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Kimball A, Funkhouser-Jones L, Huang W, Xu R, Witola WH, Sibley LD. Mendelian segregation and high recombination rates facilitate genetic analyses in Cryptosporidium parvum. PLoS Genet 2024; 20:e1011162. [PMID: 38885280 PMCID: PMC11213348 DOI: 10.1371/journal.pgen.1011162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/28/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024] Open
Abstract
Very little is known about the process of meiosis in the apicomplexan parasite Cryptosporidium despite the essentiality of sex in its life cycle. Most cell lines only support asexual growth of Cryptosporidium parvum (C. parvum), but stem cell derived intestinal epithelial cells grown under air-liquid interface (ALI) conditions support the sexual cycle. To examine chromosomal dynamics during meiosis in C. parvum, we generated two transgenic lines of parasites that were fluorescently tagged with mCherry or GFP on chromosomes 1 or 5, respectively. Infection of ALI cultures or Ifngr1-/- mice with mCherry and GFP parasites resulted in cross-fertilization and the formation of "yellow" oocysts, which contain 4 haploid sporozoites that are the product of meiosis. Recombinant oocysts from the F1 generation were purified and used to infect HCT-8 cultures, and phenotypes of the progeny were observed by microscopy. All possible phenotypes predicted by independent segregation were represented equally (~25%) in the population, indicating that C. parvum chromosomes exhibit a Mendelian inheritance pattern. The most common pattern observed from the outgrowth of single oocysts included all possible parental and recombinant phenotypes derived from a single meiotic event, suggesting a high rate of crossover. To estimate the frequency of crossover, additional loci on chromosomes 1 and 5 were tagged and used to monitor intrachromosomal crosses in Ifngr1-/- mice. Both chromosomes showed a high frequency of crossover compared to other apicomplexans with map distances (i.e., 1% recombination) of 3-12 kb. Overall, a high recombination rate may explain many unique characteristics observed in Cryptosporidium spp. such as high rates of speciation, wide variation in host range, and rapid evolution of host-specific virulence factors.
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Affiliation(s)
- Abigail Kimball
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lisa Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wanyi Huang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - William H. Witola
- Department of Pathobiology, University of Illinois Urbana-Champaign College of Veterinary Medicine, Urbana, Illinois, United States of America
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Kimball A, Funkhouser-Jones L, Huang W, Xu R, Witola WH, Sibley LD. Mendelian segregation and high recombination rates facilitate genetic analyses in Cryptosporidium parvum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578536. [PMID: 38352509 PMCID: PMC10862819 DOI: 10.1101/2024.02.02.578536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Very little is known about the process of meiosis in the apicomplexan parasite Cryptosporidium despite the essentiality of sex in its life cycle. Most cell lines only support asexual growth of Cryptosporidium parvum (C. parvum), but stem cell derived intestinal epithelial cells grown under air-liquid interface (ALI) conditions support the sexual cycle. To examine chromosomal dynamics during meiosis in C. parvum, we generated two transgenic lines of parasites that were fluorescently tagged with mCherry or GFP on chromosomes 1 or 5, respectively. Infection of ALI cultures or Ifngr1-/- mice with mCherry and GFP parasites produced "yellow" oocysts generated by cross-fertilization. Outcrossed oocysts from the F1 generation were purified and used to infect HCT-8 cultures, and phenotypes of the progeny were observed by microscopy. All possible phenotypes predicted by independent segregation were represented equally (~25%) in the population, indicating that C. parvum chromosomes exhibit a Mendelian inheritance pattern. Unexpectedly, the most common pattern observed from the outgrowth of single oocysts included all possible parental and recombinant phenotypes derived from a single meiotic event, suggesting a high rate of crossover. To estimate the frequency of crossover, additional loci on chromosomes 1 and 5 were tagged and used to monitor intrachromosomal crosses in Ifngr1-/- mice. Both chromosomes showed a high frequency of crossover compared to other apicomplexans with map distances (i.e., 1% recombination) of 3-12 kb. Overall, a high recombination rate may explain many unique characteristics observed in Cryptosporidium spp. such as high rates of speciation, wide variation in host range, and rapid evolution of host-specific virulence factors.
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Affiliation(s)
- Abigail Kimball
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lisa Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wanyi Huang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - William H. Witola
- Department of Pathobiology, University of Illinois Urbana-Champaign College of Veterinary Medicine, Urbana, IL 61802, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Zingales B, Macedo AM. Fifteen Years after the Definition of Trypanosoma cruzi DTUs: What Have We Learned? Life (Basel) 2023; 13:2339. [PMID: 38137940 PMCID: PMC10744745 DOI: 10.3390/life13122339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Trypanosoma cruzi, the protozoan causative of Chagas disease (ChD), exhibits striking genetic and phenotypic intraspecific diversity, along with ecoepidemiological complexity. Human-pathogen interactions lead to distinct clinical presentations of ChD. In 2009, an international consensus classified T. cruzi strains into six discrete typing units (DTUs), TcI to TcVI, later including TcBat, and proposed reproducible genotyping schemes for DTU identification. This article aims to review the impact of classifying T. cruzi strains into DTUs on our understanding of biological, ecoepidemiological, and pathogenic aspects of T. cruzi. We will explore the likely origin of DTUs and the intrinsic characteristics of each group of strains concerning genome organization, genomics, and susceptibility to drugs used in ChD treatment. We will also provide an overview of the association of DTUs with mammalian reservoirs, and summarize the geographic distribution, and the clinical implications, of prevalent specific DTUs in ChD patients. Throughout this review, we will emphasize the crucial roles of both parasite and human genetics in defining ChD pathogenesis and chemotherapy outcome.
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Affiliation(s)
- Bianca Zingales
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, São Paulo, Brazil
| | - Andréa M. Macedo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil;
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Barnabé C, Brenière SF, Santillán-Guayasamín S, Douzery EJP, Waleckx E. Revisiting gene typing and phylogeny of Trypanosoma cruzi reference strains: Comparison of the relevance of mitochondrial DNA, single-copy nuclear DNA, and the intergenic region of mini-exon gene. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105504. [PMID: 37739149 DOI: 10.1016/j.meegid.2023.105504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Chagas disease is a widespread neglected disease in Latin America. Trypanosoma cruzi, the causative agent of the disease, is currently subdivided into six DTUs (discrete typing units) named TcI-TcVI, and although no clear association has been found between parasite genetics and different clinical outcomes of the disease or different transmission cycles, genetic characterization of T. cruzi strains remains crucial for integrated epidemiological studies. Numerous markers have been used for this purpose, although without consensus. These include mitochondrial genes, single or multiple-copy nuclear genes, ribosomal RNA genes, and the intergenic region of the repeated mini-exon gene. To increase our knowledge of these gene sequences and their usefulness for strain typing, we sequenced fragments of three mitochondrial genes, nine single-copy nuclear genes, and the repeated intergenic part of the mini-exon gene by Next Generation Sequencing (NGS) on a sample constituted of 16 strains representative of T. cruzi genetic diversity, to which we added the corresponding genetic data of the 38 T. cruzi genomes fully sequenced until 2022. Our results show that single-copy nuclear genes remain the gold standard for characterizing T. cruzi strains; the phylogenetic tree from concatenated genes (3959 bp) confirms the six DTUs previously recognized and provides additional information about the alleles present in the hybrid strains. In the tree built from the three mitochondrial concatenated genes (1274 bp), three main clusters are identified, including one with TcIII, TcIV, TcV, and TcVI DTUs which are not separated. Nevertheless, mitochondrial markers remain necessary for detecting introgression and heteroplasmy. The phylogenetic tree built from the sequence alignment of the repeated mini-exon gene fragment (327 bp) displayed six clusters, but only TcI was associated with a single cluster. The sequences obtained from strains belonging to the other DTUs were scattered into different clusters. Therefore, while the mini-exon marker may bring, for some biological samples, some advantages in terms of sensibility due to its repeated nature, mini-exon sequences must be used with caution and, when possible, avoided for T. cruzi typing and phylogenetic studies.
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Affiliation(s)
- Christian Barnabé
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD, CIRAD, University of Montpellier, Montpellier, France.
| | - Simone Frédérique Brenière
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD, CIRAD, University of Montpellier, Montpellier, France
| | - Soledad Santillán-Guayasamín
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD, CIRAD, University of Montpellier, Montpellier, France; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Emmanuel J P Douzery
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.
| | - Etienne Waleckx
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD, CIRAD, University of Montpellier, Montpellier, France; Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Mexico; ACCyC, Asociación Chagas con Ciencia y Conocimiento, A. C, Orizaba, Mexico.
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Buffi G, Ceccarelli M, Diotallevi A, Abruzzese M, Bruno F, Castelli G, Vitale F, Andreoni F, Bencardino D, Magnani M, Galluzzi L. High-resolution melting (HRM)-based detection of polymorphisms in the malic enzyme and glucose-6-phosphate isomerase genes for Leishmania infantum genotyping. Parasit Vectors 2023; 16:282. [PMID: 37580789 PMCID: PMC10426199 DOI: 10.1186/s13071-023-05878-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/11/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Leishmaniasis is a zoonotic disease endemic in the Mediterranean region where Leishmania infantum is the causative agent of human and canine infection. Characterization of this parasite at the subspecies level can be useful in epidemiological studies, to evaluate the clinical course of the disease (e.g. resistant strains, visceral and cutaneous forms of leishmaniasis) as well as to identify infection reservoirs. Multilocus enzyme electrophoresis (MLEE), a method currently recognized as the reference method for characterizing and identifying strains of Leishmania, is cumbersome and time-consuming and requires cultured parasites. These disadvantages have led to the development of other methods, such as multilocus microsatellite typing (MLMT) and multilocus sequence typing (MLST), for typing Leishmania parasites; however, these methods have not yet been applied for routine use. In this study, we first used MLST to identify informative polymorphisms on single-copy genes coding for metabolic enzymes, following which we developed two rapid genotyping assays based on high-resolution melting (HRM) analysis to explore these polymorphisms in L. infantum parasites. METHODS A customized sequencing panel targeting 14 housekeeping genes was designed and MLST analysis was performed on nine L. infantum canine and human strains/isolates. Two quantitative real-time PCR-HRM assays were designed to analyze two informative polymorphisms on malic enzyme (ME) and glucose-6-phosphate isomerase (GPI) genes (390T/G and 1831A/G, respectively). The two assays were applied to 73 clinical samples/isolates from central/southern Italy and Pantelleria island, and the results were confirmed by DNA sequencing in a subset of samples. RESULTS The MLST analysis, together with sequences available in the Genbank database, enabled the identification of two informative polymorphisms on the genes coding for ME and GPI. The fast screening of these polymorphisms using two HRM-based assays in 73 clinical samples/isolates resulted in the identification of seven genotypes. Overall, genotype 1 (sequence type 390T/1831G) was the most highly represented (45.2%) in the overall sample and correlated with the most common L. infantum zymodemes (MON-1, MON-72). Interestingly, in Pantelleria island, the most prevalent genotype (70.6%) was genotype 6 (sequence type 390T/1831A). CONCLUSIONS Applying our HRM assays on clinical samples allowed us to identify seven different genotypes without the need for parasite isolation and cultivation. We have demonstrated that these assays could be used as fast, routine and inexpensive tools for epidemiological surveillance of L. infantum or for the identification of new infection reservoirs.
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Affiliation(s)
- Gloria Buffi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Marcello Ceccarelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Aurora Diotallevi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | | | - Federica Bruno
- OIE Leishmania Reference Laboratory, Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), Istituto Zooprofilattico Sperimentale Della Sicilia, Palermo, PA, Italy
| | - Germano Castelli
- OIE Leishmania Reference Laboratory, Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), Istituto Zooprofilattico Sperimentale Della Sicilia, Palermo, PA, Italy
| | - Fabrizio Vitale
- OIE Leishmania Reference Laboratory, Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), Istituto Zooprofilattico Sperimentale Della Sicilia, Palermo, PA, Italy
| | - Francesca Andreoni
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Daniela Bencardino
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Luca Galluzzi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy.
