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Stefan Geisen - One of the best experts on this subject based on the ideXlab platform.
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Soil protist life matters
2020Co-Authors: Stefan Geisen, Enrique Lara, Edward A. D. Mitchell, Eckhard Völcker, Valentyna KrashevskaAbstract:Soils host most biodiversity on Earth, with a major fraction of its taxonomic diversity still to be uncovered and most of its functional knowledge to be determined. Much focus has been - and still is - on bacteria, fungi and animals. Clearly, without any of those components, soils would not function as they do. However, the group that constitutes the bulk of eukaryotic diversity and plays a central role for soil functioning is missing: Protists. As the main consumers of the microbiome, Protists shape its composition and functioning. Other less known functions performed by Protists may be equally important. Protists also include primary producers, decomposers, animal parasites and plant pathogens. We briefly review the many functions Protists perform in soils and argue that soil biodiversity studies that ignore Protists miss some potential mechanistic insight into the drivers of observed patterns. We highlight that the immense functional repertoire of protist affects virtually every soil process, from carbon cycling to primary production, including crop production. Therefore, we call for truly integrated biodiversity assessments including Protists, without which the soil food-web and processes cannot reliably be understood: Protists matter!
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The global-scale distributions of soil Protists and their contributions to belowground systems
Science advances, 2020Co-Authors: Angela M. Oliverio, Stefan Geisen, Manuel Delgado-baquerizo, Fernando T. Maestre, Benjamin L. Turner, Noah FiererAbstract:Protists are ubiquitous in soil, where they are key contributors to nutrient cycling and energy transfer. However, Protists have received far less attention than other components of the soil microbiome. We used amplicon sequencing of soils from 180 locations across six continents to investigate the ecological preferences of Protists and their functional contributions to belowground systems. We complemented these analyses with shotgun metagenomic sequencing of 46 soils to validate the identities of the more abundant protist lineages. We found that most soils are dominated by consumers, although parasites and phototrophs are particularly abundant in tropical and arid ecosystems, respectively. The best predictors of protist composition (primarily annual precipitation) are fundamentally distinct from those shaping bacterial and archaeal communities (namely, soil pH). Some Protists and bacteria co-occur globally, highlighting the potential importance of these largely undescribed belowground interactions. Together, this study allowed us to identify the most abundant and ubiquitous Protists living in soil, with our work providing a cross-ecosystem perspective on the factors structuring soil protist communities and their likely contributions to soil functioning.
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Microbial amendments alter protist communities within the soil microbiome
Soil Biology and Biochemistry, 2019Co-Authors: Wu Xiong, Qirong Shen, Sai Guo, Ida Karlsson, George A. Kowalchuk, Zixuan Jiao, Weibing Xun, Stefan GeisenAbstract:Plant-beneficial microbes improve while pathogens reduce plant performance. When introduced in soils, such microbes can induce entire microbiome changes. However, the impact of those microbial introductions on Protists – key predators within the soil microbiome – remain unknown. Here, we tracked how soil Protists respond to bacterial (Bacillus and Ralstonia) and fungal (Trichoderma and Fusarium) introductions, with both microbial groups represented by one beneficial and one pathogenic taxon. We found that plant-beneficial Bacillus bacteria change the protist community structure. This community-shift was likely induced by an increased fungi/bacteria ratio, supported by a negative correlation of the fungi/bacteria ratio with the relative abundance of phagotrophic Protists across all treatments. Our results indicate that microbial introductions can impact protist communities, thereby altering microbiome-derived multi-functionality.
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Soil protist communities form a dynamic hub in the soil microbiome
The ISME journal, 2017Co-Authors: Wu Xiong, Qirong Shen, Alexandre Jousset, Sai Guo, Ida Karlsson, Qingyun Zhao, George A. Kowalchuk, Stefan GeisenAbstract:Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, Protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic Protists and increased bacterivorous and omnivorous Protists. The addition of individual biocontrol bacteria and fungi further altered the soil protist community composition, and eventually function. Network analysis integrating protist, bacterial and fungal community data, placed Protists as a central hub in the soil microbiome, linking diverse bacterial and fungal populations. Given their dynamic response to soil management practices and key position in linking soil microbial networks, Protists may provide the leverage between soil management and the enhancement of bacterial and fungal microbiota at the service of improved soil health.
