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DEOP: a database on osmoprotectants and associated pathways.

Salim Bougouffa1, Aleksandar Radovanovic1, Magbubah Essack1

  • 1King 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 : the Journal of Biological Databases and Curation
|October 19, 2014
PubMed
Summary
This summary is machine-generated.

Microorganisms manage salt stress using osmoprotectants. A new online tool, DEOP, explores pathways for these compounds, aiding crop halotolerance and biotechnology research.

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Area of Science:

  • Microbiology
  • Biotechnology
  • Bioinformatics

Background:

  • Microorganisms counteract salt stress via salt influx or osmoprotectant accumulation.
  • Understanding osmoprotectant pathways is crucial for crop halotolerance and microbial biotechnology.
  • Osmoprotectants, also known as compatible solutes, play a key role in cellular stress response.

Purpose of the Study:

  • To develop a comprehensive online resource for exploring osmoprotection-associated pathways.
  • To facilitate research into the synthesis and breakdown of osmoprotectants.
  • To link microbial genes and genomes to relevant osmoprotection pathways.

Main Methods:

  • Developed 'Dragon Explorer of Osmoprotection associated Pathways' (DEOP), an online database.
  • Curated information on 141 confirmed osmoprotectants, linked to 1883 reactions and 834 pathways.
  • Integrated a text-mining utility for literature-based discovery of associations.

Main Results:

  • DEOP consolidates curated data on osmoprotectants, reactions, and pathways.
  • The resource enables mapping of genes and genomes to osmoprotection pathways.
  • A text-mining tool enhances literature exploration for new osmoprotectant associations.

Conclusions:

  • DEOP serves as a valuable resource for studying microbial osmoprotection.
  • The tool supports research in crop science and industrial biotechnology.
  • DEOP facilitates deeper understanding and discovery within osmoprotection research.