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6
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Cruz-Saavedra L, Caceres T, Ballesteros N, Posada-Forero B, Ramírez JD. Differential expression of meiosis and homologous recombination-related genes in the life cycle of Trypanosoma cruzi. Parasitol Res 2023:10.1007/s00436-023-07850-2. [PMID: 37272974 DOI: 10.1007/s00436-023-07850-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023]
Abstract
Trypanosoma cruzi has a complex life cycle consisting of four morphological and distinct biological stages. Although some authors suggest that T. cruzi primarily follows clonal reproduction, recent genomic and transcriptomic studies indicate an unorthodox capacity for recombination. We aimed to estimate the differential gene expression of 10 meiosis/homologous recombination-related genes during the T. cruzi life cycle, including epimastigotes, under two different types of stress (oxidative stress and pH changes). We performed RT-qPCR tests using novel-designed primers to estimate the differential gene expression (∆Ct and ∆∆Ct) of nine genes (SPO11, HAP2, RAD50, MRN complex, BRCA2, DMC1, MND1, and RPA1) and RAD51, which was previously reported. Our results show basal expression of all genes during the life cycle, indicating their hypothetical role in several cellular processes but with specific signatures of differential gene expression during the life cycle (HAP2, RPA, RAD50, BRCA2, MND1, and DMC1) and oxidative stress (RPA, MRE11, NBS1, BRCA2, MND1, and RAD51). Additionally, we found that the MRN complex has an independent level of expression in T. cruzi, with profiles of MRE11 and NBS1 upregulated in some stages. Recent studies on other trypanosomatids have highlighted the influence of HAP2 and RPA in recombination and hybridization. If T. cruzi uses the same repertoire of genes, our findings could suggest that metacyclogenesis may be the putative step that the parasite uses to undergo recombination. Likewise, our study reveals the differential profiles of genes expressed in response to oxidative and pH stress. Further studies are necessary to confirm our findings and understand the recombination mechanism in T. cruzi.
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Affiliation(s)
- Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Tatiana Caceres
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | | | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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7
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Darwish AM, Sharaf A, Gaouar SBS, Ali NI, El-Aziz THA, Abushady AM, Kaouadji Z, Othman OE, Obornik M. Biochemical and genotyping analyses of camels (Camelus dromedaries) trypanosomiasis in North Africa. Sci Rep 2023; 13:7176. [PMID: 37137920 PMCID: PMC10156784 DOI: 10.1038/s41598-023-34086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/24/2023] [Indexed: 05/05/2023] Open
Abstract
Camels are considered an important food source in North Africa. Trypanosomiasis in camels is a life-threatening disease that causes severe economic losses in milk and meat production. Therefore, the objective of this study was to determine the trypanosome genotypes in the North African region. Trypanosome infection rates were determined by microscopic examination of blood smears and polymerase chain reaction (PCR). In addition, total antioxidant capacity (TAC), lipid peroxides (MDA), reduced glutathione (GSH), superoxide dismutase (SOD) and catalase (CAT) were determined in erythrocyte lysate. Furthermore, 18S amplicon sequencing was used to barcode and characterizes the genetic diversity of trypanosome genotypes in camel blood. In addition to Trypanosoma, Babesia and Thelieria were also detected in the blood samples. PCR showed that the trypanosome infection rate was higher in Algerian samples (25.7%) than in Egyptian samples (7.2%). Parameters such as MDA, GSH, SOD and CAT had significantly increased in camels infected with trypanosomes compared to uninfected control animals, while TAC level was not significantly changed. The results of relative amplicon abundance showed that the range of trypanosome infection was higher in Egypt than in Algeria. Moreover, phylogenetic analysis showed that the Trypanosoma sequences of Egyptian and Algerian camels are related to Trypanosoma evansi. Unexpectedly, diversity within T. evansi was higher in Egyptian camels than in Algerian camels. We present here the first molecular report providing a picture of trypanosomiasis in camels, covering wide geographical areas in Egypt and Algeria.
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Affiliation(s)
- Ahmed M Darwish
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622, Giza, Egypt.
| | - Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, 78464, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Semir Bechir Suheil Gaouar
- Applied Genetic in Agriculture, Ecology and Public Health Laboratory, SNV/STU Faculty, University of Tlemcen, Chetouane, Algeria
| | - Neama I Ali
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Tamer H Abd El-Aziz
- Parasitology and Animal Diseases, Veterinary Research Institute, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Asmaa M Abushady
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Biotechnology School, Nile University, Sheikh Zayed, Giza, Egypt
| | - Zoubeyda Kaouadji
- Applied Genetic in Agriculture, Ecology and Public Health Laboratory, SNV/STU Faculty, University of Tlemcen, Chetouane, Algeria
| | - Othman E Othman
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Miroslav Obornik
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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8
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Majeau A, Cloherty E, Anderson AN, Straif-Bourgeois SC, Dumonteil E, Herrera C. Genetic diversity of Trypanosoma cruzi infecting raccoons ( Procyon lotor) in 2 metropolitan areas of southern Louisiana: implications for parasite transmission networks. Parasitology 2023; 150:1-8. [PMID: 36788672 PMCID: PMC10090583 DOI: 10.1017/s0031182023000070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
Trypanosoma cruzi, the aetiological agent of Chagas disease, exists as an anthropozoonosis in Louisiana. Raccoons are an important reservoir, as they demonstrate high prevalence and maintain high parasitaemia longer than other mammals. Given the complex nature of parasite transmission networks and importance of raccoons as reservoirs that move between sylvatic and domestic environments, detailing the genetic diversity of T. cruzi in raccoons is crucial to assess risk to human health. Using a next-generation sequencing approach targeting the mini-exon, parasite diversity was assessed in 2 metropolitan areas of Louisiana. Sequences were analysed along with those previously identified in other mammals and vectors to determine if any association exists between ecoregion and parasite diversity. Parasites were identified from discrete typing units (DTUs) TcI, TcII, TcIV, TcV and TcVI. DTUs TcII, TcV and TcVI are previously unreported in raccoons in the United States (US). TcI was the most abundant DTU, comprising nearly 80% of all sequences. All but 1 raccoon harboured multiple haplotypes, some demonstrating mixed infections of different DTUs. Furthermore, there is significant association between DTU distribution and level III ecoregion in Louisiana. Finally, while certain sequences were distributed across multiple tissues, others appeared to have tissue-specific tropism. Taken together, these findings indicate that ongoing surveillance of T. cruzi in the US should be undertaken across ecoregions to fully assess risk to human health. Given potential connections between parasite diversity and clinical outcomes, deep sequencing technologies are crucial and interventions targeting raccoons may prove useful in mitigating human health risk.
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Affiliation(s)
- Alicia Majeau
- Tulane University School of Public Health & Tropical Medicine, New Orleans, LA, USA
| | - Erin Cloherty
- New Orleans Mosquito, Rodent, and Termite Control, New Orleans, LA, USA
| | - A. Nikki Anderson
- Louisiana Department of Wildlife and Fisheries, Baton Rouge, LA, USA
| | | | - Eric Dumonteil
- Tulane University School of Public Health & Tropical Medicine, New Orleans, LA, USA
| | - Claudia Herrera
- Tulane University School of Public Health & Tropical Medicine, New Orleans, LA, USA
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9
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da Silva VS, Machado CR. Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids. Genet Mol Biol 2022; 45:e20220065. [PMID: 36218381 PMCID: PMC9552303 DOI: 10.1590/1678-4685-gmb-2022-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
The Protist kingdom individuals are the most ancestral representatives of
eukaryotes. They have inhabited Earth since ancient times and are currently
found in the most diverse environments presenting a great heterogeneity of life
forms. The unicellular and multicellular algae, photosynthetic and heterotrophic
organisms, as well as free-living and pathogenic protozoa represents the protist
group. The evolution of sex is directly associated with the origin of eukaryotes
being protists the earliest protagonists of sexual reproduction on earth. In
eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism
that can be stimulated by DNA damage. Scientific evidences support the
hypothesis that reactive oxygen species (ROS) induced DNA damage can promote
sexual recombination in eukaryotes which might have been a decisive factor for
the origin of sex. The fact that some recombination enzymes also participate in
meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction
emerged as consequence of specific mechanisms to cope with mutations and
alterations in genetic material. In this review we will discuss about origin of
sex and different strategies of evolve sexual reproduction in some protists such
that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas
disease, and leishmaniasis.
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Affiliation(s)
- Verônica Santana da Silva
- Universidade Federal de Minas Gerais, Departamento de Genética,
Ecologia e Evolução, Belo Horizonte, MG, Brazil
| | - Carlos Renato Machado
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e
Imunologia, Belo Horizonte, MG, Brazil
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10
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Jameson SB, Cloherty E, Londono-Renteria B, Wesson DM. Chagas Disease in the Southeastern USA. CURRENT TROPICAL MEDICINE REPORTS 2022. [DOI: 10.1007/s40475-022-00260-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Tibayrenc M, Ayala FJ. Microevolution and subspecific taxonomy of Trypanosoma cruzi. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105344. [PMID: 35926722 DOI: 10.1016/j.meegid.2022.105344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Trypanosoma cruzi, the agent of Chagas disease, is a highly polymorphic species, subdivided into 6 main evolutionary lineages or near-clades (formerly discrete typing units or DTUs). An additional near-clade (TC-bat) has recently been evidenced. This pattern is considered to be the result of predominant clonal evolution (PCE). PCE is compatible with occasional mating/hybridization, which do not break the prevalent pattern of clonal evolution, the main trait of it being the presence of Multigene Bifurcating Trees (MGBTs) at all evolutionary levels ("clonal frame"). The development of highly resolutive genetic (microsatellites*) and genomic (sequencing and multi-single nucleotide polymorphism {SNP}* typing) markers shows that PCE also operates at a microevolutionary* level within each of the near-clades ("Russian doll pattern"), in spite of occasional meiosis and hybridization events. Within each near-clade, one can evidence widespread clonal multilocus genotypes*, linkage disequilibrium*, Multigene Bifurcating Trees and lesser near-clades. The within near-clade population structure is like a miniature picture of that of the whole species, suggesting gradual rather than saltatory evolution. Additional data are required to evaluate the stability of these lesser near-clades in the long run and to evaluate the need for an adequate nomenclature for this microevolutionary level.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Institut de Recherche Pour le Développement, BP 6450134394 Montpellier Cedex 5, France.
| | - Francisco J Ayala
- Catedra Francisco Jose Ayala of Science, Technology, and Religion, University of Comillas, 28015 Madrid, Spain. 2 Locke Court, Irvine, CA 92617, USA
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Martín-Escolano J, Marín C, Rosales MJ, Tsaousis AD, Medina-Carmona E, Martín-Escolano R. An Updated View of the Trypanosoma cruzi Life Cycle: Intervention Points for an Effective Treatment. ACS Infect Dis 2022; 8:1107-1115. [PMID: 35652513 PMCID: PMC9194904 DOI: 10.1021/acsinfecdis.2c00123] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Chagas disease (CD)
is a parasitic, systemic, chronic, and often
fatal illness caused by infection with the protozoan Trypanosoma
cruzi. The World Health Organization classifies CD as the
most prevalent of poverty-promoting neglected tropical diseases, the
most important parasitic one, and the third most infectious disease
in Latin America. Currently, CD is a global public health issue that
affects 6–8 million people. However, the current approved treatments
are limited to two nitroheterocyclic drugs developed more than 50
years ago. Many efforts have been made in recent decades to find new
therapies, but our limited understanding of the infection process,
pathology development, and long-term nature of this disease has made
it impossible to develop new drugs, effective treatment, or vaccines.
This Review aims to provide a comprehensive update on our understanding
of the current life cycle, new morphological forms, and genetic diversity
of T. cruzi, as well as identify intervention points
in the life cycle where new drugs and treatments could achieve a parasitic
cure.
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Affiliation(s)
- Javier Martín-Escolano
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
| | - Clotilde Marín
- Department of Parasitology, University of Granada, Severo Ochoa s/n, 18071 Granada, Spain
| | - María J. Rosales
- Department of Parasitology, University of Granada, Severo Ochoa s/n, 18071 Granada, Spain
| | - Anastasios D. Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K
| | - Encarnación Medina-Carmona
- Department of Physical Chemistry, University of Granada, 18071 Granada, Spain
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K
| | - Rubén Martín-Escolano
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K
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Cruz-Saavedra L, Schwabl P, Vallejo GA, Carranza JC, Muñoz M, Patino LH, Paniz-Mondolfi A, Llewellyn MS, Ramírez JD. Genome plasticity driven by aneuploidy and loss of heterozygosity in Trypanosoma cruzi. Microb Genom 2022; 8. [PMID: 35748878 PMCID: PMC9455712 DOI: 10.1099/mgen.0.000843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi the causative agent of Chagas disease shows a marked genetic diversity and divided into at least six Discrete Typing Units (DTUs). High intra genetic variability has been observed in the TcI DTU, the most widely distributed DTU, where patterns of genomic diversity can provide information on ecological and evolutionary processes driving parasite population structure and genome organization. Chromosomal aneuploidies and rearrangements across multigene families represent an evidence of T. cruzi genome plasticity. We explored genomic diversity among 18 Colombian T. cruzi I clones and 15 T. cruzi I South American strains. Our results confirm high genomic variability, heterozygosity and presence of a clade compatible with the TcIdom genotype, described for strains from humans in Colombia and Venezuela. TcI showed high structural plasticity across the geographical region studied. Differential events of whole and segmental aneuploidy (SA) along chromosomes even between clones from the same strain were found and corroborated by the depth and allelic frequency. We detected loss of heterozygosity (LOH) events in different chromosomes, however, the size and location of segments under LOH varied between clones. Genes adjacent to breakpoints were evaluated, and retrotransposon hot spot genes flanked the beginning of segmental aneuploidies. Our results suggest that T. cruzi genomes, like those of Leishmania, may have a highly unstable structure and there is now an urgent need to design experiments to explore any potential adaptive role for the plasticity observed.
