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Pandey M, Sarkar S, Ghosh SK. Ancestral TALE homeobox protein transcription factor regulates actin dynamics and cellular activities of protozoan parasite Entamoeba invadens. Mol Microbiol 2024. [PMID: 38654540 DOI: 10.1111/mmi.15266] [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: 06/30/2023] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Entamoeba histolytica causes invasive amoebiasis, an important neglected tropical disease with a significant global health impact. The pathogenicity and survival of E. histolytica and its reptilian equivalent, Entamoeba invadens, relies on its ability to exhibit efficient motility, evade host immune responses, and exploit host resources, all of which are governed by the actin cytoskeleton remodeling. Our study demonstrates the early origin and the regulatory role of TALE homeobox protein EiHbox1 in actin-related cellular processes. Several genes involved in different biological pathways, including actin dynamics are differentially expressed in EiHbox1 silenced cells. EiHbox1 silenced parasites showed disrupted F-actin organization and loss of cellular polarity. EiHbox1's presence in the anterior region of migrating cells further suggests its involvement in maintaining cellular polarity. Loss of polarized morphology of EiHbox1 silenced parasites leads to altered motility from fast, directionally persistent, and highly chemotactic to slow, random, and less chemotactic, which subsequently leads to defective aggregation during encystation. EiHbox1 knockdown also resulted in a significant reduction in phagocytic capacity and poor capping response. These findings highlight the importance of EiHbox1 of E. invadens in governing cellular processes crucial for their survival, pathogenicity, and evasion of the host immune system.
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Affiliation(s)
- Meenakshi Pandey
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Shilpa Sarkar
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Sudip K Ghosh
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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Krishnan D, Pandey M, Nayak S, Ghosh SK. Novel Insights into the Wattle and Daub Model of Entamoeba Cyst Wall Formation and the Importance of Actin Cytoskeleton. Pathogens 2023; 13:20. [PMID: 38251328 PMCID: PMC10818507 DOI: 10.3390/pathogens13010020] [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: 11/16/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
The "Wattle and Daub" model of cyst wall formation in Entamoeba invadens has been used to explain encystment in Entamoeba histolytica, the causal agent of amoebiasis, and this process could be a potential target for new antiamoebic drugs. In this study, we studied the morphological stages of chitin wall formation in E. invadens in more detail using fluorescent chitin-binding dyes and the immunolocalization of cyst wall proteins. It was found that chitin deposition was mainly initiated on the cell surface at a specific point or at different points at the same time. The cystic wall grew outward and gradually covered the entire surface of the cyst over time, following the model of Wattle and Daub. The onset of chitin deposition was guided by the localization of chitin synthase 1 to the plasma membrane, occurring on the basis of the Jacob lectin in the cell membrane. During encystation, F-actin was reorganized into the cortical region within the early stages of encystation and remained intact until the completion of the chitin wall. The disruption of actin polymerization in the cortical region inhibited proper wall formation, producing wall-less cysts or cysts with defective chitin walls, indicating the importance of the cortical actin cytoskeleton for proper cyst wall formation.
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Affiliation(s)
| | | | | | - Sudip K. Ghosh
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India; (D.K.); (M.P.); (S.N.)
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Goswami P, Samanta SK, Agarwal T, Ghosh SK. Stress-responsive AMP Kinase like protein regulates encystation of Entamoeba invadens. Mol Biochem Parasitol 2022; 251:111507. [PMID: 35870645 DOI: 10.1016/j.molbiopara.2022.111507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 11/25/2022]
Abstract
Starvation is always accompanied by an increase in the ratio of AMP/ATP followed by activation of AMPK. It is one of the sensors for cellular energy status and is highly conserved across various species. Its role in the stage differentiation process of protozoan species like Giardia, Plasmodium, Trypanosome, and Toxoplasma has been reported. Since Entamoeba undergoes encystation in glucose-starved conditions; it intrigued us to investigate the existence and role of AMPK during the differentiation of trophozoites to the cyst. By employing in silico approaches, we have identified an AMPK homologue which is denominated here as EiAMPK (AMPK-like protein in Entamoeba invadens). Sequence and structural analysis indicate that EiAMPK is sequentially and structurally similar to the AMPK alpha subunit of other organisms. The recombinant form of EiAMPK was functionally active and in accordance, its activity was inhibited by an AMPK-specific inhibitor (eg. Compound C). The increased expression of EiAMPK during different stresses indicated that EiAMPK is a stress-responsive gene. To further investigate, whether EiAMPK has any role in encystation, we employed RNAi-mediated gene silencing that demonstrated its active involvement in encystation. It is known that Entamoeba maintains a flow of glucose from the glycolytic pathway to chitin synthesis for cyst wall formation during encystation. It is conceivable that EiAMPK might have a command over such glucose metabolism. As anticipated, the chitin synthesis was found greatly inhibited in both EiAMPK knockdown and Compound C treated cells, indicating that EiAMPK regulates the cyst wall chitin synthesis.
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Affiliation(s)
- Piyali Goswami
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sintu Kumar Samanta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Tarun Agarwal
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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RNA Sequencing Reveals Widespread Transcription of Natural Antisense RNAs in Entamoeba Species. Microorganisms 2022; 10:microorganisms10020396. [PMID: 35208849 PMCID: PMC8874941 DOI: 10.3390/microorganisms10020396] [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: 12/07/2021] [Revised: 01/26/2022] [Accepted: 02/05/2022] [Indexed: 11/17/2022] Open
Abstract
Entamoeba is a genus of Amoebozoa that includes the intestine-colonizing pathogenic species Entamoeba histolytica. To understand the basis of gene regulation in E. histolytica from an evolutionary perspective, we have profiled the transcriptomes of its closely related species E. dispar, E. moshkovskii and E. invadens. Genome-wide identification of transcription start sites (TSS) and polyadenylation sites (PAS) revealed the similarities and differences of their gene regulatory sequences. In particular, we found the widespread initiation of antisense transcription from within the gene coding sequences is a common feature among all Entamoeba species. Interestingly, we observed the enrichment of antisense transcription in genes involved in several processes that are common to species infecting the human intestine, e.g., the metabolism of phospholipids. These results suggest a potentially conserved and compact gene regulatory system in Entamoeba.
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Bai Y, Zhou Z, Zhao J, Ke Q, Pu F, Wu L, Zheng W, Chi H, Gong H, Zhou T, Xu P. The Draft Genome of Cryptocaryon irritans Provides Preliminary Insights on the Phylogeny of Ciliates. Front Genet 2022; 12:808366. [PMID: 35096020 PMCID: PMC8790277 DOI: 10.3389/fgene.2021.808366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yulin Bai
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ji Zhao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qiaozhen Ke
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Linni Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Weiqiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hongshu Chi
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Hui Gong
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Tao Zhou
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Rawat A, Singh P, Jyoti A, Kaushik S, Srivastava VK. Averting transmission: A pivotal target to manage amoebiasis. Chem Biol Drug Des 2020; 96:731-744. [PMID: 32356312 DOI: 10.1111/cbdd.13699] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 12/18/2022]
Abstract
Amoebiasis is a parasitic infectious disease caused by the enteric protozoan Entamoeba histolytica, a leading basis of deaths accounted to parasites, succeeding malaria and schistosomiasis. Conventional treatment methodologies used to deal with amoebiasis mainly rely on the administration of anti-amoebic compounds and vaccines but are often linked with substantial side-effects on the patient. Besides, cases of development of drug resistance in protozoans have been recorded, contributing further to the reduction in the efficiency of the treatment. Loopholes in the efficacious management of the disease call for the development of novel methodologies to manage amoebiasis. A way to achieve this is by targeting the essential metabolic processes of 'encystation' and 'excystation', and the associated biomolecules, thus interrupting the biphasic life cycle of the parasite. Technologies like the CRISPR-Cas9 system can efficiently be exploited to discover novel and essential molecules that regulate the protozoan's metabolism, while efficiently manipulating and managing the known drug targets, leading to an effective halt and forestall to the enteric infection. This review presents a perspective on these essential metabolic processes and the associated molecules that can be targeted efficaciously to prevent the transmission of amoebiasis, thus managing the disease and proving to be a fruitful endeavour.