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the prey s scent volatile organic compound mediated interactions between soil bacteria and their protist predators
The ISME Journal, 2017Co-Authors: Kristin Schulzbohm, Stefan Geisen, E Jasper R Wubs, Chunxu Song, Wietse De Boer, Paolina GarbevaAbstract:Protists are major predators of bacteria in soils. However, it remains unknown how Protists sense their prey in this highly complex environment. Here, we investigated whether volatile organic compounds (VOCs) of six phylogenetic distinct soil bacteria affect the performance of three different soil Protists and how that relates to direct feeding interactions. We observed that most bacteria affected protist activity by VOCs. However, the response of Protists to the VOCs was strongly dependent on both the bacterial and protist interacting partner. Stimulation of protist activity by volatiles and in direct trophic interaction assays often coincided, suggesting that VOCs serve as signals for Protists to sense suitable prey. Furthermore, bacterial terpene synthase mutants lost the ability to affect Protists, indicating that terpenes represent key components of VOC-mediated communication. Overall, we demonstrate that volatiles are directly involved in protist−bacterial predator−prey interactions.
Petrus Tang - One of the best experts on this subject based on the ideXlab platform.
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Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins
BMC Bioinformatics, 2019Co-Authors: Po-jung Huang, Sin-you Chen, Cheng-hsun Chiu, Wei-hung Cheng, Petrus TangAbstract:Background Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Currently, there is no centralized protist membrane transporter database published, which makes system-wide comparisons and studies of host-pathogen membranomes difficult to achieve. Results We analyzed over one million protein sequences from 139 Protists with full or partial genome sequences. Putative transmembrane proteins were annotated by primary sequence alignments, conserved secondary structural elements, and functional domains. We have constructed the PPTdb (Pathogenic Protist Transmembranome database), a comprehensive membrane transporter protein portal for pathogenic Protists and their human hosts. The PPTdb is a web-based database with a user-friendly searching and data querying interface, including hierarchical transporter classification (TC) numbers, protein sequences, functional annotations, conserved functional domains, batch sequence retrieving and downloads. The PPTdb also serves as an analytical platform to provide useful comparison/mining tools, including transmembrane ability evaluation, annotation of unknown proteins, informative visualization charts, and iterative functional mining of host-pathogen transporter proteins. Conclusions The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface. Moreover, a pairwise functional comparison ability can provide useful information for identifying functional uniqueness of each protist. Finally, the host and non-host protein similarity search can fulfill the needs of comprehensive studies of Protists and their hosts. The PPTdb is freely accessible at http://pptdb.cgu.edu.tw .
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Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins.
BMC Bioinformatics, 2019Co-Authors: Chi-ching Lee, Po-jung Huang, Sin-you Chen, Cheng-hsun Chiu, Wei-hung Cheng, Yuan-ming Yeh, Petrus TangAbstract:Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Currently, there is no centralized protist membrane transporter database published, which makes system-wide comparisons and studies of host-pathogen membranomes difficult to achieve. We analyzed over one million protein sequences from 139 Protists with full or partial genome sequences. Putative transmembrane proteins were annotated by primary sequence alignments, conserved secondary structural elements, and functional domains. We have constructed the PPTdb (Pathogenic Protist Transmembranome database), a comprehensive membrane transporter protein portal for pathogenic Protists and their human hosts. The PPTdb is a web-based database with a user-friendly searching and data querying interface, including hierarchical transporter classification (TC) numbers, protein sequences, functional annotations, conserved functional domains, batch sequence retrieving and downloads. The PPTdb also serves as an analytical platform to provide useful comparison/mining tools, including transmembrane ability evaluation, annotation of unknown proteins, informative visualization charts, and iterative functional mining of host-pathogen transporter proteins. The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface. Moreover, a pairwise functional comparison ability can provide useful information for identifying functional uniqueness of each protist. Finally, the host and non-host protein similarity search can fulfill the needs of comprehensive studies of Protists and their hosts. The PPTdb is freely accessible at http://pptdb.cgu.edu.tw .
Michael Bonkowski - One of the best experts on this subject based on the ideXlab platform.
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Protists in the Plant Microbiome: An Untapped Field of Research.
Methods in molecular biology (Clifton N.J.), 2020Co-Authors: Kenneth Dumack, Michael BonkowskiAbstract:Protists are mostly unicellular eukaryotes. Some Protists are beneficial for plants, while others live as endosymbionts and can cause severe plant diseases. More detailed studies on plant-protist interactions exist only for plant pathogens and parasites. A number of Protists live as inconspicuous endophytes and cause no visible disease symptoms, while others appear closely associated with the rhizosphere or phyllosphere of plants, but we still have only a vague understanding on their identities and functions. Here, we provide a protocol on how to assess the plant-associated protist community via Illumina-sequencing of ribosomal marker-amplicons and describe how to assign taxonomic affiliation to the obtained sequences.
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What drives the assembly of plant-associated protist microbiomes?
