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Yu M, Yao Y, Li X, Su A, Xie M, Xiong Y, Yang S, Ni Q, Xiao H, Xu H. Epidemiological investigation of Entamoeba in wild rhesus macaques in China: A novel ribosomal lineage and genetic differentiation of Entamoeba nuttalli. Int J Parasitol 2024:S0020-7519(24)00072-9. [PMID: 38604548 DOI: 10.1016/j.ijpara.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/23/2024] [Accepted: 04/07/2024] [Indexed: 04/13/2024]
Abstract
Wild rhesus macaques are a potential source of zoonotic parasites for humans, and Entamoeba spp. are common intestinal parasites. To investigate the prevalence of Entamoeba in wild rhesus macaques in China and explore the genetic differentiation of the potentially pathogenic species Entamoeba nuttalli, a total of 276 fecal samples from five populations at high altitudes (HAG, 2,800-4,100 m above sea level) and four populations at low altitudes (LAG, 5-1,000 m above sea level) were collected. PCR methods based on the ssrRNA gene were used to detect Entamoeba infection. Genotyping of E. nuttalli was performed based on six tRNA-linked short tandem repeat (STR) loci for further genetic analyses. The results revealed that Entamoeba infection (69.2%) was common in wild rhesus macaques in China, especially in LAG which had a significantly higher prevalence rate than that in HAG (P < 0.001). Three zoonotic species were identified: Entamoeba chattoni (60.9%) was the most prevalent species and distributed in all the populations, followed by Entamoeba coli (33.3%) and Entamoeba nuttalli (17.4%). In addition, a novel Entamoeba ribosomal lineage named RL13 (22.8%) was identified, and phylogenetic analysis revealed a close genetic relationship between RL13 and Entamoeba. hartmanni. Genotyping of E. nuttalli obtained 24 genotypes from five populations and further analysis showed E. nuttalli had a high degree of genetic differentiation (FST > 0.25, Nm < 1) between the host populations. The result of analysis of molecular variance (AMOVA) revealed that observed genetic differences mainly originate from differences among populations (FST = 0.91). Meanwhile, the phylogenetic tree showed that these genotypes of E. nuttalli were clustered according to geographical populations, indicating a significant phylogeographic distribution pattern. Considering the potential pathogenicity of E. nuttalli, attention should be paid to its risk of zoonotic transmission.
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Affiliation(s)
- Mengshi Yu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Xin Li
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Aoxing Su
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Ying Xiong
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongtao Xiao
- College of Life Science, Sichuan Agricultural University, Ya'an, China.
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, China.
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Upadhyay S, Das K, Ghosal A, Saito-Nakano Y, Dutta S, Nozaki T, Ganguly S. Short tandem repeat (STR) based sequence typing of Entamoeba histolytica identifies S TGA-D locus as a genetic marker, associated with disease outcomes. Parasitol Int 2024; 99:102846. [PMID: 38110172 DOI: 10.1016/j.parint.2023.102846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023]
Abstract
Amoebiasis, caused by the enteric parasite Entamoeba histolytica has differential disease outcomes. The association of parasite genotypes with outcomes of amoebic infection is still a paradox and requires to be explored. The genetic information of infecting strains from endemic settings of different geographical regions is essential to evaluate the relation. Comparative genetics of E. histolytica clinical isolates from different disease outcomes have been explored based on two tRNA-linked STR loci (STGA-D and A-L). All of the repeat patterns in the A-L locus were newly identified and unique to Indian isolates. The majority of newly identified repeat patterns in STGA-D locus have outcome-specific distributions, predicting the emergence of disease-specific mutations in this target locus. Statistical analysis further reinforces this observation, as identified repeat patterns only from STGA-D but not A-L locus were significantly associated with disease outcomes. Phylogenetic analysis indicates independent segregation and divergence of tRNA-linked STR arrays for each STR locus.
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Affiliation(s)
- Shashi Upadhyay
- Department of Allied Health Sciences, School of Health Science and Technology, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Koushik Das
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India.
| | - Ajanta Ghosal
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Sandipan Ganguly
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), Kolkata 700010, India.
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Morán P, Serrano-Vázquez A, Rojas-Velázquez L, González E, Pérez-Juárez H, Hernández EG, Padilla MDLA, Zaragoza ME, Portillo-Bobadilla T, Ramiro M, Ximénez C. Amoebiasis: Advances in Diagnosis, Treatment, Immunology Features and the Interaction with the Intestinal Ecosystem. Int J Mol Sci 2023; 24:11755. [PMID: 37511519 PMCID: PMC10380210 DOI: 10.3390/ijms241411755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
This review of human amoebiasis is based on the most current knowledge of pathogenesis, diagnosis, treatment, and Entamoeba/microbiota interactions. The most relevant findings during this last decade about the Entamoeba parasite and the disease are related to the possibility of culturing trophozoites of different isolates from infected individuals that allowed the characterization of the multiple pathogenic mechanisms of the parasite and the understanding of the host-parasite relationship in the human. Second, the considerable advances in molecular biology and genetics help us to analyze the genome of Entamoeba, their genetic diversity, and the association of specific genotypes with the different amoebic forms of human amoebiasis. Based on this knowledge, culture and/or molecular diagnostic strategies are now available to determine the Entamoeba species and genotype responsible for invasive intestinal or extraintestinal amoebiasis cases. Likewise, the extensive knowledge of the immune response in amoebiasis with the appearance of new technologies made it possible to design diagnostic tools now available worldwide. Finally, the understanding of the interaction between the Entamoeba species and the intestinal microbiota aids the understanding of the ecology of this parasite in the human environment. These relevant findings will be discussed in this review.
