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Korenková V, Weisz F, Perglerová A, Cacciò SM, Nohýnková E, Tůmová P. Comprehensive analysis of flavohemoprotein copy number variation in Giardia intestinalis: exploring links to metronidazole resistance. Parasit Vectors 2024; 17:336. [PMID: 39127700 DOI: 10.1186/s13071-024-06392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/03/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Giardiasis, caused by the protozoan parasite Giardia intestinalis, often presents a treatment challenge, particularly in terms of resistance to metronidazole. Despite extensive research, markers for metronidazole resistance have not yet been identified. METHODS This study analysed 28 clinical samples of G. intestinalis from sub-assemblage AII, characterised by varying responses to metronidazole treatment. We focussed on copy number variation (CNV) of the multi-copy flavohemoprotein gene, analysed using digital polymerase chain reaction (dPCR) and next generation sequencing (NGS). Additionally, chromosomal ploidy was tested in 18 of these samples. Flavohemoprotein CNV was also assessed in 17 samples from other sub-assemblages. RESULTS Analyses revealed variable CNVs of the flavohemoprotein gene among the isolates, with no correlation to clinical metronidazole resistance. Discrepancies in CNVs detected from NGS data were attributed to biases linked to the whole genome amplification. However, dPCR helped to clarify these discrepancies by providing more consistent CNV data. Significant differences in flavohemoprotein CNVs were observed across different G. intestinalis sub-assemblages. Notably, Giardia exhibits a propensity for aneuploidy, contributing to genomic variability within and between sub-assemblages. CONCLUSIONS The complexity of the clinical metronidazole resistance in Giardia is influenced by multiple genetic factors, including CNVs and aneuploidy. No significant differences in the CNV of the flavohemoprotein gene between isolates from metronidazole-resistant and metronidazole-sensitive cases of giardiasis were found, underscoring the need for further research to identify reliable genetic markers for resistance. We demonstrate that dPCR and NGS are robust methods for analysing CNVs and provide cross-validating results, highlighting their utility in the genetic analyses of this parasite.
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Affiliation(s)
- Vlasta Korenková
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Filip Weisz
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Aneta Perglerová
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore Di Sanita, Rome, Italy
| | - Eva Nohýnková
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavla Tůmová
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
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2
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de Paula Baptista R, Tucker MS, Valente MJ, Srivastava SK, Chehab N, Li A, Shaik JS, Ramirez JD, Rosenthal BM, Khan A. Comparative genomics of Giardia duodenalis sub-assemblage AI beaver (Be-2) and human (WB-C6) strains show remarkable homozygosity, sequence similarity, and conservation of VSP genes. Sci Rep 2024; 14:13582. [PMID: 38866814 PMCID: PMC11169602 DOI: 10.1038/s41598-024-63783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Giardia duodenalis, a major cause of waterborne infection, infects a wide range of mammalian hosts and is subdivided into eight genetically well-defined assemblages named A through H. However, fragmented genomes and a lack of comparative analysis within and between the assemblages render unclear the molecular mechanisms controlling host specificity and differential disease outcomes. To address this, we generated a near-complete de novo genome of AI assemblage using the Oxford Nanopore platform by sequencing the Be-2 genome. We generated 148,144 long-reads with quality scores of > 7. The final genome assembly consists of only nine contigs with an N50 of 3,045,186 bp. This assembly agrees closely with the assembly of another strain in the AI assemblage (WB-C6). However, a critical difference is that a region previously placed in the five-prime region of Chr5 belongs to Chr4 of Be-2. We find a high degree of conservation in the ploidy, homozygosity, and the presence of cysteine-rich variant-specific surface proteins (VSPs) within the AI assemblage. Our assembly provides a nearly complete genome of a member of the AI assemblage of G. duodenalis, aiding population genomic studies capable of elucidating Giardia transmission, host range, and pathogenicity.
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Affiliation(s)
- Rodrigo de Paula Baptista
- Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Medicine, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Matthew S Tucker
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Matthew J Valente
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Subodh K Srivastava
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Nadya Chehab
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Alison Li
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Jahangheer S Shaik
- Insights and Analytics, Applied Data Science and Learning, Data Science Institute, Takeda, Cambridge, MA, 02142, USA
| | - Juan David Ramirez
- 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
| | - Benjamin M Rosenthal
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Asis Khan
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA.