2020Co-Authors: Kenneth Dumack, Kai Feng, Sebastian Flues, Melanie Sapp, Susanne Schreiter, Rita Grosch, Laura E. Rose, Ye Deng, Kornelia Smalla, Michael BonkowskiAbstract:Abstract In a field experiment we investigated the influence of the environmental filters soil type and plant species identity on rhizosphere community assembly of Cercozoa, a dominant group of (mostly bacterivorous) soil Protists. The experiment was set up with two plant species, lettuce and potato, grown in an experimental plot system with three contrasting soils. Plant species (14%) and rhizosphere origin (vs. bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation in beta diversity). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of Protists has a strong impact on the composition and functioning of bacteria communities, Protists expand the repertoire of plant genes by functional traits, and should be considered as ‘protist microbiomes’ in analogy to ‘bacterial microbiomes’. Highlight Microbiomes of rhizosphere Protists are plant species-specific and tightly co-evolving with their bacterial prey, thereby extending and modifying the functional repertoire of the bacterial-plant symbiosis.
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Microplastic and soil Protists: A call for research
Environmental Pollution, 2018Co-Authors: Michael BonkowskiAbstract:Abstract Microplastic is an emerging contaminant of concern in soils globally, probably gradually increasing in soil due to slow degradation. Few studies on microplastic effects on soil biota are available, and no study in a microplastic contamination context has specifically addressed soil Protists. Soil Protists, a phylogenetically and functionally diverse group of eukaryotic, unicellular soil organisms, are major consumers of bacteria in soils and are potentially important vehicles for the delivery of microplastics into the soil food chain. Here we build a case for focusing research on soil Protists by drawing on data from previous, older studies of phagocytosis in protist taxa, which have long made use of polystyrene latex beads (microspheres). Various soil-borne taxa, including ciliates, flagellates and amoebae take up microplastic beads in the size range of a few micrometers. This included filter feeders as well as amoebae which engulf their prey. Discrimination in microplastic particle uptake depended on species, physiological state as well as particle size. Based on the results of the studies we review here, there is now a need to study microplastic effects in a pollution ecology context: this means considering a broad range of particle types under realistic conditions in the soil, and exploring longer-term effects on soil protist communities and functions.
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the soil food web revisited diverse and widespread mycophagous soil Protists
Soil Biology & Biochemistry, 2016Co-Authors: Stefan Geisen, Robert Koller, Maike Hunninghaus, Kenneth Dumack, Tim Urich, Michael BonkowskiAbstract:Abstract Soil Protists are commonly suggested being solely bacterivorous, serving together with bacterivorous nematodes as the main controllers of the bacterial energy channel in soil food webs. In contrast, the fungal energy channel is assumed to be controlled by arthropods and mycophagous nematodes. This perspective accepted by most soil biologists is, however, challenged by functional studies conducted by taxonomists that revealed a range of mycophagous Protists. In order to increase the knowledge on the functional importance of mycophagous Protists we isolated and initiated cultures of protist taxa and tested eight for facultative feeding on diverse fungi in microcosm experiments. Two different flagellate species of the genus Cercomonas, the testate amoeba Cryptodifflugia operculata and four genera of naked amoebae (Acanthamoeba sp., Leptomyxa sp., two Mayorella spp. and Thecamoeba spp.) fed and grew on yeasts with four taxa (Cercomonas sp., Leptomyxa sp., Mayorella sp., and Thecamoeba sp.) also thriving on spores of the plant pathogenic hyphal-forming fungus Fusarium culmorum. To identify the potential importance of mycophagous Protists in the environment we applied a data-mining approach targeting small subunit (SSU) rRNA data obtained in metatranscriptomes of five fundamentally different terrestrial samples. We focused our analyses on the distribution and relative abundances of two well-studied mycophagous protist groups, vampyrellid amoebae and grossglockneriid ciliates. Both groups were detected in all of the highly contrasting terrestrial samples, comprising up to 3% of all protist SSU rRNA transcripts. SSU transcripts of these two groups, in contrast to all remaining protist SSU transcripts, showed strong correlations with the relative abundance of fungal sequences indicating close direct trophic interactions. Taken together, this study provides evidence that mycophagy among soil Protists is common and might be of substantial but hitherto overlooked ecological importance in terrestrial ecosystems. Future studies should aim at evaluating taxon-specific (facultative) mycophagy, decipher changes caused in the fungal community and quantitatively evaluate the functional importance of this trophic position in soil ecosystems.
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Metatranscriptomic census of active Protists in soils
The ISME Journal, 2015Co-Authors: Stefan Geisen, Michael Bonkowski, Alexander T Tveit, Ian M Clark, Andreas Richter, Mette M Svenning, Tim UrichAbstract:The high numbers and diversity of Protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil Protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil Protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater Protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of Protists in the complex soil system.
