomal subunits 24Salpha rRNA and 18S rRNA. In T. rangeli, differences in the organization of the kinetoplast DNA separate two forms denoted T. rangeli KP1+ and KP1-, although differences in the intergenic mini-exon gene and of the small subunit rRNA (SSU rRNA) suggest four subpopulations denoted T. rangeli A, B, C and D. The interactions of these subpopulations of the trypanosomes with different species and populations of Triatominae determine the epidemiology of the human-infecting trypanosomes in Latin America. Often, specific subpopulations of the trypanosomes are transmitted by specific vectors in a particular geographic area. Studies centered on trypanosome-triatomine interaction may allow identification of co-evolutionary processes, which, in turn, could consolidate hypotheses of the evolution and the distribution of T. cruzi/T. rangeli-vectors in America, and they may help to identify the mechanisms that either facilitate or impede the transmission of the parasites in different vector species. Such mechanisms seem to involve intestinal bacteria, especially the symbionts which are needed by the triatomines to complete nymphal development and to produce eggs. Development of the symbionts is regulated by the vector. T. cruzi and T. rangeli interfere with this system and induce the production of antibacterial substances. Whereas T. cruzi is only subpathogenic for the insect host, T. rangeli strongly affects species of the genus Rhodnius and this pathogenicity seems based on a reduction of the number of symbionts.
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Venegas JA, Aslund L, Solari A. Cloning and characterization of a DNA polymerase beta gene from Trypanosoma cruzi. Parasitol Int 2009; 58:187-92. [PMID: 19567232 DOI: 10.1016/j.parint.2009.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2008] [Revised: 01/21/2009] [Accepted: 01/23/2009] [Indexed: 11/15/2022]
Abstract
A gene coding for a DNA polymerase beta from the Trypanosoma cruzi Miranda clone, belonging to the TcI lineage, was cloned (Miranda Tcpol beta), using the information from eight peptides of the T. cruzi beta-like DNA polymerase purified previously. The gene encodes for a protein of 403 amino acids which is very similar to the two T. cruzi CL Brener (TcIIe lineage) sequences published, but has three different residues in highly conserved segments. At the amino acid level, the identity of TcI-pol beta with mitochondrial pol beta and pol beta-PAK from other trypanosomatids was between 68-80% and 22-30%, respectively. Miranda Tc-pol beta protein has an N-terminal sequence similar to that described in the mitochondrial Crithidia fasciculata pol beta, which suggests that the TcI-pol beta plays a role in the organelle. Northern and Western analyses showed that this T. cruzi gene is highly expressed both in proliferative and non-proliferative developmental forms. These results suggest that, in addition to replication of kDNA in proliferative cells, this enzyme may have another function in non-proliferative cells, such as DNA repair role similar to that which has extensively been described in a vast spectrum of eukaryotic cells.
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Affiliation(s)
- Juan A Venegas
- Programa de Biología Celular y Molecular, ICBM, Universidad de Chile, Casilla 70086, Santiago-7, Chile.
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14
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Abstract
SUMMARYTrypanosoma cruzi, the agent of Chagas disease is associated with a very high clinical and epidemiological pleomorphism. This might be better understood through studies on the evolutionary history of the parasite. We explored here the value of antigen genes for the understanding of the evolution withinT. cruzi. We selected 11 genes and 12 loci associated with different functions and considered to be involved in host-parasite interaction (cell adhesion, infection, molecular mimicry). The polymorphism of the respective genes in a sample representative of the diversity ofT. cruziwas screened by PCR-RFLP and evolutionary relationships were inferred by phenetic analysis. Our results support the classification ofT. cruziin 2 major lineages and 6 discrete typing units (DTUs). The topology of the PCR-RFLP tree was the one that better fitted with the epidemiological features of the different DTUs: (i) lineage I, being encountered in sylvatic as well as domestic transmission cycles, (ii) IIa/c being associated with a sylvatic transmission cycle and (iii) IIb/d/e being associated with a domestic transmission cycle. Our study also supported the hypothesis that the evolutionary history ofT. cruzihas been shaped by a series of hybridization events in the framework of a predominant clonal evolution pattern.
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Kosec G, Alvarez VE, Agüero F, Sánchez D, Dolinar M, Turk B, Turk V, Cazzulo JJ. Metacaspases of Trypanosoma cruzi: possible candidates for programmed cell death mediators. Mol Biochem Parasitol 2005; 145:18-28. [PMID: 16213036 DOI: 10.1016/j.molbiopara.2005.09.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Revised: 09/01/2005] [Accepted: 09/06/2005] [Indexed: 01/07/2023]
Abstract
The genome of Trypanosoma cruzi, the Protozoan parasite causing the American Trypanosomiasis, Chagas disease, contains two genes, TcMCA3 and TcMCA5, with homology to those encoding metacaspases, distantly related to the caspases involved in programmed cell death (PCD) in higher eukaryotes. TcMCA3 is present in the CL Brener clone at 16 copies per haploid genome, arrayed in two tandems located in chromosomes of 0.54 and 0.98 Mbp. TcMCA5, on the other hand, is present as a single copy gene. The proteins encoded were expressed in Escherichia coli BL21 [DE3] cells, and used to generate antibodies, which allowed demonstrating that TcMCA3 is expressed in the four major developmental stages of the parasite, whereas TcMCA5 is expressed only in the epimastigote form. Moreover, recombinant TcMCA3, but not TcMCA5, was recognized by most sera from chronic Chagasic patients, showing that the protein is expressed during natural infections. All attempts to show processing and enzyme activity in the recombinant proteins have been unsuccessful so far; however, indirect evidence suggests that the metacaspases might be involved in PCD of the parasite. (1) Immunofluorescence experiments showed that both proteins change their subcellular localization during fresh human serum (FHS)-induced PCD migrating into the nucleus. (2) Epimastigotes over-expressing TcMCA5 were more sensitive to FHS-induced PCD than the controls. (3) PCD was parallelled by an increase in peptidase activity against Z-YVAD-AFC, a typical caspase substrate, and the apoptotic nuclei cells were labeled in vivo with the pan-caspase fluorescent inhibitor SR-VAD-FMK. Further experiments will be required to complete the characterization of these proteins and elucidate their role in the parasite.
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Affiliation(s)
- Gregor Kosec
- Jozef Stefan Institute, Jamova 39, SI 1000 Ljubljana, Slovenia
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16
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Campetella O, Sánchez D, Cazzulo JJ, Frasch AC. A superfamily of Trypanosoma cruzi surface antigens. ACTA ACUST UNITED AC 2005; 8:378-81. [PMID: 15463546 DOI: 10.1016/0169-4758(92)90175-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Several genes o f Trypanosoma cruzi encode surface antigens that include an amino acid motif that is conserved among bacterial neurominidases. Oscar Campetella, Daniel Sdnchez, Juan Jose Cazzulo and Alberto Carlos Frasch here suggest grouping these gene families in a superfamily.