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Hagen KD, Hart CJS, McInally SG, Dawson SC. Harnessing the power of new genetic tools to illuminate Giardia biology and pathogenesis. Genetics 2024; 227:iyae038. [PMID: 38626297 PMCID: PMC11151923 DOI: 10.1093/genetics/iyae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 04/18/2024] Open
Abstract
Giardia is a prevalent single-celled microaerophilic intestinal parasite causing diarrheal disease and significantly impacting global health. Double diploid (essentially tetraploid) Giardia trophozoites have presented a formidable challenge to the development of molecular genetic tools to interrogate gene function. High sequence divergence and the high percentage of hypothetical proteins lacking homology to proteins in other eukaryotes have limited our understanding of Giardia protein function, slowing drug target validation and development. For more than 25 years, Giardia A and B assemblages have been readily amenable to transfection with plasmids or linear DNA templates. Here, we highlight the utility and power of genetic approaches developed to assess protein function in Giardia, with particular emphasis on the more recent clustered regularly interspaced palindromic repeats/Cas9-based methods for knockdowns and knockouts. Robust and reliable molecular genetic approaches are fundamental toward the interrogation of Giardia protein function and evaluation of druggable targets. New genetic approaches tailored for the double diploid Giardia are imperative for understanding Giardia's unique biology and pathogenesis.
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Affiliation(s)
- Kari D Hagen
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
| | - Christopher J S Hart
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
| | - Shane G McInally
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Scott C Dawson
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
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4
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Lagunas-Rangel FA. Giardia telomeres and telomerase. Parasitol Res 2024; 123:179. [PMID: 38584235 PMCID: PMC10999387 DOI: 10.1007/s00436-024-08200-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Giardia duodenalis, the protozoan responsible for giardiasis, is a significant contributor to millions of diarrheal diseases worldwide. Despite the availability of treatments for this parasitic infection, therapeutic failures are alarmingly frequent. Thus, there is a clear need to identify new therapeutic targets. Giardia telomeres were previously identified, but our understanding of these structures and the critical role played by Giardia telomerase in maintaining genomic stability and its influence on cellular processes remains limited. In this regard, it is known that all Giardia chromosomes are capped by small telomeres, organized and protected by specific proteins that regulate their functions. To counteract natural telomere shortening and maintain high proliferation, Giardia exhibits constant telomerase activity and employs additional mechanisms, such as the formation of G-quadruplex structures and the involvement of transposable elements linked to telomeric repeats. Thus, this study aims to address the existing knowledge gap by compiling the available information (until 2023) about Giardia telomeres and telomerase, focusing on highlighting the distinctive features within this parasite. Furthermore, the potential feasibility of targeting Giardia telomeres and/or telomerase as an innovative therapeutic strategy is discussed.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Surgical Sciences, Uppsala University, Husargatan 3, BMC Box 593, 751 24, Uppsala, Sweden.
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360, Mexico City, Mexico.
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5
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Negreira GH, de Groote R, Van Giel D, Monsieurs P, Maes I, de Muylder G, Van den Broeck F, Dujardin J, Domagalska MA. The adaptive roles of aneuploidy and polyclonality in Leishmania in response to environmental stress. EMBO Rep 2023; 24:e57413. [PMID: 37470283 PMCID: PMC10481652 DOI: 10.15252/embr.202357413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/21/2023] Open
Abstract
Aneuploidy is generally considered harmful, but in some microorganisms, it can act as an adaptive mechanism against environmental stress. Here, we use Leishmania-a protozoan parasite with remarkable genome plasticity-to study the early steps of aneuploidy evolution under high drug pressure (using antimony or miltefosine as stressors). By combining single-cell genomics, lineage tracing with cellular barcodes, and longitudinal genome characterization, we reveal that aneuploidy changes under antimony pressure result from polyclonal selection of pre-existing karyotypes, complemented by further and rapid de novo alterations in chromosome copy number along evolution. In the case of miltefosine, early parasite adaptation is associated with independent point mutations in a miltefosine transporter gene, while aneuploidy changes only emerge later, upon exposure to increased drug levels. Therefore, polyclonality and genome plasticity are hallmarks of parasite adaptation, but the scenario of aneuploidy dynamics depends on the nature and strength of the environmental stress as well as on the existence of other pre-adaptive mechanisms.
