Whole genome sequencing of Entamoeba nuttalli reveals mammalian host-related molecular signatures and a novel octapeptide-repeat surface protein

Tanaka, Masayuki; Makiuchi, Takashi; Komiyama, Tomoyoshi; Shiina, Takashi; Osaki, Ken; Tachibana, Hiroshi

doi:10.1371/journal.pntd.0007923

Cited by 13 publications

(11 citation statements)

References 96 publications

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“…E. nuttalli is the species most closely related to E. histolytica . Different species of wild macaques, as well as other non-human primates kept in captivity, have been identified as hosts for E. nuttalli ( Tachibana et al, 2007 ; Tachibana et al, 2009 ; Levecke et al, 2010 ; Wei et al, 2018 ; Tanaka et al, 2019 ). In addition to the genomes of E. histolytica and E. dispar , the genome of E. nuttalli was recently sequenced and all genomes are available on AmoebaDB ( Tanaka et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

“…Different species of wild macaques, as well as other non-human primates kept in captivity, have been identified as hosts for E. nuttalli ( Tachibana et al, 2007 ; Tachibana et al, 2009 ; Levecke et al, 2010 ; Wei et al, 2018 ; Tanaka et al, 2019 ). In addition to the genomes of E. histolytica and E. dispar , the genome of E. nuttalli was recently sequenced and all genomes are available on AmoebaDB ( Tanaka et al, 2019 ). The ability to compare the genomes of E. histolytica , E. dispar and E. nuttalli now opens up the possibility of identifying additional molecules responsible for the development of extraintestinal amoebiasis in human or non-human primates.…”

Section: Introductionmentioning

confidence: 99%

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Taxon-Specific Proteins of the Pathogenic Entamoeba Species E. histolytica and E. nuttalli

König

Honecker

Wilson

et al. 2021

Front. Cell. Infect. Microbiol.

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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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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Taxon-Specific Proteins of the Pathogenic Entamoeba Species E. histolytica and E. nuttalli

König

Honecker

Wilson

et al. 2021

Front. Cell. Infect. Microbiol.

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“…In addition, we used the software TMHMM2.0 [ 37 ] to predict transmembrane proteins in Foc4 proteins. If the number of transmembrane helices predicted by TMHMM is greater than 1, the proteins are considered to be transmembrane proteins [ 38 ].…”

Section: Methodsmentioning

confidence: 99%

Predicting protein–protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification

2022

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Background The pathogen of banana Fusarium oxysporum f. sp. cubense race 4(Foc4) infects almost all banana species, and it is the most destructive. The molecular mechanism of the interactions between Fusarium oxysporum and banana still needs to be further investigated. Methods We use both the interolog and domain-domain method to predict the protein–protein interactions (PPIs) between banana and Foc4. The predicted protein interaction sequences are encoded by the conjoint triad and autocovariance method respectively to obtain continuous and discontinuous information of protein sequences. This information is used as the input data of the neural network model. The Long Short-Term Memory (LSTM) neural network five-fold cross-validation and independent test methods are used to verify the predicted protein interaction sequences. To further confirm the PPIs between banana and Foc4, the GO (Gene Ontology) and KEGG (Kyoto Encylopedia of Genes and Genomics) functional annotation and interaction network analysis are carried out. Results The experimental results show that the PPIs for banana and foc4 predicted by our proposed method may interact with each other in terms of sequence structure, GO and KEGG functional annotation, and Foc4 protein plays a more active role in the process of Foc4 infecting banana. Conclusions This study obtained the PPIs between banana and Foc4 by using computing means for the first time, which will provide data support for molecular biology experiments.

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“…Geographic distribution. Native to Southeast Asia, probably worldwide in zoos and from the animal trade ( Tanaka et al 2019 ).…”

Section: Checklist Of Eukaryotic Human Parasitesmentioning

confidence: 99%

An annotated checklist of the eukaryotic parasites of humans, exclusive of fungi and algae

Mathison¹,

Sapp²

2021

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The classification of “parasites” in the medical field is a challenging notion, a group which historically has included all eukaryotes exclusive of fungi that invade and derive resources from the human host. Since antiquity, humans have been identifying and documenting parasitic infections, and this collective catalog of parasitic agents has expanded considerably with technology. As our understanding of species boundaries and the use of molecular tools has evolved, so has our concept of the taxonomy of human parasites. Consequently, new species have been recognized while others have been relegated to synonyms. On the other hand, the decline of expertise in classical parasitology and limited curricula have led to a loss of awareness of many rarely encountered species. Here, we provide a comprehensive checklist of all reported eukaryotic organisms (excluding fungi and allied taxa) parasitizing humans resulting in 274 genus-group taxa and 848 species-group taxa. For each species, or genus where indicated, a concise summary of geographic distribution, natural hosts, route of transmission and site within human host, and vectored pathogens are presented. Ubiquitous, human-adapted species as well as very rare, incidental zoonotic organisms are discussed in this annotated checklist. We also provide a list of 79 excluded genera and species that have been previously reported as human parasites but are not believed to be true human parasites or represent misidentifications or taxonomic changes.

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Whole genome sequencing of Entamoeba nuttalli reveals mammalian host-related molecular signatures and a novel octapeptide-repeat surface protein

Cited by 13 publications

References 96 publications

Taxon-Specific Proteins of the Pathogenic Entamoeba Species E. histolytica and E. nuttalli

Taxon-Specific Proteins of the Pathogenic Entamoeba Species E. histolytica and E. nuttalli

Predicting protein–protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification

An annotated checklist of the eukaryotic parasites of humans, exclusive of fungi and algae

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