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Affiliation(s)
- Patricia Morán
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
| | - Angélica Serrano-Vázquez
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
| | - Liliana Rojas-Velázquez
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
| | - Enrique González
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
| | - Horacio Pérez-Juárez
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
| | - Eric G Hernández
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
| | - Maria de Los Angeles Padilla
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
| | - Martha E Zaragoza
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
| | - Tobías Portillo-Bobadilla
- Unidad de Bioinformática, Bioestadística y Biología Computacional, Red de Apoyo a la Investigación, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico
| | - Manuel Ramiro
- División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - Cecilia Ximénez
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 06726, Mexico
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Yanagawa Y, Singh U. Diversity and Plasticity of Virulent Characteristics of Entamoeba histolytica. Trop Med Infect Dis 2023; 8:tropicalmed8050255. [PMID: 37235303 DOI: 10.3390/tropicalmed8050255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
The complexity of clinical syndromes of amebiasis, caused by the parasite Entamoeba histolytica, stems from the intricate interplay between the host immune system, the virulence of the invading parasite, and the surrounding environment. Although there is still a relative paucity of information about the precise relationship between virulence factors and the pathogenesis of Entamoeba histolytica, by accumulating data from clinical and basic research, researchers have identified essential pathogenic factors that play a critical role in the pathogenesis of amebiasis, providing important insights into disease development through animal models. Moreover, the parasite's genetic variability has been associated with differences in virulence and disease outcomes, making it important to fully understand the epidemiology and pathogenesis of amebiasis. Deciphering the true mechanism of disease progression in humans caused by this parasite is made more difficult through its ability to demonstrate both genomic and pathological plasticity. The objective of this article is to underscore the heterogeneous nature of disease states and the malleable virulence characteristics in experimental models, while also identifying persistent scientific issues that need to be addressed.
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Affiliation(s)
- Yasuaki Yanagawa
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Upinder Singh
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Huaman JL, Pacioni C, Kenchington-Evans L, Doyle M, Helbig KJ, Carvalho TG. First Evidence of Entamoeba Parasites in Australian Wild Deer and Assessment of Transmission to Cattle. Front Cell Infect Microbiol 2022; 12:883031. [PMID: 35755840 PMCID: PMC9226911 DOI: 10.3389/fcimb.2022.883031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022] Open
Abstract
Australian wild deer populations have significantly expanded in size and distribution in recent decades. Due to their role in pathogen transmission, these deer populations pose a biosecurity risk to the livestock industry. However, little is known about the infection status of wild deer in Australia. The intestinal parasite Entamoeba bovis has been previously detected in farm and wild ruminants worldwide, but its epidemiology and distribution in wild ruminants remain largely unexplored. To investigate this knowledge gap, faecal samples of wild deer and domestic cattle from south-eastern Australia were collected and analysed for the presence of Entamoeba spp. using PCR and phylogenetic analysis of the conserved 18S rRNA gene. E. bovis parasites were detected at high prevalence in cattle and wild deer hosts, and two distinct Entamoeba ribosomal lineages (RLs), RL1 and RL8, were identified in wild deer. Phylogenetic analysis further revealed the existance of a novel Entamoeba species in sambar deer and a novel Entamoeba RL in fallow deer. While we anticipated cross-species transmission of E. bovis between wild deer and cattle, the data generated in this study demonstrated transmission is yet to occur in Australia. Overall, this study has identified novel variants of Entamoeba and constitutes the first report of Entamoeba in fallow deer and sambar deer, expanding the host range of this parasite. Epidemiological investigations and continued surveillance of Entamoeba parasites in farm ruminants and wild animals will be required to evaluate pathogen emergence and transmission to livestock.
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Affiliation(s)
- Jose L Huaman
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, Australia
| | - Carlo Pacioni
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Melbourne, VIC, Australia.,Environmental and Conservation Sciences, Murdoch University, Perth, WA, Australia
| | - Lily Kenchington-Evans
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, Australia
| | - Mark Doyle
- Far South Coast, South East Local Land Services, Bega, NSW, Australia
| | - Karla J Helbig
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, Australia
| | - Teresa G Carvalho
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, Australia
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6
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Elmallawany MA, EL-Dardiry MA, Nahnoush RK, Akmal M, Afife AA, Badr MS. Structural and Genetic Diversity of Entamoeba gingivalis Trophozoites Isolated from Diseased and Healthy Periodontal Sites. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.8713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: At present, there is little documented about the variability aspects of Entamoeba gingivalis (E. gingivalis) in relation to periodontal diseases. This is perhaps due to several specialists rejecting the notion that E. gingivalis can cause periodontal disease.
AIM: The aim of the present study was to compare the morphological and genetic variability within trophozoites isolated from diseased (n = 26) and healthy periodontal sites (n = 14).