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Affiliation(s)
- Gabriel H Negreira
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Robin de Groote
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Dorien Van Giel
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Pieter Monsieurs
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Ilse Maes
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | | | - Frederik Van den Broeck
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical ResearchKatholieke Universiteit LeuvenLeuvenBelgium
| | - Jean‐Claude Dujardin
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
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6
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Lagunas-Rangel FA. The nucleolus of Giardia and its ribosomal biogenesis. Parasitol Res 2023; 122:1961-1971. [PMID: 37400534 DOI: 10.1007/s00436-023-07915-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Giardia duodenalis is a protozoan intestinal parasite that causes a significant number of infections worldwide each year, particularly in low-income and developing countries. Despite the availability of treatments for this parasitic infection, treatment failures are alarmingly common. As a result, new therapeutic strategies are urgently needed to effectively combat this disease. On the other hand, within the eukaryotic nucleus, the nucleolus stands out as the most prominent structure. It plays a crucial role in coordinating ribosome biogenesis and is involved in vital processes such as maintaining genome stability, regulating cell cycle progression, controlling cell senescence, and responding to stress. Given its significance, the nucleolus presents itself as a valuable target for selectively inducing cell death in undesirable cells, making it a potential avenue for anti-Giardia treatments. Despite its potential importance, the Giardia nucleolus remains poorly studied and often overlooked. In light of this, the objective of this study is to provide a detailed molecular description of the structure and function of the Giardia nucleolus, with a primary focus on its involvement in ribosomal biogenesis. Likewise, it discusses the targeting of the Giardia nucleolus as a therapeutic strategy, its feasibility, and the challenges involved.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360, Mexico City, Mexico.
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7
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Subspecific Nomenclature of Giardia duodenalis in the Light of a Compared Population Genomics of Pathogens. Pathogens 2023; 12:pathogens12020249. [PMID: 36839521 PMCID: PMC9960469 DOI: 10.3390/pathogens12020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Genetic and genomic data have long recognized that the species Giardia duodenalis is subdivided into at least eight genetic clusters that have been named "assemblages" by specialists in the field. Some of these assemblages have been given the status of species, with Linnean binames. In the framework of the predominant clonal evolution model (PCE), we have shown that, from an evolutionary point of view, G. duodenalis assemblages are equatable to "near-clades", that is to say: clades whose discreteness is somewhat clouded by occasional genetic exchange, but remain discrete and stable in space and time. The implications of this evolutionary status for the species described within G. duodenalis are discussed in light of the most recent genetic and genomic studies. The pattern of this species' subspecific genetic variability and genetic clustering appears to be very similar to the ones of various parasitic, fungal and bacteria species. This underlines the relevance of a compared population genomics of pathogenic species allowed by the broad framework of the PCE model.
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Naranjo-Ortiz MA, Molina M, Fuentes D, Mixão V, Gabaldón T. Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies. Gigascience 2022; 11:6751106. [PMID: 36205401 PMCID: PMC9540331 DOI: 10.1093/gigascience/giac088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/23/2021] [Accepted: 08/24/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, heterokaryosis, or extreme compositional biases can challenge current standard assembly procedures and result in highly fragmented assemblies. Hence, we hypothesized that genome databases must contain a nonnegligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors. FINDINGS Here we present Karyon, a Python-based toolkit that uses raw sequencing data and de novo genome assembly to assess several parameters and generate informative plots to assist in the identification of nonchanonical genomic traits. Karyon includes automated de novo genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species. CONCLUSIONS Our results show that 10 (28.57%) of the assemblies presented signs of unusual genomic configurations, suggesting that these are common, at least for some lineages within the Fungi.
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Affiliation(s)
- Miguel A Naranjo-Ortiz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain,Health and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain,Biology Department, Clark University, Worcester, MA 01610, USA,Naturhistoriskmuseum, University of Oslo, Oslo 0562, Norway
| | - Manu Molina
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain,Health and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain,Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona 08034, Spain
| | - Diego Fuentes
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona 08034, Spain,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Verónica Mixão
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain,Health and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain,Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona 08034, Spain,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Toni Gabaldón
- Correspondence address. Toni Gabaldón, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain. E-mail:
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9
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Goetz EJ, Greco M, Rappaport HB, Weiner AKM, Walker LM, Bowser S, Goldstein S, Katz LA. Foraminifera as a model of the extensive variability in genome dynamics among eukaryotes. Bioessays 2022; 44:e2100267. [PMID: 36050893 DOI: 10.1002/bies.202100267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 06/30/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
Knowledge of eukaryotic life cycles and associated genome dynamics stems largely from research on animals, plants, and a small number of "model" (i.e., easily cultivable) lineages. This skewed sampling results in an underappreciation of the variability among the many microeukaryotic lineages, which represent the bulk of eukaryotic biodiversity. The range of complex nuclear transformations that exists within lineages of microbial eukaryotes challenges the textbook understanding of genome and nuclear cycles. Here, we look in-depth at Foraminifera, an ancient (∼600 million-year-old) lineage widely studied as proxies in paleoceanography and environmental biomonitoring. We demonstrate that Foraminifera challenge the "rules" of life cycles developed largely from studies of plants and animals. To this end, we synthesize data on foraminiferal life cycles, focusing on extensive endoreplication within individuals (i.e., single cells), the unusual nuclear process called Zerfall, and the separation of germline and somatic function into distinct nuclei (i.e., heterokaryosis). These processes highlight complexities within lineages and expand our understanding of the dynamics of eukaryotic genomes.