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Affiliation(s)
- Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Gustavo A Vallejo
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Julio C Carranza
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patino
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Alberto Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.,Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Matos GM, Lewis MD, Talavera-López C, Yeo M, Grisard EC, Messenger LA, Miles MA, Andersson B. Microevolution of Trypanosoma cruzi reveals hybridization and clonal mechanisms driving rapid genome diversification. eLife 2022; 11:75237. [PMID: 35535495 PMCID: PMC9098224 DOI: 10.7554/elife.75237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/22/2022] [Indexed: 12/11/2022] Open
Abstract
Protozoa and fungi are known to have extraordinarily diverse mechanisms of genetic exchange. However, the presence and epidemiological relevance of genetic exchange in Trypanosoma cruzi, the agent of Chagas disease, has been controversial and debated for many years. Field studies have identified both predominantly clonal and sexually recombining natural populations. Two of six natural T. cruzi lineages (TcV and TcVI) show hybrid mosaicism, using analysis of single-gene locus markers. The formation of hybrid strains in vitro has been achieved and this provides a framework to study the mechanisms and adaptive significance of genetic exchange. Using whole genome sequencing of a set of experimental hybrids strains, we have confirmed that hybrid formation initially results in tetraploid parasites. The hybrid progeny showed novel mutations that were not attributable to either (diploid) parent showing an increase in amino acid changes. In long-term culture, up to 800 generations, there was a variable but gradual erosion of progeny genomes towards triploidy, yet retention of elevated copy number was observed at several core housekeeping loci. Our findings indicate hybrid formation by fusion of diploid T. cruzi, followed by sporadic genome erosion, but with substantial potential for adaptive evolution, as has been described as a genetic feature of other organisms, such as some fungi.
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Affiliation(s)
- Gabriel Machado Matos
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianopolis, Brazil.,Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Michael D Lewis
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlos Talavera-López
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.,Institute of Computational Biology, Computational Health Centre, Helmholtz Munich, Munich, Germany
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Edmundo C Grisard
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianopolis, Brazil
| | - Louisa A Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael A Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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Cortez DR, Lima FM, Reis-Cunha JL, Bartholomeu DC, Villacis RAR, Rogatto SR, Costa-Martins AG, Marchiano FS, do Carmo RA, da Silveira JF, Marini MM. Trypanosoma cruzi Genomic Variability: Array Comparative Genomic Hybridization Analysis of Clone and Parental Strain. Front Cell Infect Microbiol 2022; 12:760830. [PMID: 35402315 PMCID: PMC8992781 DOI: 10.3389/fcimb.2022.760830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, exhibits extensive inter- and intrastrain genetic diversity. As we have previously described, there are some genetic differences between the parental G strain and its clone D11, which was isolated by the limiting dilution method and infection of cultured mammalian cells. Electrophoretic karyotyping and Southern blot hybridization of chromosomal bands with specific markers revealed chromosome length polymorphisms of small size with additional chromosomal bands in clone D11 and the maintenance of large syntenic groups. Both G strain and clone D11 belong to the T. cruzi lineage TcI. Here, we designed intraspecific array-based comparative genomic hybridization (aCGH) to identify chromosomal regions harboring copy-number variations between clone D11 and the G strain. DNA losses were more extensive than DNA gains in clone D11. Most alterations were flanked by repeated sequences from multigene families that could be involved in the duplication and deletion events. Several rearrangements were detected by chromoblot hybridization and confirmed by aCGH. We have integrated the information of genomic sequence data obtained by aCGH to the electrophoretic karyotype, allowing the reconstruction of possible recombination events that could have generated the karyotype of clone D11. These rearrangements may be explained by unequal crossing over between sister or homologous chromatids mediated by flanking repeated sequences and unequal homologous recombination via break-induced replication. The genomic changes detected by aCGH suggest the presence of a dynamic genome that responds to environmental stress by varying the number of gene copies and generating segmental aneuploidy.
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Affiliation(s)
- Danielle Rodrigues Cortez
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fabio Mitsuo Lima
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Centro Universitário São Camilo, Biomedicina, São Paulo, Brazil
| | - João Luís Reis-Cunha
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Silvia Regina Rogatto
- Department of Clinical Genetics, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
| | - André Guilherme Costa-Martins
- Department of Clinical and Toxicological Analyses, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda Sycko Marchiano
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rafaela Andrade do Carmo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jose Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- *Correspondence: Marjorie Mendes Marini, ; Jose Franco da Silveira,
| | - Marjorie Mendes Marini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Centro Universitário São Camilo, Biomedicina, São Paulo, Brazil
- *Correspondence: Marjorie Mendes Marini, ; Jose Franco da Silveira,
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Silveira KRD, Nogueira PM, Soares RP. Effect of hybridization on Lipophosphoglycan expression in Leishmania major. Cell Biol Int 2022; 46:1169-1174. [PMID: 35312138 DOI: 10.1002/cbin.11798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/07/2022]
Abstract
Leishmania major is the causative agent of cutaneous leishmaniasis (CL). It is one of the most studied Leishmania species not only during vector interaction, but also in the vertebrate host. Lipophosphoglycan (LPG) is the Leishmania multifunctional virulence factor during host-parasite interaction, whose polymorphisms are involved in the immunopathology of leishmaniasis. Although natural hybrids occur in nature, hybridization of L. major strains in the laboratory was successfully demonstrated. However, LPG expression in the hybrids remains unknown. LPGs from parental (Friedlin-Fn and Seidman-Sd) and hybrids (FnSd3, FnSd4A, FnSd4B and FnSd6F) were extracted, purified and their repeat units analyzed by immunoblotting and fluorophore-assisted carbohydrate electrophoresis (FACE). Parental strains have distinct profiles in LPG expression, and a mixed profile was observed for all hybrids. Variable levels of NO production by macrophages were detected after LPG exposure (parental and hybrids) and were strain specific. This article is protected by copyright. All rights reserved.
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Pathogen diversity, immunity, and the fate of infections: lessons learned from Trypanosoma cruzi human–host interactions. THE LANCET MICROBE 2022; 3:e711-e722. [DOI: 10.1016/s2666-5247(21)00265-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/02/2023] Open
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Kay C, Peacock L, Williams TA, Gibson W. Signatures of hybridization in Trypanosoma brucei. PLoS Pathog 2022; 18:e1010300. [PMID: 35139131 PMCID: PMC8863249 DOI: 10.1371/journal.ppat.1010300] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 02/22/2022] [Accepted: 01/22/2022] [Indexed: 11/19/2022] Open
Abstract
Genetic exchange among disease-causing micro-organisms can generate progeny that combine different pathogenic traits. Though sexual reproduction has been described in trypanosomes, its impact on the epidemiology of Human African Trypanosomiasis (HAT) remains controversial. However, human infective and non-human infective strains of Trypanosoma brucei circulate in the same transmission cycles in HAT endemic areas in subsaharan Africa, providing the opportunity for mating during the developmental cycle in the tsetse fly vector. Here we investigated inheritance among progeny from a laboratory cross of T. brucei and then applied these insights to genomic analysis of field-collected isolates to identify signatures of past genetic exchange. Genomes of two parental and four hybrid progeny clones with a range of DNA contents were assembled and analysed by k-mer and single nucleotide polymorphism (SNP) frequencies to determine heterozygosity and chromosomal inheritance. Variant surface glycoprotein (VSG) genes and kinetoplast (mitochondrial) DNA maxi- and minicircles were extracted from each genome to examine how each of these components was inherited in the hybrid progeny. The same bioinformatic approaches were applied to an additional 37 genomes representing the diversity of T. brucei in subsaharan Africa and T. evansi. SNP analysis provided evidence of crossover events affecting all 11 pairs of megabase chromosomes and demonstrated that polyploid hybrids were formed post-meiotically and not by fusion of the parental diploid cells. VSGs and kinetoplast DNA minicircles were inherited biparentally, with approximately equal numbers from each parent, whereas maxicircles were inherited uniparentally. Extrapolation of these findings to field isolates allowed us to distinguish clonal descent from hybridization by comparing maxicircle genotype to VSG and minicircle repertoires. Discordance between maxicircle genotype and VSG and minicircle repertoires indicated inter-lineage hybridization. Significantly, some of the hybridization events we identified involved human infective and non-human infective trypanosomes circulating in the same geographic areas.
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Affiliation(s)
- Christopher Kay
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Lori Peacock
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Veterinary School, University of Bristol, Bristol, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Wendy Gibson
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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Pinello JF, Clark TG. HAP2-Mediated Gamete Fusion: Lessons From the World of Unicellular Eukaryotes. Front Cell Dev Biol 2022; 9:807313. [PMID: 35071241 PMCID: PMC8777248 DOI: 10.3389/fcell.2021.807313] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 01/29/2023] Open
Abstract
Most, if not all the cellular requirements for fertilization and sexual reproduction arose early in evolution and are retained in extant lineages of single-celled organisms including a number of important model organism species. In recent years, work in two such species, the green alga, Chlamydomonas reinhardtii, and the free-living ciliate, Tetrahymena thermophila, have lent important new insights into the role of HAP2/GCS1 as a catalyst for gamete fusion in organisms ranging from protists to flowering plants and insects. Here we summarize the current state of knowledge around how mating types from these algal and ciliate systems recognize, adhere and fuse to one another, current gaps in our understanding of HAP2-mediated gamete fusion, and opportunities for applying what we know in practical terms, especially for the control of protozoan parasites.
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Affiliation(s)
- Jennifer F. Pinello
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Theodore G. Clark
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
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Zingales B, Bartholomeu DC. Trypanosoma cruzi genetic diversity: impact on transmission cycles and Chagas disease. Mem Inst Oswaldo Cruz 2022; 117:e210193. [PMID: 35544857 PMCID: PMC9088421 DOI: 10.1590/0074-02760210193] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Trypanosoma cruzi, the agent of Chagas disease (ChD), exhibits remarkable biological and genetic diversity, along with eco-epidemiological complexity. In order to facilitate communication among researchers aiming at the characterisation of biological and epidemiological aspects of T. cruzi, parasite isolates and strains were partitioned into seven discrete typing units (DTUs), TcI-TcVI and TcBat, identifiable by reproducible genotyping protocols. Here we present the potential origin of the genetic diversity of T. cruzi and summarise knowledge about eco-epidemiological associations of DTUs with mammalian reservoirs and vectors. Circumstantial evidence of a connection between T. cruzi genotype and ChD manifestations is also discussed emphasising the role of the host’s immune response in clinical ChD progression. We describe genomic aspects of DTUs focusing on polymorphisms in multigene families encoding surface antigens that play essential functions for parasite survival both in the insect vector and the mammalian host. Such antigens most probably contributed to the parasite success in establishing infections in different hosts and exploring several niches. Gaps in the current knowledge and challenges for future research are pointed out.