METHODS: Detailed microscopic analyses were performed, in addition to post real-time polymerase chain reaction 18S-SSU rRNA gene scanning technology, using reference synthetic genes to analyze melting curve features from different isolates.
RESULTS: All trophozoites isolated from diseased sites were significantly larger in size than those isolated from healthy sites. In addition, they were found in clusters, containing many leukophagocytosis and in a significantly higher number than those from healthy sites. Gene scanning revealed diversity within the isolates with a significantly higher number of mutant forms (18 out of 26) within the trophozoites isolated from diseased sites, 14 of them were of unknown origin. Four melting curves matched E. gingivalis H57 strain and the remaining eight were related to the wild strain (ATCC-30927). Isolates from healthy sites corresponded to the wild type (12 out of 14) with only two related to H57 strain.
CONCLUSION: The study confirmed morphological and genetic variability between different isolates; We still recommend further in-depth molecular studies to investigate the role of this oral protozoan in the pathogenicity of periodontal affection. The study highlighted the importance of real engagement of multidisciplinary diagnostic strategies, involving experts from variable medical fields to reach truthful scientific outcomes concerning the association of certain microorganism to particular diseases or disorders.
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García-lerena JA, González-blanco G, Saucedo-cárdenas O, Valdés J. Promoter-Bound Full-Length Intronic Circular RNAs-RNA Polymerase II Complexes Regulate Gene Expression in the Human Parasite Entamoeba histolytica. Noncoding RNA 2022; 8:12. [PMID: 35202086 PMCID: PMC8876499 DOI: 10.3390/ncrna8010012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/12/2022] Open
Abstract
Ubiquitous eukaryotic non-coding circular RNAs are involved in numerous co- and post-transcriptional regulatory mechanisms. Recently, we reported full-length intronic circular RNAs (flicRNAs) in Entamoeba histolytica, with 3′ss–5′ss ligation points and 5′ss GU-rich elements essential for their biogenesis and their suggested role in transcription regulation. Here, we explored how flicRNAs impact gene expression regulation. Using CLIP assays, followed by qRT-PCR, we identified that the RabX13 control flicRNA and virulence-associated flicRNAs were bound to the HA-tagged RNA Pol II C-terminus domain in E. histolytica transformants. The U2 snRNA was also present in such complexes, indicating that they belonged to transcription initiation/elongation complexes. Correspondingly, inhibition of the second step of splicing using boric acid reduced flicRNA formation and modified the expression of their parental genes and non-related genes. flicRNAs were also recovered from chromatin immunoprecipitation eluates, indicating that the flicRNA-Pol II complex was formed in the promoter of their cognate genes. Finally, two flicRNAs were found to be cytosolic, whose functions remain to be uncovered. Here, we provide novel evidence of the role of flicRNAs in gene expression regulation in cis, apparently in a widespread fashion, as an element bound to the RNA polymerase II transcription initiation complex, in E. histolytica.
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Das K, Sardar SK, Ghosal A, Saito-Nakano Y, Dutta S, Nozaki T, Ganguly S. Multilocus sequence typing (MLST) of Entamoeba histolytica identifies kerp2 as a genetic marker associated with disease outcomes. Parasitol Int 2021; 83:102370. [PMID: 33932601 DOI: 10.1016/j.parint.2021.102370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/25/2021] [Accepted: 04/25/2021] [Indexed: 12/29/2022]
Abstract
Amoebiasis caused by protozoan parasite Entamoeba histolytica has diverse infection outcomes. The relationship between parasite genotypes and outcome of amoebic infection is still a paradox and needs to be explored. Genome information of infecting strains from endemic areas throughout the world is essential to explore this relation. Comparative genetics between E. histolytica populations from different disease outcomes have been studied to identify potential genetic markers having single nucleotide polymorphisms (SNPs) significantly associated with specific clinical outcome. Coding and non-coding regions have significantly different rates of polymorphism. Non-synonymous base substitutions were significantly more frequent than synonymous within coding loci. Both synonymous and non-synonymous SNPs within lysine- and glutamic acid rich protein 2 (kerp2) locus were significantly associated with disease outcomes. An incomplete linkage disequilibrium (LD) value with potential recombination events and significant population differentiation (FST) value have also been identified at kerp2 locus within the study population. Presence of disease specific SNPs, potential recombination events, and significant FST value at kerp2 locus indicate that kerp2 gene and its gene product are under constant selection pressure exerted by host on parasite and could also be a potential determinant of disease outcome of E. histolytica infection. Furthermore, E. histolytica isolated from asymptomatic carriers are phylogenetically closer to those causing liver abscess in human and exhibit potential inter-population recombination among them. Individuals with persistent asymptomatic E. histolytica infection may be under high risk of developing amoebic liver abscess formation in future and detailed investigation of asymptomatic individuals from endemic areas should be always required.
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Affiliation(s)
- Koushik Das
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Sanjib Kumar Sardar
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Ajanta Ghosal
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Shanta Dutta
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo, Japan
| | - Sandipan Ganguly
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India.