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Affiliation(s)
- Eleanor J Goetz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
| | - Mattia Greco
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
| | - Hannah B Rappaport
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
| | - Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA.,NORCE Climate and Environment, NORCE Norwegian Research Centre, Bergen, Norway
| | - Laura M Walker
- Department of Biology, Washington University in St. Louis, Missouri, USA
| | - Samuel Bowser
- Department of Environmental Health Sciences, School of Public Health, State University of New York, Albany, New York, USA
| | - Susan Goldstein
- Department of Geology, University of Georgia, Athens, Georgia, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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10
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Veldhuis FL, Nijsse R, Wagenaar JA, Arkesteijn G, Kooyman FNJ. Variation in haplotypes in single cysts of assemblages C and D, but not of assemblage E of Giardia duodenalis. BMC Microbiol 2022; 22:166. [PMID: 35754024 PMCID: PMC9235224 DOI: 10.1186/s12866-022-02581-3] [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: 04/28/2022] [Accepted: 06/21/2022] [Indexed: 11/14/2022] Open
Abstract
Background Giardia duodenalis, a single-celled intestinal parasite, is divided into eight assemblages (A-H), with differences in host specificity. Giardia duodenalis reproduces asexually and cycles between the binucleated trophozoite (4 N) and the infectious cyst with four nuclei (16 N). Interaction between the nuclei is limited. Therefore, genetic drift causes differences in genetic make-up between the non-daughter nuclei; the allelic sequence heterozygosity (ASH). The ASH is low (0.01%—0.0023%) for the related assemblages A and E, higher (0.43–0.53) for assemblage B and much higher (0.74% -0.89%) for the assemblage C and D at the root of the phylogenetic tree. The heterozygosity in assemblage F, in the same clade as assemblage A and E, was unknown. The heterozygosity in the sequences of the gdh and dis3 genes was used as proxy for the ASH and whole genome amplification of single cysts followed by cloning and Sanger sequencing of dis3 fragment could reveal the genetic variation within the cyst. The aim of the study was to determine the level of heterozygosity within pooled and single cysts of different assemblages. Results The heterozygosity in gdh and dis3 was determined in pooled cysts of the assemblages A to F. Heterozygosity in the isolates of the assemblages C (n = 2) and D (n = 1) ranged from 0.41% to 0.82% for gdh and dis3 and no heterozygosity was found in the isolates of the assemblages A (n = 4), E (n = 3) and F (n = 3). The heterozygosity in assemblage B (n = 7) was intermediate (0% to 0.62%). Next, the number of haplotypes of dis3 was determined for single cysts of assemblages C, D and E. In the assemblages C and D, two to four haplotypes were found per cyst, while in assemblage E only one haplotype was identified. Conclusions Having high heterozygosity is characteristic for the assemblages C and D, while having a low heterozygosity is characteristic for the clade with the assemblages A, E and F. Presence of more than 1 haplotype per cyst in assemblage C and D suggests differences between the non-daughter nuclei, in contrast to the one haplotype in assemblage E.
Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02581-3.
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Affiliation(s)
- Floor L Veldhuis
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rolf Nijsse
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ger Arkesteijn
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frans N J Kooyman
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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11
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Horáčková V, Voleman L, Hagen KD, Petrů M, Vinopalová M, Weisz F, Janowicz N, Marková L, Motyčková A, Najdrová V, Tůmová P, Dawson SC, Doležal P. Efficient CRISPR/Cas9-mediated gene disruption in the tetraploid protist Giardia intestinalis. Open Biol 2022; 12:210361. [PMID: 35472287 PMCID: PMC9042576 DOI: 10.1098/rsob.210361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/14/2022] [Indexed: 01/07/2023] Open
Abstract
CRISPR/Cas9-mediated genome editing has become an extremely powerful technique used to modify gene expression in many organisms, including parasitic protists. Giardia intestinalis, a protist parasite that infects approximately 280 million people around the world each year, has been eluding the use of CRISPR/Cas9 to generate knockout cell lines due to its tetraploid genome. In this work, we show the ability of the in vitro assembled CRISPR/Cas9 components to successfully edit the genome of G. intestinalis. The cell line that stably expresses Cas9 in both nuclei of G. intestinalis showed effective recombination of the cassette containing the transcription units for the gRNA and the resistance marker. This highly efficient process led to the removal of all gene copies at once for three independent experimental genes, mem, cwp1 and mlf1. The method was also applicable to incomplete disruption of the essential gene, as evidenced by significantly reduced expression of tom40. Finally, testing the efficiency of Cas9-induced recombination revealed that homologous arms as short as 150 bp can be sufficient to establish a complete knockout cell line in G. intestinalis.