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Souza TKMD, Westphalen EVN, Westphalen SDR, Taniguchi HH, Elias CR, Motoie G, Gava R, Pereira-Chioccola VL, Novaes CTG, Carvalho NB, Bocchi EA, Cruz FDDD, Rocha MC, Shinjo SK, Shikanai-Yasuda MA, Ortiz PA, Teixeira MMG, Tolezano JE. Genetic diversity of Trypanosoma cruzi strains isolated from chronic chagasic patients and non-human hosts in the state of São Paulo, Brazil. Mem Inst Oswaldo Cruz 2022; 117:e220125. [PMID: 36383785 PMCID: PMC9651066 DOI: 10.1590/0074-02760220125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi shows an exuberant genetic diversity. Currently, seven phylogenetic lineages, called discrete typing units (DTUs), are recognised: TcI-TcVI and Tcbat. Despite advances in studies on T. cruzi and its populations, there is no consensus regarding its heterogeneity. OBJECTIVES This study aimed to perform molecular characterisation of T. cruzi strains, isolated in the state of São Paulo, to identify the DTUs involved and evaluate their genetic diversity. METHODS T. cruzi strains were isolated from biological samples of chronic chagasic patients, marsupials and triatomines through culture techniques and subjected to molecular characterisation using the fluorescent fragment length barcoding (FFLB) technique. Subsequently, the results were correlated with complementary information to enable better discrimination between the identified DTUs. FINDINGS It was possible to identify TcI in two humans and two triatomines; TcII/VI in 19 humans, two marsupials and one triatomine; and TcIII in one human host, an individual that also presented a result for TcI, which indicated the possibility of a mixed infection. Regarding the strains characterised by the TcII/VI profile, the correlation with complementary information allowed to suggest that, in general, these parasite populations indeed correspond to the TcII genotype. MAIN CONCLUSIONS The TcII/VI profile, associated with domestic cycles and patients with chronic Chagas disease, was the most prevalent among the identified DTUs. Furthermore, the correlation of the study results with complementary information made it possible to suggest that TcII is the predominant lineage of this work.
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Glans H, Lind Karlberg M, Advani R, Bradley M, Alm E, Andersson B, Downing T. High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria. PLoS Negl Trop Dis 2021; 15:e0010110. [PMID: 34968388 PMCID: PMC8754299 DOI: 10.1371/journal.pntd.0010110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/12/2022] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Background The kinetoplastid protozoan Leishmania tropica mainly causes cutaneous leishmaniasis in humans in the Middle East, and relapse or treatment failure after treatment are common in this area. L. tropica’s digenic life cycle includes distinct stages in the vector sandfly and the mammalian host. Sexual reproduction and genetic exchange appear to occur more frequently than in other Leishmania species. Understanding these processes is complicated by chromosome instability during cell division that yields aneuploidy, recombination and heterozygosity. This combination of rare recombination and aneuploid permits may reveal signs of hypothetical parasexual mating, where diploid cells fuse to form a transient tetraploid that undergoes chromosomal recombination and gradual chromosomal loss. Methodology/principal findings The genome-wide SNP diversity from 22 L. tropica isolates showed chromosome-specific runs of patchy heterozygosity and extensive chromosome copy number variation. All these isolates were collected during 2007–2017 in Sweden from patients infected in the Middle East and included isolates from a patient possessing two genetically distinct leishmaniasis infections three years apart with no evidence of re-infection. We found differing ancestries on the same chromosome (chr36) across multiple samples: matching the reference genome with few derived alleles, followed by blocks of heterozygous SNPs, and then by clusters of homozygous SNPs with specific recombination breakpoints at an inferred origin of replication. Other chromosomes had similar marked changes in heterozygosity at strand-switch regions separating polycistronic transcriptional units. Conclusion/significance These large-scale intra- and inter-chromosomal changes in diversity driven by recombination and aneuploidy suggest multiple mechanisms of cell reproduction and diversification in L. tropica, including mitotic, meiotic and parasexual processes. It underpins the need for more genomic surveillance of Leishmania, to detect emerging hybrids that could spread more widely and to better understand the association between genetic variation and treatment outcome. Furthering our understanding of Leishmania genome evolution and ancestry will aid better diagnostics and treatment for cutaneous leishmaniasis caused by L.tropica in the Middle East. Cutaneous leishmaniasis is mainly caused by Leishmania tropica in the Middle East, where it is known for treatment failure and a need for prolonged and/or multiple treatments. Several factors affect the clinical presentation and treatment outcome, such as host genetic variability and specific immune response, as well as environmental factors and the vector species. Little is known about the parasite genome and its influence on treatment response. By analysing the genome of 22 isolates of L. tropica, we have revealed extensive genomic variation and a complex population structure with evidence of genetic exchange within and among the isolates, indicating a possible presence of sexual or parasexual mechanisms. Understanding the Leishmania genome better may improve future treatment and better understanding of treatment failure and relapse.
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Affiliation(s)
- Hedvig Glans
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Maria Lind Karlberg
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Reza Advani
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Maria Bradley
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venerology, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Alm
- The European Center for Disease Prevention and Control, Stockholm, Sweden
| | - Björn Andersson
- Department of Cell & Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
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23
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Medina-Rincón GJ, Gallo-Bernal S, Jiménez PA, Cruz-Saavedra L, Ramírez JD, Rodríguez MJ, Medina-Mur R, Díaz-Nassif G, Valderrama-Achury MD, Medina HM. Molecular and Clinical Aspects of Chronic Manifestations in Chagas Disease: A State-of-the-Art Review. Pathogens 2021; 10:pathogens10111493. [PMID: 34832648 PMCID: PMC8619182 DOI: 10.3390/pathogens10111493] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/11/2022] Open
Abstract
Chronic manifestations of Chagas disease present as disabling and life-threatening conditions affecting mainly the cardiovascular and gastrointestinal systems. Although meaningful research has outlined the different molecular mechanisms underlying Trypanosoma cruzi’s infection and the host-parasite interactions that follow, prompt diagnosis and treatment remain a challenge, particularly in developing countries and also in those where the disease is considered non-endemic. This review intends to present an up-to-date review of the parasite’s life cycle, genetic diversity, virulence factors, and infective mechanisms, as well as the epidemiology, clinical presentation, diagnosis, and treatment options of the main chronic complications of Chagas disease.
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Affiliation(s)
- Germán J. Medina-Rincón
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (S.G.-B.); (M.D.V.-A.); (H.M.M.)
- Correspondence: ; Tel.: +57-310-817-2369
| | - Sebastián Gallo-Bernal
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (S.G.-B.); (M.D.V.-A.); (H.M.M.)
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Radiology, Harvard Medical School, Boston, MA 02114, USA
| | - Paula A. Jiménez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (P.A.J.); (L.C.-S.); (J.D.R.)
| | - Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (P.A.J.); (L.C.-S.); (J.D.R.)
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (P.A.J.); (L.C.-S.); (J.D.R.)
| | - María Juliana Rodríguez
- Division of Cardiology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá 110131, Colombia; (M.J.R.); (R.M.-M.)
| | - Ramón Medina-Mur
- Division of Cardiology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá 110131, Colombia; (M.J.R.); (R.M.-M.)
| | - Gustavo Díaz-Nassif
- Division of Gastroenterology and Liver Diseases, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá 111221, Colombia;
| | | | - Héctor M. Medina
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (S.G.-B.); (M.D.V.-A.); (H.M.M.)
- Division of Cardiology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá 110131, Colombia; (M.J.R.); (R.M.-M.)
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24
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Vangalis V, Likhotkin I, Knop M, Typas MA, Papaioannou IA. Starvation-induced cell fusion and heterokaryosis frequently escape imperfect allorecognition systems in an asexual fungal pathogen. BMC Biol 2021; 19:169. [PMID: 34429100 PMCID: PMC8385987 DOI: 10.1186/s12915-021-01101-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/16/2021] [Indexed: 01/02/2023] Open
Abstract
Background Asexual fungi include important pathogens of plants and other organisms, and their effective management requires understanding of their evolutionary dynamics. Genetic recombination is critical for adaptability and could be achieved via heterokaryosis — the co-existence of genetically different nuclei in a cell resulting from fusion of non-self spores or hyphae — and the parasexual cycle in the absence of sexual reproduction. Fusion between different strains and establishment of viable heterokaryons are believed to be rare due to non-self recognition systems. Here, we investigate the extent and mechanisms of cell fusion and heterokaryosis in the important asexual plant pathogen Verticillium dahliae. Results We used live-cell imaging and genetic complementation assays of tagged V. dahliae strains to analyze the extent of non-self vegetative fusion, heterokaryotic cell fate, and nuclear behavior. An efficient CRISPR/Cas9-mediated system was developed to investigate the involvement of autophagy in heterokaryosis. Under starvation, non-self fusion of germinating spores occurs frequently regardless of the previously assessed vegetative compatibility of the partners. Supposedly “incompatible” fusions often establish viable heterokaryotic cells and mosaic mycelia, where nuclei can engage in fusion or transfer of genetic material. The molecular machinery of autophagy has a protective function against the destruction of “incompatible” heterokaryons. Conclusions We demonstrate an imperfect function of somatic incompatibility systems in V. dahliae. These systems frequently tolerate the establishment of heterokaryons and potentially the initiation of the parasexual cycle even between strains that were previously regarded as “incompatible.” Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01101-5.
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Affiliation(s)
- Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ilya Likhotkin
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.,German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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25
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Cruz-Saavedra L, Vallejo GA, Guhl F, Messenger LA, Ramírez JD. Transcriptional remodeling during metacyclogenesis in Trypanosoma cruzi I. Virulence 2021; 11:969-980. [PMID: 32715914 PMCID: PMC7549971 DOI: 10.1080/21505594.2020.1797274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Metacyclogenesis is one of the most important processes in the life cycle of Trypanosoma cruzi. In this stage, noninfective epimastigotes become infective metacyclic trypomastigotes. However, the transcriptomic changes that occur during this transformation remain uncertain. Illumina RNA-sequencing of epimastigotes and metacyclic trypomastigotes belonging to T. cruzi DTU I was undertaken. Sequencing reads were aligned and mapped against the reference genome, differentially expressed genes between the two life cycle stages were identified, and metabolic pathways were reconstructed. Gene expression differed significantly between epimastigotes and metacyclic trypomastigotes. The cellular pathways that were mostly downregulated during metacyclogenesis involved glucose energy metabolism (glycolysis, pyruvate metabolism, the Krebs cycle, and oxidative phosphorylation), amino acid metabolism, and DNA replication. By contrast, the processes where an increase in gene expression was observed included those related to autophagy (particularly Atg7 and Atg8 transcripts), corroborating its importance during metacyclogenesis, endocytosis, by an increase in the expression of the AP-2 complex subunit alpha, protein processing in the endoplasmic reticulum and meiosis. Study findings indicate that in T. cruzi metacyclic trypomastigotes, metabolic processes are decreased, and expression of genes involved in specific cell cycle processes is increased to facilitate transformation to this infective stage.
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Affiliation(s)
- Lissa Cruz-Saavedra
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario , Bogotá, Colombia
| | - Gustavo A Vallejo
- Laboratorio de Investigaciones en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima , Ibagué, Colombia
| | - Felipe Guhl
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de Los Andes , Bogotá, Colombia
| | | | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario , Bogotá, Colombia
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26
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Zuma AA, Dos Santos Barrias E, de Souza W. Basic Biology of Trypanosoma cruzi. Curr Pharm Des 2021; 27:1671-1732. [PMID: 33272165 DOI: 10.2174/1381612826999201203213527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022]
Abstract
The present review addresses basic aspects of the biology of the pathogenic protozoa Trypanosoma cruzi and some comparative information of Trypanosoma brucei. Like eukaryotic cells, their cellular organization is similar to that of mammalian hosts. However, these parasites present structural particularities. That is why the following topics are emphasized in this paper: developmental stages of the life cycle in the vertebrate and invertebrate hosts; the cytoskeleton of the protozoa, especially the sub-pellicular microtubules; the flagellum and its attachment to the protozoan body through specialized junctions; the kinetoplast-mitochondrion complex, including its structural organization and DNA replication; glycosome and its role in the metabolism of the cell; acidocalcisome, describing its morphology, biochemistry, and functional role; cytostome and the endocytic pathway; the organization of the endoplasmic reticulum and Golgi complex; the nucleus, describing its structural organization during interphase and division; and the process of interaction of the parasite with host cells. The unique characteristics of these structures also make them interesting chemotherapeutic targets. Therefore, further understanding of cell biology aspects contributes to the development of drugs for chemotherapy.
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Affiliation(s)
- Aline A Zuma
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho - Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emile Dos Santos Barrias
- Laboratorio de Metrologia Aplicada a Ciencias da Vida, Diretoria de Metrologia Aplicada a Ciencias da Vida - Instituto Nacional de Metrologia, Qualidade e Tecnologia (Inmetro), Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho - Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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27
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Reproduction in Trypanosomatids: Past and Present. BIOLOGY 2021; 10:biology10060471. [PMID: 34071741 PMCID: PMC8230138 DOI: 10.3390/biology10060471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023]
Abstract
Simple Summary The reproduction of trypanosomatids is a fundamental issue for host–parasite interaction, and its biological importance lies in knowing how these species acquire new defense mechanisms against the countermeasures imposed by the host, which is consistent with the theory of the endless race or the Red Queen hypothesis for the existence of meiotic sex. Moreover, the way these species re-produce may also be at the origin of novel and more virulent clades and is relevant from a thera-peutic or vaccination point of view, as sex may contribute to increased tolerance and even to the rapid acquisition of drug resistance mechanisms. Kinetoplastids are single-celled organisms, many of them being responsible for important parasitic diseases, globally termed neglected diseases, which are endemic in low-income countries. Leishmaniasis, African (sleeping sickness) and American trypanosomiasis (Chagas disease) caused by trypanosomatids are among the most ne-glected tropical scourges related to poverty and poor health systems. The reproduction of these microorganisms has long been considered to be clonal due to population genetic observations. However, there is increasing evidence of true sex and genetic exchange events under laboratory conditions. We would like to highlight the importance of this topic in the field of host/parasite in-terplay, virulence, and drug resistance. Abstract Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.