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Affiliation(s)
- Aadish Rawat
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Parikshit Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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Nayak S, Ghosh SK. Nucleotide sugar transporters of Entamoeba histolytica and Entamoeba invadens involved in chitin synthesis. Mol Biochem Parasitol 2019; 234:111224. [PMID: 31585127 DOI: 10.1016/j.molbiopara.2019.111224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 11/26/2022]
Abstract
Chitin, a homopolymer of β-(1,4) linked N-acetylglucosamine (GlcNAc), is a major component of cyst wall in the protozoan parasites Entamoeba histolytica (Eh) and Entamoeba invadens (Ei). The Entamoeba chitin synthase makes chitin at the vesicular membrane rather than the plasma membrane in fungi, even though the chemistry of chitin synthesis is most likely the same. However, the role of nucleotide sugar transporter(s) (NSTs) that are involved in chitin synthesis in Entamoeba are not yet established. In this study, we have identified the putative UDP-GlcNAc transporter (EiNst5) of Ei by BLASTP analysis using the amino acid sequence of EhNst3, the UDP-GlcNAc transporter of Eh. Heterologous expression of both EhNst3 and EiNst5 was found to complement the function of Yea4p (UDP-GlcNAc transporter of S. cerevisiae) in YEA4 null mutant and increased the cell wall chitin content. Like Yea4p in S. cerevisiae, Myc-epitope tagged EhNst3 and EiNst5 were localized to the endoplasmic reticulum in Δyea4 cells. The EiNST5 transcript was up-regulated during the in vitro encystation and oxidative stress in E. invadens. Similar up-regulation was also seen for EhNST3 under oxidative stress in E. histolytica. Down-regulation of EiNst5 expression using gene-specific dsRNA significantly reduced cyst formation during in vitro encystation in E. invadens. Our observations suggest for the first time the involvement of EhNst3 and EiNst5 in chitin synthesis and so in encystation of Entamoeba.
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Affiliation(s)
- Santoshi Nayak
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721 302, India.
| | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721 302, India.
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Shilton CM, Šlapeta J, Shine R, Brown GP. Pathology Associated With an Outbreak of Entamoebiasis in Wild Cane Toads ( Rhinella marina) in Tropical Australia. Vet Pathol 2019; 56:921-931. [PMID: 31526112 DOI: 10.1177/0300985819868729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Infection due to Entamoeba spp. is known to cause serious disease in primates (Entamoeba histolytica) and snakes (Entamoeba invadens), but there are no detailed descriptions of the pathology associated with Entamoeba spp. infection in amphibians. In 2014, an outbreak of entamoebiasis associated with a novel species of Entamoeba induced clinical illness and poor body condition in free-ranging cane toads in Australia's Northern Territory. Here, we describe the gross pathology, histology, and clinical pathology linked to the outbreak. The study compared 25 toads with invasive entamoebiasis, defined as histologically visible amoebas within tissue, and 12 toads without invasive entamoebiasis. Grossly, affected toads had mild to marked congestion of colonic serosal vasculature, with variable thickening of the intestinal wall and serosanguineous to hemorrhagic colonic content. Histologically, invasive entamoebiasis manifested primarily as moderate to severe, variably hyperplastic to ulcerative colitis. The small intestine was affected in 10 of 25 toads, and 5 of 25 toads also had gastric lesions. Amoebas consistent in morphology with Entamoeba sp. were commonly intermingled with mucosal epithelium, frequently along the basement membrane, with deeper invasion into the superficial lamina propria in only 5 toads. Toads with invasive entamoebiasis had neutrophilia, monocytosis, and lymphopenia, and thus elevated neutrophil to lymphocyte ratios, suggestive of an inflammatory and/or stress leukogram.
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Affiliation(s)
- Catherine M Shilton
- Berrimah Veterinary Laboratory, Northern Territory Department of Primary Industry and Resources, Darwin, Northern Territory, Australia
| | - Jan Šlapeta
- University of Sydney, Sydney, NSW, Australia
| | - Richard Shine
- University of Sydney, Sydney, NSW, Australia.,Macquarie University, Sydney, NSW, Australia
| | - Gregory P Brown
- University of Sydney, Sydney, NSW, Australia.,Macquarie University, Sydney, NSW, Australia
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Wilson IW, Weedall GD, Lorenzi H, Howcroft T, Hon CC, Deloger M, Guillén N, Paterson S, Clark CG, Hall N. Genetic Diversity and Gene Family Expansions in Members of the Genus Entamoeba. Genome Biol Evol 2019; 11:688-705. [PMID: 30668670 PMCID: PMC6414313 DOI: 10.1093/gbe/evz009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2019] [Indexed: 12/18/2022] Open
Abstract
Amoebiasis is the third-most common cause of mortality worldwide from a parasitic disease. Although the primary etiological agent of amoebiasis is the obligate human parasite Entamoeba histolytica, other members of the genus Entamoeba can infect humans and may be pathogenic. Here, we present the first annotated reference genome for Entamoeba moshkovskii, a species that has been associated with human infections, and compare the genomes of E. moshkovskii, E. histolytica, the human commensal Entamoeba dispar, and the nonhuman pathogen Entamoeba invadens. Gene clustering and phylogenetic analyses show differences in expansion and contraction of families of proteins associated with host or bacterial interactions. They intimate the importance to parasitic Entamoeba species of surface-bound proteins involved in adhesion to extracellular membranes, such as the Gal/GalNAc lectin and members of the BspA and Ariel1 families. Furthermore, E. dispar is the only one of the four species to lack a functional copy of the key virulence factor cysteine protease CP-A5, whereas the gene's presence in E. moshkovskii is consistent with the species' potentially pathogenic nature. Entamoeba moshkovskii was found to be more diverse than E. histolytica across all sequence classes. The former is ∼200 times more diverse than latter, with the four E. moshkovskii strains tested having a most recent common ancestor nearly 500 times more ancient than the tested E. histolytica strains. A four-haplotype test indicates that these E. moshkovskii strains are not the same species and should be regarded as a species complex.
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Affiliation(s)
- Ian W Wilson
- Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - Gareth D Weedall
- Institute of Integrative Biology, University of Liverpool, United Kingdom.,School of Natural Sciences and Psychology, Liverpool John Moores University, United Kingdom
| | | | - Timothy Howcroft
- Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - Chung-Chau Hon
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France
| | - Marc Deloger
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France
| | - Nancy Guillén
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - C Graham Clark
- London School of Hygiene & Tropical Medicine, Faculty of Infectious and Tropical Diseases, London, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ United Kingdom
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Schaap P, Schilde C. Encystation: the most prevalent and underinvestigated differentiation pathway of eukaryotes. MICROBIOLOGY-SGM 2018; 164:727-739. [PMID: 29620506 DOI: 10.1099/mic.0.000653] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Not long ago, protists were considered one of four eukaryote kingdoms, but recent gene-based phylogenies show that they contribute to all nine eukaryote subdomains. The former kingdoms of animals, plants and fungi are now relegated to lower ranks within subdomains. Most unicellular protists respond to adverse conditions by differentiating into dormant walled cysts. As cysts, they survive long periods of starvation, drought and other environmental threats, only to re-emerge when conditions improve. For protists pathogens, the resilience of their cysts can prevent successful treatment or eradication of the disease. In this context, effort has been directed towards understanding the molecular mechanisms that control encystation. We here firstly summarize the prevalence of encystation across protists and next focus on Amoebozoa, where most of the health-related issues occur. We review current data on processes and genes involved in encystation of the obligate parasite Entamoeba histolytica and the opportunistic pathogen Acanthamoeba. We show how the cAMP-mediated signalling pathway that controls spore and stalk cell encapsulation in Dictyostelium fruiting bodies could be retraced to a stress-induced pathway controlling encystation in solitary Amoebozoa. We highlight the conservation and prevalence of cAMP signalling genes in Amoebozoan genomes and the suprisingly large and varied repertoire of proteins for sensing and processing environmental signals in individual species.
