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Gene expression of axenically-isolated clinical Entamoeba histolytica strains and its impact on disease severity of amebiasis. PLoS Pathog 2022; 18:e1010880. [PMID: 36178974 PMCID: PMC9555656 DOI: 10.1371/journal.ppat.1010880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/12/2022] [Accepted: 09/14/2022] [Indexed: 11/30/2022] Open
Abstract
The severity of Entamoeba histolytica infection is determined by host immunology, pathogen virulence, and the intestinal environment. Conventional research for assessing pathogen virulence has been mainly performed using laboratory strains, such as a virulent HM-1: IMSS (HM-1) and an avirulent Rahman, under various artificial environmental conditions because of the difficulties of axenic isolation of the clinical strains. However, it is still unclear whether scientific knowledge based on laboratory strains are universally applicable to the true pathogenesis. Hereby, we performed transcriptomic analysis of clinical strains from patients with different degrees of disease severity, as well as HM-1 under different conditions. Even after several months of axenization, Clinical strains show the distinct profile in gene expression during in vitro passage, moreover, difference between any 2 of these strains was much greater than the changes on the liver challenge. Interestingly, 26 DEGs, which were closely related to the biological functions, were oppositely up- or down regulated between virulent Ax 19 (liver abscess) and avirulent Ax 11 (asymptomatic carrier). Additionally, RNAseq using laboratory strain (HM1) showed more than half of genes were differently expressed between continuously in vitro passaged HM1 (in vitro HM1) and periodically liver passaged HM1 (virulent HM1), which was much greater than the changes on the liver passage of virulent HM1. Also, transcriptomic analysis of a laboratory strain revealed that continuous environmental stress enhances its virulence via a shift in its gene expression profile. Changes in gene expression patterns on liver abscess formation were not consistent between clinical and laboratory strains. Various genotypes of Entamoeba histolytica are prevalent in the field. Some papers suggest the association between genotypes and disease severity. However, most studies for assessing pathogen virulence were performed using laboratory strains, such as virulent HM1: IMSS (HM1) and avirulent Rahman, because axenic isolation from clinical specimen is technically complex and time consuming. This transcriptomic analysis using clinical strains from the patients with different clinical severity, as well as the laboratory strain HM1 under different conditions showed unique gene expression patterns. Following things were confirmed; 1. Virulent clinical strain maintains its virulence with unique gene expression pattern after axenic isolation, 2. Continuous environmental stress enhances its virulence via the accumulation of altered gene expressions, and 3. Changes in gene expression on the liver abscess formation are not always the same amongst strains. For an accurate understanding the pathogenesis, comprehensive analyses of various clinical strains under different environmental conditions should be promoted.
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König C, Honecker B, Wilson IW, Weedall GD, Hall N, Roeder T, Metwally NG, Bruchhaus I. Taxon-Specific Proteins of the Pathogenic Entamoeba Species E. histolytica and E. nuttalli. Front Cell Infect Microbiol 2021; 11:641472. [PMID: 33816346 PMCID: PMC8017271 DOI: 10.3389/fcimb.2021.641472] [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: 12/14/2020] [Accepted: 03/03/2021] [Indexed: 01/30/2023] Open
Abstract
The human protozoan parasite Entamoeba histolytica can live in the human intestine for months or years without generating any symptoms in the host. For unknown reasons, amoebae can suddenly destroy the intestinal mucosa and become invasive. This can lead to amoebic colitis or extraintestinal amoebiasis whereby the amoebae spread to other organs via the blood vessels, most commonly the liver where abscesses develop. Entamoeba nuttalli is the closest genetic relative of E. histolytica and is found in wild macaques. Another close relative is E. dispar, which asyptomatically infects the human intestine. Although all three species are closely related, only E. histolytica and E. nuttalli are able to penetrate their host’s intestinal epithelium. Lineage-specific genes and gene families may hold the key to understanding differences in virulence among species. Here we discuss those genes found in E. histolytica that have relatives in only one or neither of its sister species, with particular focus on the peptidase, AIG, Ariel, and BspA families.
