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PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena
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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282748/ https://www.ncbi.nlm.nih.gov/pubmed/22363733 http://dx.doi.org/10.1371/journal.pone.0031785 |
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author | Harbi, Djamel Parthiban, Marimuthu Gendoo, Deena M. A. Ehsani, Sepehr Kumar, Manish Schmitt-Ulms, Gerold Sowdhamini, Ramanathan Harrison, Paul M. |
author_facet | Harbi, Djamel Parthiban, Marimuthu Gendoo, Deena M. A. Ehsani, Sepehr Kumar, Manish Schmitt-Ulms, Gerold Sowdhamini, Ramanathan Harrison, Paul M. |
author_sort | Harbi, Djamel |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3282748 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-32827482012-02-23 PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena Harbi, Djamel Parthiban, Marimuthu Gendoo, Deena M. A. Ehsani, Sepehr Kumar, Manish Schmitt-Ulms, Gerold Sowdhamini, Ramanathan Harrison, Paul M. PLoS One Research Article 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. Public Library of Science 2012-02-20 /pmc/articles/PMC3282748/ /pubmed/22363733 http://dx.doi.org/10.1371/journal.pone.0031785 Text en Harbi et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Harbi, Djamel Parthiban, Marimuthu Gendoo, Deena M. A. Ehsani, Sepehr Kumar, Manish Schmitt-Ulms, Gerold Sowdhamini, Ramanathan Harrison, Paul M. PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena |
title | PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena |
title_full | PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena |
title_fullStr | PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena |
title_full_unstemmed | PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena |
title_short | PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena |
title_sort | prionhome: a database of prions and other sequences relevant to prion phenomena |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282748/ https://www.ncbi.nlm.nih.gov/pubmed/22363733 http://dx.doi.org/10.1371/journal.pone.0031785 |
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