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König C, Honecker B, Wilson IW, Weedall GD, Hall N, Roeder T, Metwally NG, Bruchhaus I. Taxon-Specific Proteins of the Pathogenic Entamoeba Species E. histolytica and E. nuttalli. Front Cell Infect Microbiol 2021; 11:641472. [PMID: 33816346 PMCID: PMC8017271 DOI: 10.3389/fcimb.2021.641472] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/03/2021] [Indexed: 01/30/2023] Open
Abstract
The human protozoan parasite Entamoeba histolytica can live in the human intestine for months or years without generating any symptoms in the host. For unknown reasons, amoebae can suddenly destroy the intestinal mucosa and become invasive. This can lead to amoebic colitis or extraintestinal amoebiasis whereby the amoebae spread to other organs via the blood vessels, most commonly the liver where abscesses develop. Entamoeba nuttalli is the closest genetic relative of E. histolytica and is found in wild macaques. Another close relative is E. dispar, which asyptomatically infects the human intestine. Although all three species are closely related, only E. histolytica and E. nuttalli are able to penetrate their host’s intestinal epithelium. Lineage-specific genes and gene families may hold the key to understanding differences in virulence among species. Here we discuss those genes found in E. histolytica that have relatives in only one or neither of its sister species, with particular focus on the peptidase, AIG, Ariel, and BspA families.
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Affiliation(s)
- Constantin König
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Barbara Honecker
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ian W Wilson
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Gareth D Weedall
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Thomas Roeder
- Zoology, Department of Molecular Physiology, Kiel University, Kiel, Germany.,Airway Research Center North (ARCN), German Center for Lung Research (DZL), Kiel, Germany
| | | | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Department of Biology, University of Hamburg, Hamburg, Germany
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Das K, Nair LV, Ghosal A, Sardar SK, Dutta S, Ganguly S. Genetic characterization reveals evidence for an association between water contamination and zoonotic transmission of a Cryptosporidium sp. from dairy cattle in West Bengal, India. Food Waterborne Parasitol 2020; 17:e00064. [PMID: 32095634 PMCID: PMC7034051 DOI: 10.1016/j.fawpar.2019.e00064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 08/08/2019] [Accepted: 08/15/2019] [Indexed: 11/27/2022] Open
Abstract
Cryptosporidium sp. is an enteric parasite with zoonotic potential, and can infect a wide range of vertebrates, including human. Determining the source of infection and the mode of transmission in a new endemic region is crucial for the control of cryptosporidiosis. In the present study, we have assessed the importance of dairy cattle as a potential source of Cryptosporidium infection for humans in a newly recognized endemic region. Cryptosporidium isolates from dairy calves, humans (farm workers) and nearby water bodies were genetically characterized based on 18SrRNA and hsp70 genes. A high incidence of Cryptosporidium infection was identified in our study region. This finding is of public health concern. Cryptosporidium ryanae rather than Cryptosporidium parvum has been identified as the most prevalent infecting species in the study region. Infections were associated with clinical symptoms of infected animals. An incomplete linkage disequilibrium (LD) value with potential recombination events at 18SrRNA locus were identified for the first time in C. ryanae, which was previously reported as a clonal population. Phylogenetic analysis revealed the presence of identical genotypes of a Cryptosporidium sp. from dairy calves, farm workers and nearby water bodies and indicates an association between water contamination and zoonotic transmission of Cryptosporidiosis in our study region.
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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, West Bengal, India
| | - Lakshmi V Nair
- Department of Microbiology, All India Institute of Hygiene and Public Health, 110 Chittaranjan Avenue, Kolkata 700073, West Bengal, India
| | - Ajanta Ghosal
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Sanjib Kumar Sardar
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Shanta Dutta
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Sandipan Ganguly
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India
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11
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Tomii K, Santos HJ, Nozaki T. Genome-Wide Analysis of Known and Potential Tetraspanins in Entamoeba histolytica. Genes (Basel) 2019; 10:genes10110885. [PMID: 31684194 PMCID: PMC6895871 DOI: 10.3390/genes10110885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022] Open
Abstract
Tetraspanins are membrane proteins involved in intra- and/or intercellular signaling, and membrane protein complex formation. In some organisms, their role is associated with virulence and pathogenesis. Here, we investigate known and potential tetraspanins in the human intestinal protozoan parasite Entamoeba histolytica. We conducted sequence similarity searches against the proteome data of E. histolytica and newly identified nine uncharacterized proteins as potential tetraspanins in E. histolytica. We found three subgroups within known and potential tetraspanins, as well as subgroup-associated features in both their amino acid and nucleotide sequences. We also examined the subcellular localization of a few representative tetraspanins that might be potentially related to pathogenicity. The results in this study could be useful resources for further understanding and downstream analyses of tetraspanins in Entamoeba.
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Affiliation(s)
- Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
| | - Herbert J Santos
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Cui Z, Li J, Chen Y, Zhang L. Molecular epidemiology, evolution, and phylogeny of Entamoeba spp. Infect Genet Evol 2019; 75:104018. [PMID: 31465857 DOI: 10.1016/j.meegid.2019.104018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 01/11/2023]
Abstract
Entamoeba histolytica is a protozoan parasite and the causative agent of amoebiasis in humans. The estimations of the worldwide burden of amoebiasis by the WHO indicated that approximately 500 million people were infected with the parasite and 10% of these individuals had invasive amoebiasis. However, our understanding of the disease burden and epidemiology of human amebiasis has undergone dramatic changes over the last two decades based on molecular analyses. The development of Entamoeba genomics has also provided some interesting and valuable information on the evolution and population structure of this parasite. In addition, the use of a number of molecular markers has greatly expanded our understanding of Entamoeba host range and genetic diversity. In this review, we re-assessed Entamoeba prevalence and species in humans, non-human primates, other animals, and the environment in the context of molecular data. Some issues regarding the evolution and phylogeny of different Entamoeba species lineages are also discussed.
