Background: Prions are a particular type of amyloids that are related to a great variety of important processes in cells, but also responsible for serious diseases in mammals and human. Prion-related aggregation is mediated by specific protein domains with remarkable compositional bias towards glutamine/asparagine and against charged residues and prolines. The number of prions experimentally characterized nowadays corresponds to a handful of examples in microorganisms and mammals, thus these compositional features have been used to try to predict new prion proteins at genomic scale. However, the number of algorithms for achieving this task is scarce and there are few data sources available containing prion predictions in the genomes of organisms.
Description: Here we present PrionScan a new database of predicted prion-like domains in the complete proteomes of organisms. By using a predictive methodology previously developed by us to identify and score prionogenic stretches in protein sequences, we have scanned all the protein sequences in public databases and compiled a repository containing relevant information of proteins bearing prion-like domains. The database is updated regularly alongside UniprotKB and in its present version contains approximately 28000 predictions in proteins from different functional categories in more than 3200 organisms from all the taxonomic subdivisions. The site is designed to be used in two ways: database query and analysis of protein sequences submitted by the users. In the first mode, easy queries allow to retrieve a detailed description of the prion-like properties for a specified protein, while more complex queries can adapt to many possible combinations of search patterns. In the second mode, we provide a service that allows users to submit and analyze their own sequences.
Conclusions: It is expected that this database would provide relevant insights on prion functions and regulation from a genome-wide perspective, and provide researches with a source for performing cross-species studies of prion biology in all the known organisms. Our database might also be useful for guiding experimentalist in the identification of new candidates for further experimental characterization.
prion domain, protein aggregation, amyloid fibrils, prion prediction
Prions are a special type of amyloids, which have the distinctive properties of acting as heritable elements when in their aggregated forms, constituting self-replicating entities that can perpetuate and transmit over generations. Prions are generally ubiquitous proteins with specific functions when folded, that also perform important functions in cells following their amyloid conversion as epigenetic elements [1, 2], evolutionary capacitors [3, 4] and bet-hedging devices [5, 6] in the processes of adaptation to environmental fluctuations in microorganisms, and in mechanisms crucial to maintain long-term physiological states in invertebrates [7-9]....