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28
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Peacock L, Kay C, Farren C, Bailey M, Carrington M, Gibson W. Sequential production of gametes during meiosis in trypanosomes. Commun Biol 2021; 4:555. [PMID: 33976359 PMCID: PMC8113336 DOI: 10.1038/s42003-021-02058-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023] Open
Abstract
Meiosis is a core feature of eukaryotes that occurs in all major groups, including the early diverging excavates. In this group, meiosis and production of haploid gametes have been described in the pathogenic protist, Trypanosoma brucei, and mating occurs in the salivary glands of the insect vector, the tsetse fly. Here, we searched for intermediate meiotic stages among trypanosomes from tsetse salivary glands. Many different cell types were recovered, including trypanosomes in Meiosis I and gametes. Significantly, we found trypanosomes containing three nuclei with a 1:2:1 ratio of DNA contents. Some of these cells were undergoing cytokinesis, yielding a mononucleate gamete and a binucleate cell with a nuclear DNA content ratio of 1:2. This cell subsequently produced three more gametes in two further rounds of division. Expression of the cell fusion protein HAP2 (GCS1) was not confined to gametes, but also extended to meiotic intermediates. We propose a model whereby the two nuclei resulting from Meiosis I undergo asynchronous Meiosis II divisions with sequential production of haploid gametes.
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Affiliation(s)
- Lori Peacock
- School of Biological Sciences University of Bristol, Bristol, UK
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Chris Kay
- School of Biological Sciences University of Bristol, Bristol, UK
| | - Chloe Farren
- School of Biological Sciences University of Bristol, Bristol, UK
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Wendy Gibson
- School of Biological Sciences University of Bristol, Bristol, UK.
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29
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Lima ACS, Gomes CMC, Tomokane TY, Campos MB, Zampieri RA, Jorge CL, Laurenti MD, Silveira FT, Corbett CEP, Floeter-Winter LM. Molecular tools confirm natural Leishmania (Viannia) guyanensis/L. (V.) shawi hybrids causing cutaneous leishmaniasis in the Amazon region of Brazil. Genet Mol Biol 2021; 44:e20200123. [PMID: 33949621 PMCID: PMC8108439 DOI: 10.1590/1678-4685-gmb-2020-0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 03/03/2021] [Indexed: 11/22/2022] Open
Abstract
Seven isolates from patients with American cutaneous leishmaniasis in the Amazon region of Brazil were phenotypically suggestive of Leishmania (Viannia) guyanensis/L. (V.) shawi hybrids. In this work, two molecular targets were employed to check the hybrid identity of the putative hybrids. Heat shock protein 70 (hsp70) gene sequences were analyzed by three different polymerase chain reaction (PCR) approaches, and two different patterns of inherited hsp70 alleles were found. Three isolates presented heterozygous L. (V.) guyanensis/L. (V.) shawi patterns, and four presented homozygous hsp70 patterns involving only L. (V.) shawi alleles. The amplicon sequences confirmed the RFLP patterns. The high-resolution melting method detected variant heterozygous and homozygous profiles. Single-nucleotide polymorphism genotyping/cleaved amplified polymorphic site analysis suggested a higher contribution from L. (V.) guyanensis in hsp70 heterozygous hybrids. Additionally, PCR-RFLP analysis targeting the enzyme mannose phosphate isomerase (mpi) gene indicated heterozygous and homozygous cleavage patterns for L. (V.) shawi and L. (V.) guyanensis, corroborating the hsp70 findings. In this communication, we present molecular findings based on partial informative regions of the coding sequences of hsp70 and mpi as markers confirming that some of the parasite strains from the Brazilian Amazon region are indeed hybrids between L. (V.) guyanensis and L. (V.) shawi.
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Affiliation(s)
- Ana Carolina S Lima
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil.,Ministério da Saúde, Secretaria de Vigilância em Saúde, Instituto Evandro Chagas, Belém, PA, Brazil
| | - Claudia Maria C Gomes
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil
| | - Thaise Y Tomokane
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil
| | - Marliane Batista Campos
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Instituto Evandro Chagas, Belém, PA, Brazil
| | - Ricardo A Zampieri
- Universidade de São Paulo, Instituto de Biociências, Departamento de Fisiologia, São Paulo, SP, Brazil
| | - Carolina L Jorge
- Universidade de São Paulo, Instituto de Biociências, Departamento de Fisiologia, São Paulo, SP, Brazil
| | - Marcia D Laurenti
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil
| | - Fernando T Silveira
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Instituto Evandro Chagas, Belém, PA, Brazil
| | - Carlos Eduardo P Corbett
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil
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30
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Gibson W. The sexual side of parasitic protists. Mol Biochem Parasitol 2021; 243:111371. [PMID: 33872659 DOI: 10.1016/j.molbiopara.2021.111371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 01/09/2023]
Abstract
Much of the vast evolutionary landscape occupied by Eukaryotes is dominated by protists. Though parasitism has arisen in many lineages, there are three main groups of parasitic protists of relevance to human and livestock health: the Apicomplexa, including the malaria parasite Plasmodium and coccidian pathogens of livestock such as Eimeria; the excavate flagellates, encompassing a diverse range of protist pathogens including trypanosomes, Leishmania, Giardia and Trichomonas; and the Amoebozoa, including pathogenic amoebae such as Entamoeba. These three groups represent separate, deep branches of the eukaryote tree, underlining their divergent evolutionary histories. Here, I explore what is known about sex in these three main groups of parasitic protists.
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Affiliation(s)
- Wendy Gibson
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom.
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31
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da Silva MS. DNA Double-Strand Breaks: A Double-Edged Sword for Trypanosomatids. Front Cell Dev Biol 2021; 9:669041. [PMID: 33937271 PMCID: PMC8085331 DOI: 10.3389/fcell.2021.669041] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/29/2021] [Indexed: 01/09/2023] Open
Abstract
For nearly all eukaryotic cells, stochastic DNA double-strand breaks (DSBs) are one of the most deleterious types of DNA lesions. DSB processing and repair can cause sequence deletions, loss of heterozygosity, and chromosome rearrangements resulting in cell death or carcinogenesis. However, trypanosomatids (single-celled eukaryotes parasites) do not seem to follow this premise strictly. Several studies have shown that trypanosomatids depend on DSBs to perform several events of paramount importance during their life cycle. For Trypanosoma brucei, DSBs formation is associated with host immune evasion via antigenic variation. In Trypanosoma cruzi, DSBs play a crucial role in the genetic exchange, a mechanism that is still little explored but appear to be of fundamental importance for generating variability. In Leishmania spp., DSBs are necessary to generate genomic changes by gene copy number variation (CNVs), events that are essential for these organisms to overcome inhospitable conditions. As DSB repair in trypanosomatids is primarily conducted via homologous recombination (HR), most of the events associated with DSBs are HR-dependent. This review will discuss the latest findings on how trypanosomatids balance the benefits and inexorable challenges caused by DSBs.
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Affiliation(s)
- Marcelo Santos da Silva
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
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32
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Vasconcelos LASD, Oliveira JC, Silva Junior RCAD, Justiniano SCB, Souza ÉDS, Magalhães LKC, Silveira H, Silva GAVD, Guerra JADO, Guerra MDGVB. Trypanosoma cruzi discrete typing unit TcIV implicated in a case of acute Chagas disease in a domiciliated dog in the western Amazon. Rev Soc Bras Med Trop 2021; 54:e0873-2020. [PMID: 33759934 PMCID: PMC8008907 DOI: 10.1590/0037-8682-0873-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/10/2021] [Indexed: 11/21/2022] Open
Abstract
Chagas disease is caused by the protozoan Trypanosoma cruzi. Seven lineages have been identified based on different molecular markers, namely TcI, TcII, TcIII, TcIV, TcV, TcVI, and TcBat. Dogs play the role of epidemiological sentinels being domestic reservoirs of T. cruzi. The aim of the current study was to report the first case of CD in a domestic dog in Manaus, Amazonas, Brazil, infected with T. cruzi DTU TcIV. We hope our report encourages veterinarians and surveillance professionals to a take a deeper look at T. cruzi infection in domestic animals.
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Affiliation(s)
| | - Josué Costa Oliveira
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Centro de Entomologia, Manaus, AM, Brasil
| | | | | | - Éder Dos Santos Souza
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Centro de Entomologia, Manaus, AM, Brasil
| | | | - Henrique Silveira
- Universidade Nova de Lisboa, Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
| | | | | | - Maria das Graças Vale Barbosa Guerra
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Centro de Entomologia, Manaus, AM, Brasil.,Universidade do Estado do Amazonas, Programa de Pós-graduação em Medicina Tropical, Manaus, AM, Brasil
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33
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Talavera-López C, Messenger LA, Lewis MD, Yeo M, Reis-Cunha JL, Matos GM, Bartholomeu DC, Calzada JE, Saldaña A, Ramírez JD, Guhl F, Ocaña-Mayorga S, Costales JA, Gorchakov R, Jones K, Nolan MS, Teixeira SMR, Carrasco HJ, Bottazzi ME, Hotez PJ, Murray KO, Grijalva MJ, Burleigh B, Grisard EC, Miles MA, Andersson B. Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi. Front Cell Infect Microbiol 2021; 11:614665. [PMID: 33747978 PMCID: PMC7966520 DOI: 10.3389/fcimb.2021.614665] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
Trypanosoma cruzi, a zoonotic kinetoplastid protozoan parasite, is the causative agent of American trypanosomiasis (Chagas disease). Having a very plastic, repetitive and complex genome, the parasite displays a highly diverse repertoire of surface molecules, with pivotal roles in cell invasion, immune evasion and pathogenesis. Before 2016, the complexity of the genomic regions containing these genes impaired the assembly of a genome at chromosomal level, making it impossible to study the structure and function of the several thousand repetitive genes encoding the surface molecules of the parasite. We here describe the genome assembly of the Sylvio X10/1 genome sequence, which since 2016 has been used as a reference genome sequence for T. cruzi clade I (TcI), produced using high coverage PacBio single-molecule sequencing. It was used to analyze deep Illumina sequence data from 34 T. cruzi TcI isolates and clones from different geographic locations, sample sources and clinical outcomes. Resolution of the surface molecule gene distribution showed the unusual duality in the organization of the parasite genome, a synteny of the core genomic region with related protozoa flanked by unique and highly plastic multigene family clusters encoding surface antigens. The presence of abundant interspersed retrotransposons in these multigene family clusters suggests that these elements are involved in a recombination mechanism for the generation of antigenic variation and evasion of the host immune response on these TcI strains. The comparative genomic analysis of the cohort of TcI strains revealed multiple cases of such recombination events involving surface molecule genes and has provided new insights into T. cruzi population structure.
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Affiliation(s)
- Carlos Talavera-López
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- European Bioinformatics Institute, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Louisa A. Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael D. Lewis
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - João Luís Reis-Cunha
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Machado Matos
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal Santa Catarina, Florianópolis, Brazil
| | | | - José E. Calzada
- Departamento de Parasitología, Instituto Conmemorativo Gorgas de Estudios de la Salud, Ciudad de Panamá, Panama
| | - Azael Saldaña
- Departamento de Parasitología, Instituto Conmemorativo Gorgas de Estudios de la Salud, Ciudad de Panamá, Panama
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Felipe Guhl
- Grupo de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Tropical Parasitology Research Center, Universidad de Los Andes, Bogotá, Colombia
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Rodion Gorchakov
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Kathryn Jones
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Melissa S. Nolan
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hernán José Carrasco
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | - Maria Elena Bottazzi
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Peter J. Hotez
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Kristy O. Murray
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Department of Pediatrics - Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina (CISeAL), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Infectious and Tropical Disease Institute, Ohio University, Athens, OH, United States
| | - Barbara Burleigh
- Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Edmundo C. Grisard
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal Santa Catarina, Florianópolis, Brazil
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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Martín-Escolano J, Medina-Carmona E, Martín-Escolano R. Chagas Disease: Current View of an Ancient and Global Chemotherapy Challenge. ACS Infect Dis 2020; 6:2830-2843. [PMID: 33034192 DOI: 10.1021/acsinfecdis.0c00353] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chagas disease is a neglected tropical disease and a global public health issue. In terms of treatment, no progress has been made since the 1960s, when benznidazole and nifurtimox, two obsolete drugs still prescribed, were used to treat this disease. Hence, currently, there are no effective treatments available to tackle Chagas disease. Over the past 20 years, there has been an increasing interest in the disease. However, parasite genetic diversity, drug resistance, tropism, and complex life cycle, along with the limited understanding of the disease and inadequate methodologies and strategies, have resulted in the absence of new insights in drugs development and disappointing outcomes in clinical trials so far. In summary, new drugs are urgently needed. This Review considers the relevant aspects related to the lack of drugs for Chagas disease, resumes the advances in tools for drug discovery, and discusses the main features to be taken into account to develop new effective drugs.