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Affiliation(s)
- Zhaohui Cui
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; National International Joint Research Center for Veterinary Immunology, Zhengzhou, China
| | - Junqiang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; National International Joint Research Center for Veterinary Immunology, Zhengzhou, China; Scientific Research Experiment Center & Laboratory Animal Center, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yuancai Chen
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; National International Joint Research Center for Veterinary Immunology, Zhengzhou, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; National International Joint Research Center for Veterinary Immunology, Zhengzhou, China.
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14
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Serradell MC, Rupil LL, Martino RA, Prucca CG, Carranza PG, Saura A, Fernández EA, Gargantini PR, Tenaglia AH, Petiti JP, Tonelli RR, Reinoso-Vizcaino N, Echenique J, Berod L, Piaggio E, Bellier B, Sparwasser T, Klatzmann D, Luján HD. Efficient oral vaccination by bioengineering virus-like particles with protozoan surface proteins. Nat Commun 2019; 10:361. [PMID: 30664644 DOI: 10.1038/s41467-018-08265-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/22/2018] [Indexed: 12/13/2022] Open
Abstract
Intestinal and free-living protozoa, such as Giardia lamblia, express a dense coat of variant-specific surface proteins (VSPs) on trophozoites that protects the parasite inside the host’s intestine. Here we show that VSPs not only are resistant to proteolytic digestion and extreme pH and temperatures but also stimulate host innate immune responses in a TLR-4 dependent manner. We show that these properties can be exploited to both protect and adjuvant vaccine antigens for oral administration. Chimeric Virus-like Particles (VLPs) decorated with VSPs and expressing model surface antigens, such as influenza virus hemagglutinin (HA) and neuraminidase (NA), are protected from degradation and activate antigen presenting cells in vitro. Orally administered VSP-pseudotyped VLPs, but not plain VLPs, generate robust immune responses that protect mice from influenza infection and HA-expressing tumors. This versatile vaccine platform has the attributes to meet the ultimate challenge of generating safe, stable and efficient oral vaccines. Giardia lamblia express a dense coat of variant-specific surface proteins (VSPs) on trophozoites that protects the parasite inside the host´s intestine. Here the authors show that stability and immunomodulatory properties of VSPs can be exploited to both protect and adjuvant vaccine antigens for oral administration.
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15
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Avendaño-Borromeo B, Narayanasamy RK, García-Rivera G, Labra-Barrios ML, Lagunes-Guillén AE, Munguía-Chávez B, Castañón-Sánchez CA, Orozco E, Luna-Arias JP. Identification of the gene encoding the TATA box-binding protein-associated factor 1 (TAF1) and its putative role in the heat shock response in the protozoan parasite Entamoeba histolytica. Parasitol Res 2018; 118:517-538. [PMID: 30552577 DOI: 10.1007/s00436-018-6170-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/29/2018] [Indexed: 11/26/2022]
Abstract
Transcription factor IID (TFIID) is a cornerstone in the transcription initiation in eukaryotes. It is composed of TBP and approximately 14 different subunits named TBP-associated factors (TAFs). TFIID has a key role in transcription of many genes involved in cell proliferation, cell growth, cell cycle, cell cycle checkpoint, and various other processes as well. Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, represents a major global health concern. Our research group has previously reported the genes coding the TATA box-binding protein (EhTBP) and TBP-related factor 1 (EhTRF1), which displayed different mRNA levels in trophozoites under different stress conditions. In this work, we identified the TBP-associated factor 1 (Ehtaf1) gene in the E. histolytica genome, which possess a well-conserved DUF domain and a Bromo domain located in the middle and C-terminus of the protein, respectively. The EhTAF1-DUF domain tertiary structure is similar to the corresponding HsTAF1 DUF domain. RT-qPCR experiments with RNA isolated from trophozoites harvested at different time points of the growth curve and under different stress conditions revealed that the Ehtaf1 gene was found slightly upregulated in the death phase of growth curve, but under heat shock stress, it was found upregulated 10 times, suggesting that Ehtaf1 might have an important role in the heat shock stress response. We also found that EhTAF1 is expressed in the nucleus and cytoplasm at 37 °C, but under heat shock stress, it is overexpressed in both the nucleus and cytoplasm, and partially colocalized with EhHSP70 in cytoplasm.
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Affiliation(s)
- Bartolo Avendaño-Borromeo
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Ravi Kumar Narayanasamy
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - María Luisa Labra-Barrios
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Anel E Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Bibiana Munguía-Chávez
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Carlos Alberto Castañón-Sánchez
- Laboratorio de Investigación Biomédica, Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, Aldama S/N, San Bartolo Coyotepec, 71256, Oaxaca, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Juan Pedro Luna-Arias
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico.