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Affiliation(s)
- O Campetella
- Instituto de Investigaciones Bioquímicas 'Luis F. Leloir', Fundación Campomar, CONICET Facultad de Ciencios Exactas y Naturales, Universidad de Buenos Aires, Antonio Machado 151, 1405 Buenos Aires, Argentina
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17
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Ejchel TF, Ramirez MI, Vargas N, Azevedo EB, Elias MC, Zingales B, Schenkman S. The largest subunit of the RNA polymerase II of Trypanosoma cruzi lacks the repeats in the carboxy-terminal domain and is encoded by several genes. Parasitol Int 2004; 52:243-9. [PMID: 14550480 DOI: 10.1016/s1383-5769(03)00009-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The largest subunit of eukaryotic RNA polymerase II (RNA Pol II) of several members of Kinetoplastida order and other early diverging eukaryote contains a serine, tyrosine and proline-rich domain in the carboxyl-terminal instead of the typical heptapeptides repeats found in most eukaryotes. The lack of these repeats seems to reflect the different control of gene transcription found in these organisms. To provide further understanding in these mechanisms, we have characterized the largest subunit of RNA polymerase II (RNA Pol II LSU) in Trypanosoma cruzi. We found that it also lacks the heptapeptide repeats in the carboxy-terminal domain, but is quite similar to the same region in the Trypanosoma brucei enzyme, suggesting a conserved role for this domain. In addition, we found several genes encoding the RNA Pol II in T. cruzi, distributed in different chromosomal bands in several isolates. Two of these genes were entirely sequenced and shown to be quite similar. The presence of several gene copies of the RNA Pol II LSU, also described in African trypanosomes might reflect a gene amplification requirement that appeared early in the evolution of these organisms.
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Affiliation(s)
- Tatiana Flank Ejchel
- Departamento de Microbiologia, Imunologia e Parasitologia Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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18
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García GA, Joensen LG, Búa J, Ainciart N, Perry SJ, Ruiz AM. Trypanosoma cruzi: molecular identification and characterization of new members of the Tc13 family. Description of the interaction between the Tc13 antigen from Tulahuén strain and the second extracellular loop of the beta(1)-adrenergic receptor. Exp Parasitol 2003; 103:112-9. [PMID: 12880587 DOI: 10.1016/s0014-4894(03)00087-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Trypanosoma cruzi Tc13 antigens belong to the trans-sialidase superfamily. Their sequences have been described only partially and, up to now, their physiological activity has not been elucidated. Here we present two new members of this family from the Tulahuén strain (Tc13 Tul) and the CL Brener clone (Tc13 CL), being the latter the first Tc13 sequence fully described. Alignment of all Tc13 sequences allowed us to define two sub-families that differ in the number of repeats and the presence or absence of the GPI addition site. Chromoblots demonstrate that Tc13 antigens are mainly located in chromosome III and its homologous. Pull down assays suggest that recombinant MBP-Tc13 Tul interacts with the second extracellular loop of the beta(1)-adrenergic receptor. This is the first evidence that a Tc13 antigen acts as a ligand interacting with a neurotransmitter receptor. These observations might add some light to the development of chagasic pathology.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Protozoan/chemistry
- Antigens, Protozoan/genetics
- Antigens, Protozoan/metabolism
- Antigens, Surface/chemistry
- Antigens, Surface/genetics
- Antigens, Surface/metabolism
- Base Sequence
- Glycoproteins
- Humans
- Molecular Sequence Data
- Neuraminidase/chemistry
- Neuraminidase/genetics
- Neuraminidase/metabolism
- Receptors, Adrenergic, beta-1/chemistry
- Receptors, Adrenergic, beta-1/metabolism
- Restriction Mapping
- Sequence Alignment
- Sequence Analysis, DNA
- Trypanosoma cruzi/classification
- Trypanosoma cruzi/enzymology
- Trypanosoma cruzi/genetics
- Trypanosoma cruzi/immunology
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Affiliation(s)
- Gabriela A García
- Dr. Mario Fatala Chabén National Institute of Parasitology (ANLIS/Malbrán), Paseo Colón 568, (1063) Buenos Aires, Argentina.
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19
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Brisse S, Henriksson J, Barnabé C, Douzery EJP, Berkvens D, Serrano M, De Carvalho MRC, Buck GA, Dujardin JC, Tibayrenc M. Evidence for genetic exchange and hybridization in Trypanosoma cruzi based on nucleotide sequences and molecular karyotype. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2003; 2:173-83. [PMID: 12797979 DOI: 10.1016/s1567-1348(02)00097-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Trypanosoma cruzi is thought to undergo predominant clonal evolution, as determined by population genetics studies. However, this model does not exclude occasional recombination, which existence is strongly suggested by several recent studies. We sequenced a portion of the maxicircle cytochrome b (CYb) gene and of the nuclear rRNA promoter region from representative strains of six T. cruzi genetic lineages isolated from anthroponotic environments and man (lineages IIb, IId and IIe), sylvatic environments (lineages IIa and IIc) or both (lineage I). Phylogenetic analyses based on the two genes were incongruent. Remarkably, in lineage IIe, CYb and rRNA sequences were very closely related to those of lineages IIc and IIb, respectively. One stock of lineage IId showed rRNA sequence heterogeneity, with both IIb-like and IIc-like copies. Analysis of the size variation of six distinct pairs of putative homologous chromosomes revealed a bimodal distribution of chromosomal sizes across T. cruzi. Notably, stocks of lineages IId and IIe had several chromosomal pairs distributed in distinct modes, with the corresponding modes individually found in lineages IIb and IIc. Together, these data indicate the origin of lineages IId and IIe by hybridization between representatives of lineages IIb and IIc. CYb and rRNA sequences clustered into three and four major lineages, respectively. Data were in agreement with the distinction of six genetic lineages, but not with their proposed grouping into two primary lineages, as lineage II was not monophyletic. Based on a CYb substitution rate of 1% per million years (Myr), the major lineages are estimated to have diverged around 10 million years ago.
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Affiliation(s)
- Sylvain Brisse
- Génétique des Maladies Infectieuses, UMR CNRS/IRD No. 9926, Institut de Recherches pour le Dévelopement, Montpellier, France.