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Affiliation(s)
- Javier Martín-Escolano
- Department of Parasitology, Instituto de Investigación Biosanitaria (ibs.Granada), Hospitales Universitarios De Granada/University of Granada, Severo Ochoa s/n, 18071 Granada, Spain
| | | | - Rubén Martín-Escolano
- Department of Parasitology, Instituto de Investigación Biosanitaria (ibs.Granada), Hospitales Universitarios De Granada/University of Granada, Severo Ochoa s/n, 18071 Granada, Spain
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Genomic Organization and Generation of Genetic Variability in the RHS (Retrotransposon Hot Spot) Protein Multigene Family in Trypanosoma cruzi. Genes (Basel) 2020; 11:genes11091085. [PMID: 32957642 PMCID: PMC7563717 DOI: 10.3390/genes11091085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Retrotransposon Hot Spot (RHS) is the most abundant gene family in Trypanosoma cruzi, with unknown function in this parasite. The aim of this work was to shed light on the organization and expression of RHS in T. cruzi. The diversity of the RHS protein family in T. cruzi was demonstrated by phylogenetic and recombination analyses. Transcribed sequences carrying the RHS domain were classified into ten distinct groups of monophyletic origin. We identified numerous recombination events among the RHS and traced the origins of the donors and target sequences. The transcribed RHS genes have a mosaic structure that may contain fragments of different RHS inserted in the target sequence. About 30% of RHS sequences are located in the subtelomere, a region very susceptible to recombination. The evolution of the RHS family has been marked by many events, including gene duplication by unequal mitotic crossing-over, homologous, as well as ectopic recombination, and gene conversion. The expression of RHS was analyzed by immunofluorescence and immunoblotting using anti-RHS antibodies. RHS proteins are evenly distributed in the nuclear region of T. cruzi replicative forms (amastigote and epimastigote), suggesting that they could be involved in the control of the chromatin structure and gene expression, as has been proposed for T. brucei.
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Ramirez JL. Trypanosoma cruzi Genome 15 Years Later: What Has Been Accomplished? Trop Med Infect Dis 2020; 5:E129. [PMID: 32781761 PMCID: PMC7559697 DOI: 10.3390/tropicalmed5030129] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022] Open
Abstract
On 15 July 2020 was the 15th anniversary of the Science Magazine issue that reported three trypanosomatid genomes, namely Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. That publication was a milestone for the research community working with trypanosomatids, even more so, when considering that the first draft of the human genome was published only four years earlier after 15 years of research. Although nowadays, genome sequencing has become commonplace, the work done by researchers before that publication represented a huge challenge and a good example of international cooperation. Research in neglected diseases often faces obstacles, not only because of the unique characteristics of each biological model but also due to the lower funds the research projects receive. In the case of Trypanosoma cruzi the etiologic agent of Chagas disease, the first genome draft published in 2005 was not complete, and even after the implementation of more advanced sequencing strategies, to this date no final chromosomal map is available. However, the first genome draft enabled researchers to pick genes a la carte, produce proteins in vitro for immunological studies, and predict drug targets for the treatment of the disease or to be used in PCR diagnostic protocols. Besides, the analysis of the T. cruzi genome is revealing unique features about its organization and dynamics. In this work, I briefly summarize the actions of Latin American researchers that contributed to the first publication of the T. cruzi genome and discuss some features of the genome that may help to understand the parasite's robustness and adaptive capabilities.
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Affiliation(s)
- Jose Luis Ramirez
- Instituto de Estudios Avanzados, Caracas, Venezuela and Universidad Central de Venezuela, Caracas 1080, Venezuela
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Cruz-Saavedra L, Vallejo GA, Guhl F, Ramírez JD. Transcriptomic changes across the life cycle of Trypanosoma cruzi II. PeerJ 2020; 8:e8947. [PMID: 32461822 PMCID: PMC7231504 DOI: 10.7717/peerj.8947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Trypanosoma cruzi is a flagellated protozoan that causes Chagas disease; it presents a complex life cycle comprising four morphological stages: epimastigote (EP), metacyclic trypomastigote (MT), cell-derived trypomastigote (CDT) and amastigote (AM). Previous transcriptomic studies on three stages (EPs, CDTs and AMs) have demonstrated differences in gene expressions among them; however, to the best of our knowledge, no studies have reported on gene expressions in MTs. Therefore, the present study compared differentially expressed genes (DEGs), and signaling pathway reconstruction in EPs, MTs, AMs and CDTs. The results revealed differences in gene expressions in the stages evaluated; these differences were greater between MTs and AMs-PTs. The signaling pathway that presented the highest number of DEGs in all the stages was associated with ribosomes protein profiles, whereas the other related pathways activated were processes related to energy metabolism from glucose, amino acid metabolism, or RNA regulation. However, the role of autophagy in the entire life cycle of T. cruzi and the presence of processes such as meiosis and homologous recombination in MTs (where the expressions of SPO11 and Rad51 plays a role) are crucial. These findings represent an important step towards the full understanding of the molecular basis during the life cycle of T. cruzi.
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Affiliation(s)
- Lissa Cruz-Saavedra
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Gustavo A Vallejo
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Felipe Guhl
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de Los Andes, Bogota, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
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Jiang H, Li S, Liu W, Zheng H, Liu J, Zhang Y. Geometry-Aware Cell Detection with Deep Learning. mSystems 2020; 5:e00840-19. [PMID: 32019836 PMCID: PMC7002118 DOI: 10.1128/msystems.00840-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
Analyzing cells and tissues under a microscope is a cornerstone of biological research and clinical practice. However, the challenge faced by conventional microscopy image analysis is the fact that cell recognition through a microscope is still time-consuming and lacks both accuracy and consistency. Despite enormous progress in computer-aided microscopy cell detection, especially with recent deep-learning-based techniques, it is still difficult to translate an established method directly to a new cell target without extensive modification. The morphology of a cell is complex and highly varied, but it has long been known that cells show a nonrandom geometrical order in which a distinct and defined shape can be formed in a given type of cell. Thus, we have proposed a geometry-aware deep-learning method, geometric-feature spectrum ExtremeNet (GFS-ExtremeNet), for cell detection. GFS-ExtremeNet is built on the framework of ExtremeNet with a collection of geometric features, resulting in the accurate detection of any given cell target. We obtained promising detection results with microscopic images of publicly available mammalian cell nuclei and newly collected protozoa, whose cell shapes and sizes varied. Even more striking, our method was able to detect unicellular parasites within red blood cells without misdiagnosis of each other.IMPORTANCE Automated diagnostic microscopy powered by deep learning is useful, particularly in rural areas. However, there is no general method for object detection of different cells. In this study, we developed GFS-ExtremeNet, a geometry-aware deep-learning method which is based on the detection of four extreme key points for each object (topmost, bottommost, rightmost, and leftmost) and its center point. A postprocessing step, namely, adjacency spectrum, was employed to measure whether the distances between the key points were below a certain threshold for a particular cell candidate. Our newly proposed geometry-aware deep-learning method outperformed other conventional object detection methods and could be applied to any type of cell with a certain geometrical order. Our GFS-ExtremeNet approach opens a new window for the development of an automated cell detection system.
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Affiliation(s)
- Hao Jiang
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Sen Li
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Weihuang Liu
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Hongjin Zheng
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Jinghao Liu
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Yang Zhang
- College of Science, Harbin Institute of Technology, Shenzhen, China
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Rusman F, Floridia-Yapur N, Ragone PG, Diosque P, Tomasini N. Evidence of hybridization, mitochondrial introgression and biparental inheritance of the kDNA minicircles in Trypanosoma cruzi I. PLoS Negl Trop Dis 2020; 14:e0007770. [PMID: 32004318 PMCID: PMC7015434 DOI: 10.1371/journal.pntd.0007770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 02/12/2020] [Accepted: 01/13/2020] [Indexed: 11/21/2022] Open
Abstract
Background Genetic exchange in Trypanosoma cruzi is controversial not only in relation to its frequency, but also to its mechanism. Parasexual genetic exchange has been proposed based on laboratory hybrids, but population genomics strongly suggests meiosis in T. cruzi. In addition, mitochondrial introgression has been reported several times in natural isolates although its mechanism is not fully understood yet. Moreover, hybrid T. cruzi DTUs (TcV and TcVI) have inherited at least part of the kinetoplastic DNA (kDNA = mitochondrial DNA) from both parents. Methodology/Principal findings In order to address such topics, we sequenced and analyzed fourteen nuclear DNA fragments and three kDNA maxicircle genes in three TcI stocks which are natural clones potentially involved in events of genetic exchange. We also deep-sequenced (a total of 6,146,686 paired-end reads) the minicircle hypervariable region (mHVR) of the kDNA in such three strains. In addition, we analyzed the DNA content by flow cytometry to address cell ploidy. We observed that most polymorphic sites in nuclear loci showed a hybrid pattern in one cloned strain and the other two cloned strains were compatible as parental strains (or nearly related to the true parents). The three clones had almost the same ploidy and the DNA content was similar to the reference strain Sylvio (a nearly diploid strain). Despite maxicircle genes evolve faster than nuclear housekeeping ones, we detected no polymorphisms in the sequence of three maxicircle genes showing mito-nuclear discordance. Lastly, the hybrid stock shared 66% of its mHVR clusters with one putative parent and 47% with the other one; in contrast, the putative parental stocks shared less than 30% of the mHVR clusters between them. Conclusions/significance The results suggest a reductive division, a natural hybridization, biparental inheritance of the minicircles in the hybrid and maxicircle introgression. The models including such phenomena and explaining the relationships between these three clones are discussed. Chagas disease, an important public health problem in Latin America, is caused by the parasite Trypanosoma cruzi. Despite being a widely studied parasite, several questions on the biology of genetic exchange remain unanswered. Population genomic studies have inferred meiosis in T. cruzi, but this cellular division mechanism has not been observed in laboratory yet. In addition, previous results suggest that mitochondrial DNA (called kDNA) may be inherited from both parents in hybrids. Here, we analyzed a hybrid strain and its potential parents to address the mechanisms of genetic exchange at nuclear and mitochondrial levels. We observed that the hybrid strain had heterozygous patterns and DNA content compatible with a meiosis event. Also, we observed that the evolutionary histories of nuclear DNA and kDNA maxicircles were discordant and that the three strains shared identical DNA sequences. Mitochondrial introgression of maxicircle DNA from one genotype to another may explain this observation. In addition, we demonstrated that the hybrid strain shared kDNA minicircles with both parental strains. Our results suggest that hybridization implied meiosis and biparental inheritance of the kDNA. Further research is required to address such phenomena in detail.
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Affiliation(s)
- Fanny Rusman
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Noelia Floridia-Yapur
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Paula G. Ragone
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Patricio Diosque
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Nicolás Tomasini
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
- * E-mail:
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A 'parameiosis' drives depolyploidization and homologous recombination in Candida albicans. Nat Commun 2019; 10:4388. [PMID: 31558727 PMCID: PMC6763455 DOI: 10.1038/s41467-019-12376-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/28/2019] [Indexed: 12/14/2022] Open
Abstract
Meiosis is a conserved tenet of sexual reproduction in eukaryotes, yet this program is seemingly absent from many extant species. In the human fungal pathogen Candida albicans, mating of diploid cells generates tetraploid products that return to the diploid state via a non-meiotic process of depolyploidization known as concerted chromosome loss (CCL). Here, we report that recombination rates are more than three orders of magnitude higher during CCL than during normal mitotic growth. Furthermore, two conserved ‘meiosis-specific’ factors play central roles in CCL as SPO11 mediates DNA double-strand break formation while both SPO11 and REC8 regulate chromosome stability and promote inter-homolog recombination. Unexpectedly, SPO11 also promotes DNA repair and recombination during normal mitotic divisions. These results indicate that C. albicans CCL represents a ‘parameiosis’ that blurs the conventional boundaries between mitosis and meiosis. They also reveal parallels with depolyploidization in mammalian cells and provide potential insights into the evolution of meiosis. Mating of Candida albicans produces tetraploid products that return to the diploid state via a non-meiotic process known as concerted chromosome loss (CCL). Here, Anderson et al. show high recombination rates during CCL and identify factors that are essential for chromosome stability and recombination during CCL.
