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DEOP: a database on osmoprotectants and associated pathways

Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology a...

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Autores principales: Bougouffa, Salim, Radovanovic, Aleksandar, Essack, Magbubah, Bajic, Vladimir B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201361/
https://www.ncbi.nlm.nih.gov/pubmed/25326239
http://dx.doi.org/10.1093/database/bau100
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author Bougouffa, Salim
Radovanovic, Aleksandar
Essack, Magbubah
Bajic, Vladimir B.
author_facet Bougouffa, Salim
Radovanovic, Aleksandar
Essack, Magbubah
Bajic, Vladimir B.
author_sort Bougouffa, Salim
collection PubMed
description Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, ‘Dragon Explorer of Osmoprotection associated Pathways’ (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at. Database URL: http://www.cbrc.kaust.edu.sa/deop/
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spelling pubmed-42013612014-10-22 DEOP: a database on osmoprotectants and associated pathways Bougouffa, Salim Radovanovic, Aleksandar Essack, Magbubah Bajic, Vladimir B. Database (Oxford) Original Article Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, ‘Dragon Explorer of Osmoprotection associated Pathways’ (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at. Database URL: http://www.cbrc.kaust.edu.sa/deop/ Oxford University Press 2014-10-09 /pmc/articles/PMC4201361/ /pubmed/25326239 http://dx.doi.org/10.1093/database/bau100 Text en © The Author(s) 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Bougouffa, Salim
Radovanovic, Aleksandar
Essack, Magbubah
Bajic, Vladimir B.
DEOP: a database on osmoprotectants and associated pathways
title DEOP: a database on osmoprotectants and associated pathways
title_full DEOP: a database on osmoprotectants and associated pathways
title_fullStr DEOP: a database on osmoprotectants and associated pathways
title_full_unstemmed DEOP: a database on osmoprotectants and associated pathways
title_short DEOP: a database on osmoprotectants and associated pathways
title_sort deop: a database on osmoprotectants and associated pathways
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201361/
https://www.ncbi.nlm.nih.gov/pubmed/25326239
http://dx.doi.org/10.1093/database/bau100
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