However, constraint-based comparison, which allowed users to pre-define specific search parameters or select a subset from the whole genome, was still lacking in protist resources. The PPTdb provided pairwise functional element comparison through the Venn diagrams. Users could select unique left- and right-hand side or shared intersecting region of the Venn diagram functional elements. PPTdb were consisted by two exactly the same virtual machines — the stable version for public use and the standby version for latest data integration.
And the stable version will go off-line for next data updating. Currently, there was no published transporter-system database specifically designed for protists. However, both databases collected a limited number of protists, which could not provide sufficient resources for protist transporter protein studies. However, there were only 75 protists in this database and fewer than protist transporters. Both TCDB and TransportDB provided interfaces for transporter protein studies; however, neither of them offered mining tools for protist versus human homolog gene searches, protist to protist comparison, or further protist-associated studies.
Horizontal gene transfer events were known as evolutionary driving forces of eukaryotes [ 19 ]. For example, nucleotide transporter NTT gene acquisition was reported as a major evolutionary innovation of Microsporidia which were intracellular parasites of animals and human [ 20 ]. Algerae PRA This two-way search interface offered a high flexibility especially on multiple keyword combinations which could not be searched by one-way search, for example, nucleotide-sugar transmembrane transporter activity GO , guanine nucleotide transmembrane transporter activity GO , and nucleotide transmembrane transporter activity GO Moreover, the type-n-search table instantly returned database query candidates.
Users could obtain putative results by just entering a few characters instead of entire searching keywords. Interestingly, more than half of the results are hypothetical proteins. The protist uniqueness genes and human transporter homologs could be easily separated from the search. Tools such as MAFFT [ 21 ] and ClustalW [ 22 ] could do the multiple sequence alignment and deliver the phylogenetic tree of these sequences. It was complicated to mimic all possible search movements for every user of these databases that provided several advanced search tools. The most straightforward search strategy was the keyword search and filters provided by each database.
The search would be set if the database offers pre-set filters, such as number of transmembrane domains. However, the keyword search was used without pre-set filters, such as putative transporter proteins.
The result showed that the functional filter and iterative search functionalities could make the search more user-friendly than other general purposed databases. All the searched genes Ids from PPTdb could be downloaded in a text format and then be executed more detailed data retrieving processes, such as genetic information from Entrez Gene database, protein 3D structures and pathways from UniProt database.
PPTdb collected all the putative transporter protist proteins and provides a user-friendly data querying interface. The next goal is to collect the human validated transporter proteins by offering a system for putative and validated proteins comparison. The collection of 3D structures of protist transporters will be the goal as well. We believe these future works will make PPTdb more useful on potential protist associated treatment or drug development.
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The PPTdb had been specifically designed for protist transporter system studies and provides a data query portal, an online comparison tool, and a flexible functional search interface. For all putative, hypothetical, or curated protist proteins, the PPTdb provided functional annotations. The PPTdb also offered a straightforward protist-human homology search interface for pathogen and host studies.
Transport proteins of parasitic protists and their role in nutrient salvage. Front Plant Sci. Cloning of Leishmania nucleoside transporter genes by rescue of a transport-deficient mutant. A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi.
Biogenesis and Function of Cellular Organelles in Pathogenic Protozoa | Biocev
Mol Microbiol. Landfear SM. Glucose transporters in parasitic protozoa. Methods Mol Biol. A constitutive pan-hexose permease for the Plasmodium life cycle and transgenic models for screening of antimalarial sugar analogs. Biochem J. A novel high-affinity arginine transporter from the human parasitic protozoan Leishmania donovani. Mutations in the P.
Mol Cell. Trends in the exploitation of novel drug targets. Nat Rev Drug Discov.
Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol. The transporter classification database TCDB : recent advances. Nucleic Acids Res. Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes. PLoS One.
YTPdb: a wiki database of yeast membrane transporters. Biochim Biophys Acta. EuPathDB: the eukaryotic pathogen genomics database resource. Database resources of the National Center for biotechnology information.
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Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Transporter gene acquisition and innovation in the evolution of microsporidia intracellular parasites. Nat Commun. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.
Brief Bioinform. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Bateman A. UniProt: a hub for protein information. Download references. Software, CC.
All authors have read and approved the final manuscript. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Reprints and Permissions. Search all BMC articles Search. Article metrics Accesses 2 Altmetric Metrics details. Abstract 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.
Results We analyzed over one million protein sequences from protists with full or partial genome sequences. Conclusions The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface.
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Background Bioactive molecules that cross through the extracellular barrier mainly rely on channels, pores, or energy-consuming pumps composed of transporter proteins [ 1 ]. Construction and content Sequence characterization and annotation The data processing pipeline was mainly built by service-side command-line PHP and a suite of in-house developed text-processing and data retrieval modules which were implemented by Bash scripting language. Web-interface and database architecture The PPTdb is a database providing real-time user interaction functionalities.
Full size image. One-click potential transporter gene finder We collected all 16, transporter proteins downloaded from the TCDB and annotated them by Gene Ontology terms to construct a transporter protein functional ontology dataset. Sequence homology search for human transporters Primary sequence alignment is an effective method to identify proteins as human homologs. Dynamic type-n-search table All the listed data including genes and GO terms were delivered by a Type-n-Search table, allowing users to narrow down the selection data.
Download page for sequence and annotation retrieval The PPTdb provided a data retrieval tool for protein sequences and annotations targeting genes selected by the functional filters and homology search tool mentioned above. Pairwise functional compositional comparisons Interspecies comparisons of current protist resources focused on the number of genes, transporter classes, or sequence similarities. Comparison to other protist transporter resources Currently, there was no published transporter-system database specifically designed for protists.
Conclusions The PPTdb had been specifically designed for protist transporter system studies and provides a data query portal, an online comparison tool, and a flexible functional search interface. References 1. Article Google Scholar 2. Article Google Scholar Google Scholar Article Google Scholar Download references. Ethics declarations Ethics approval and consent to participate Not applicable Consent for publication Not applicable Competing interests The authors declare that they have no competing interests.
Metabolic pathways have been discovered in these organelles which open up new possibilities for drug targets. This work presents reviews dealing with cytoskeletal structures such as the mastigont system found in trichomonads, the sub-pellicular microtubules in trypanosomatids and the paraflagellar rod. Further chapters cover structures involved in the synthesis, secretion and uptake of molecules, including the flagellar pocket of trypanosomatids, the reservosome of Trypanosoma and the megasome found in Leishmania, the traffic of vesicles in Entamoeba histolytica, secretory organelles and the secretory events of intestinal parasites during encystation.
Reviews on special organelles, such as the kinetoplast-mitochondrion complex, the apicoplast found in Apicomplexa, the glycosomes in Kinetoplastida and the acidocalcisomes found in several protozoa complete the volume. Enter your Postcode or Suburb to view availability and delivery times.