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Schwabl P, Imamura H, Van den Broeck F, Costales JA, Maiguashca-Sánchez J, Miles MA, Andersson B, Grijalva MJ, Llewellyn MS. Meiotic sex in Chagas disease parasite Trypanosoma cruzi. Nat Commun 2019; 10:3972. [PMID: 31481692 PMCID: PMC6722143 DOI: 10.1038/s41467-019-11771-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 07/27/2019] [Indexed: 12/11/2022] Open
Abstract
Genetic exchange enables parasites to rapidly transform disease phenotypes and exploit new host populations. Trypanosoma cruzi, the parasitic agent of Chagas disease and a public health concern throughout Latin America, has for decades been presumed to exchange genetic material rarely and without classic meiotic sex. We present compelling evidence from 45 genomes sequenced from southern Ecuador that T. cruzi in fact maintains truly sexual, panmictic groups that can occur alongside others that remain highly clonal after past hybridization events. These groups with divergent reproductive strategies appear genetically isolated despite possible co-occurrence in vectors and hosts. We propose biological explanations for the fine-scale disconnectivity we observe and discuss the epidemiological consequences of flexible reproductive modes. Our study reinvigorates the hunt for the site of genetic exchange in the T. cruzi life cycle, provides tools to define the genetic determinants of parasite virulence, and reforms longstanding theory on clonality in trypanosomatid parasites.
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Affiliation(s)
- Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Hideo Imamura
- Unit of Molecular Parasitology, Institute of Tropical Medicine Antwerp, 155 Nationalestraat, 2000, Antwerp, Belgium
| | - Frederik Van den Broeck
- Unit of Molecular Parasitology, Institute of Tropical Medicine Antwerp, 155 Nationalestraat, 2000, Antwerp, Belgium
| | - Jaime A Costales
- Center for Research on Health in Latin America, School of Biological Sciences, Pontifical Catholic University of Ecuador, Quito, Ecuador
| | - Jalil Maiguashca-Sánchez
- Center for Research on Health in Latin America, School of Biological Sciences, Pontifical Catholic University of Ecuador, Quito, Ecuador
| | - Michael A Miles
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Bjorn Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Biomedicum 9C, 171 77, Stockholm, Sweden
| | - Mario J Grijalva
- Center for Research on Health in Latin America, School of Biological Sciences, Pontifical Catholic University of Ecuador, Quito, Ecuador
- Infectious and Tropical Disease Institute, Biomedical Sciences Department, Heritage College of Osteopathic Medicine, Ohio University, 45701, Athens, OH, USA
| | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
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Kemmerling U, Osuna A, Schijman AG, Truyens C. Congenital Transmission of Trypanosoma cruzi: A Review About the Interactions Between the Parasite, the Placenta, the Maternal and the Fetal/Neonatal Immune Responses. Front Microbiol 2019; 10:1854. [PMID: 31474955 PMCID: PMC6702454 DOI: 10.3389/fmicb.2019.01854] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Chagas disease (CD), caused by the protozoan parasite Trypanosoma cruzi, is considered a neglected tropical disease by the World Health Organization. Congenital transmission of CD is an increasingly relevant public health problem. It progressively becomes the main transmission route over others and can occur in both endemic and non-endemic countries. Though most congenitally infected newborns are asymptomatic at birth, they display higher frequencies of prematurity, low birth weight, and lower Apgar scores compared to uninfected ones, and some suffer from severe symptoms. If not diagnosed and treated, infected newborns are at risk of developing disabling and life-threatening chronic pathologies later in life. The success or failure of congenital transmission depends on interactions between the parasite, the placenta, the mother, and the fetus. We review and discuss here the current knowledge about these parameters, including parasite virulence factors such as exovesicles, placental tropism, potential placental defense mechanisms, the placental transcriptome of infected women, gene polymorphism, and the maternal and fetal/neonatal immune responses, that might modulate the risk of T. cruzi congenital transmission.
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Affiliation(s)
- Ulrike Kemmerling
- Programa de Anatomía y Biología del Desarrollo, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Antonio Osuna
- Grupo de Bioquímica y Parasitología Molecular, Departamento de Parasitología, Instituto de Biotecnología, Universidad de Granada, Granada, Spain
| | - Alejandro Gabriel Schijman
- Molecular Biology of Chagas Disease Laboratory, Genetic Engineering and Molecular Biology Research Institute Dr. Héctor Torres (INGEBI-CONICET), Buenos Aires, Argentina
| | - Carine Truyens
- Laboratory of Parasitology, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
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Santana RAG, Guerra MGVB, Sousa DR, Couceiro K, Ortiz JV, Oliveira M, Ferreira LS, Souza KR, Tavares IC, Morais RF, Silva GAV, Melo GC, Vergel GM, Albuquerque BC, Arcanjo ARL, Monteiro WM, Ferreira JMBB, Lacerda MVG, Silveira H, Guerra JAO. Oral Transmission of Trypanosoma cruzi, Brazilian Amazon. Emerg Infect Dis 2019; 25:132-135. [PMID: 30561299 PMCID: PMC6302584 DOI: 10.3201/eid2501.180646] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the Brazilian Amazon, the suspected source of infection in an outbreak of acute Chagas disease involving 10 patients was Euterpe oleracea (açaí berry) juice. Patient blood and juice samples contained Trypanosoma cruzi TcIV, indicating oral transmission of the Chagas disease agent.
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Elucidating diversity in the class composition of the minicircle hypervariable region of Trypanosoma cruzi: New perspectives on typing and kDNA inheritance. PLoS Negl Trop Dis 2019; 13:e0007536. [PMID: 31247047 PMCID: PMC6619836 DOI: 10.1371/journal.pntd.0007536] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/10/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022] Open
Abstract
Background Trypanosoma cruzi, the protozoan causative of Chagas disease, is classified into six main Discrete Typing Units (DTUs): TcI-TcVI. This parasite has around 105 copies of the minicircle hypervariable region (mHVR) in their kinetoplastic DNA (kDNA). The genetic diversity of the mHVR is virtually unknown. However, cross-hybridization assays using mHVRs showed hybridization only between isolates belonging to the same genetic group. Nowadays there is no methodologic approach with a good sensibility, specificity and reproducibility for direct typing on biological samples. Due to its high copy number and apparently high diversity, mHVR becomes a good target for typing. Methodology/Principal findings Around 22 million reads, obtained by amplicon sequencing of the mHVR, were analyzed for nine strains belonging to six T. cruzi DTUs. The number and diversity of mHVR clusters was variable among DTUs and even within a DTU. However, strains of the same DTU shared more mHVR clusters than strains of different DTUs and clustered together. In addition, hybrid DTUs (TcV and TcVI) shared similar percentages (1.9–3.4%) of mHVR clusters with their parentals (TcII and TcIII). Conversely, just 0.2% of clusters were shared between TcII and TcIII suggesting biparental inheritance of the kDNA in hybrids. Sequencing at low depth (20,000–40,000 reads) also revealed 95% of the mHVR clusters for each of the analyzed strains. Finally, the method revealed good correlation in cluster identity and abundance between different replications of the experiment (r = 0.999). Conclusions/Significance Our work sheds light on the sequence diversity of mHVRs at intra and inter-DTU level. The mHVR amplicon sequencing workflow described here is a reproducible technique, that allows multiplexed analysis of hundreds of strains and results promissory for direct typing on biological samples in a future. In addition, such approach may help to gain knowledge on the mechanisms of the minicircle evolution and phylogenetic relationships among strains. Chagas disease is an important public health problem in Latin America showing a wide diversity of clinical manifestations and epidemiological patterns. It is caused by the parasite Trypanosoma cruzi. This parasite is genetically diverse and classified into six main lineages. However, the relationship between intra-specific genetic diversity and clinical or epidemiological features is not clear, mainly because low sensitivity for direct typing on biological samples. For this reason, genetic markers with high copy number are required to achieve sensitivity. Here, we deep sequenced and analyzed a DNA region present in the large mitochondria of the parasite (named as mHVR, 105 copies per parasite) from strains belonging to the six main lineages in order to analyze mHVR diversity and to evaluate its usefulness for typing. Despite the high sequence diversity, strains of the same lineage shared more sequences than strains of different lineages. Curiously, hybrid lineages shared mHVR sequences with both parents suggesting that mHVR (and DNA minicircles from the mitochondria) are inherited from both parentals. The mHVR amplicon sequencing workflow proposed here is reproducible and, potentially, it would be useful for typing hundreds of biological samples at time. It also provides a valuable approach to perform evolutionary and functional studies.
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Berry ASF, Salazar-Sánchez R, Castillo-Neyra R, Borrini-Mayorí K, Chipana-Ramos C, Vargas-Maquera M, Ancca-Juarez J, Náquira-Velarde C, Levy MZ, Brisson D. Sexual reproduction in a natural Trypanosoma cruzi population. PLoS Negl Trop Dis 2019; 13:e0007392. [PMID: 31107905 PMCID: PMC6544315 DOI: 10.1371/journal.pntd.0007392] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/31/2019] [Accepted: 04/15/2019] [Indexed: 12/21/2022] Open
Abstract
Background Sexual reproduction provides an evolutionary advantageous mechanism that combines favorable mutations that have arisen in separate lineages into the same individual. This advantage is especially pronounced in microparasites as allelic reassortment among individuals caused by sexual reproduction promotes allelic diversity at immune evasion genes within individuals which is often essential to evade host immune systems. Despite these advantages, many eukaryotic microparasites exhibit highly-clonal population structures suggesting that genetic exchange through sexual reproduction is rare. Evidence supporting clonality is particularly convincing in the causative agent of Chagas disease, Trypanosoma cruzi, despite equally convincing evidence of the capacity to engage in sexual reproduction. Methodology/ Principle Findings In the present study, we investigated two hypotheses that can reconcile the apparent contradiction between the observed clonal population structure and the capacity to engage in sexual reproduction by analyzing the genome sequences of 123 T. cruzi isolates from a natural population in Arequipa, Peru. The distribution of polymorphic markers within and among isolates provides clear evidence of the occurrence of sexual reproduction. Large genetic segments are rearranged among chromosomes due to crossing over during meiosis leading to a decay in the genetic linkage among polymorphic markers compared to the expectations from a purely asexually-reproducing population. Nevertheless, the population structure appears clonal due to a high level of inbreeding during sexual reproduction which increases homozygosity, and thus reduces diversity, within each inbreeding lineage. Conclusions/ Significance These results effectively reconcile the apparent contradiction by demonstrating that the clonal population structure is derived not from infrequent sex in natural populations but from high levels of inbreeding. We discuss epidemiological consequences of this reproductive strategy on genome evolution, population structure, and phenotypic diversity of this medically important parasite. The rearrangement of alleles among individuals in a population during sexual reproduction maintains high allelic diversity within individuals in a population at polymorphic genes. Allelic diversity within individuals can be particularly important for parasites as it enhances their ability to evade host immune systems. Despite the potential benefits of sexual reproduction for parasites, natural populations of the protozoan parasite—and causative agent of human Chagas disease—Trypanosoma cruzi, exhibit clonal population structures indicative of asexual reproduction. This is particularly surprising as T. cruzi has the capacity for sexual reproduction. Here, we resolve this apparent contradiction by sequencing whole genomes of 123 T. cruzi isolates from a natural population in Arequipa, Peru. Evidence of past sexual reproduction and allelic rearrangements are common in this T. cruzi population. However, the majority of sexual reproduction events occur between close relatives resulting in an apparent clonal population structure. Sexual reproduction with distant relatives in areas with greater strain diversity has the potential to affect public health by increasing diversity in immune evasion genes within individuals and enhancing within-host survival, rapidly diversifying antigens that could affect the sensitivity of serological diagnostics, and by generating diversity in pathogenicity or drug resistance.