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16
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Kazama M, Yoshida K, Ogiwara S, Makiuchi T, Tachibana H. Influence of Heterologous Transplant of DNA-lacking Mitochondria from Entamoeba histolytica on Proliferation of Entamoeba invadens. J Eukaryot Microbiol 2018; 66:483-493. [PMID: 30329208 DOI: 10.1111/jeu.12693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/30/2018] [Accepted: 10/08/2018] [Indexed: 11/27/2022]
Abstract
In mitochondria, compatibility of proteins encoded in mitochondrial DNA and nuclear DNA is essential for the normal functioning of the organelle. Incompatibility between mitochondrial and nuclear DNA can lead to dysfunctional respiration, mitochondrial diseases, and lethal problems, which suggests that the presence of heterologous mitochondria is unfavorable. In a previous study, we established a transplant method for DNA-lacking mitochondria (mitosomes) in the anaerobic protozoan Entamoeba histolytica. In this study, interspecies transplant of mitosomes from E. histolytica into Entamoeba invadens, which is a parasitic protozoon of reptiles, was performed using the microinjection method at various temperatures and injection volumes. When E. invadens was used as recipient, it showed higher tolerance to a lower temperature and larger injection volume, in comparison with E. histolytica. After microinjection, donor mitosomes expressing HA-tag conjugated protein were observed in recipient cells by immunofluorescent staining. The heterologous mitosomes-injected cells proliferated and growth rate of the microinjected-cells was similar to that of intact cells. Therefore, we conclude that interspecies transplant of DNA-lacking mitochondria does not result in incompatibility.
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Affiliation(s)
- Makoto Kazama
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan.,NEKKEN Bio-Resource Center, Institute of Tropical Medicine, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Kazuhiro Yoshida
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan.,Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Sanae Ogiwara
- Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Takashi Makiuchi
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Hiroshi Tachibana
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
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17
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Valdés-Flores J, López-Rosas I, López-Camarillo C, Ramírez-Moreno E, Ospina-Villa JD, Marchat LA. Life and Death of mRNA Molecules in Entamoeba histolytica. Front Cell Infect Microbiol 2018; 8:199. [PMID: 29971219 PMCID: PMC6018208 DOI: 10.3389/fcimb.2018.00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/28/2018] [Indexed: 02/05/2023] Open
Abstract
In eukaryotic cells, the life cycle of mRNA molecules is modulated in response to environmental signals and cell-cell communication in order to support cellular homeostasis. Capping, splicing and polyadenylation in the nucleus lead to the formation of transcripts that are suitable for translation in cytoplasm, until mRNA decay occurs in P-bodies. Although pre-mRNA processing and degradation mechanisms have usually been studied separately, they occur simultaneously and in a coordinated manner through protein-protein interactions, maintaining the integrity of gene expression. In the past few years, the availability of the genome sequence of Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, coupled to the development of the so-called “omics” technologies provided new opportunities for the study of mRNA processing and turnover in this pathogen. Here, we review the current knowledge about the molecular basis for splicing, 3′ end formation and mRNA degradation in amoeba, which suggest the conservation of events related to mRNA life throughout evolution. We also present the functional characterization of some key proteins and describe some interactions that indicate the relevance of cooperative regulatory events for gene expression in this human parasite.
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Affiliation(s)
- Jesús Valdés-Flores
- Departamento de Bioquímica, CINVESTAV, Ciudad de Mexico, Mexico City, Mexico
| | - Itzel López-Rosas
- CONACyT Research Fellow - Colegio de Postgraduados Campus Campeche, Campeche, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México Ciudad de Mexico, Mexico City, Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Juan D Ospina-Villa
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Laurence A Marchat
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
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18
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García G, Ramos F, Martínez-Hernández F, Hernández L, Yáñez J, Gaytán P. A new subtype of Entamoeba gingivalis: "E. gingivalis ST2, kamaktli variant". Parasitol Res 2018; 117:1277-1284. [PMID: 29429011 PMCID: PMC5978907 DOI: 10.1007/s00436-018-5798-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/31/2018] [Indexed: 11/24/2022]
Abstract
Entamoeba gingivalis is a protozoan that resides in the oral cavity. Using molecular biology techniques, we identified a novel organism that shares the same ecological niche as E. gingivalis. To differentiate this organism from E. gingivalis, we named it “kamaktli variant.” By sequencing the 18S-ITS1-5.8S-ITS2 rRNA region, we demonstrated that kamaktli variant is 89% identical to E. gingivalis. To elucidate the relationship between kamaktli variant and E. gingivalis, we performed a phylogenetic analysis. Both taxa clustered in the same clade with high support, indicating that the amoebas are closely related (98/99/1.00, maximum parsimony/maximum likelihood/MrBayes, respectively). Given this information, we propose that these molecular differences between kamaktli variant and E. gingivalis ST1 are sufficient to distinguish them as independent subtypes, and we name the new subtype “E. gingivalis ST2, kamaktli variant.”