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Affiliation(s)
- Vendula Horáčková
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
| | - Kari D. Hagen
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, UC Davis, Davis, CA, USA
| | - Markéta Petrů
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
| | - Martina Vinopalová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
| | - Filip Weisz
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Natalia Janowicz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
| | - Lenka Marková
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
| | - Alžběta Motyčková
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
| | - Vladimíra Najdrová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
| | - Pavla Tůmová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Scott C. Dawson
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, UC Davis, Davis, CA, USA
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Praha, Czech Republic
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Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun 2021; 12:6003. [PMID: 34650064 PMCID: PMC8516963 DOI: 10.1038/s41467-021-26077-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.
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Affiliation(s)
- Dayana E. Salas-Leiva
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada ,grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eelco C. Tromer
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom ,grid.4830.f0000 0004 0407 1981Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Bruce A. Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Martin Kolisko
- grid.418095.10000 0001 1015 3316Institute of Parasitology, Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic
| | - Zhenzhen Yi
- grid.263785.d0000 0004 0368 7397Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Joan S. Salas-Leiva
- grid.466575.30000 0001 1835 194XCONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih. México
| | - Lucie Gallot-Lavallée
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Shelby K. Williams
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Geert J. P. L. Kops
- grid.7692.a0000000090126352Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - John M. Archibald
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Alastair G. B. Simpson
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
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Abstract
Giardia duodenalis captured the attention of Leeuwenhoek in 1681 while he was examining his own diarrheal stool, but, ironically, it did not really gain attention as a human pathogen until the 1960s, when outbreaks were reported. Key technological advances, including in vitro cultivation, genomic and proteomic databases, and advances in microscopic and molecular approaches, have led to an understanding that this is a eukaryotic organism with a reduced genome rather than a truly premitochondriate eukaryote. This has included the discovery of mitosomes (vestiges of mitochondria), a transport system with many of the features of the Golgi apparatus, and even evidence for a sexual or parasexual cycle. Cell biology approaches have led to a better understanding of how Giardia survives with two nuclei and how it goes through its life cycle as a noninvasive organism in the hostile environment of the lumen of the host intestine. Studies of its immunology and pathogenesis have moved past the general understanding of the importance of the antibody response in controlling infection to determining the key role of the Th17 response. This work has led to understanding of the requirement for a balanced host immune response that avoids the extremes of an excessive response with collateral damage or one that is unable to clear the organism. This understanding is especially important in view of the remarkable ranges of early manifestations, which range from asymptomatic to persistent diarrhea and weight loss, and longer-term sequelae that include growth stunting in children who had no obvious symptoms and a high frequency of postinfectious irritable bowel syndrome (IBS).
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Lagunas-Rangel FA, Yee J, Bermúdez-Cruz RM. An update on cell division of Giardia duodenalis trophozoites. Microbiol Res 2021; 250:126807. [PMID: 34130067 DOI: 10.1016/j.micres.2021.126807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
Giardia duodenalis is a flagellated protozoan that is responsible for many cases of diarrheal disease worldwide and is characterized by its great divergence from the model organisms commonly used in studies of basic cellular processes. The life cycle of Giardia involves an infectious cyst form and a proliferative and mobile trophozoite form. Each Giardia trophozoite has two nuclei and a complex microtubule cytoskeleton that consists of eight flagellar axonemes, basal bodies, the adhesive disc, the funis and the median body. Since the success of Giardia infecting other organisms depends on its ability to divide and proliferate efficiently, Giardia must coordinate its cell division to ensure the duplication and partitioning of both nuclei and the multiple cytoskeletal structures. The purpose of this review is to summarize current knowledge about cell division and its regulation in this protist.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico; Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Janet Yee
- Department of Biology, Biochemistry and Molecular Biology Program, Trent University, Peterborough, ON, Canada
| | - Rosa María Bermúdez-Cruz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico.