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20
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Murta SM, dos Santos WG, Anacleto C, Nirdé P, Moreira ES, Romanha AJ. Drug resistance in Trypanosoma cruzi is not associated with amplification or overexpression of P-glycoprotein (PGP) genes. Mol Biochem Parasitol 2001; 117:223-8. [PMID: 11606233 DOI: 10.1016/s0166-6851(01)00350-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- S M Murta
- Laboratório de Parasitologia Celular e Molecular, Centro de Pesquisas René Rachou, FIOCRUZ, Av. Augusto de Lima 1715, Caixa Postal 1743, CEP 30190-002, Belo Horizonte, MG, Brazil
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21
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Fárez-Vidal ME, Gallego C, Ruiz-Pérez LM, González-Pacanowska D. Characterization of uracil-DNA glycosylase activity from Trypanosoma cruzi and its stimulation by AP endonuclease. Nucleic Acids Res 2001; 29:1549-55. [PMID: 11266557 PMCID: PMC31275 DOI: 10.1093/nar/29.7.1549] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The intracellular pathogen Trypanosoma cruzi is the etiological agent of Chagas' disease. We have isolated a full-length cDNA encoding uracil-DNA glycosylase (UDGase), a key enzyme involved in DNA repair, from this organism. The deduced protein sequence is highly conserved at the C-terminus of the molecule and shares key residues involved in binding or catalysis with most of the UDGases described so far, while the N-terminal part is highly variable. The gene is single copy and is located on a chromosome of approximately 1.9 Mb. A His-tagged recombinant protein was overexpressed, purified and used to raise polyclonal antibodies. Western blot analysis revealed the existence of a single UDGase species in parasite extracts. Using a specific ethidium bromide fluorescence assay, recombinant T.cruzi UDGase was shown to specifically excise uracil from DNA. The addition of both Leishmania major AP endonuclease and exonuclease III, the major AP endonuclease from Escherichia coli, produces stimulation of UDGase activity. This activation is specific for AP endonuclease and suggests functional communication between the two enzymes.
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Affiliation(s)
- M E Fárez-Vidal
- Instituto de Parasitología y Biomedicina 'López Neyra', Consejo Superior de Investigaciones Científicas, C/ Ventanilla 11, 18001 Granada, Spain
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22
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Toaldo CB, Steindel M, Sousa MA, Tavares CC. Molecular karyotype and chromosomal localization of genes encoding beta-tubulin, cysteine proteinase, hsp 70 and actin in Trypanosoma rangeli. Mem Inst Oswaldo Cruz 2001; 96:113-21. [PMID: 11285482 DOI: 10.1590/s0074-02762001000100013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The molecular karyotype of nine Trypanosoma rangeli strains was analyzed by contour-clamped homogeneous electric field electrophoresis, followed by the chromosomal localization of beta-tubulin, cysteine proteinase, 70 kDa heat shock protein (hsp 70) and actin genes. The T. rangeli strains were isolated from either insects or mammals from El Salvador, Honduras, Venezuela, Colombia, Panama and southern Brazil. Also, T. cruzi CL-Brener clone was included for comparison. Despite the great similarity observed among strains from Brazil, the molecular karyotype of all T. rangeli strains analyzed revealed extensive chromosome polymorphism. In addition, it was possible to distinguish T. rangeli from T. cruzi by the chromosomal DNA electrophoresis pattern. The localization of beta-tubulin genes revealed differences among T. rangeli strains and confirmed the similarity between the isolates from Brazil. Hybridization assays using probes directed to the cysteine proteinase, hsp 70 and actin genes discriminated T. rangeli from T. cruzi, proving that these genes are useful molecular markers for the differential diagnosis between these two species. Numerical analysis based on the molecular karyotype data revealed a high degree of polymorphism among T. rangeli strains isolated from southern Brazil and strains isolated from Central and the northern South America. The T. cruzi reference strain was not clustered with any T. rangeli strain.
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Affiliation(s)
- C B Toaldo
- Departamento de Biologia Celular e Genética, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, 20550-013, Brasil
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23
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Brisse S, Dujardin JC, Tibayrenc M. Identification of six Trypanosoma cruzi lineages by sequence-characterised amplified region markers. Mol Biochem Parasitol 2000; 111:95-105. [PMID: 11087920 DOI: 10.1016/s0166-6851(00)00302-9] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Six discrete phylogenetic lineages were recently identified in Trypanosoma cruzi, on the basis of multilocus enzyme electrophoresis and random amplified polymorphic DNA (RAPD) characterisation. The objective of the present study was to develop specific PCR-based markers for the identification of each of the six lineages. Eighty-seven T. cruzi stocks representative of all the lineages were characterised by RAPD with three primers, resulting in the identification of three fragments that were specifically amplified in the given sets of lineages. After cloning and sequencing these fragments, three pairs of sequence-characterised amplified region (SCAR) primers were designed. After PCR amplification using the SCAR primers, the initial polymorphism was retained either as the presence or absence of amplification, or as size variation between the PCR products. Although most PCR products, taken individually, were distributed across several lineages, the combination of the three SCAR markers resulted in characteristic patterns that were distinct in the six lineages. Furthermore, T. cruzi lineages were distinguished from Trypanosoma rangeli, T. cruzi marinkellei and T. cruzi-like organisms. The excellent correspondence of these new PCR markers with the phylogenetic lineages, allied with their sensitivity, makes them reliable tools for lineage identification and strain characterisation in T. cruzi. The approach described here could be generalised to any species of microorganism harbouring clear-cut phylogenetic subdivisions.
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Affiliation(s)
- S Brisse
- Centre d'Etudes sur le Polymorphisme des Microorganismes, UMR CNRS/IRD 9926, IRD, 911 avenue Agropolis, BP 5045, 34 032 Montpellier Cedex, France.
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24
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Zingales B, Stolf BS, Souto RP, Fernandes O, Briones MR. Epidemiology, biochemistry and evolution of Trypanosoma cruzi lineages based on ribosomal RNA sequences. Mem Inst Oswaldo Cruz 2000; 94 Suppl 1:159-64. [PMID: 10677706 DOI: 10.1590/s0074-02761999000700020] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- B Zingales
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brasil.
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25
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Affiliation(s)
- S M Murta
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 30270-010, Brasil
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26
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Dujardin JC, Henriksson J, Victoir K, Brisse S, Gamboa D, Arevalo J, Le Ray D. Genomic rearrangements in trypanosomatids: an alternative to the "one gene" evolutionary hypotheses? Mem Inst Oswaldo Cruz 2000; 95:527-34. [PMID: 10904411 DOI: 10.1590/s0074-02762000000400015] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Most molecular trees of trypanosomatids are based on point mutations within DNA sequences. In contrast, there are very few evolutionary studies considering DNA (re) arrangement as genetic characters. Waiting for the completion of the various parasite genome projects, first information may already be obtained from chromosome size-polymorphism, using the appropriate algorithms for data processing. Three illustrative models are presented here. First, the case of Leishmania (Viannia) braziliensis/L. (V.) peruviana is described. Thanks to a fast evolution rate (due essentially to amplification/deletion of tandemly repeated genes), molecular karyotyping seems particularly appropriate for studying recent evolutionary divergence, including eco-geographical diversification. Secondly, karyotype evolution is considered at the level of whole genus Leishmania. Despite the fast chromosome evolution rate, there is qualitative congruence with MLEE- and RAPD-based evolutionary hypotheses. Significant differences may be observed between major lineages, likely corresponding to major and less frequent rearrangements (fusion/fission, translocation). Thirdly, comparison is made with Trypanosoma cruzi. Again congruence is observed with other hypotheses and major lineages are delineated by significant chromosome rearrangements. The level of karyotype polymorphism within that "species" is similar to the one observed in "genus" Leishmania. The relativity of the species concept among these two groups of parasites is discussed.