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Affiliation(s)
- Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee DD15EH, UK
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Yang D, Pan L, Chen Z, Du H, Luo B, Luo J, Pan G. The roles of microsporidia spore wall proteins in the spore wall formation and polar tube anchorage to spore wall during development and infection processes. Exp Parasitol 2018. [PMID: 29522765 DOI: 10.1016/j.exppara.2018.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microsporidia are highly specialized obligate intracellular, spore forming divergent fungi with a wide variety host range that includes most vertebrates and invertebrates. The resistant spores are surrounded by a rigid cell wall which consists of three layers: the electron-lucent chitin and protein inner endospore, the outer-electron-dense and mainly proteinaceous exospore and plasma membrane. Interestingly, microsporidia owns a special invasion organelle, called polar tube, coiled within the interior of the spore wall and attached to anchoring disk at the anterior end of spore. Spore wall and polar tube are the major apparatuses for mature spores adhering and infecting to the host cells. In this review, we summarize the research advances in spore wall proteins (SWPs) related to spore adherence and infection, and SWPs and deproteinated chitin spore coats (DCSCs) interaction associated with SWPs deposit processes and spore wall assembly. Furthermore, we highlight the SWPs-polar tube proteins (PTPs) interaction correlated to polar tube orderly orientation, arrangement and anchorage to anchoring disk. Based on results obtained, it is helpful to improve understanding of the spore wall assembly and polar tube orderly arrangement mechanisms and molecular pathogenesis of microsporidia infection. Also, such information will provide a basis for developing effective control strategies against microporidia.
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Affiliation(s)
- Donglin Yang
- International Academy of Targeted Therapeutics and Innovation, Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Chongqing University of Arts and Sciences, Chongqing, China.
| | - Lixia Pan
- Chongqing Water Resources and Electric Engineering College, Chongqing, China
| | - Zhongzhu Chen
- International Academy of Targeted Therapeutics and Innovation, Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Chongqing University of Arts and Sciences, Chongqing, China
| | - Huihui Du
- Chongqing Three Gorges University, Chongqing, China
| | - Bo Luo
- Zunyi Medical University, Zunyi, Guizhou province, China
| | - Jie Luo
- College of Forestry and Life Sciences, Chongqing University of Arts and Sciences, Chongqing, China
| | - Guoqing Pan
- The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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12
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Wojtkowska M, Buczek D, Suzuki Y, Shabardina V, Makałowski W, Kmita H. The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup. BMC Genomics 2017; 18:997. [PMID: 29284403 PMCID: PMC5747110 DOI: 10.1186/s12864-017-4383-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/14/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The existence of mitochondria-related organelles (MROs) is proposed for eukaryotic organisms. The Amoebozoa includes some organisms that are known to have mitosomes but also organisms that have aerobic mitochondria. However, the mitochondrial protein apparatus of this supergroup remains largely unsampled, except for the mitochondrial outer membrane import complexes studied recently. Therefore, in this study we investigated the mitochondrial inner membrane and intermembrane space complexes, using the available genome and transcriptome sequences. RESULTS When compared with the canonical cognate complexes described for the yeast Saccharomyces cerevisiae, amoebozoans with aerobic mitochondria, display lower differences in the number of subunits predicted for these complexes than the mitochondrial outer membrane complexes, although the predicted subunits appear to display different levels of diversity in regard to phylogenetic position and isoform numbers. For the putative mitosome-bearing amoebozoans, the number of predicted subunits suggests the complex elimination distinctly more pronounced than in the case of the outer membrane ones. CONCLUSION The results concern the problem of mitochondrial and mitosome protein import machinery structural variability and the reduction of their complexity within the currently defined supergroup of Amoebozoa. This results are crucial for better understanding of the Amoebozoa taxa of both biomedical and evolutionary importance.
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Affiliation(s)
- Małgorzata Wojtkowska
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Dorota Buczek
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562 Japan
| | - Victoria Shabardina
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Hanna Kmita
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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Sarjapuram N, Mekala N, Singh M, Tatu U. The Potential of Lactobacillus casei and Entercoccus faecium Combination as a Preventive Probiotic Against Entamoeba. Probiotics Antimicrob Proteins 2016; 9:142-149. [DOI: 10.1007/s12602-016-9232-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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14
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Development of RNA Interference Trigger-Mediated Gene Silencing in Entamoeba invadens. Infect Immun 2016; 84:964-975. [PMID: 26787723 DOI: 10.1128/iai.01161-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/14/2016] [Indexed: 01/08/2023] Open
Abstract
Entamoeba histolytica, a protozoan parasite, is an important human pathogen and a leading parasitic cause of death. The organism has two life cycle stages, trophozoites, which are responsible for tissue invasion, and cysts, which are involved in pathogen transmission. Entamoeba invadens is the model system to study Entamoeba developmental biology, as high-grade regulated encystation and excystation are readily achievable. However, the lack of gene-silencing tools in E. invadens has limited the molecular studies that can be performed. Using the endogenous RNA interference (RNAi) pathway in Entamoeba, we developed an RNAi-based trigger gene-silencing approach inE. invadens We demonstrate that a gene's coding region that has abundant antisense small RNAs (sRNAs) can trigger silencing of a gene that is fused to it. The trigger fusion leads to the generation of abundant antisense sRNAs that map to the target gene, with silencing occurring independently of trigger location at the 5' or 3' end of a gene. Gene silencing is stably maintained during development, including encystation and excystation. We have used this approach to successfully silence two E. invadens genes: a putative rhomboid protease gene and a SHAQKY family Myb gene. The Myb gene is upregulated during oxidative stress and development, and its downregulation led, as predicted, to decreased viability under oxidative stress and decreased cyst formation. Thus, the RNAi trigger silencing method can be used to successfully investigate the molecular functions of genes inE. invadens Dissection of the molecular basis of Entamoeba stage conversion is now possible, representing an important technical advance for the system.
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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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Jex AR, Koehler AV, Ansell BR, Baker L, Karunajeewa H, Gasser RB. Getting to the guts of the matter: The status and potential of ‘omics’ research of parasitic protists of the human gastrointestinal system. Int J Parasitol 2013; 43:971-82. [DOI: 10.1016/j.ijpara.2013.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/07/2013] [Accepted: 06/07/2013] [Indexed: 11/17/2022]
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The ribosomal RNA transcription unit of Entamoeba invadens: Accumulation of unprocessed pre-rRNA and a long non coding RNA during encystation. Mol Biochem Parasitol 2013; 192:30-8. [DOI: 10.1016/j.molbiopara.2013.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/25/2013] [Accepted: 10/29/2013] [Indexed: 01/20/2023]
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De Cádiz AE, Jeelani G, Nakada-Tsukui K, Caler E, Nozaki T. Transcriptome analysis of encystation in Entamoeba invadens. PLoS One 2013; 8:e74840. [PMID: 24040350 PMCID: PMC3770568 DOI: 10.1371/journal.pone.0074840] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 08/08/2013] [Indexed: 11/23/2022] Open
Abstract
Encystation is an essential differentiation process for the completion of the life cycle of a group of intestinal protozoa including Entamoeba histolytica, the causative agent of intestinal and extraintestinal amebiasis. However, regulation of gene expression during encystation is poorly understood. To comprehensively understand the process at the molecular level, the transcriptomic profiles of E. invadens, which is a related reptilian species that causes an invasive disease similar to that of E. histolytica, was investigated during encystation. Using a custom-generated Affymetrix platform microarray, we performed time course (0.5, 2, 8, 24, 48, and 120 h) gene expression analysis of encysting E. invadens. ANOVA analysis revealed that a total of 1,528 genes showed ≥3 fold up-regulation at one or more time points, relative to the trophozoite stage. Of these modulated genes, 8% (116 genes) were up-regulated at the early time points (0.5, 2 and 8h), while 63% (962 genes) were up-regulated at the later time points (24, 48, and 120 h). Twenty nine percent (450 genes) are either up-regulated at 2 to 5 time points or constitutively up-regulated in both early and late stages. Among the up-regulated genes are the genes encoding transporters, cytoskeletal proteins, proteins involved in vesicular trafficking (small GTPases), Myb transcription factors, cysteine proteases, components of the proteasome, and enzymes for chitin biosynthesis. This study represents the first kinetic analysis of gene expression during differentiation from the invasive trophozoite to the dormant, infective cyst stage in Entamoeba. Functional analysis on individual genes and their encoded products that are modulated during encystation may lead to the discovery of targets for the development of new chemotherapeutics that interfere with stage conversion of the parasite.