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15
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Saghaug CS, Klotz C, Kallio JP, Aebischer T, Langeland N, Hanevik K. Genetic Diversity of the Flavohemoprotein Gene of Giardia lamblia: Evidence for High Allelic Heterozygosity and Copy Number Variation. Infect Drug Resist 2020; 13:4531-4545. [PMID: 33376360 PMCID: PMC7755369 DOI: 10.2147/idr.s274543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose The flavohemoprotein (gFlHb) in Giardia plays an important role in managing nitrosative and oxidative stress, and potentially also in virulence and nitroimidazole drug tolerance. The aim of this study was to analyze the genetic diversity of gFlHb in Giardia assemblages A and B clinical isolates. Methods gFlHb genes from 20 cultured clinical Giardia isolates were subjected to PCR amplification and cloning, followed by Sanger sequencing. Sequences of all cloned PCR fragments from each isolate were analyzed for single nucleotide variants (SNVs) and compared to genomic Illumina sequence data. Identical clone sequences were sorted into alleles, and diversity was further analyzed. The number of gFlHb gene copies was assessed by mining PacBio de novo assembled genomes in eight isolates. Homology models for assessment of SNV's potential impact on protein function were created using Phyre2. Results A variable copy number of the gFlHb gene, between two and six copies, depending on isolate, was found. A total of 37 distinct sequences, representing different alleles of the gFlHb gene, were identified in AII isolates, and 41 were identified in B isolates. In some isolates, up to 12 different alleles were found. The total allelic diversity was high for both assemblages (>0.9) and was coupled with a nucleotide diversity of <0.01. The genetic variation (SNVs per CDS length) was 4.8% in sub-assemblage AII and 5.4% in assemblage B. The number of non-synonymous (ns) SNVs was high in gFIHb of both assemblages, 1.6% in A and 3.0% in B, respectively. Some of the identified nsSNV are predicted to alter protein structure and possibly function. Conclusion In this study, we present evidence that gFlHb, a putative protective enzyme against oxidative and nitrosative stress in Giardia, is a variable copy number gene with high allelic diversity. The genetic variability of gFlHb may contribute metabolic adaptability against metronidazole toxicity.
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Affiliation(s)
- Christina S Saghaug
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Toni Aebischer
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
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16
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Mizuno T, Matey EJ, Bi X, Songok EM, Ichimura H, Tokoro M. Extremely diversified haplotypes observed among assemblage B population of Giardia intestinalis in Kenya. Parasitol Int 2019; 75:102038. [PMID: 31837398 DOI: 10.1016/j.parint.2019.102038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022]
Abstract
In molecular epidemiological studies of Giardia intestinalis, an pathogenic intestinal flagellate, due to the presence of allelic sequence heterogeneity (ASH) on the tetraploid genome, the image of haplotype diversity in the field remains uncertain. Here we employed the nine assemblage B positive stool samples, which had previously reported from Kenyan children, for the clonal sequence analysis of multiple gene loci (glutamate dehydrogenase (GDH), triosephosphate isomerase (TPI), and beta-giardin (BG)). The diversified unique assemblage B haplotypes as GDH (n = 67), TPI (n = 84), and BG (n = 62), and the assemblage A haplotypes as GDH (n = 7), TPI (n = 14), and BG (n = 15), which were hidden in the previous direct-sequence results, were detected. Among the assemblage B haplotypes, Bayesian phylogeny revealed multiple statistically significant clusters (9, 7, and 7 clusters for GDH, TPI, and BG, respectively). A part of the clusters (2 for GDH and 1 for BG), which included >4 haplotypes from an individual sample, indicated the presence of co-transmission with multiple strains sharing a recent ancestor. Locus-dependent discrepancies, such as different compositions of derived samples in clusters and different genotyping results for the assemblages, were also observed and considered to be the traces of both intra- and inter-assemblage genetic recombination respectively. Our clonal sequence analysis for giardial population, which applied firstly in Kenya, could reveal the higher rates of ASH far beyond the levels reported in other areas and address the complex population structure. The clonal analysis is indispensable for the molecular field study of G. intestinalis.
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Affiliation(s)
- Tetsushi Mizuno
- Department of Parasitology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Xiuqiong Bi
- Department of Viral Infection and International Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Hiroshi Ichimura
- Department of Viral Infection and International Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Masaharu Tokoro
- Department of Parasitology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.