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Affiliation(s)
- J C Dujardin
- Prins Leopold Instituut voor Tropische Geneeskunde, Belgium.
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27
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Brisse S, Barnabé C, Tibayrenc M. Identification of six Trypanosoma cruzi phylogenetic lineages by random amplified polymorphic DNA and multilocus enzyme electrophoresis. Int J Parasitol 2000; 30:35-44. [PMID: 10675742 DOI: 10.1016/s0020-7519(99)00168-x] [Citation(s) in RCA: 230] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Genetic characterisation of Trypanosoma cruzi variants is of foremost importance, due to considerable genetic and biological heterogeneity in the parasite populations. Two major phylogenetic lineages, each highly heterogeneous, have been previously described within this species. Here we characterised a geographically and ecologically diverse sample of stocks representative of the breadth of the known clonal diversity of each major lineage, using random amplified polymorphic DNA with 20 primers and multilocus enzyme electrophoresis at 22 loci. Molecular hybridisation experiments were performed to control the homology of randomly amplified DNA markers. Both sets of data were highly consistent and supported the existence of two major lineages. Additionally, we found that lineage 2 appeared further partitioned into five sharply delineated phylogenetic clusters, each comprising one of the following reference strains: CanIII cl1 (Z3 reference), M5631 cl5, Esmeraldo cl3 (Z2 reference), CL Brener, and MN cl2. The two first clusters were found mainly in sylvatic environments, whereas the three latter were restricted to domestic transmission cycles and were only collected South to the Amazon Basin. In contrast, lineage 1, which included Miles' Z1 reference strain X10 cl1, was not further subdivided and was encountered across the entire endemic area, in both domestic and sylvatic cycles. Thus, T. cruzi appeared to be subdivided into six discrete typing units, or DTUs, exhibiting distinct geographic and ecological ranges. Reliable diagnostic markers for the two major lineages and the five smaller DTUs of lineage 2 are described, and correspondence with previous classifications of T. cruzi genotypes is given in order to help communication on T. cruzi phylogenetic diversity.
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Affiliation(s)
- S Brisse
- Centre d'Etudes sur le Polymorphisme des Microorganismes (CEPM,) UMR No. 9926 Centre National de la Recherche Scientifique/Institut de Recherche pour le Développement, IRD, 911 avenue Agropolis, BP 5045, 34 032, Montpellier, France.
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Tran AN, Andersson B, Pettersson U, Aslund L. A chromosome-specific dispersed gene family in Trypanosoma cruzi. Mol Biochem Parasitol 1999; 100:229-34. [PMID: 10391385 DOI: 10.1016/s0166-6851(99)00049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A N Tran
- Department of Genetics and Pathology, Biomedical Center, Uppsala University, Sweden
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29
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Gao G, Nara T, Nakajima-Shimada J, Aoki T. Novel organization and sequences of five genes encoding all six enzymes for de novo pyrimidine biosynthesis in Trypanosoma cruzi. J Mol Biol 1999; 285:149-61. [PMID: 9878395 DOI: 10.1006/jmbi.1998.2293] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A 25 kb segment of genomic DNA from Trypanosoma cruzi, the causative agent of Chagas' disease, was sequenced. It contains five genes, pyr1, pyr2, pyr3, pyr4, and pyr6-5, encoding all six enzymes involved in de novo pyrimidine biosynthesis, glutamine-dependent carbamoyl-phosphate synthetase, aspartate carbamoyltransferase, dihydroorotase, dihydroorotate dehydrogenase, and orotidine-5'-phosphate decarboxylase linked with orotate phosphoribosyltransferase, respectively. The pyr genes constitute a polycistronic transcription unit on an 800 kb chromosomal DNA in the order of pyr1, pyr3, pyr6-5, pyr2, and pyr4 from the 5' terminus, with intervening sequences of 2.2, 0.4, 8.1, and 0.8 kb. The amino acid sequences deduced from the trypanosomatid pyr genes, except for pyr6, showed closer similarities to mammalian and yeast sequences, and less similarity to archaeal and bacterial sequences. The last two enzymes encoded by a single gene, pyr6-5, are covalently linked in the order opposite to mammalian pyr5-6, and possess a putative glycosomal targeting signal tripeptide, serine-lysine-leucine, at the C terminus. The calculated isoelectric points of 9.3 and 9.9 are also diagnostic of the glycosomal localization of these enzymes. We conclude that the T. cruzi pyr gene organization represents an early progenitor in de novo pyrimidine biosynthesis in eukaryotic lineage, and that the independent pyr genes may have evolved before the gene fusion events that resulted in the three mammalian-type genes, pyr1-3-2, pyr4, and pyr5-6, for UMP synthesis. Peculiarities in the trypanosomatid pyr6-5 gene product are discussed.
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Affiliation(s)
- G Gao
- Department of Parasitology, Juntendo University School of Medicine, Hongo 2-1-1, Tokyo, Bunkyo-ku, 113-8421, Japan
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30
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Dos Santos WG, Buck GA. Polymorphisms at the topoisomerase II gene locus provide more evidence for the partition of Trypanosoma cruzi into two major groups. J Eukaryot Microbiol 1999; 46:17-23. [PMID: 10188257 DOI: 10.1111/j.1550-7408.1999.tb04577.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have dissected the topoisomerase II gene of members of the two recently characterized subgroups of Trypanosoma cruzi to obtain further evidence to support this dichotomy of isolates in this important parasite. Pulsed field gel electrophoresis showed a striking heterogeneity in the molecular karyotypes of the strains analyzed. Southern analysis of these chromosome gels also showed heterogeneity in the size and number of chromosomes containing the topoisomerase II gene. Analysis of DNA restriction fragment length polymorphisms of the topoisomerase II gene also showed two principal patterns consistent with the two previously characterized groups. Finally, the sequences of portions of the topoisomerase II genes from members of the T. cruzi groups showed two distinct patterns, again consistent with the previous grouping of this parasite. Thus, this work clearly supports previous observations suggesting an ancient divergence of known T. cruzi isolates into two main branches.
