title: PrionHome: a database of prions and other sequences relevant to prion phenomena.
abstract: Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion.
authors.affiliation: Department of Biology, McGill University, Montreal, Quebec, Canada.
authors.forename: Djamel
authors.initials: D
authors.lastname: Harbi
authors.forename: Marimuthu
authors.initials: M
authors.lastname: Parthiban
authors.forename: Deena M A
authors.initials: DM
authors.lastname: Gendoo
authors.forename: Sepehr
authors.initials: S
authors.lastname: Ehsani
authors.forename: Manish
authors.initials: M
authors.lastname: Kumar
authors.forename: Gerold
authors.initials: G
authors.lastname: Schmitt-Ulms
authors.forename: Ramanathan
authors.initials: R
authors.lastname: Sowdhamini
authors.forename: Paul M
authors.initials: PM
authors.lastname: Harrison
mesh_terms: D000595:Amino Acid Sequence; D000682:Amyloid / Q000378:metabolism; D030562:Databases, Protein; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D011328:Prions / Q000737:chemistry* / Q000378:metabolism; D011544:Pseudogenes; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism; D012985:Software Design; D014584:User-Computer Interface
chemical_list: D000682:Amyloid; D011328:Prions; D029701:Saccharomyces cerevisiae Proteins