Moriya Ohkuma - One of the best experts on this subject based on the ideXlab platform.
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Division of functional roles for termite gut Protists revealed by single-cell transcriptomes
The ISME Journal, 2020Co-Authors: Yuki Nishimura, Masato Otagiri, Masahiro Yuki, Michiru Shimizu, Jun-ichi Inoue, Shigeharu Moriya, Moriya OhkumaAbstract:The microbiome in the hindgut of wood-feeding termites comprises various species of bacteria, archaea, and Protists. This gut community is indispensable for the termite, which thrives solely on recalcitrant and nitrogen-poor wood. However, the difficulty in culturing these microorganisms has hindered our understanding of the function of each species in the gut. Although Protists predominate in the termite gut microbiome and play a major role in wood digestion, very few culture-independent studies have explored the contribution of each species to digestion. Here, we report single-cell transcriptomes of four Protists species comprising the protist population in worldwide pest Coptotermes formosanus . Comparative transcriptomic analysis revealed that the expression patterns of the genes involved in wood digestion were different among species, reinforcing their division of roles in wood degradation. Transcriptomes, together with enzyme assays, also suggested that one of the Protists, Cononympha leidyi , actively degrades chitin and assimilates it into amino acids. We propose that C. leidyi contributes to nitrogen recycling and inhibiting infection from entomopathogenic fungi through chitin degradation. Two of the genes for chitin degradation were further revealed to be acquired via lateral gene transfer (LGT) implying the importance of LGT in the evolution of symbiosis. Our single-cell-based approach successfully characterized the function of each protist in termite hindgut and explained why the gut community includes multiple species.
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Identification of Endosymbiotic Methanogen and Ectosymbiotic Spirochetes of Gut Protists of the Termite Coptotermes formosanus
Microbes and environments, 2008Co-Authors: Jun-ichi Inoue, Satoko Noda, Yuichi Hongoh, Moriya OhkumaAbstract:Prokaryotic associations with gut Protists of the termite Coptotermes formosanus were investigated based on 16S rRNA gene sequences. An endosymbiotic methanogen of Spirotrichonympha leidyi phylogenetically grouped with endosymbionts of other gut Protists in the genus Methanobrevibacter, seemed to be unrelated to the host protist phylogeny. Three different lineages of ectosymbiotic spirochetes in the genus Treponema were identified in single cells of Holomastigotoides mirabile, indicating their simultaneous occurrence. Although these symbionts represented mere minor populations in the gut, their phylogenetic assignments suggest a common symbiotic relationship involving H2 metabolism.
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identification and characterization of ectosymbionts of distinct lineages in bacteroidales attached to flagellated Protists in the gut of termites and a wood feeding cockroach
Environmental Microbiology, 2006Co-Authors: Satoko Noda, Yuichi Hongoh, Toshiaki Kudo, Tetsushi Inoue, Miho Kawai, Christine A Nalepa, Charunee Vongkaluang, Moriya OhkumaAbstract:Bacterial attachments to nearly the entire surface of flagellated Protists in the guts of termites and the wood-feeding cockroach Cryptocercus are often observed. Based on the polymerase chain reaction-amplified 16S rRNA gene sequences, we investigated the phylogenetic relationships of the rod-shaped, attached bacteria (ectosymbionts) of several protist species from five host taxa and confirmed their identity by fluorescence in situ hybridizations. These ectosymbionts are affiliated with the order Bacteroidales but formed three distinct lineages, each of which may represent novel bacterial genera. One lineage consisted of the closely related ectosymbionts of two species of the protist genus Devescovina (Cristamonadida). The second lineage comprised three phylotypes identified from the protist Streblomastix sp. (Oxymonadida). The third lineage included ectosymbionts of the three protist genera Hoplonympha, Barbulanympha and Urinympha in the family Hoplonymphidae (Trichonymphida). The ultrastructural observations indicated that these rod-shaped ectosymbionts share morphological similarities of their cell walls and their point of attachment with the protist but differ in shape. Elongated forms of the ectosymbionts appeared in all the three lineages. The protist cells Streblomastix sp. and Hoplonympha sp. display deep furrows and vane-like structures, but these impressive structures are probably evolutionarily convergent because both the host Protists and their ectosymbionts are distantly related.
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Phylogenetic position and in situ identification of ectosymbiotic spirochetes on Protists in the termite gut.