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Affiliation(s)
- Aleyla Escueta De Cádiz
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao, Philippines
| | - Ghulam Jeelani
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Elisabet Caler
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail:
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Samanta SK, Ghosh SK. The chitin biosynthesis pathway in Entamoeba and the role of glucosamine-6-P isomerase by RNA interference. Mol Biochem Parasitol 2012; 186:60-8. [DOI: 10.1016/j.molbiopara.2012.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 09/17/2012] [Accepted: 09/28/2012] [Indexed: 02/05/2023]
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Kaur D, Gupta AK, Kumari V, Sharma R, Bhattacharya A, Bhattacharya S. Computational prediction and validation of C/D, H/ACA and Eh_U3 snoRNAs of Entamoeba histolytica. BMC Genomics 2012; 13:390. [PMID: 22892049 PMCID: PMC3542256 DOI: 10.1186/1471-2164-13-390] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 07/25/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small nucleolar RNAs are a highly conserved group of small RNAs found in eukaryotic cells. Genes encoding these RNAs are diversely located throughout the genome. They are functionally conserved, performing post transcriptional modification (methylation and pseudouridylation) of rRNA and other nuclear RNAs. They belong to two major categories: the C/D box and H/ACA box containing snoRNAs. U3 snoRNA is an exceptional member of C/D box snoRNAs and is involved in early processing of pre-rRNA. An antisense sequence is present in each snoRNA which guides the modification or processing of target RNA. However, some snoRNAs lack this sequence and often they are called orphan snoRNAs. RESULTS We have searched snoRNAs of Entamoeba histolytica from the genome sequence using computational programmes (snoscan and snoSeeker) and we obtained 99 snoRNAs (C/D and H/ACA box snoRNAs) along with 5 copies of Eh_U3 snoRNAs. These are located diversely in the genome, mostly in intergenic regions, while some are found in ORFs of protein coding genes, intron and UTRs. The computationally predicted snoRNAs were validated by RT-PCR and northern blotting. The expected sizes were in agreement with the observed sizes for all C/D box snoRNAs tested, while for some of the H/ACA box there was indication of processing to generate shorter products. CONCLUSION Our results showed the presence of snoRNAs in E. histolytica, an early branching eukaryote, and the structural features of E. histolytica snoRNAs were well conserved when compared with yeast and human snoRNAs. This study will help in understanding the evolution of these conserved RNAs in diverse phylogenetic groups.
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Affiliation(s)
- Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Transient and stable transfection in the protozoan parasite Entamoeba invadens. Mol Biochem Parasitol 2012; 184:59-62. [PMID: 22561071 DOI: 10.1016/j.molbiopara.2012.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 11/22/2022]
Abstract
Entamoeba histolytica is an important human pathogen and a major health problem worldwide. Many aspects of parasite biology can be studied with the exception of stage conversion, which cannot be reproduced adequately in E. histolytica. The reptile parasite Entamoeba invadens is a vital model system for studying stage conversion since it can be induced to undergo both encystation and excystation with high efficiency in vitro. However, functional studies using E. invadens have been limited by the lack of genetic tools in this species. Here, we report a new method for both transient and stable transfection of E. invadens. These new tools will greatly enhance research into Entamoeba development.
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Weedall GD, Hall N. Evolutionary genomics of Entamoeba. Res Microbiol 2011; 162:637-45. [PMID: 21288488 PMCID: PMC3268252 DOI: 10.1016/j.resmic.2011.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 12/17/2010] [Indexed: 11/06/2022]
Abstract
Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population structure. The imminent expansion of the amount genome data will greatly improve our knowledge of the genus and of pathogenic species within it.
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Affiliation(s)
- Gareth D Weedall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
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Ghosh SK, Van Dellen KL, Chatterjee A, Dey T, Haque R, Robbins PW, Samuelson J. The Jacob2 lectin of the Entamoeba histolytica cyst wall binds chitin and is polymorphic. PLoS Negl Trop Dis 2010; 4:e750. [PMID: 20652032 PMCID: PMC2907411 DOI: 10.1371/journal.pntd.0000750] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 06/02/2010] [Indexed: 11/30/2022] Open
Abstract
Background The infectious and diagnostic form of Entamoeba histolytica (Eh), cause of amebic dysentery and liver abscess, is the quadranucleate cyst. The cyst wall of Entamoeba invadens (Ei), a model for Eh, is composed of chitin fibrils and three sets of chitin-binding lectins that cross-link chitin fibrils (multivalent Jacob lectins), self-aggregate (Jessie lectins), and remodel chitin (chitinase). The goal here was to determine how well the Ei model applies to Entamoeba cysts from humans. Methods/Results An Eh Jacob lectin (EhJacob2) has three predicted chitin-binding domains surrounding a large, Ser-rich spacer. Recombinant EhJacob2 made in transfected Eh trophozoites binds to particulate chitin. Sequences of PCR products using primers flanking the highly polymorphic spacer of EhJacob2 may be used to distinguish Entamoeba isolates. Antibodies to the EhJacob2, EhJessie3, and chitinase each recognize cyst walls of clinical isolates of Entamoeba. While numerous sera from patients with amebic intestinal infections and liver abscess recognize recombinant EhJacob1 and EhJessie3 lectins, few of these sera recognize recombinant EhJacob2. Conclusions/Significance The EhJacob2 lectin binds chitin and is polymorphic, and Jacob2, Jessie3, and chitinase are present in cyst walls of clinical isolates of Entamoeba. These results suggest there are substantial similarities between cysts of the human pathogen (Eh) and the in vitro model (Ei), even though there are quantitative and qualitative differences in their chitin-binding lectins. For many years, we and others have used cysts of Entamoeba invadens (Ei), a reptilian parasite, to model the infectious and diagnostic cysts of the human pathogen Entamoeba histolytica (Eh). The Ei cyst wall is composed of chitin fibrils, as well as Jacob and Jessie lectins that have unique chitin-binding domains. Our recent results suggest a “wattle and daub” model of the Ei cyst wall, where the wattle or sticks (chitin fibrils bound by multivalent Jacob lectins) is constructed prior to the addition of the mortar or daub (self-aggregating Jessie3 lectins). Here we “humanize” the Ei model of the cyst wall with four findings. First, a recombinant Eh Jacob2 lectin, which has three predicted chitin-binding domains surrounding a large spacer domain, binds chitin beads. Second, polymorphisms in the spacer domain of EhJacob2 discriminate clinical isolates of Entamoeba. Third, chitinase, Jacob2 lectin, and Jessie3 lectin are present in cyst walls of clinical isolates of Entamoeba. Finally, numerous sera from patients infected with Entamoeba recognize recombinant Eh Jacob1 and Jessie3 lectins.
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Affiliation(s)
- Sudip K. Ghosh
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Katrina L. Van Dellen
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Anirban Chatterjee
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Tuli Dey
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Phillips W. Robbins
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
| | - John Samuelson
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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Lorenzi HA, Puiu D, Miller JR, Brinkac LM, Amedeo P, Hall N, Caler EV. New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. PLoS Negl Trop Dis 2010; 4:e716. [PMID: 20559563 PMCID: PMC2886108 DOI: 10.1371/journal.pntd.0000716] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 04/26/2010] [Indexed: 11/18/2022] Open
Abstract
Background In order to maintain genome information accurately and relevantly, original genome annotations need to be updated and evaluated regularly. Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken research. For this reason, after five years from the initial submission of the Entamoeba histolytica draft genome publication, we have re-examined the original 23 Mb assembly and the annotation of the predicted genes. Principal Findings The evaluation of the genomic sequence led to the identification of more than one hundred artifactual tandem duplications that were eliminated by re-assembling the genome. The reannotation was done using a combination of manual and automated genome analysis. The new 20 Mb assembly contains 1,496 scaffolds and 8,201 predicted genes, of which 60% are identical to the initial annotation and the remaining 40% underwent structural changes. Functional classification of 60% of the genes was modified based on recent sequence comparisons and new experimental data. We have assigned putative function to 3,788 proteins (46% of the predicted proteome) based on the annotation of predicted gene families, and have identified 58 protein families of five or more members that share no homology with known proteins and thus could be entamoeba specific. Genome analysis also revealed new features such as the presence of segmental duplications of up to 16 kb flanked by inverted repeats, and the tight association of some gene families with transposable elements. Significance This new genome annotation and analysis represents a more refined and accurate blueprint of the pathogen genome, and provides an upgraded tool as reference for the study of many important aspects of E. histolytica biology, such as genome evolution and pathogenesis. Entamoeba histolytica is an anaerobic parasitic protozoan that causes amoebic dysentery. The parasites colonize the large intestine, but under some circumstances may invade the intestinal mucosa, enter the bloodstream and lead to the formation of abscesses such amoebic liver abscesses. The draft genome of E. histolytica, published in 2005, provided the scientific community with the first comprehensive view of the gene set for this parasite and important tools for elucidating the genetic basis of Entamoeba pathogenicity. Because complete genetic knowledge is critical for drug discovery and potential vaccine development for amoebiases, we have re-examined the original draft genome for E. histolytica. We have corrected the sequence assembly, improved the gene predictions and refreshed the functional gene assignments. As a result, this effort has led to a more accurate gene annotation, and the discovery of novel features, such as the presence of genome segmental duplications and the close association of some gene families with transposable elements. We believe that continuing efforts to improve genomic data will undoubtedly help to identify and characterize potential targets for amoebiasis control, as well as to contribute to a better understanding of genome evolution and pathogenesis for this parasite.
