Bougouffa Salim, Radovanovic Aleksandar, Essack Magbubah, Bajic Vladimir B
King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Centre (CBRC); Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE); Thuwal, Jeddah, 23955-6900, Saudi Arabia.
King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Centre (CBRC); Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE); Thuwal, Jeddah, 23955-6900, Saudi Arabia
Database (Oxford). 2014 Oct 17;2014. doi: 10.1093/database/bau100. Print 2014.
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/
已知微生物可通过盐分流入或积累渗透保护剂（也称为相容性溶质）来应对盐胁迫。了解合成和/或分解这些渗透保护剂的途径，对于作物耐盐性研究以及将微生物用作生产生物质或商业化学品的细胞工厂的生物技术应用而言是很有意义的。为了便于探索渗透保护剂，我们开发了首个在线资源“渗透保护相关途径的龙探索器”（DEOP），它收集并展示有关渗透保护剂的精选信息，并辅以有关使用或影响它们的反应和途径的信息。总共141种化合物被确认为渗透保护剂，它们与1883个反应和834条途径相匹配。DEOP还可用于将基因或微生物基因组映射到潜在的渗透保护相关途径，从而将基因和基因组与其他相关的渗透保护信息联系起来。此外，DEOP提供了一个文本挖掘工具，以便更深入地在科学文献中搜索支持证据或寻找渗透保护剂与途径、反应、酶、基因或生物体的新关联。提供了两个案例研究以证明DEOP的实用性。可通过以下网址访问该系统。数据库网址：http://www.cbrc.kaust.edu.sa/deop/
