DEOP: a database on osmoprotectants and associated pathways

Abstract

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/

Figure 1.

DEOP conceptual diagram.

Figure 2.

Values in the left panel are pathway completeness estimates. The values in the right panel are the total hits for each pathway that was normalized against its completeness. A minimum completeness of 50% was applied to both panels, where at least one sample had to satisfy for each pathway. The left panel demonstrates the presence or absence of selected pathways in the mangrove samples vs the control data sets, whereas the right panel shows the enrichment of these pathways.

Figure 3.

Values in the left panel are pathway completeness estimates. The values in the right panel are the total hits for each pathway that was normalized against its completeness. A minimum completeness of 75% was applied to both panels, where at least one sample had to satisfy for each pathway. The left panel demonstrates the presence or absence of selected pathways in the mangrove samples vs the control data sets, whereas the right panel shows the enrichment of these pathways.