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Affiliation(s)
- W G Dos Santos
- Department of Microbiology and Immunology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond 23298-0678, USA
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31
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De Leon MP, Yanagi T, Kikuchi M, Mu J, Ayau O, Matta V, Paz M, Juarez S, Kanbara H, Tada I, Hirayama K. Characterisation of Trypanosoma cruzi populations by DNA polymorphism of the cruzipain gene detected by single-stranded DNA conformation polymorphism (SSCP) and direct sequencing. Int J Parasitol 1998; 28:1867-74. [PMID: 9925265 DOI: 10.1016/s0020-7519(98)00154-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fifty fresh isolates of Trypanosoma cruzi from Triatoma dimidiata vectors and 31 from patients with Chagas' disease were analysed for DNA polymorphisms within the 432-bp core region of the cruzipain gene which encodes the active site of cathepsin L-like cystein proteinase. The cruzipain gene showed signs of polymorphism consisting of four different DNA sequences in Central and South American isolates of T. cruzi. The PCR fragments of Guatemalan isolates could be divided into three groups, Groups 1, 2 and 3, based on different patterns of single-stranded DNA conformation polymorphism. All of the strains isolated from Brazil, Chile, and Paraguay, except for the CL strain, showed a Group 4 pattern. Two to four isolates from each group were analysed by cloning and sequencing. A silent mutation occurred between Groups 1 and 2, and five nucleotides and two aa substitutions were detected between Groups 1 and 3. The DNA sequence of Group 4 contained five nucleotides and one aa substitution from Group 1. All of the DNA sequences corresponded well with the single-stranded DNA conformation polymorphism. The Group 1 isolates, the majority in the Guatemalan population (70/81, 86.4%), were isolated from both triatomines and humans, but Group 3 were isolated only from humans. Moreover, the Group 2 isolates were detected only in triatomine vectors (9/50; 18%), but never in humans (0/32, P<0.05) suggesting that this group has an independent life-cycle in sylvatic animals and is maintained by reservoir hosts other than humans.
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Affiliation(s)
- M P De Leon
- Department of Medical Zoology, Saitama Medical School, Moroyama, Iruma, Japan
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32
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Persson K, Aslund L, Grahn B, Hanke J, Heby O. Trypanosoma cruzi has not lost its S-adenosylmethionine decarboxylase: characterization of the gene and the encoded enzyme. Biochem J 1998; 333 ( Pt 3):527-37. [PMID: 9677309 PMCID: PMC1219613 DOI: 10.1042/bj3330527] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
All attempts to identify ornithine decarboxylase in the human pathogen Trypanosoma cruzi have failed. The parasites have instead been assumed to depend on putrescine uptake and S-adenosylmethionine decarboxylase (AdoMetDC) for their synthesis of the polyamines spermidine and spermine. We have now identified the gene encoding AdoMetDC in T. cruzi by PCR cloning, with degenerate primers corresponding to conserved amino acid sequences in AdoMetDC proteins of other trypanosomatids. The amplified DNA fragment was used as a probe to isolate the complete AdoMetDC gene from a T. cruzi genomic library. The AdoMetDC gene was located on chromosomes with a size of approx. 1.4 Mbp, and contained a coding region of 1110 bp, specifying a sequence of 370 amino acid residues. The protein showed a sequence identity of only 25% with human AdoMetDC, the major differences being additional amino acids present in the terminal regions of the T. cruzi enzyme. As expected, a higher sequence identity (68-72%) was found in comparison with trypanosomatid AdoMetDCs. When the coding region was expressed in Escherichia coli, the recombinant protein underwent autocatalytic cleavage, generating a 33-34 kDa alpha subunit and a 9 kDa beta subunit. The encoded protein catalysed the decarboxylation of AdoMet (Km 0.21 mM) and was stimulated by putrescine but inhibited by the polyamines, weakly by spermidine and strongly by spermine. Methylglyoxal-bis(guanylhydrazone) (MGBG), a potent inhibitor of human AdoMetDC, was a poor inhibitor of the T. cruzi enzyme. This differential sensitivity to MGBG suggests that the two enzymes are sufficiently different to warrant the search for compounds that might interfere with the progression of Chagas' disease by selectively inhibiting T. cruzi AdoMetDC.
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Affiliation(s)
- K Persson
- Department of Cellular and Developmental Biology, Umeâ University, S-901 87 Umeå, Sweden
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33
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Solari A, Wallace A, Ortiz S, Venegas J, Sanchez G. Biological characterization of Trypanosoma cruzi stocks from Chilean insect vectors. Exp Parasitol 1998; 89:312-22. [PMID: 9676709 DOI: 10.1006/expr.1998.4289] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fifty-seven Trypanosoma cruzi stocks isolated from Triatoma infestans and Triatoma spinolai of the five different geographic endemic areas of Chile were studied by schizodeme and molecular karyotype analysis. Four different genotypes are found in the sylvatic T. spinolai vector and five in the T. infestans domiciliary vector. Of these genotypes, two common genotypes overlap on both transmission cycles exclusively in the extreme northern endemic areas of Chile. Metacyclic trypomastigotes obtained in vitro or cell-derived trypomastigotes proved to be infective in gamma-irradiated Balb/c mice for the study of the immune response and biological behavior. Of a total of 57 T. cruzi stocks obtained, 19 of them, representing all the different genotypes found in Chile, were tested on a murine experimental model and then fully studied. Female compared with male animals demonstrated greater resistance to Chagas disease with all the T. cruzi stocks tested. The immune response was assessed by lytic antibodies that were studied by the in vitro antibody-dependent complement-mediated lytic assay with the use of bloodstream trypomastigotes as target cells. In one unique parasite genotype the elicited lytic antibodies reacted in a genotype-specific manner, in contrast with lytic antibodies generated by other T. cruzi genotypes. Parasitemias were high, moderate, and low, with mortality ranges of 6-50%, 0-45%, and 0-10%, respectively. No association was found between specific infective genotypes and virulence or mortality. Independently of the T. cruzi strain studied, each population displayed a characteristic parasitemia curve and prepatent period. A considerable number of the parasite stocks proved to be mixed populations, according to molecular karyotype patterns obtained before and after differentiation and amplification of the parasites. This fact created difficulty in assessing the identity of the genotype really infective to mice.
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Affiliation(s)
- A Solari
- Department of Biochemistry, Faculty of Medicine, University of Chile, Casilla, Santiago
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34
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Frohme M, Hanke J, Aslund L, Pettersson U, Hoheisel JD. Selective generation of chromosomal cosmid libraries within the Trypanosoma cruzi genome project. Electrophoresis 1998; 19:478-81. [PMID: 9588790 DOI: 10.1002/elps.1150190404] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
From a total genomic cosmid library of the pathogen Trypanosoma cruzi, specific sublibraries of the smallest four chromosomes were isolated by hybridization of the respective chromosomal bands obtained from pulsed-field gels. These libraries form the basis for initial mapping analyses that should provide information useful for both the ongoing physical mapping of the entire genome and eventual sequence analyses. Selectivity of the procedure was high with 75% to 92%, although cross-hybridization had to be expected from ubiquitous DNA features, such as centromeric and telomeric sequences, and other regions homologous between individual chromosomes. Overall, the number of identified clones was slightly higher than expected but well within the intrinsic experimental variation considering the uncertainty about the exact genome size, the variability in clonability and the higher frequency of repeat sequences in larger chromosomes. Chromosome III- and IV-specific cosmids were analyzed on Southern blots of chromosomal separations. For strain CL Brener, all clones tested exhibited cross-hybridization to a homologous chromosome larger than 1 Mbp, supporting the assumption of the respective chromosome couple being diploid pairs.