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17
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Brás R, Sunkel CE, Resende LP. Tissue stem cells: the new actors in the aneuploidy field. Cell Cycle 2019; 18:1813-1823. [PMID: 31242809 DOI: 10.1080/15384101.2019.1635867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The development of multicellular organisms and the maintenance of its tissues relies on mitosis. However, this process represents a major challenge for genomic stability as each time a cell division occurs there are multiple steps where errors can lead to an abnormal chromosomal content in daughter cells - aneuploidy. Aneuploidy was first postulated to act as a tumour promoting agent over one century ago. Since then, we have learned to appreciate the complexity involving the cellular responses to aneuploidy and to value the importance of models where aneuploidy is induced in vivo and in a cell-type specific manner. Recent data suggests that stem cells evolved a distinct response to aneuploidy, being able to survive and proliferate as aneuploid. Since stem cells are the main cells responsible for tissue renewal, it is of the utmost importance to place the spotlight on stem cells within the aneuploidy field. Here, we briefly review some of the biological mechanisms implicated in aneuploidy, the relationship between aneuploidy and tissue pathologies, and summarize the most recent findings in Drosophila on how tissue stem cells respond to aneuploidy. Once we understand how stem cell behavior is impacted by aneuploidy, we might be able to better describe the complicated link between aneuploidy and tumourigenesis.
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Affiliation(s)
- Rita Brás
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,b IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal
| | - Claudio E Sunkel
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,c ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto , Porto , Portugal
| | - Luís Pedro Resende
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,b IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal
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18
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Tůmová P, Dluhošová J, Weisz F, Nohýnková E. Unequal distribution of genes and chromosomes refers to nuclear diversification in the binucleated Giardia intestinalis. Int J Parasitol 2019; 49:463-470. [DOI: 10.1016/j.ijpara.2019.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/18/2019] [Accepted: 01/27/2019] [Indexed: 01/13/2023]
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19
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Chunduri NK, Storchová Z. The diverse consequences of aneuploidy. Nat Cell Biol 2019; 21:54-62. [PMID: 30602769 DOI: 10.1038/s41556-018-0243-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/31/2018] [Indexed: 12/25/2022]
Abstract
Aneuploidy, or imbalanced chromosome number, has profound effects on eukaryotic cells. In humans, aneuploidy is associated with various pathologies, including cancer, which suggests that it mediates a proliferative advantage under these conditions. Here, we discuss physiological changes triggered by aneuploidy, such as altered cell growth, transcriptional changes, proteotoxic stress, genomic instability and response to interferons, and how cancer cells adapt to the changing aneuploid genome.
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Affiliation(s)
| | - Zuzana Storchová
- Department of Molecular Genetics, TU Kaiserslautern, Kaiserslautern, Germany.
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20
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A natural zoonotic giardiasis: Infection of a child via Giardia cysts in pet chinchilla droppings. Parasitol Int 2018; 67:759-762. [PMID: 30053544 DOI: 10.1016/j.parint.2018.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/14/2018] [Accepted: 07/23/2018] [Indexed: 11/23/2022]
Abstract
Here, we report a case of direct zoonotic transmission of giardiasis between a pet chinchilla and a human. Microscopic and molecular examinations of stool samples from a child and samples of chinchilla droppings revealed cysts/DNA of Giardia intestinalis. The transmission from the chinchilla to the child has been confirmed as coprophagous after the 1-year-old toddler ingested pet chinchilla droppings. Molecular analysis of the gdh gene from both hosts classified the G. intestinalis cysts into the assemblage B genetic group, which has been previously shown to be characteristic of both human and chinchilla giardiasis. Both Giardia sub-assemblages BIII and BIV were present in the chinchilla droppings, whereas only the sub-assemblage BIV was isolated from the child's stool sample. To the best of our knowledge, this is the first report of a true zoonotic transmission of giardiasis, supporting the zoonotic potential of assemblage B.
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21
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Ankarklev J, Lebbad M, Einarsson E, Franzén O, Ahola H, Troell K, Svärd SG. A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination. INFECTION GENETICS AND EVOLUTION 2018; 60:7-16. [DOI: 10.1016/j.meegid.2018.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022]
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22
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Zhu J, Tsai HJ, Gordon MR, Li R. Cellular Stress Associated with Aneuploidy. Dev Cell 2018; 44:420-431. [PMID: 29486194 DOI: 10.1016/j.devcel.2018.02.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 01/10/2023]
Abstract
Aneuploidy, chromosome stoichiometry that deviates from exact multiples of the haploid compliment of an organism, exists in eukaryotic microbes, several normal human tissues, and the majority of solid tumors. Here, we review the current understanding about the cellular stress states that may result from aneuploidy. The topics of aneuploidy-induced proteotoxic, metabolic, replication, and mitotic stress are assessed in the context of the gene dosage imbalance observed in aneuploid cells. We also highlight emerging findings related to the downstream effects of aneuploidy-induced cellular stress on the immune surveillance against aneuploid cells.