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Affiliation(s)
- Constantin König
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Barbara Honecker
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ian W Wilson
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Gareth D Weedall
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Thomas Roeder
- Zoology, Department of Molecular Physiology, Kiel University, Kiel, Germany.,Airway Research Center North (ARCN), German Center for Lung Research (DZL), Kiel, Germany
| | | | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Department of Biology, University of Hamburg, Hamburg, Germany
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Whole genome sequencing of Entamoeba nuttalli reveals mammalian host-related molecular signatures and a novel octapeptide-repeat surface protein. PLoS Negl Trop Dis 2019; 13:e0007923. [PMID: 31805050 PMCID: PMC6917348 DOI: 10.1371/journal.pntd.0007923] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 12/17/2019] [Accepted: 11/12/2019] [Indexed: 11/19/2022] Open
Abstract
The enteric protozoa Entamoeba histolytica is the causative agent of amebiasis, which is one of the most common parasitic diseases in developed and developing countries. Entamoeba nuttalli is the genetically closest species to E. histolytica in current phylogenetic analyses of Entamoeba species, and is prevalent in wild macaques. Therefore, E. nuttalli may be a key organism in which to investigate molecules required for infection of human or non-human primates. To explore the molecular signatures of host-parasite interactions, we conducted de novo assembly of the E. nuttalli genome, utilizing self-correction of PacBio long reads and polishing corrected reads using Illumina short reads, followed by comparative genomic analysis with two other mammalian and a reptilian Entamoeba species. The final draft assembly of E. nuttalli included 395 contigs with a total length of approximately 23 Mb, and 9,647 predicted genes, of which 6,940 were conserved with E. histolytica. In addition, we found an E. histolytica-specific repeat known as ERE2 in the E. nuttalli genome. GO-term enrichment analysis of mammalian host-related molecules indicated diversification of transmembrane proteins, including AIG1 family and BspA-like proteins that may be involved in the host-parasite interaction. Furthermore, we identified an E. nuttalli-specific protein that contained 42 repeats of an octapeptide ([G,E]KPTDTPS). This protein was shown to be localized on the cell surface using immunofluorescence. Since many repeat-containing proteins in parasites play important roles in interactions with host cells, this unique octapeptide repeat-containing protein may be involved in colonization of E. nuttalli in the intestine of macaques. Overall, our draft assembly provides a valuable resource for studying Entamoeba evolution and host-parasite selection.
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Krishnan D, Ghosh SK. Cellular Events of Multinucleated Giant Cells Formation During the Encystation of Entamoeba invadens. Front Cell Infect Microbiol 2018; 8:262. [PMID: 30109218 PMCID: PMC6079502 DOI: 10.3389/fcimb.2018.00262] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/13/2018] [Indexed: 12/21/2022] Open
Abstract
Entamoeba histolytica, the causative agent of amoebiasis, does not form cysts in vitro, so reptilian pathogen Entamoeba invadens is used as an Entamoeba encystation model. During the in vitro encystation of E. invadens, a few multinucleated giant cells (MGC) were also appeared in the culture along with cysts. Like the cyst, these MGC's were also formed in the multicellular aggregates found in the encystation culture. Time-lapse live cell imaging revealed that MGC's were the result of repeated cellular fusion with fusion-competent trophozoites as a starting point. The early MGC were non-adherent, and they moved slowly and randomly in the media, but under confinement, MGC became highly motile and directionally persistent. The increased motility resulted in rapid cytoplasmic fissions, which indicated the possibility of continuous cell fusion and division taking place inside the compact multicellular aggregates. Following cell fusion, each nucleus obtained from the fusion-competent trophozoites gave rise to four nuclei with half genomic content. All the haploid nuclei in MGC later aggregated and fused to form a polyploid nucleus. These observations have important implications on Entamoeba biology as they point toward the possibility of E. invadens undergoing sexual or parasexual reproduction.