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Affiliation(s)
- M Frohme
- Molecular-Genetic Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany.
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35
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Barderi P, Campetella O, Frasch AC, Santomé JA, Hellman U, Pettersson U, Cazzulo JJ. The NADP+-linked glutamate dehydrogenase from Trypanosoma cruzi: sequence, genomic organization and expression. Biochem J 1998; 330 ( Pt 2):951-8. [PMID: 9480915 PMCID: PMC1219230 DOI: 10.1042/bj3300951] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NADP-linked glutamate dehydrogenase (NADP+-GluDH, EC 1.4.1.4) has been purified to homogeneity from epimastigotes of Trypanosoma cruzi by an improved procedure, and the amino acid sequences of 11 internal peptides obtained by digestion with trypsin, endopeptidase Lys-C, endopeptidase Arg-C or CNBr have been obtained. Using oligonucleotide primers synthesized according to the amino acid sequence of the N-terminus of the mature enzyme and to the nucleotide sequence of a clone corresponding to the C-terminus, obtained by immunological screening of an expression library, two complete open reading frames (TcGluDH1 and TcGluDH2) were isolated and sequenced. The sequences obtained are most similar to that of the NADP+-GluDH of Escherichia coli (70-72% identity), and less similar (50-56%) to those of lower eukaryotes. Using TcGluDH1 as a probe, evidence for the presence of several genes and developmental regulation of the expression of NADP+-GluDH in different parasite stages was obtained. TcGluDH1 encodes an enzymically active protein, since its expression in E. coli resulted in the production of a GluDH activity with kinetic parameters similar to those of the natural enzyme.
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Affiliation(s)
- P Barderi
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de General San Martín. Av. General Paz y Albarellos, Casilla de Correo 30, 1650 San Martín, Prov. de Buenos Aires, Argentina
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36
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Affiliation(s)
- Alexey S. Kondrashov
- Section of Ecology and Systematics, Cornell University, Ithaca, New York; 14853 e-mail:
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37
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Santos MR, Cano MI, Schijman A, Lorenzi H, Vázquez M, Levin MJ, Ramirez JL, Brandão A, Degrave WM, da Silveira JF. The Trypanosoma cruzi genome project: nuclear karyotype and gene mapping of clone CL Brener. Mem Inst Oswaldo Cruz 1997; 92:821-8. [PMID: 9580491 DOI: 10.1590/s0074-02761997000600018] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
By using improved pulsed field gel electrophoresis conditions, the molecular karyotype of the reference clone CL Brener selected for Trypanosoma cruzi genome project was established. A total of 20 uniform chromosomal bands ranging in size from 0.45 to 3.5 Megabase pairs (Mbp) were resolved in a single run. The weighted sum of the chromosomal bands was approximately 87 Mbp. Chromoblots were hybridized with 39 different homologous probes, 13 of which identified single chromosomes. Several markers showed linkage and four different linkage groups were identified, each comprising two markers. Densitometric analysis suggests that most of the chromosomal bands contain two or more chromosomes representing either homologous chromosomes and/or heterologous chromosomes with similar sizes.
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Affiliation(s)
- M R Santos
- Universidade Federal de São Paulo (UNIFESP-EPM), Brasil
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38
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Egima CM, Briones MR, Freitas Júnior LH, Schenkman RP, Uemura H, Schenkman S. Organization of trans-sialidase genes in Trypanosoma cruzi. Mol Biochem Parasitol 1996; 77:115-25. [PMID: 8813658 DOI: 10.1016/0166-6851(96)02582-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Trypanosoma cruzi trans-sialidase is encoded by a family of genes containing a conserved region, which corresponds to the catalytic and amino-terminal domain of the enzyme. Most, but not all genes, also encode a variable region formed by 12 amino acid repeats at the carboxy-terminus of the protein that are not required for enzymatic activity. To design gene knock-out strategies and understand how trans-sialidase expression is regulated, we have studied the genome organization of trans-sialidase genes. We show here that the different types of trans-sialidase genes are distributed in more than one chromosomal band with sizes ranging from 0.8 to 1.5 Mb pairs in several T. cruzi strains. In the Y-strain, all repeat-containing genes are localized in one chromosomal band of 1.1 Mb, while the repeat-minus genes are in two chromosomes of 0.82 and 0.79 Mb. The repeat-containing genes have similar catalytic and intergenic regions, but variable lengths of the repeated region. The trans-sialidase genes with the repeats are in tandem of up to 12 genes in at least four different clusters. Each cluster contains genes with different numbers of repeats, according to the physical maps of eight independent cosmids, and in the same cluster there are genes that code for active and inactive trans-sialidases. There are 80 +/- 30 copies of the repeat-containing genes grouped in two NotI fragments of 120 and 180 Kb. Therefore, in the Y-strain, the trans-sialidase genes containing repeats might be arranged in three to four clusters in two homologous chromosomes, each cluster having up to 12 genes with different repeat numbers.
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Affiliation(s)
- C M Egima
- Departmento de Microbiologia, Immunologia e Parasitologia, Universidade Federal de São Paulo, Brasil
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39
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Alves AM, de Almeida DF, von Krüger WM. Genomic variation in Trypanosoma cruzi clonal cultures. Parasitol Res 1996; 82:410-5. [PMID: 8738279 DOI: 10.1007/s004360050137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Spontaneous changes in restriction DNA profiles and pulsed-field gel electrophoresis (PFGE) patterns, along with a concomitant loss of infectivity, were observed in infective clones of Trypanosoma cruzi strain Y either following a number of passages during the exponential growth phase of after subcloning in liver infusion tryptone (LIT) medium using as the probe a genomic fragment of the parasite (pMYP16), indicating naturally occurring rearrangements of DNA sequences. No variation could be detected when the genomic DNA was probed with conserved T. cruzi tubulin and actin genes. There was no correlation between such rearrangements and the life-cycle forms of the parasites, since trypomastigote forms showed the same karyotype and hybridization patterns as did epimastigote forms. The variations observed could be reverted and infectivity, recovered after inoculation of the parasites in newborn mice.
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Affiliation(s)
- A M Alves
- Laboratório de Fisiologia Celular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
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40
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Henriksson J, Solari A, Rydåker M, Sousa OE, Pettersson U. Karyotype variability in Trypanosoma rangeli. Parasitology 1996; 112 ( Pt 4):385-91. [PMID: 8935949 DOI: 10.1017/s0031182000066610] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The molecular karyotypes of several different protozoan parasites show high intra-species variation, including different kinetoplastids such as Trypanosoma brucei, Trypanosoma cruzi and Leishmania ssp. In this study, the molecular karyotype of Trypanosoma rangeli was examined. To evaluate potential intra-species molecular karyotype variations, 16 different samples were studied by pulsed field gel electrophoresis (PFGE) followed by ethidium bromide staining and hybridizations with 6 different probes. The result showed that different T. rangeli populations are highly polymorphic regarding the molecular karyotype, and thus suggests that PFGE analysis can be used for classification of different T. rangeli isolates. In addition, the molecular karyotype of T. rangeli was compared to molecular karyotypes of other kinetoplastids, and was shown to be distinctly different from that of T. cruzi, but shows some similarities with the karyotype described for T. brucei. Among the probes used one was identified as highly polymorphic, and thus informative for studies of different T. rangeli populations, and another was useful for differentiation between T. rangeli and T. cruzi.