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Affiliation(s)
- Alexander S. F. Berry
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Renzo Salazar-Sánchez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Ricardo Castillo-Neyra
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katty Borrini-Mayorí
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Claudia Chipana-Ramos
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Melina Vargas-Maquera
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Jenny Ancca-Juarez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - César Náquira-Velarde
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Michael Z. Levy
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Inbar E, Shaik J, Iantorno SA, Romano A, Nzelu CO, Owens K, Sanders MJ, Dobson D, Cotton JA, Grigg ME, Beverley SM, Sacks D. Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania. PLoS Genet 2019; 15:e1008042. [PMID: 31091230 PMCID: PMC6519804 DOI: 10.1371/journal.pgen.1008042] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/21/2019] [Indexed: 11/29/2022] Open
Abstract
Hybrid genotypes have been repeatedly described among natural isolates of Leishmania, and the recovery of experimental hybrids from sand flies co-infected with different strains or species of Leishmania has formally demonstrated that members of the genus possess the machinery for genetic exchange. As neither gamete stages nor cell fusion events have been directly observed during parasite development in the vector, we have relied on a classical genetic analysis to determine if Leishmania has a true sexual cycle. Here, we used whole genome sequencing to follow the chromosomal inheritance patterns of experimental hybrids generated within and between different strains of L. major and L. infantum. We also generated and sequenced the first experimental hybrids in L. tropica. We found that in each case the parental somy and allele contributions matched the inheritance patterns expected under meiosis 97–99% of the time. The hybrids were equivalent to F1 progeny, heterozygous throughout most of the genome for the markers that were homozygous and different between the parents. Rare, non-Mendelian patterns of chromosomal inheritance were observed, including a gain or loss of somy, and loss of heterozygosity, that likely arose during meiosis or during mitotic divisions of the progeny clones in the fly or culture. While the interspecies hybrids appeared to be sterile, the intraspecies hybrids were able to produce backcross and outcross progeny. Analysis of 5 backcross and outcross progeny clones generated from an L. major F1 hybrid, as well as 17 progeny clones generated from backcrosses involving a natural hybrid of L. tropica, revealed genome wide patterns of recombination, demonstrating that classical crossing over occurs at meiosis, and allowed us to construct the first physical and genetic maps in Leishmania. Altogether, the findings provide strong evidence for meiosis-like sexual recombination in Leishmania, presenting clear opportunities for forward genetic analysis and positional cloning of important genes. Leishmania promastigotes are able to undergo genetic exchange during their growth and development in the sand fly vector, however, it is still not known if they have a true sexual cycle involving meiosis. Here, we used whole genome sequencing to follow the chromosomal inheritance patterns of 44 experimental hybrids generated between different strains of L. major, L. infantum, and L. tropica. In almost every case the number of chromosomes and the allele contributions from each parent matched the inheritance patterns expected under meiosis. Rare instances of hybrid chromosomes that did not fit Mendelian expectations were observed, including gain or loss of somy, and loss of heterozygosity. Strong evidence for a meiotic-like process was also obtained from the genome wide patterns of recombination observed in the offspring generated from backcrosses involving an experimental or natural hybrid, consistent with crossing over occurring between homologous chromosomes during meiosis. The frequency and position of the recombination breakpoints observed on each chromosome allowed us to construct the first physical and genetic maps in Leishmania. The results demonstrate that forward genetic approaches are possible for positional cloning of important genes.
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Affiliation(s)
- Ehud Inbar
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jahangheer Shaik
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, Missouri, United States of America
| | - Stefano A. Iantorno
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Audrey Romano
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chukwunonso O. Nzelu
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Katherine Owens
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, Missouri, United States of America
| | - Mandy J. Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Deborah Dobson
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, Missouri, United States of America
| | - James A. Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Michael E. Grigg
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen M. Beverley
- Department of Molecular Microbiology, Washington University School of Medicine in St Louis, St Louis, Missouri, United States of America
| | - David Sacks
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: ,
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Caballero E Z, Correa R, Nascimento MS, Villarreal A, Llanes A, Kesper N. High sensitivity and reproducibility of in-house ELISAs using different genotypes of Trypanosoma cruzi. Parasite Immunol 2019; 41:e12627. [PMID: 30908676 DOI: 10.1111/pim.12627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 02/08/2019] [Accepted: 03/20/2019] [Indexed: 02/01/2023]
Abstract
The adequate choice of Trypanosoma cruzi strains as antigen source for the diagnosis of Chagas disease is still controversial due to differences in terms of accuracy reported between different diagnostic tests. In this study was determined if the genetic variability between different genotypes of T. cruzi (TcI, TcII and TcIV) affect the final diagnosis of Chagas disease. The sensitivity and specificity index of in-house ELISA tests prepared with different T. cruzi strains were evaluated with chagasic and non-chagasic control sera and using the TESA-blot as a reference test. The results of this study revealed that the sensitivity index did not vary, with percentages of 100% for all strains in both tests. However, the specificity index for ELISA tests showed differences between 92% and 98%, but were reduced to 78%-89% when Leishmania-positive sera were included. All ELISAs and TESA-blot prepared with different antigens and the recombinant Wiener test were challenged in an endemic community for Chagas disease in Panama. Both ELISAs and TESA-blot recognized the same positive sera, corroborating the sensitivity indexes (100%) found with the control sera. The TESA-blot maintained the specificity index of 100% and did not display false positives. However, the recombinant Wiener test decreased its sensitivity to 81.25%.
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Affiliation(s)
- Zuleima Caballero E
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Asociación de Interés Público (INDICASAT-AIP), Panamá, República of Panamá.,Sistema Nacional de Investigación - Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panamá, República de Panamá
| | - Ricardo Correa
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Asociación de Interés Público (INDICASAT-AIP), Panamá, República of Panamá.,Sistema Nacional de Investigación - Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panamá, República de Panamá
| | - Marilda S Nascimento
- Instituto de Medicina Tropical da Universidade de São Paulo (IMT-USP), São Paulo, Brasil
| | - Alcibiades Villarreal
- Sistema Nacional de Investigación - Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panamá, República de Panamá
| | - Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Asociación de Interés Público (INDICASAT-AIP), Panamá, República of Panamá
| | - Norival Kesper
- Instituto de Medicina Tropical da Universidade de São Paulo (IMT-USP), São Paulo, Brasil
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Espinosa A, Paz-Y-Miño-C G. Discrimination Experiments in Entamoeba and Evidence from Other Protists Suggest Pathogenic Amebas Cooperate with Kin to Colonize Hosts and Deter Rivals. J Eukaryot Microbiol 2019; 66:354-368. [PMID: 30055104 PMCID: PMC6349510 DOI: 10.1111/jeu.12673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/27/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023]
Abstract
Entamoeba histolytica is one of the least understood protists in terms of taxa, clone, and kin discrimination/recognition ability. However, the capacity to tell apart same or self (clone/kin) from different or nonself (nonclone/nonkin) has long been demonstrated in pathogenic eukaryotes like Trypanosoma and Plasmodium, free-living social amebas (Dictyostelium, Polysphondylium), budding yeast (Saccharomyces), and in numerous bacteria and archaea (prokaryotes). Kin discrimination/recognition is explained under inclusive fitness theory; that is, the reproductive advantage that genetically closely related organisms (kin) can gain by cooperating preferably with one another (rather than with distantly related or unrelated individuals), minimizing antagonism and competition with kin, and excluding genetic strangers (or cheaters = noncooperators that benefit from others' investments in altruistic cooperation). In this review, we rely on the outcomes of in vitro pairwise discrimination/recognition encounters between seven Entamoeba lineages to discuss the biological significance of taxa, clone, and kin discrimination/recognition in a range of generalist and specialist species (close or distantly related phylogenetically). We then focus our discussion on the importance of these laboratory observations for E. histolytica's life cycle, host infestation, and implications of these features of the amebas' natural history for human health (including mitigation of amebiasis).
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Affiliation(s)
- Avelina Espinosa
- Department of Biology, Roger Williams University, Bristol, Rhode Island
- New England Center for the Public Understanding of Science, Roger Williams University, Bristol, Rhode Island
| | - Guillermo Paz-Y-Miño-C
- New England Center for the Public Understanding of Science, Roger Williams University, Bristol, Rhode Island
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Berry ASF, Salazar-Sánchez R, Castillo-Neyra R, Borrini-Mayorí K, Chipana-Ramos C, Vargas-Maquera M, Ancca-Juarez J, Náquira-Velarde C, Levy MZ, Brisson D. Immigration and establishment of Trypanosoma cruzi in Arequipa, Peru. PLoS One 2019; 14:e0221678. [PMID: 31454370 PMCID: PMC6711515 DOI: 10.1371/journal.pone.0221678] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 08/13/2019] [Indexed: 01/21/2023] Open
Abstract
Changing environmental conditions, including those caused by human activities, reshape biological communities through both loss of native species and establishment of non-native species in the altered habitats. Dynamic interactions with the abiotic environment impact both immigration and initial establishment of non-native species into these altered habitats. The repeated emergence of disease systems in urban areas worldwide highlights the importance of understanding how dynamic migratory processes affect the current and future distribution and abundance of pathogens in urban environments. In this study, we examine the pattern of invasion of Trypanosoma cruzi-the causative agent of human Chagas disease-in the city of Arequipa, Peru. Phylogenetic analyses of 136 T. cruzi isolates from Arequipa and other South American locations suggest that only one T. cruzi lineage established a population in Arequipa as all T. cruzi isolated from vectors in Arequipa form a recent monophyletic group within the broader South American phylogeny. We discuss several hypotheses that may explain the limited number of established T. cruzi lineages despite multiple introductions of the parasite.
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Affiliation(s)
- Alexander S. F. Berry
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Renzo Salazar-Sánchez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Zoonotic Disease Research Laboratory, Arequipa, Peru
| | - Ricardo Castillo-Neyra
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Zoonotic Disease Research Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States of America
| | - Katty Borrini-Mayorí
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Zoonotic Disease Research Laboratory, Arequipa, Peru
| | - Claudia Chipana-Ramos
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Zoonotic Disease Research Laboratory, Arequipa, Peru
| | - Melina Vargas-Maquera
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Zoonotic Disease Research Laboratory, Arequipa, Peru
| | - Jenny Ancca-Juarez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Zoonotic Disease Research Laboratory, Arequipa, Peru
| | - César Náquira-Velarde
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Zoonotic Disease Research Laboratory, Arequipa, Peru
| | - Michael Z. Levy
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Zoonotic Disease Research Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States of America
- * E-mail:
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da Silva MS, Marin PA, Repolês BM, Elias MC, Machado CR. Analysis of DNA Exchange Using Thymidine Analogs (ADExTA) in Trypanosoma cruzi. Bio Protoc 2018; 8:e3125. [PMID: 34532563 PMCID: PMC8342059 DOI: 10.21769/bioprotoc.3125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 10/20/2018] [Indexed: 11/02/2022] Open
Abstract
Trypanosoma cruzi is a protozoan parasite belonging to the Trypanosomatidae family. Although the trypanosomatids multiply predominantly by clonal generation, the presence of DNA exchange in some of them has been puzzling researchers over the years, mainly because it may represent a novel form that these organisms use to gain variability. Analysis of DNA Exchange using Thymidine Analogs (ADExTA) is a method that allows the in vitro detection and measurement of rates of DNA exchange, particularly in trypanosomatid cells, in a rapid and simple manner by indirect immunofluorescence assay (IFA). The method can be used to detect DNA exchange within one trypanosomatid lineage or among different lineages by paired analysis. The principle of this assay is based on the incorporation of two distinguishable halogenated thymidine analogs called 5'-chloro-2'-deoxyuridine (CldU) and 5'-iodo-2'-deoxyuridine (IdU) during DNA replication. After mixing the two cell cultures that had been previously incorporated with CldU and IdU separately, the presence of these unusual deoxynucleosides in the genome can be detected by specific antibodies. For this, a DNA denaturation step is required to expose the sites of thymidine analogs incorporated. Subsequently, a secondary reaction using fluorochrome-labeled antibodies will generate distinct signals under fluorescence analysis. By using this method, DNA exchange verification (i.e., the presence of both CldU and IdU in the same cell) is possible using a standard fluorescence microscope. It typically takes 2-3 days from the thymidine analogs incorporation to results. Of note, ADExTA is relatively cheap and does not require transfections or harsh genetic manipulation. These features represent an advantage when compared to other time-consuming protocols that demand DNA manipulation to introduce distinct drug-resistance markers in different cells for posterior selection.
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Affiliation(s)
- Marcelo S. da Silva
- Laboratório Especial de Ciclo Celular (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Paula A. Marin
- Laboratório Especial de Ciclo Celular (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Bruno M. Repolês
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria C. Elias
- Laboratório Especial de Ciclo Celular (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Carlos R. Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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