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Affiliation(s)
- Hernan A Lorenzi
- J. Craig Venter Institute, Rockville, Maryland, United States of America
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Shrimal S, Bhattacharya S, Bhattacharya A. Serum-dependent selective expression of EhTMKB1-9, a member of Entamoeba histolytica B1 family of transmembrane kinases. PLoS Pathog 2010; 6:e1000929. [PMID: 20532220 PMCID: PMC2880585 DOI: 10.1371/journal.ppat.1000929] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 04/28/2010] [Indexed: 11/29/2022] Open
Abstract
Entamoeba histolytica transmembrane kinases (EhTMKs) can be grouped into six distinct families on the basis of motifs and sequences. Analysis of the E. histolytica genome revealed the presence of 35 EhTMKB1 members on the basis of sequence identity (≥95%). Only six homologs were full length containing an extracellular domain, a transmembrane segment and an intracellular kinase domain. Reverse transcription followed by polymerase chain reaction (RT-PCR) of the kinase domain was used to generate a library of expressed sequences. Sequencing of randomly picked clones from this library revealed that about 95% of the clones were identical with a single member, EhTMKB1-9, in proliferating cells. On serum starvation, the relative number of EhTMKB1-9 derived sequences decreased with concomitant increase in the sequences derived from another member, EhTMKB1-18. The change in their relative expression was quantified by real time PCR. Northern analysis and RNase protection assay were used to study the temporal nature of EhTMKB1-9 expression after serum replenishment of starved cells. The results showed that the expression of EhTMKB1-9 was sinusoidal. Specific transcriptional induction of EhTMKB1-9 upon serum replenishment was further confirmed by reporter gene (luciferase) expression and the upstream sequence responsible for serum responsiveness was identified. EhTMKB1-9 is one of the first examples of an inducible gene in Entamoeba. The protein encoded by this member was functionally characterized. The recombinant kinase domain of EhTMKB1-9 displayed protein kinase activity. It is likely to have dual specificity as judged from its sensitivity to different kinase inhibitors. Immuno-localization showed EhTMKB1-9 to be a surface protein which decreased on serum starvation and got relocalized on serum replenishment. Cell lines expressing either EhTMKB1-9 without kinase domain, or EhTMKB1-9 antisense RNA, showed decreased cellular proliferation and target cell killing. Our results suggest that E. histolytica TMKs of B1 family are functional kinases likely to be involved in serum response and cellular proliferation. The presence of a vast array of putative transmembrane kinase genes suggests an extensive network of signaling systems in E. histolytica, particularly the ability to perceive signals from the extracellular environment and transduce these intracellularly. However, it has been very difficult to work with these molecules due to the presence of a large number of homologs. It is also not clear if these molecules are indeed protein kinases, as no kinase activity has yet been shown associated with these molecules. In this report, we show that EhTMKB1-9 is a protein kinase and it is one of the early serum-induced genes. It is a predominant EhTMKB1 molecule that is expressed in proliferating cells and its expression is modulated by serum. Cells containing a reduced level of EhTMKB1-9 or high level of a mutant protein result in decreased proliferation, target cell killing and adherence. The results presented in this report suggest that EhTMKB1-9 is an important signaling molecule likely to be involved in E. histolytica proliferation and virulence. We have also identified a serum starvation induced response where expression of EhTMKB1-18 was found to be induced.
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Affiliation(s)
- Shiteshu Shrimal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- School of Information Technology, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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Nakada-Tsukui K, Saito-Nakano Y, Husain A, Nozaki T. Conservation and function of Rab small GTPases in Entamoeba: annotation of E. invadens Rab and its use for the understanding of Entamoeba biology. Exp Parasitol 2010; 126:337-47. [PMID: 20434444 DOI: 10.1016/j.exppara.2010.04.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2009] [Revised: 04/19/2010] [Accepted: 04/19/2010] [Indexed: 12/25/2022]
Abstract
Entamoeba invadens is a reptilian enteric protozoan parasite closely related to the human pathogen Entamoeba histolytica and a good model organism of encystation. To understand the molecular mechanism of vesicular trafficking involved in the encystation of Entamoeba, we examined the conservation of Rab small GTPases between the two species. E. invadens has over 100 Rab genes, similar to E. histolytica. Most of the Rab subfamilies are conserved between the two species, while a number of species-specific Rabs are also present. We annotated all E. invadens Rabs according to the previous nomenclature [Saito-Nakano, Y., Loftus, B.J., Hall, N., Nozaki, T., 2005. The diversity of Rab GTPases in Entamoeba histolytica. Experimental Parasitology 110, 244-252]. Comparative genomic analysis suggested that the fundamental vesicular traffic machinery is well conserved, while there are species-specific protein transport mechanisms. We also reviewed the function of Rabs in Entamoeba, and proposed the use of the annotation of E. invadens Rab genes to understand the ubiquitous importance of Rab-mediated membrane trafficking during important biological processes including differentiation in Entamoeba.
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Affiliation(s)
- Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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Dey T, Basu R, Ghosh SK. Entamoeba invadens: Cloning and molecular characterization of chitinases. Exp Parasitol 2009; 123:244-9. [DOI: 10.1016/j.exppara.2009.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 06/02/2009] [Accepted: 07/24/2009] [Indexed: 11/29/2022]
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Wang Y, Song JZ, Yang Q, Liu ZH, Huang XM, Chen Y. Cloning of a heat-stable chitin deacetylase gene from Aspergillus nidulans and its functional expression in Escherichia coli. Appl Biochem Biotechnol 2009; 162:843-54. [PMID: 19760058 DOI: 10.1007/s12010-009-8772-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 09/03/2009] [Indexed: 11/28/2022]
Abstract
A gene encoding chitin deacetylase was cloned by polymerase chain reaction from Aspergillus nidulans. Sequencing result showed 40% homology to the corresponding gene from Colletotrichum lindemuthianum. The complete gene contains an open reading frame of 747 nucleotides encoding a sequence of 249 amino acid residues. The chitin deacetylase gene was subcloned into a pET28a expression vector and expressed in Escherichia coli BL21 and then purified by metal affinity chromatography using a His-bind column. The purified chitin deacetylase demonstrated an activity of 0.77 U ml(-1) for the glycol chitin substrates, and its specific activity was 4.17 U mg(-1) for it. The optimal temperature and pH of the purified enzyme were 50 degrees C and 8.0, respectively. When glycol chitin was used as the substrate, K (m) was 4.92 mg ml(-1), and K (cat) showed 6.25 s(-1), thus the ratio of K (cat) and K (m) was 1.27 ml s(-1) mg(-1). The activity of chitin deacetylase was affected by a range of metal ions and ethylenediaminetetraacetic acid.