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Affiliation(s)
- Deepak Krishnan
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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Shabardina V, Kischka T, Kmita H, Suzuki Y, Makałowski W. Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by comparative genomic analysis. Int J Biol Sci 2018; 14:306-320. [PMID: 29559848 PMCID: PMC5859476 DOI: 10.7150/ijbs.23869] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/30/2017] [Indexed: 11/17/2022] Open
Abstract
Amoebozoans are in many aspects interesting research objects, as they combine features of single-cell organisms with complex signaling and defense systems, comparable to multicellular organisms. Acanthamoeba castellanii is a cosmopolitan species and developed diverged feeding abilities and strong anti-bacterial resistance; Entamoeba histolytica is a parasitic amoeba, who underwent massive gene loss and its genome is almost twice smaller than that of A. castellanii. Nevertheless, both species prosper, demonstrating fitness to their specific environments. Here we compare transcriptomes of A. castellanii and E. histolytica with application of orthologs' search and gene ontology to learn how different life strategies influence genome evolution and restructuring of physiology. A. castellanii demonstrates great metabolic activity and plasticity, while E. histolytica reveals several interesting features in its translational machinery, cytoskeleton, antioxidant protection, and nutritional behavior. In addition, we suggest new features in E. histolytica physiology that may explain its successful colonization of human colon and may facilitate medical research.
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Affiliation(s)
- Victoria Shabardina
- Institute of Bioinformatics, University Münster, Niels-Stensen Strasse 14, Münster 48149, Germany
| | - Tabea Kischka
- Institute of Bioinformatics, University Münster, Niels-Stensen Strasse 14, Münster 48149, Germany
| | - Hanna Kmita
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Wojciech Makałowski
- Institute of Bioinformatics, University Münster, Niels-Stensen Strasse 14, Münster 48149, Germany
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Abstract
The outcome of an Entamoeba histolytica infection is variable and the contribution of genetic diversity within E. histolytica to human disease is not fully understood. The information provided by the whole genome sequence of the E. histolytica reference laboratory strain (HM-1:IMSS) and thirteen additional laboratory strains have been made publically available. In this review theories on the source of the unexpected level of structural diversity found in E. histolytica will be discussed.
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Affiliation(s)
- Carol A Gilchrist
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
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Singh RS, Walia AK, Kanwar JR, Kennedy JF. Amoebiasis vaccine development: A snapshot on E. histolytica with emphasis on perspectives of Gal/GalNAc lectin. Int J Biol Macromol 2016; 91:258-68. [DOI: 10.1016/j.ijbiomac.2016.05.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 01/10/2023]
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Gilchrist CA, Petri SE, Schneider BN, Reichman DJ, Jiang N, Begum S, Watanabe K, Jansen CS, Elliott KP, Burgess SL, Ma JZ, Alam M, Kabir M, Haque R, Petri WA. Role of the Gut Microbiota of Children in Diarrhea Due to the Protozoan Parasite Entamoeba histolytica. J Infect Dis 2015; 213:1579-85. [PMID: 26712950 PMCID: PMC4837909 DOI: 10.1093/infdis/jiv772] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/21/2015] [Indexed: 12/26/2022] Open
Abstract
Background. An estimated 1 million children die each year before their fifth birthday from diarrhea. Previous population-based surveys of pediatric diarrheal diseases have identified the protozoan parasite Entamoeba histolytica, the etiological agent of amebiasis, as one of the causes of moderate-to-severe diarrhea in sub-Saharan Africa and South Asia. Methods. We prospectively studied the natural history of E. histolytica colonization and diarrhea among infants in an urban slum of Dhaka, Bangladesh. Results. Approximately 80% of children were infected with E. histolytica by the age of 2 years. Fecal anti-galactose/N-acetylgalactosamine lectin immunoglobulin A was associated with protection from reinfection, while a high parasite burden and expansion of the Prevotella copri level was associated with diarrhea. Conclusions. E. histolytica infection was prevalent in this population, with most infections asymptomatic and diarrhea associated with both the amount of parasite and the composition of the microbiota.
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Affiliation(s)
| | | | | | | | | | - Sharmin Begum
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | | | | | | | | | - Jennie Z Ma
- Division of Biostatistics, Department of Public Health Sciences School of Medicine, University of Virginia, Charlottesville
| | - Masud Alam
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Mamun Kabir
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
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Das K, Ganguly S. Evolutionary genomics and population structure of Entamoeba histolytica. Comput Struct Biotechnol J 2014; 12:26-33. [PMID: 25505504 PMCID: PMC4262060 DOI: 10.1016/j.csbj.2014.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 01/02/2023] Open
Abstract
Amoebiasis caused by the gastrointestinal parasite Entamoeba histolytica has diverse disease outcomes. Study of genome and evolution of this fascinating parasite will help us to understand the basis of its virulence and explain why, when and how it causes diseases. In this review, we have summarized current knowledge regarding evolutionary genomics of E. histolytica and discussed their association with parasite phenotypes and its differential pathogenic behavior. How genetic diversity reveals parasite population structure has also been discussed. Queries concerning their evolution and population structure which were required to be addressed have also been highlighted. This significantly large amount of genomic data will improve our knowledge about this pathogenic species of Entamoeba.