Applied and environmental microbiology, 2003Co-Authors: Satoko Noda, Moriya Ohkuma, Akinori Yamada, Yuichi Hongoh, Toshiaki KudoAbstract:Phylogenetic relationships, diversity, and in situ identification of spirochetes in the gut of the termite Neotermes koshunensis were examined without cultivation, with an emphasis on ectosymbionts attached to flagellated Protists. Spirochetes in the gut microbial community investigated so far are related to the genus Treponema and divided into two phylogenetic clusters. In situ hybridizations with a 16S rRNA-targeting consensus oligonucleotide probe for one cluster (known as termite Treponema cluster I) detected both the ectosymbiotic spirochetes on gut Protists and the free-swimming spirochetes in the gut fluid of N. koshunensis. The probe for the other cluster (cluster II), which has been identified as ectosymbionts on gut Protists of two other termite species, Reticulitermes speratus and Hodotermopsis sjoestedti, failed to detect any spirochete population. The absence of cluster II spirochetes in N. koshunensis was confirmed by intensive 16S ribosomal DNA (rDNA) clone analysis, in which remarkably diverse spirochetes of 45 phylotypes were identified, almost all belonging to cluster I. Ectosymbiotic spirochetes of the three gut protist species Devescovina sp., Stephanonympha sp., and Oxymonas sp. in N. koshunensis were identified by their 16S rDNA and by in situ hybridizations using specific probes. The probes specific for these ectosymbionts did not receive a signal from the free-swimming spirochetes. The ectosymbionts were dispersed in cluster I of the phylogeny, and they formed distinct phylogenetic lineages, suggesting multiple origins of the spirochete attachment. Each single protist cell harbored multiple spirochete species, and some of the spirochetes were common among protist species. The results indicate complex relationships of the ectosymbiotic spirochetes with the gut Protists.
Po-jung Huang - One of the best experts on this subject based on the ideXlab platform.
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Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins
BMC Bioinformatics, 2019Co-Authors: Po-jung Huang, Sin-you Chen, Cheng-hsun Chiu, Wei-hung Cheng, Petrus TangAbstract:Background Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Currently, there is no centralized protist membrane transporter database published, which makes system-wide comparisons and studies of host-pathogen membranomes difficult to achieve. Results We analyzed over one million protein sequences from 139 Protists with full or partial genome sequences. Putative transmembrane proteins were annotated by primary sequence alignments, conserved secondary structural elements, and functional domains. We have constructed the PPTdb (Pathogenic Protist Transmembranome database), a comprehensive membrane transporter protein portal for pathogenic Protists and their human hosts. The PPTdb is a web-based database with a user-friendly searching and data querying interface, including hierarchical transporter classification (TC) numbers, protein sequences, functional annotations, conserved functional domains, batch sequence retrieving and downloads. The PPTdb also serves as an analytical platform to provide useful comparison/mining tools, including transmembrane ability evaluation, annotation of unknown proteins, informative visualization charts, and iterative functional mining of host-pathogen transporter proteins. Conclusions The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface. Moreover, a pairwise functional comparison ability can provide useful information for identifying functional uniqueness of each protist. Finally, the host and non-host protein similarity search can fulfill the needs of comprehensive studies of Protists and their hosts. The PPTdb is freely accessible at http://pptdb.cgu.edu.tw .
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Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins.
BMC Bioinformatics, 2019Co-Authors: Chi-ching Lee, Po-jung Huang, Sin-you Chen, Cheng-hsun Chiu, Wei-hung Cheng, Yuan-ming Yeh, Petrus TangAbstract:Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Currently, there is no centralized protist membrane transporter database published, which makes system-wide comparisons and studies of host-pathogen membranomes difficult to achieve. We analyzed over one million protein sequences from 139 Protists with full or partial genome sequences. Putative transmembrane proteins were annotated by primary sequence alignments, conserved secondary structural elements, and functional domains. We have constructed the PPTdb (Pathogenic Protist Transmembranome database), a comprehensive membrane transporter protein portal for pathogenic Protists and their human hosts. The PPTdb is a web-based database with a user-friendly searching and data querying interface, including hierarchical transporter classification (TC) numbers, protein sequences, functional annotations, conserved functional domains, batch sequence retrieving and downloads. The PPTdb also serves as an analytical platform to provide useful comparison/mining tools, including transmembrane ability evaluation, annotation of unknown proteins, informative visualization charts, and iterative functional mining of host-pathogen transporter proteins. The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface. Moreover, a pairwise functional comparison ability can provide useful information for identifying functional uniqueness of each protist. Finally, the host and non-host protein similarity search can fulfill the needs of comprehensive studies of Protists and their hosts. The PPTdb is freely accessible at http://pptdb.cgu.edu.tw .