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Affiliation(s)
- Jin Zhu
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hung-Ji Tsai
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Molly R Gordon
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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23
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Cacciò SM, Lalle M, Svärd SG. Host specificity in the Giardia duodenalis species complex. INFECTION GENETICS AND EVOLUTION 2017; 66:335-345. [PMID: 29225147 DOI: 10.1016/j.meegid.2017.12.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/15/2022]
Abstract
Giardia duodenalis is a unicellular flagellated parasite that infects the gastrointestinal tract of a wide range of mammalian species, including humans. Investigations of protein and DNA polymorphisms revealed that G. duodenalis should be considered as a species complex, whose members, despite being morphologically indistinguishable, can be classified into eight groups, or Assemblages, separated by large genetic distances. Assemblages display various degree of host specificity, with Assemblages A and B occurring in humans and many other hosts, Assemblage C and D in canids, Assemblage E in hoofed animals, Assemblage F in cats, Assemblage G in rodents, and Assemblage H in pinnipeds. The factors determining host specificity are only partially understood, and clearly involve both the host and the parasite. Here, we review the results of in vitro and in vivo experiments, and clinical observations to highlight relevant biological and genetic differences between Assemblages, with a focus on human infection.
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Affiliation(s)
- Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Marco Lalle
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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Uzlíková M, Fulnečková J, Weisz F, Sýkorová E, Nohýnková E, Tůmová P. Characterization of telomeres and telomerase from the single-celled eukaryote Giardia intestinalis. Mol Biochem Parasitol 2017; 211:31-38. [DOI: 10.1016/j.molbiopara.2016.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
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25
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Markova K, Uzlikova M, Tumova P, Jirakova K, Hagen G, Kulda J, Nohynkova E. Absence of a conventional spindle mitotic checkpoint in the binucleated single-celled parasite Giardia intestinalis. Eur J Cell Biol 2016; 95:355-367. [DOI: 10.1016/j.ejcb.2016.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/19/2016] [Accepted: 07/13/2016] [Indexed: 01/26/2023] Open
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26
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Tůmová P, Uzlíková M, Jurczyk T, Nohýnková E. Constitutive aneuploidy and genomic instability in the single-celled eukaryote Giardia intestinalis. Microbiologyopen 2016; 5:560-74. [PMID: 27004936 PMCID: PMC4985590 DOI: 10.1002/mbo3.351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 11/23/2022] Open
Abstract
Giardia intestinalis is an important single‐celled human pathogen. Interestingly, this organism has two equal‐sized transcriptionally active nuclei, each considered diploid. By evaluating condensed chromosome numbers and visualizing homologous chromosomes by fluorescent in situ hybridization, we determined that the Giardia cells are constitutively aneuploid. We observed karyotype inter‐and intra‐population heterogeneity in eight cell lines from two clinical isolates, suggesting constant karyotype evolution during in vitro cultivation. High levels of chromosomal instability and frequent mitotic missegregations observed in four cell lines correlated with a proliferative disadvantage and growth retardation. Other cell lines, although derived from the same clinical isolate, revealed a stable yet aneuploid karyotype. We suggest that both chromatid missegregations and structural rearrangements contribute to shaping the Giardia genome, leading to whole‐chromosome aneuploidy, unequal gene distribution, and a genomic divergence of the two nuclei within one cell. Aneuploidy in Giardia is further propagated without p53‐mediated cell cycle arrest and might have been a key mechanism in generating the genetic diversity of this human pathogen.
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Affiliation(s)
- Pavla Tůmová
- Department of Tropical Medicine, First Faculty of Medicine, Charles University in Prague, Studnickova 7, Praha 2, 12800, Czech Republic
| | - Magdalena Uzlíková
- Department of Tropical Medicine, First Faculty of Medicine, Charles University in Prague, Studnickova 7, Praha 2, 12800, Czech Republic
| | - Tomáš Jurczyk
- Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University in Prague, Praha 2, Czech Republic
| | - Eva Nohýnková
- Department of Tropical Medicine, First Faculty of Medicine, Charles University in Prague, Studnickova 7, Praha 2, 12800, Czech Republic
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