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Affiliation(s)
- Koushik Das
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India
| | - Sandipan Ganguly
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India
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Singh N, Bhattacharya A, Bhattacharya S. Homologous Recombination Occurs in Entamoeba and Is Enhanced during Growth Stress and Stage Conversion. PLoS One 2013; 8:e74465. [PMID: 24098652 PMCID: PMC3787063 DOI: 10.1371/journal.pone.0074465] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/01/2013] [Indexed: 12/28/2022] Open
Abstract
Homologous recombination (HR) has not been demonstrated in the parasitic protists Entamoeba histolytica or Entamoeba invadens, as no convenient method is available to measure it. However, HR must exist to ensure genome integrity, and possible genetic exchange, especially during stage conversion from trophozoite to cyst. Here we show the up regulation of mitotic and meiotic HR genes in Entamoeba during serum starvation, and encystation. To directly demonstrate HR we use a simple PCR-based method involving inverted repeats, which gives a reliable read out, as the recombination junctions can be determined by sequencing the amplicons. Using this read out, we demonstrate enhanced HR under growth stress in E. histolytica, and during encystation in E. invadens. We also demonstrate recombination between chromosomal inverted repeats. This is the first experimental demonstration of HR in Entamoeba and will help future investigations into this process, and to explore the possibility of meiosis in Entamoeba.
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Affiliation(s)
- Nishant Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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Manoharan SS, Miao VPW, Andrésson ÓS. LEC-2, a highly variable lectin in the lichen Peltigera membranacea.. Symbiosis 2012; 58:91-98. [PMID: 23482294 PMCID: PMC3589653 DOI: 10.1007/s13199-012-0206-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/26/2012] [Indexed: 12/31/2022]
Abstract
Lectins are a diverse group of carbohydrate binding proteins often involved in cellular interactions. A lectin gene, lec-2, was identified in the mycobiont of the lichen Peltigera membranacea. Sequencing of lec-2 open reading frames from 21 individual samples showed an unexpectedly high level of polymorphism in the deduced protein (LEC-2), which was sorted into nine haplotypes based on amino acid sequence. Calculations showed that the rates of nonsynonymous versus synonymous nucleotide substitutions deviated significantly from the null hypothesis of neutrality, indicating strong positive selection. Molecular modeling revealed that most amino acid replacements were around the putative carbohydrate-binding pocket, indicating changes in ligand binding. Lectins have been thought to be involved in the recognition of photobiont partners in lichen symbioses, and the hypothesis that positive selection of LEC-2 is driven by variation in the Nostoc photobiont partner was tested by comparing mycobiont LEC-2 haplotypes and photobiont genotypes, as represented by the rbcLX region. It was not possible to pair up the two types of marker sequences without conflicts, suggesting that positive selection of LEC-2 was not due to variation in photobiont partners.
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Affiliation(s)
- Sheeba S. Manoharan
- Department of Life and Environmental Sciences, University of Iceland, 101 Reykjavík, Iceland
| | - Vivian P. W. Miao
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Ólafur S. Andrésson
- Department of Life and Environmental Sciences, University of Iceland, 101 Reykjavík, Iceland
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Weedall GD, Clark CG, Koldkjaer P, Kay S, Bruchhaus I, Tannich E, Paterson S, Hall N. Genomic diversity of the human intestinal parasite Entamoeba histolytica. Genome Biol 2012; 13:R38. [PMID: 22630046 PMCID: PMC3446291 DOI: 10.1186/gb-2012-13-5-r38] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 04/29/2012] [Accepted: 05/25/2012] [Indexed: 11/10/2022] Open
Abstract
Background Results Conclusions
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