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Affiliation(s)
- Yun Wang
- Department of Life Science and Engineering, Harbin Institute of Technology, Harbin 150001, China
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Evidence for a "wattle and daub" model of the cyst wall of entamoeba. PLoS Pathog 2009; 5:e1000498. [PMID: 19578434 PMCID: PMC2698119 DOI: 10.1371/journal.ppat.1000498] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 06/03/2009] [Indexed: 11/19/2022] Open
Abstract
The cyst wall of Entamoeba invadens (Ei), a model for the human pathogen Entamoeba histolytica, is composed of fibrils of chitin and three chitin-binding lectins called Jacob, Jessie3, and chitinase. Here we show chitin, which was detected with wheat germ agglutinin, is made in secretory vesicles prior to its deposition on the surface of encysting Ei. Jacob lectins, which have tandemly arrayed chitin-binding domains (CBDs), and chitinase, which has an N-terminal CBD, were each made early during encystation. These results are consistent with their hypothesized roles in cross-linking chitin fibrils (Jacob lectins) and remodeling the cyst wall (chitinase). Jessie3 lectins likely form the mortar or daub of the cyst wall, because 1) Jessie lectins were made late during encystation; 2) the addition to Jessie lectins to the cyst wall correlated with a marked decrease in the permeability of cysts to nucleic acid stains (DAPI) and actin-binding heptapeptide (phalloidin); and 3) recombinant Jessie lectins, expressed as a maltose-binding proteins in the periplasm of Escherichia coli, caused transformed bacteria to agglutinate in suspension and form a hard pellet that did not dissociate after centrifugation. Jessie3 appeared as linear forms and rosettes by negative staining of secreted recombinant proteins. These findings provide evidence for a “wattle and daub” model of the Entamoeba cyst wall, where the wattle or sticks (chitin fibrils likely cross-linked by Jacob lectins) is constructed prior to the addition of the mortar or daub (Jessie3 lectins). Parasitic protists, which are spread by the fecal-oral route, have cyst walls that resist environmental insults (e.g. desiccation, stomach acids, bile, etc.). Entamoeba histolytica, the cause of amebic dysentery and liver abscess, is the only protist characterized to date that has chitin in its cyst wall. We have previously characterized Entamoeba chitin synthases, chitinases, and multivalent chitin-binding lectins called Jacob. Here we present evidence that the Entamoeba Jessie3 lectin contributes to the mortar or daub, which makes the cyst wall impenetrable to small molecules. First, the Jessie3 lectin was made after chitin and Jacob lectins had already been deposited onto the surface of encysting Entamoeba. Second, cysts became impenetrable to small molecules at the same time that Jessie3 was deposited into the wall. Third, recombinant Jessie3 lectins self-aggregated and caused transfected bacteria to agglutinate. These results suggest a “wattle and daub” model of the Ei cyst wall, where the wattle or sticks (chitin fibrils likely cross-linked by Jacob lectins) is constructed prior to the addition of the mortar or daub (Jessie3 lectins).
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Novikova OS, Blinov AG. Origin, evolution, and distribution of different groups of non-LTR retrotransposons among eukaryotes. RUSS J GENET+ 2009. [DOI: 10.1134/s102279540902001x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Recent insights into Entamoeba development: identification of transcriptional networks associated with stage conversion. Int J Parasitol 2008; 39:41-7. [PMID: 18938171 DOI: 10.1016/j.ijpara.2008.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 09/04/2008] [Indexed: 12/11/2022]
Abstract
Entamoeba histolytica is an important human pathogen and a leading parasitic cause of death globally. The parasite life cycle alternates between the trophozoite form, which is motile and causes invasive disease and the cyst stage, which is environmentally resistant and transmits infection. Understanding the triggers that initiate stage conversion is an important yet understudied area of investigation. Recent progress in dissecting the transcriptional networks that regulate E. histolytica development is outlined in this paper.
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Ebert F, Bachmann A, Nakada-Tsukui K, Hennings I, Drescher B, Nozaki T, Tannich E, Bruchhaus I. An Entamoeba cysteine peptidase specifically expressed during encystation. Parasitol Int 2008; 57:521-4. [PMID: 18723116 DOI: 10.1016/j.parint.2008.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 07/11/2008] [Accepted: 07/19/2008] [Indexed: 11/26/2022]
Abstract
Protozoan parasites of the genus Entamoeba possess a considerable number of cysteine peptidases (CPs), the function of most of these molecules for amoeba biology needs to be established. In order to determine whether CPs may play a role during Entamoeba stage conversion from trophozoites into cysts and vice versa, expression of cp genes was analysed in the reptilian parasite Entamoeba invadens, a model organism for studying Entamoeba cyst development. By homology search, 28 papain-like cp genes were identified in public E. invadens genome databases. For eight of these genes the expression profiles during stage conversion was determined. By Northern blot analysis, transcripts for eicp-a9, -b7, -b8 and -c2, respectively, were detected neither in trophozoites or cysts nor at any of the point of times analysed during stage conversion. On the other hand, eicp-a5 is constitutively expressed during all developmental stages, whereas eicp-a3 and eicp-a11, respectively, are trophozoite-specific. Only eicp-b9 was found to be cyst-specific as it is expressed exclusively 18 to 28 h after cyst induction. Cyst-specific expression was confirmed by immunofluorescence microscopy of the corresponding protein EiCP-B9. In immature cysts, the molecule is located in structures that accumulate near the cyst wall, but which are uniformly distributed in mature cysts. The precise function of EiCP-B9 during Entamoeba encystation remains to be determined. However, colocalisation studies with an Entamoeba marker for autophagosomes suggest that EiCP-B9 is not associated with Entamoeba autophagy.
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Affiliation(s)
- Frank Ebert
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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33
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Clark CG, Alsmark UCM, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N. Structure and content of the Entamoeba histolytica genome. ADVANCES IN PARASITOLOGY 2008; 65:51-190. [PMID: 18063096 DOI: 10.1016/s0065-308x(07)65002-7] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The intestinal parasite Entamoeba histolytica is one of the first protists for which a draft genome sequence has been published. Although the genome is still incomplete, it is unlikely that many genes are missing from the list of those already identified. In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes.
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Affiliation(s)
- C G Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Ehrenkaufer GM, Haque R, Hackney JA, Eichinger DJ, Singh U. Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite. Cell Microbiol 2007; 9:1426-44. [PMID: 17250591 DOI: 10.1111/j.1462-5822.2006.00882.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Developmental switching between life-cycle stages is a common feature among many pathogenic organisms. The protozoan parasite Entamoeba histolytica converts between cysts (essential for disease transmission) and trophozoites (responsible for tissue invasion). Identification of genes involved in the developmental pathway has been severely hindered by the inability to generate E. histolytica cysts in vitro. Using parasite strains derived from recent human infections and whole-genome transcriptional profiling, we determined that 1439 genes (approximately 15% of annotated genes) were potentially developmentally regulated. Genes enriched in cysts (672 in total) included cysteine proteinases and transmembrane protein kinases, which may be involved in signal transduction. Genes enriched in trophozoites (767 in total) included genes typically thought of as important in tissue invasion by trophozoites, including the Gal/GalNAc lectin light subunit and cysteine protease 1. Putative regulators of differentiation including possible G-protein coupled receptors, signal transduction proteins and transcription factors were identified. A number of E. histolytica stage-specific genes were also developmentally regulated in the reptilian parasite E. invadens, indicating that they likely have conserved functions in Entamoeba development. These advances lay the groundwork for dissection of the molecular signals that initiate stage conversion and development of novel diagnostic and therapeutic measures targeting E. histolytica cysts.
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Affiliation(s)
- Gretchen M Ehrenkaufer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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35
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Van Dellen KL, Chatterjee A, Ratner DM, Magnelli PE, Cipollo JF, Steffen M, Robbins PW, Samuelson J. Unique posttranslational modifications of chitin-binding lectins of Entamoeba invadens cyst walls. EUKARYOTIC CELL 2006; 5:836-48. [PMID: 16682461 PMCID: PMC1459681 DOI: 10.1128/ec.5.5.836-848.2006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Entamoeba histolytica, which causes amebic dysentery and liver abscesses, is spread via chitin-walled cysts. The most abundant protein in the cyst wall of Entamoeba invadens, a model for amebic encystation, is a lectin called EiJacob1. EiJacob1 has five tandemly arrayed, six-Cys chitin-binding domains separated by low-complexity Ser- and Thr-rich spacers. E. histolytica also has numerous predicted Jessie lectins and chitinases, which contain a single, N-terminal eight-Cys chitin-binding domain. We hypothesized that E. invadens cyst walls are composed entirely of proteins with six-Cys or eight-Cys chitin-binding domains and that some of these proteins contain sugars. E. invadens genomic sequences predicted seven Jacob lectins, five Jessie lectins, and three chitinases. Reverse transcription-PCR analysis showed that mRNAs encoding Jacobs, Jessies, and chitinases are increased during E. invadens encystation, while mass spectrometry showed that the cyst wall is composed of an approximately 30:70 mix of Jacob lectins (cross-linking proteins) and Jessie and chitinase lectins (possible enzymes). Three Jacob lectins were cleaved prior to Lys at conserved sites (e.g., TPSVDK) in the Ser- and Thr-rich spacers between chitin-binding domains. A model peptide was cleaved at the same site by papain and E. invadens Cys proteases, suggesting that the latter cleave Jacob lectins in vivo. Some Jacob lectins had O-phosphodiester-linked carbohydrates, which were one to seven hexoses long and had deoxysugars at reducing ends. We concluded that the major protein components of the E. invadens cyst wall all contain chitin-binding domains (chitinases, Jessie lectins, and Jacob lectins) and that the Jacob lectins are differentially modified by site-specific Cys proteases and O-phosphodiester-linked glycans.