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Affiliation(s)
- Gabriela García
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Cd. Universitaria Coyoacán, CP.04510, Ciudad de México, Mexico.
| | - Fernando Ramos
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Cd. Universitaria Coyoacán, CP.04510, Ciudad de México, Mexico
| | - Fernando Martínez-Hernández
- Departamento de Ecología de Agentes Patógenos, Hospital General Dr. Manuel Gea González, Calzada de Tlalpan 4800, Tlalpan, CP.14080, Ciudad de México, Mexico
| | - Lilian Hernández
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Cd. Universitaria Coyoacán, CP.04510, Ciudad de México, Mexico
| | - Jorge Yáñez
- Unidad de Síntesis y Secuenciación de DNA, Instituto de Biotecnología, UNAM, Av. Universidad 2001, CP.14000, Cuernavaca, Morelos, Mexico
| | - Paul Gaytán
- Unidad de Síntesis y Secuenciación de DNA, Instituto de Biotecnología, UNAM, Av. Universidad 2001, CP.14000, Cuernavaca, Morelos, Mexico
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19
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Abstract
The outcome of an Entamoeba histolytica infection is variable and the contribution of genetic diversity within E. histolytica to human disease is not fully understood. The information provided by the whole genome sequence of the E. histolytica reference laboratory strain (HM-1:IMSS) and thirteen additional laboratory strains have been made publically available. In this review theories on the source of the unexpected level of structural diversity found in E. histolytica will be discussed.
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Affiliation(s)
- Carol A Gilchrist
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
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20
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Jackson AP. Gene family phylogeny and the evolution of parasite cell surfaces. Mol Biochem Parasitol 2016; 209:64-75. [DOI: 10.1016/j.molbiopara.2016.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/18/2016] [Accepted: 03/19/2016] [Indexed: 11/30/2022]
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21
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Maurer-Alcalá XX, Katz LA. An epigenetic toolkit allows for diverse genome architectures in eukaryotes. Curr Opin Genet Dev 2015; 35:93-9. [PMID: 26649755 DOI: 10.1016/j.gde.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 02/04/2023]
Abstract
Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes are only possible due to the well-developed epigenetic toolkit, which probably existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic tree of life. Here we highlight how the changes in genome architecture in diverse eukaryotes are regulated by epigenetic processes, such as DNA elimination, genome rearrangements, and adaptive changes to genome architecture. The ability to epigenetically modify and regulate genomes has contributed greatly to the diversity of eukaryotes observed today.
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Affiliation(s)
- Xyrus X Maurer-Alcalá
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA.
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22
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Zhang H, Ehrenkaufer GM, Manna D, Hall N, Singh U. High Throughput Sequencing of Entamoeba 27nt Small RNA Population Reveals Role in Permanent Gene Silencing But No Effect on Regulating Gene Expression Changes during Stage Conversion, Oxidative, or Heat Shock Stress. PLoS One 2015; 10:e0134481. [PMID: 26248204 PMCID: PMC4527709 DOI: 10.1371/journal.pone.0134481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/10/2015] [Indexed: 01/09/2023] Open
Abstract
The human parasite Entamoeba histolytica has an active RNA interference (RNAi) pathway with an extensive repertoire of 27nt small RNAs that silence genes. However the role of this pathway in regulating amebic biology remains unknown. In this study, we address whether silencing via 27nt small RNAs may be a mechanism for controlling gene expression changes during conversion between the trophozoite and cyst stages of the parasite. We sequenced small RNA libraries generated from trophozoites, early cysts, mature cysts, and excysting cells and mapped them to the E. invadens genome. Our results show that, as in E. histolytica, small RNAs in E. invadens are largely ~27nt in length, have an unusual 5'-polyphosphate structure and mediate gene silencing. However, when comparing the libraries from each developmental time-point we found few changes in the composition of the small RNA populations. Furthermore, genes targeted by small RNAs were permanently silenced with no changes in transcript abundance during development. Thus, the E. invadens 27nt small RNA population does not mediate gene expression changes during development. In order to assess the generalizability of our observations, we examined whether small RNAs may be regulating gene expression changes during stress response in E. histolytica. Comparison of the 27nt small RNA populations from E. histolytica trophozoites from basal conditions, or after heat shock or exposure to oxidative stress showed few differences. Similar to data in E. invadens development, genes targeted by small RNAs were consistently silenced and did not change expression under tested stress conditions. Thus, the biological roles of the 27nt small RNA population in Entamoeba remain elusive. However, as the first characterization of the RNAi pathway in E. invadens these data serve as a useful resource for the study of Entamoeba development and open the door to the development of RNAi-based gene silencing tools in E. invadens.
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Affiliation(s)
- Hanbang Zhang
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gretchen M. Ehrenkaufer
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Dipak Manna
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Neil Hall
- Center for Genomic Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool, United Kingdom
| | - Upinder Singh
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cuadrat RRC, da Serra Cruz SM, Tschoeke DA, Silva E, Tosta F, Jucá H, Jardim R, Campos MLM, Mattoso M, Dávila AMR. An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs. OMICS 2014; 18:524-38. [PMID: 24960463 DOI: 10.1089/omi.2013.0172] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A key focus in 21(st) century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI's COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools.