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Affiliation(s)
- J Henriksson
- Department of Medical Genetics, Uppsala University, Sweden
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41
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Abstract
Like many other protozoam parasites, Trypanosoma cruzi (the causative agent of Chagas disease) has a plastic genome. Chromosome size polymorphisms occur in different strains of T. cruzi as well as among clones originating from the same strain, Despite this polymorphism, major interchromosomal rearrangements appear to be rare since several linkage groups of chromosomal markers are well conserved among different T. cruzi strains. In addition, some correlation has been found between karyotype variability and classification by multilocus enzyme electrophoresis. In this review, Jan Henriksson, Lena Aslund and Ulf Petterson discuss the genomic variability and suggest that amplication of repetitive sequences or members of gene families make a major contribution to the chromosomal size variation
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Affiliation(s)
- J Henriksson
- Department of Medical Genetics, Biomedical Center, Uppsala University, Box 589, S-751 23 Uppsala, Sweden
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42
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Di Noia JM, Sánchez DO, Frasch AC. The protozoan Trypanosoma cruzi has a family of genes resembling the mucin genes of mammalian cells. J Biol Chem 1995; 270:24146-9. [PMID: 7592617 DOI: 10.1074/jbc.270.41.24146] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Mucins are heavily O-glycosylated Thr/Ser/Pro-rich molecules. Given their relevant functions, mucins and their genes have been mainly studied in higher eukaryotes. In the protozoan parasite Trypanosoma cruzi, mucin-like glycoproteins were shown to play an important role in the interaction with the surface of the mammalian cell during the invasion process. We show now that this parasite has a family of putative mucin genes, whose organization resembles the one present in mammalian cells. Different parasite isolates have different sets of genes, as defined by their central domain. Central domains, rich in codons for Thr and/or Ser and Pro residues, are made up of either a variable number of repeat units in tandem or non-repetitive sequences. Conversely, 5'- and 3'-ends from different genes in different isolates have similar sequences, suggesting their common origin. Comparison of deduced amino acid sequences revealed that all members of the family have the same putative signal peptide on the N terminus and a putative sequence for glycophosphatidylinositol anchoring on the C terminus. The deduced molecular mass of the core proteins is small (from 17 to 21 kDa), in agreement with the 1-kilobase size of the mRNA detected. Putative mucin genes in T. cruzi are located on large chromosomal bands of about 1.6-2.2 megabase pairs.
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Affiliation(s)
- J M Di Noia
- Instituto de Investigaciones Bioquímicas, Fundación Campomar, Buenos Aires, Argentina
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43
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Henriksson J, Porcel B, Rydåker M, Ruiz A, Sabaj V, Galanti N, Cazzulo JJ, Frasch AC, Pettersson U. Chromosome specific markers reveal conserved linkage groups in spite of extensive chromosomal size variation in Trypanosoma cruzi. Mol Biochem Parasitol 1995; 73:63-74. [PMID: 8577348 DOI: 10.1016/0166-6851(95)00096-j] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The karyotypes of three cloned stocks, CL Brener (CL), CA I/72 (CA) and Sylvio X10/7 (X10), of Trypanosoma cruzi were studied by pulsed-field gel electrophoresis followed by ethidium bromide staining and hybridization with 35 different probes, 30 of which identified single chromosomes. The chromosome-specific probes identified between 26 and 31 chromosomal bands in the three cloned stocks, corresponding to 20 unique chromosomes in CL and 19 in CA and X10. Considering the DNA content of the parasite, it was predicted that the markers recognise at least half of all T. cruzi chromosomes. A majority of identified chromosomes showed large differences in size among different strains, in some cases by up to 50%. Interestingly, CL had in general larger chromosomes than the two other studied cloned stocks. Several of the markers showed linkage and nine different linkage groups were identified, each comprising 2-4 markers. The linkage between the markers was maintained in 8 of the 9 linkage groups when a panel comprising 26 different T. cruzi strains representing major T. cruzi populations was tested. One linkage group was found to be maintained in some strains but not in others. This result shows that chromosomal rearrangements occur in the T. cruzi genome, albeit with a low frequency. Repetitive DNA, both non-coding and in one case coding, was more abundant in the cloned stock CL Brener than in CA and X10. The information presented will make it possible to select chromosomes for the construction of physical chromosomal maps required for the T. cruzi genome project.
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Affiliation(s)
- J Henriksson
- Department of Medical Genetics, University of Uppsala, Sweden
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44
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Cano MI, Gruber A, Vazquez M, Cortés A, Levin MJ, González A, Degrave W, Rondinelli E, Zingales B, Ramirez JL. Molecular karyotype of clone CL Brener chosen for the Trypanosoma cruzi genome project. Mol Biochem Parasitol 1995; 71:273-8. [PMID: 7477112 DOI: 10.1016/0166-6851(95)00066-a] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- M I Cano
- Escola Paulisa de Medicina, São Paulo, Brazil
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45
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García-Salcedo JA, Oliver JL, Stock RP, González A. Molecular characterization and transcription of the histone H2B gene from the protozoan parasite Trypanosoma cruzi. Mol Microbiol 1994; 13:1033-43. [PMID: 7854118 DOI: 10.1111/j.1365-2958.1994.tb00494.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structure, genomic organization and transcription of the gene encoding histone H2B in the protozoan parasite Trypanosoma cruzi have been studied. This gene consists of a 746-nucleotide unit, tandemly repeated at least 18 times in each of two clusters. DNA probes corresponding to histones H2B and H3 hybridized to different chromosomes revealing that the genes coding for these two histones are not physically linked in the genome of T. cruzi. The primary transcription product of the H2B gene is processed by trans-splicing and polyadenylation. Inhibition of DNA synthesis with aphidicolin resulted in the reduction of histone H2B mRNA to undetectable levels in about two hours, suggesting that its abundance is regulated throughout the cell cycle as it occurs in other eukaryotes. In addition, a concomitant inhibition of translation by cycloheximide reverted this effect indicating that de novo protein synthesis is required for RNA instability. Histone mRNA abundance was dependent on the life-cycle stage of T. cruzi: abundant in amastigotes and epimastigotes, the dividing forms in the host cell and the insect vector, respectively, while undetected in trypomastigotes, the parasite's non-dividing life stage.