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Affiliation(s)
- Katrina L Van Dellen
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA 02118, USA
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36
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Andersson JO, Hirt RP, Foster PG, Roger AJ. Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol Biol 2006; 6:27. [PMID: 16551352 PMCID: PMC1484493 DOI: 10.1186/1471-2148-6-27] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 03/21/2006] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses. RESULTS The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time. CONCLUSION Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.
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Affiliation(s)
- Jan O Andersson
- Institute of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, S-751 24 Uppsala, Sweden
| | - Robert P Hirt
- School of Biology, The Devonshire Building, The University of Newcastle upon Tyne, NE1 7RU, UK
| | - Peter G Foster
- Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andrew J Roger
- The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
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Harony H, Bernes S, Siman-Tov R, Ankri S. DNA methylation and targeting of LINE retrotransposons in Entamoeba histolytica and Entamoeba invadens. Mol Biochem Parasitol 2006; 147:55-63. [PMID: 16530279 DOI: 10.1016/j.molbiopara.2006.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 01/25/2006] [Accepted: 02/03/2006] [Indexed: 10/25/2022]
Abstract
In this study, we have isolated by affinity chromatography, using anti-m5C antibody as a ligand, a DNA encoding reverse transcriptase of LINE retrotransposon (RT LINE) in both Entamoeba invadens and Entamoeba histolytica. RT LINE transcripts were detected in E. histolytica but were absent from E. invadens. The methylation status of genomic copies of E. invadens RT LINE was confirmed by bisulfite analysis. In contrast, all the genomic copies of the E. histolytica RT LINE analyzed in this study were not methylated. Many of these genomic copies diverge from the RT LINE isolated by m5C affinity chromatography by a number of mutations that includes conversion of C to T and G to A. These mutations are reminiscent of the conversion of C to T (and G to A on the complementary DNA strand) that occurred during primate evolution in Alu elements following accelerated deamination of methylated cytosines. E. invadens and E. histolytica RT LINEs isolated by affinity chromatography were cloned in a pEhAct Neo vector, amplified in E. coli GM2163 (dam-dcm) and transformed into E. histolytica. Bisulfite analysis of transfected amoeba showed the presence of m5C in E. invadens RT LINE replicated in E. histolytica, but not in E. histolytica RT LINE or in the neomycine phosphotransferase gene, which is also carried by the pEhAct Neo vector. These results suggest the existence of a specific mechanism based on DNA methylation that controls retrotransposons in these parasites.
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Affiliation(s)
- Hala Harony
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, P.O. Box 9649, 31096 Haifa, Israel
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38
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Loftus BJ, Hall N. Entamoeba: still more to be learned from the genome. Trends Parasitol 2005; 21:453. [PMID: 16099723 DOI: 10.1016/j.pt.2005.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Revised: 06/23/2005] [Accepted: 08/03/2005] [Indexed: 11/24/2022]
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Davis PH, Zhang Z, Chen M, Zhang X, Chakraborty S, Stanley SL. Identification of a family of BspA like surface proteins of Entamoeba histolytica with novel leucine rich repeats. Mol Biochem Parasitol 2005; 145:111-6. [PMID: 16199101 PMCID: PMC1382194 DOI: 10.1016/j.molbiopara.2005.08.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Revised: 07/26/2005] [Accepted: 08/29/2005] [Indexed: 11/25/2022]
Affiliation(s)
- Paul H Davis
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
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40
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Beck DL, Boettner DR, Dragulev B, Ready K, Nozaki T, Petri WA. Identification and gene expression analysis of a large family of transmembrane kinases related to the Gal/GalNAc lectin in Entamoeba histolytica. EUKARYOTIC CELL 2005; 4:722-32. [PMID: 15821132 PMCID: PMC1087818 DOI: 10.1128/ec.4.4.722-732.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We identified in the Entamoeba histolytica genome a family of over 80 putative transmembrane kinases (TMKs). The TMK extracellular domains had significant similarity to the intermediate subunit (Igl) of the parasite Gal/GalNAc lectin. The closest homolog to the E. histolytica TMK kinase domain was a cytoplasmic dual-specificity kinase, SplA, from Dictyostelium discoideum. Sequence analysis of the TMK family demonstrated similarities to both serine/threonine and tyrosine kinases. TMK genes from each of six phylogenetic groups were expressed as mRNA in trophozoites, as assessed by spotted oligoarray and real-time PCR assays, suggesting nonredundant functions of the TMK groups for sensing and responding to extracellular stimuli. Additionally, we observed changes in the expression profile of the TMKs in continuous culture. Antisera produced against the conserved kinase domain identified proteins of the expected molecular masses of the expressed TMKs. Confocal microscopy with anti-TMK kinase antibodies revealed a focal distribution of the TMKs on the cytoplasmic face of the trophozoite plasma membrane. We conclude that E. histolytica expresses members of each subgroup of TMKs. The presence of multiple receptor kinases in the plasma membrane offers for the first time a potential explanation of the ability of the parasite to respond to the changing environment of the host.
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Affiliation(s)
- David L Beck
- Department of Microbiology, University of Virginia, Charlottesville, VA 22908-1340, USA
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41
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Frederick JR, Petri WA. Roles for the galactose-/N-acetylgalactosamine-binding lectin of Entamoeba in parasite virulence and differentiation. Glycobiology 2005; 15:53R-59R. [PMID: 16037494 DOI: 10.1093/glycob/cwj007] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Entamoeba histolytica, an intestinal protozoan parasite, is a major cause of morbidity and mortality in developing countries. The pathology of the disease is caused by the colonization of the large intestine by the amoebic trophozoites and the invasion of the intestinal epithelium. Some of the trophozoites will eventually differentiate into the infectious cyst form, allowing them to be transmitted out of the bowel and into water supplies to be passed from person to person. Both the virulence of the organism and the differentiation process relies on a galactose-/N-acetylgalactosamine (GalNAc)-binding lectin that is expressed on the surface of trophozoites. The functional activity of this lectin has been shown to be involved in host cell binding, cytotoxicity, complement resistance, induction of encystation, and generation of the cyst wall. The role of the lectin in both differentiation and virulence suggests that it may be a pivotal molecule that determines the severity of the infection from a commensal state resulting from increased encystation to an invasive state. The lectin-glycan interactions that initiate these diverse processes are discussed with emphasis on comparing the binding of host ligands and the interactions involved in encystation.
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Affiliation(s)
- Jesse R Frederick
- Division of Infectious Diseases, University of Virginia Health System, MR4 Building, Room 2115, Charlottesville, VA 22908-1340, USA
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42
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Pritham EJ, Feschotte C, Wessler SR. Unexpected Diversity and Differential Success of DNA Transposons in Four Species of Entamoeba Protozoans. Mol Biol Evol 2005; 22:1751-63. [PMID: 15901838 DOI: 10.1093/molbev/msi169] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report the first comprehensive analysis of transposable element content in the compact genomes (approximately 20 Mb) of four species of Entamoeba unicellular protozoans for which draft sequences are now available. Entamoeba histolytica and Entamoeba dispar, two human parasites, have many retrotransposons, but few DNA transposons. In contrast, the reptile parasite Entamoeba invadens and the free-living Entamoeba moshkovskii contain few long interspersed elements but harbor diverse and recently amplified populations of DNA transposons. Representatives of three DNA transposase superfamilies (hobo/Activator/Tam3, Mutator, and piggyBac) were identified for the first time in a protozoan species in addition to a variety of members of a fourth superfamily (Tc1/mariner), previously reported only from ciliates and Trichomonas vaginalis among protozoans. The diversity of DNA transposons and their differential amplification among closely related species with similar compact genomes are discussed in the context of the biology of Entamoeba protozoans.