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Affiliation(s)
- Rafael R C Cuadrat
- 1 Computational and Systems Biology Laboratory, Computational and Systems Biology Pole, Oswaldo Cruz Institute , Fiocruz, Brazil
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Das K, Mukherjee AK, Chowdhury P, Sehgal R, Bhattacharya MK, Hashimoto T, Nozaki T, Ganguly S. Multilocus sequence typing system (MLST) reveals a significant association of Entamoeba histolytica genetic patterns with disease outcome. Parasitol Int 2013; 63:308-14. [PMID: 24321887 DOI: 10.1016/j.parint.2013.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 11/09/2013] [Accepted: 11/28/2013] [Indexed: 10/25/2022]
Abstract
The relationship between parasite genotypes and outcome of amoebic infection is still a paradox and needed to be explored. Proper identification and genetic characterization of Entamoeba histolytica clinical isolates is an effective tool for exploring this relation. Along with conventional polymorphic marker (Chitinase), tRNA linked short tandem repeat (STR) loci has been employed as multilocus genotyping tool due to its better resolution and evolutionary significance. Some common as well as exclusive repeat patterns showing significant relation with disease outcome have been identified. Phylogenetic analysis revealed that repeat patterns exclusively found in asymptomatic and amoebic liver abscess derived isolates are placed in a common lineage and has similar association pattern with the disease outcome. Assumption can be made that isolates of E. histolytica remaining asymptomatic is genetically closer siblings of those causing liver abscess rather than the diarrheal isolates.
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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.
| | - Avik K Mukherjee
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India.
| | - Punam Chowdhury
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India.
| | - Rakesh Sehgal
- Department of Parasitology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Mihir K Bhattacharya
- Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8572, Japan.
| | - Tomoyoshi Nozaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8572, Japan; Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - 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] [What about the content of this article? (0)] [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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Zermeño V, Ximénez C, Morán P, Valadez A, Valenzuela O, Rascón E, Diaz D, Cerritos R. Worldwide genealogy of Entamoeba histolytica: an overview to understand haplotype distribution and infection outcome. Infect Genet Evol 2013; 17:243-52. [PMID: 23624203 DOI: 10.1016/j.meegid.2013.04.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/18/2013] [Accepted: 04/18/2013] [Indexed: 11/17/2022]
Abstract
Although Entamoeba histolytica is one of the most prevalent intestinal parasites, how the different strains of this species are distributed all over the world and how different genotypes are associated with the infection outcome are yet to be fully understood. Recently, the use of a number of molecular markers has made the characterization of several genotypes in those regions with high incidence of amoebiasis possible. This work proposes the first genealogy of E. histolytica, with an haplotype network based on two tRNA gene-linked array of Short Tandem Repeats (STRs) reported until today, and 47 sequences from 39 new isolates of Mexican Amoebic Liver Abscesses (ALA) samples. One hundred and three sequences were obtained from D-A locus, their information about the geographic region of isolation as well as clinical diagnosis were also collected. One hundred and five sequences from N-K2 locus were also obtained as well as the region of isolation, but the information about clinical diagnosis was not available in all cases. The most abundant and widely distributed haplotype in the world is the one of E. histolytica HM1:IMSS strain. This was found in Mexico, Bangladesh, Japan, China and USA and is associated to symptomatic patients as well as asymptomatic cyst passers. Many other haplotypes were found only in a single country. Both genealogies suggest that there are no lineages within the networks that may be related to a particular geographic region or infection outcome. A concatenated analysis of the two molecular markers revealed 12 different combinations, which suggests the possibility of genetic recombination events. The present study is the first to propose a global genealogy of this species and suggests that there are still many genotypes to be discovered. The genotyping of new isolates will help to understand the great diversity and genetic structure of this parasite.
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Affiliation(s)
- Valeria Zermeño
- Departamento de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, México DF, Mexico
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Glöckner G, Noegel AA. Comparative genomics in the Amoebozoa clade. Biol Rev Camb Philos Soc 2012; 88:215-25. [PMID: 23134060 DOI: 10.1111/j.1469-185x.2012.00248.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 09/25/2012] [Accepted: 10/05/2012] [Indexed: 11/30/2022]
Abstract
Amoeboid life forms can be found throughout the evolutionary tree. The greatest proportion of these life forms is found in the Amoebozoa clade, one of the six major eukaryote evolutionary branches. Despite its common origin this clade exhibits a wide diversity of lifestyles including free-living and parasitic species and species with multicellular and multinucleate life stages. In this group, development, cooperation, and social behaviour can be studied in addition to traits common to unicellular organisms. To date, only a few Amoebozoa genomes have been sequenced completely, however a number of expressed sequence tags (ESTs) and complete and draft genomes have become available recently for several species that represent some of the major evolutionary lineages in this clade. This resource allows us to compare and analyse the evolutionary history and fate of branch-specific genes if properly exploited. Despite the large evolutionary time scale since the emergence of the major groups the genomic organization in Amoebozoa has retained common features. The number of Amoebozoa-specific genetic inventions seems to be rather small. The emergence of subgroups is accompanied by gene and domain losses and acquisitions of bacterial gene material. The sophisticated developmental cycles of Myxogastria and Dictyosteliida likely have a common origin and are deeply rooted in amoebozoan evolution. In this review we describe initial approaches to comparative genomics in Amoebozoa, summarize recent findings, and identify goals for further studies.
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Affiliation(s)
- Gernot Glöckner
- Institute for Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301, Berlin, D-12587, Germany.
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