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Affiliation(s)
- J A García-Salcedo
- Instituto de Parasitología y Biomedicina, Consejo Superior de Investigaciones Científicas, Granada, Spain
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46
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Bontempi EJ, Porcel BM, Henriksson J, Carlsson L, Rydåker M, Segura EL, Ruiz AM, Pettersson U. Genes for histone H3 in Trypanosoma cruzi. Mol Biochem Parasitol 1994; 66:147-51. [PMID: 7984178 DOI: 10.1016/0166-6851(94)90046-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- E J Bontempi
- Instituto Nacional de Diagnóstico e Investigación de la Enfermedad de Chagas, Buenos Aires, Argentina
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Reche P, Arrebola R, Olmo A, Santi DV, Gonzalez-Pacanowska D, Ruiz-Perez LM. Cloning and expression of the dihydrofolate reductase-thymidylate synthase gene from Trypanosoma cruzi. Mol Biochem Parasitol 1994; 65:247-58. [PMID: 7969266 DOI: 10.1016/0166-6851(94)90076-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have cloned, sequenced and expressed the Trypanosoma cruzi gene encoding the bifunctional protein dihydrofolate reductase-thymidylate synthase (DHFR-TS). The strategy followed for the isolation of positive clones from a genomic library was based on the construction of a probe by the amplification of highly conserved sequences of the TS domain by the polymerase chain reaction. Translation of the open reading frame of 1563 bp yields a polypeptide of 521 amino acids with a molecular mass of 58829 Da. For heterologous expression of T. cruzi DHFR-TS in Escherichia coli, the entire coding sequence was amplified by polymerase chain reaction and cloned into the plasmid vector pKK223.3. The presence of catalytically active DHFR-TS was demonstrated by complementation of the Thy- E. coli strain chi 2913 and the DHFR- Thy- E. coli strain PA414. The gene is expressed as an active protein which constitutes approximately 2% of the total cell soluble protein. Recombinant bifunctional enzyme and the DHFR domain have been purified by methotrexate-Sepharose chromatography to yield 1-2 mg of active DHFR-TS per litre of culture. Southern and electrophoretic analyses using the coding sequence as probe indicated that the T. cruzi enzyme is encoded by a single copy gene which maps to two bands of approximately 990 kb and 1047 kb. It appears that T. cruzi is diploid for the DHFR-TS gene which is located on two different-sized homologous chromosomes.
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Affiliation(s)
- P Reche
- Instituto de Parasitología y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Aslund L, Carlsson L, Henriksson J, Rydåker M, Toro GC, Galanti N, Pettersson U. A gene family encoding heterogeneous histone H1 proteins in Trypanosoma cruzi. Mol Biochem Parasitol 1994; 65:317-30. [PMID: 7969272 DOI: 10.1016/0166-6851(94)90082-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A gene family encoding a set of histone H1 proteins in Trypanosoma cruzi is described. The sequence of 3 genomic and 4 cDNA clones revealed the presence of several motifs characteristic of histone H1, although heterogeneity at the polypeptide level was evident. The clones encode histone H1 proteins of an unusually small size (74-97 amino acids), which lack the globular domain found in histone H1 of higher eukaryotes. All histone H1 mRNAs from T. cruzi are polyadenylated, although no typical polyadenylation signal was found. Furthermore, the genes encoding the histone H1 proteins in T. cruzi are found in a tandem array containing 15-20 gene copies per haploid genome. This tandem array is located on a large chromosome of 2.2 Mb.
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Affiliation(s)
- L Aslund
- Department of Medical Genetics, Biomedical Center, Uppsala, Sweden
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Tanaka T, Kaneda Y, Iida A, Tanaka M. Homologous cysteine proteinase genes located on two different chromosomes from Trypanosoma rangeli. Int J Parasitol 1994; 24:179-88. [PMID: 8026894 DOI: 10.1016/0020-7519(94)90024-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA fragments were obtained by the polymerase chain reaction (PCR) using genomic DNA from T. rangeli as template and oligonucleotide primers encoding the active site amino acids of cysteine proteinase. After amplification by PCR, several DNA products were observed. These were purified and used as templates for a second round of PCR. This resulted in two DNA products of 475 and 498 bp. The 498 bp DNA (Tr-CP) contained both the sense and antisense primer sequences, and encoded a polypeptide having substantial homology with eukaryotic cysteine proteinases. The other product (Tr-DMR), which lacked the antisense primer sequence, encoded a polypeptide having homology with the DNA mismatch repair gene from Saccharomyces cerevisiae. The overall homology of the Tr-CP-encoded polypeptide to the cysteine proteinases from other trypanosome species was 69% identity (T. cruzi) and 73% identity (T. brucei), respectively. Northern blot analysis revealed that the Tr-CP gene was specifically expressed in T. rangeli as a 1.7 kb mRNA. A karyotype map of the chromosomes was also performed using pulsed-field gradient gel electrophoresis and Southern blot hybridization with these genes. T. rangeli has 14 chromosome bands ranging from 350 kb to 1.6 Mb, which were fewer in number and smaller in size compared with those from T. cruzi. The Tr-CP fragment and the Tr-DMR fragment hybridized with equal intensity on chromosome 1 (350 kb) and chromosome 2 (470 kb), respectively. These results suggest that non-pathogenic T. rangeli contains a conserved gene corresponding to the cysteine proteinase or a closely related enzyme, and that there is more than one copy of this gene, each found on different chromosomes.
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Affiliation(s)
- T Tanaka
- Department of Infectious Diseases, Tokai University School of Medicine, Kanagawa, Japan
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Ruef BJ, Dawson BD, Tewari D, Fouts DL, Manning JE. Expression and evolution of members of the Trypanosoma cruzi trypomastigote surface antigen multigene family. Mol Biochem Parasitol 1994; 63:109-20. [PMID: 8183309 DOI: 10.1016/0166-6851(94)90013-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The trypomastigote specific surface antigens of Trypanosoma cruzi are encoded by a supergene family which includes the TSA family. The TSA family is characterized by the presence of a 27-bp tandem repeat array in the coding region. Here, we report the characterization and analysis of the three TSA family members in the Esmeraldo strain of the parasite. In this strain 2 distinct telomeric members are expressed abundantly as 3.7-kb mRNAs, while the remaining member is located at an internal chromosomal site and is expressed at less than 2% of the level seen for the telomeric members. Based on hybridization to DNA separated by PFGE, 3 chromosomes of sizes 1.8 Mb, 0.98 Mb, and 0.90 Mb each contain one of the telomeric members. In addition, the two smaller chromosomes also contain the single internal member. Since both chromosomes contain similar TSA family members, and vary only slightly in size, we suggest that they are homologues. Comparisons of the nucleotide sequences of the different members of the family show that the internal gene differs from the telomeric genes primarily in sequences found 3' of the repeat array. These comparisons also reveal that the three genes are analogous, supporting the hypothesis that short segments between the family members are exchanged by gene conversion events. We propose that similar conversion events between members of different gene families may generate some of the diversity found within the supergene family.
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Affiliation(s)
- B J Ruef
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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