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Affiliation(s)
- Ellen J Pritham
- Department of Plant Biology, The University of Georgia, USA.
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43
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Byers J, Eichinger D. Entamoeba invadens: restriction of ploidy by colonic short chain fatty acids. Exp Parasitol 2005; 110:203-6. [PMID: 15955313 DOI: 10.1016/j.exppara.2005.02.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Revised: 02/21/2005] [Accepted: 02/23/2005] [Indexed: 10/25/2022]
Abstract
The DNA content of Entamoeba parasites appears to be regulated by an unusual mechanism. This conclusion, however, was based on experiments that examined parasites grown in media that did not contain short chain fatty acids (SCFAs) normally found in the colonic lumen. Since one of these SCFAs, butyrate, is known to affect DNA replication in eukaryotic cells, we examined the effect of SCFAs on Entamoeba trophozoite DNA content. Similar to reports from others, we found that Entamoeba invadens trophozoite cultures grown in conventional medium (TYI-S-33) contained cells with 2N, 4N, 8N, and 16N amounts of DNA. In contrast, cultures grown in TYI medium containing colonic SCFAs added in place of glucose contained a minor population with 2N, a major population with 4N, and very few cells with higher amounts of DNA. SCFAs also prevented the normal increase in the number of nuclei per cell in trophozoites that were induced to encyst. These results suggest that E. invadens trophozoite stage parasites growing in the intestine in the presence of high amounts of SCFAs have a ploidy range restricted to 2N/4N. Axenic growth of trophozoites in the absence of SCFAs, however, appears to allow trophozoites to increase the amount of DNA per cell, which they must do during the normal encystment process.
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Affiliation(s)
- Jennifer Byers
- Department of Medical Parasitology, New York University School of Medicine, New York, NY 10010, USA
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44
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Worthey EA, Myler PJ. Protozoan genomes: gene identification and annotation. Int J Parasitol 2005; 35:495-512. [PMID: 15826642 DOI: 10.1016/j.ijpara.2005.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Revised: 01/25/2005] [Accepted: 02/06/2005] [Indexed: 12/01/2022]
Abstract
The draft sequence of several complete protozoan genomes is now available and genome projects are ongoing for a number of other species. Different strategies are being implemented to identify and annotate protein coding and RNA genes in these genomes, as well as study their genomic architecture. Since the genomes vary greatly in size, GC-content, nucleotide composition, and degree of repetitiveness, genome structure is often a factor in choosing the methodology utilised for annotation. In addition, the approach taken is dictated, to a greater or lesser extent, by the particular reasons for carrying out genome-wide analyses and the level of funding available for projects. Nevertheless, these projects have provided a plethora of material that will aid in understanding the biology and evolution of these parasites, as well as identifying new targets that can be used to design urgently required drug treatments for the diseases they cause.
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Affiliation(s)
- E A Worthey
- Seattle Biomedical Research Institute, 307 Westlake Ave N., Seattle, WA 98109-2591, USA
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45
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Ahren DG, Ouzounis CA. Robustness of metabolic map reconstruction. J Bioinform Comput Biol 2005; 2:589-93. [PMID: 15359428 DOI: 10.1142/s021972000400079x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Revised: 06/25/2004] [Accepted: 06/25/2004] [Indexed: 11/18/2022]
Abstract
With the ever increasing amount of genomic data available, the interest for generating biochemical pathways has grown tremendously. So far, mainly complete genomes have been used to reconstruct the biochemical pathways and their associated interactions. However, a large number of low coverage genomes, as well as other sources of partial genomic data, are currently available for many organisms. In order to be able to use incomplete data for metabolic reconstruction, the inherent properties of this procedure need to be investigated. In this short note, we describe the robustness and predictive power of metabolic reconstructions using partial information from Schizosaccharomyces pombe. We also discuss the implications of the results on reference genome projects as well as other large-scale sequencing data.
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Affiliation(s)
- Dag G Ahren
- Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
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46
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Makioka A, Kumagai M, Kobayashi S, Takeuchi T. Entamoeba invadens: cysteine protease inhibitors block excystation and metacystic development. Exp Parasitol 2004; 109:27-32. [PMID: 15639136 DOI: 10.1016/j.exppara.2004.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Revised: 10/22/2004] [Accepted: 10/25/2004] [Indexed: 11/28/2022]
Abstract
We examined the effects of six cysteine protease inhibitors on the excystation and metacystic development of Entamoeba invadens. Excystation, which was assessed by counting the number of metacystic amoebae after the induction of excystation, was inhibited by the cysteine protease inhibitors Z-Phe-Ala-DMK and E-64d in a concentration-dependent manner during incubation compared to the controls. Neither inhibitor had a significant effect on cyst viability; thus, their inhibitory effects were not due to the toxic effect on cysts. Metacystic development, when determined by the number of nuclei in amoeba, was also inhibited by these protease inhibitors, because the percentage of 4-nucleate amoebae was higher than in the controls on Day 3 of incubation. Although other cysteine protease inhibitors, Z-Phe-Phe-DMK, E-64, ALLM, and cathepsin inhibitor III, had a weak or little effect on the excystation, they inhibited cysteine protease activity in the lysates of E. invadens cysts. Broad bands with gelatinase activity of metacystic amoebae, as well as cysts and trophozoites, were detected in the gelatin substrate gel electrophores and were inhibited by Z-Phe-Ala-DMK. There was a difference in the protease composition between cysts and trophozoites, and the protease composition of metacystic amoebae changed from cyst-type to trophozoite-type during development. These results strongly suggest that cysteine proteases contribute to the excystation and metacystic development of E. invadens, which leads to successful infection.
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Affiliation(s)
- Asao Makioka
- Department of Tropical Medicine, Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan.
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Abstract
Entamoeba parasites multiply as trophozoites in the layer of mucus that overlies the colonic epithelium. In response to stimuli that are not understood, trophozoites stop multiplying and differentiate into cysts that are released to infect another host. In the colon, Entamoeba trophozoites are exposed to the large variety of biochemicals that are carried into or are produced within this organ. The normal bacterial population of the colon releases large amounts of short-chain fatty acids (SCFAs). These compounds have effects on the growth, differentiation and repair of the colonic epithelium that correlate with de-creased activity of a Class I/II histone deacetylase (HDAC). We found that the formation of cysts, but not the growth of trophozoite-stage Entamoeba invadens parasites, was inhibited by physiologic concentrations of SCFAs. Variable levels of cyst formation did occur if SCFA concentrations were lowered. Specific inhibitors of Class I/II-type HDACs also prevented encystation, and trophozoites exposed to these compounds had increased levels of acetylation of histone H4 and other nuclear proteins. These results suggest that production of the infectious cyst stage of Entamoeba parasites is regulated in part by the levels of SCFAs made by the bacterial population of the colon.
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Affiliation(s)
- Jennifer Byers
- Medical and Molecular Parasitology, New York University School of Medicine, New York, NY 10010, USA
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Abstract
The sequencing of eukaryotic genomes has lagged behind sequencing of organisms in the other domains of life, archae and bacteria, primarily due to their greater size and complexity. With recent advances in high-throughput technologies such as robotics and improved computational resources, the number of eukaryotic genome sequencing projects has increased significantly. Among these are a number of sequencing projects of tropical pathogens of medical and veterinary importance, many of which are responsible for causing widespread morbidity and mortality in peoples of developing countries. Uncovering the complete gene complement of these organisms is proving to be of immense value in the development of novel methods of parasite control, such as antiparasitic drugs and vaccines, as well as the development of new diagnostic tools. Combining pathogen genome sequences with the host and vector genome sequences is promising to be a robust method for the identification of host-pathogen interactions. Finally, comparative sequencing of related species, especially of organisms used as model systems in the study of the disease, is beginning to realize its potential in the identification of genes, and the evolutionary forces that shape the genes, that are involved in evasion of the host immune response.
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Affiliation(s)
- Jane M Carlton
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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Tannich E, Mirelman D, Petri WA. Meeting Report: EMBO Workshop “Pathogenesis of Amoebiasis: from Genomics to Disease”, Institut Pasteur, Paris, May 19–22, 2003. Protist 2003; 154:293-8. [PMID: 14658490 DOI: 10.1078/143446103322454077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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