DEOP: Dragon Explorer of
Osmoprotection Pathways

Background

Compatible solutes are small molecules either synthesised by microorganisms or transported from the outside environment into the microorganism in order to deal with sudden changes in the environments and to enable microorganisms to adapt to extreme environments.

Two principal strategies have been observed:

  1. saline cytoplasm osmoadaptation highlighted by the influx of salt into the cytoplasm (K+,NA+, Cl-).

  2. the accumulation of certain organic osmolytes (polyols, heterosides, amino acids, etoines and betaines).

Objectives

Microorganisms capable of accumulating high levels of osmolytes are potential cell factories. Also, the ability to identify genes and pathways involved in the synthesis of compatible solutes may allow for the transfer of such functional capability into other organisms by means of synthetic biology.

As far as we know, no resource exists that can provide insights into the variant genes and/or pathways from the different organisms that synthesize compatible solutes or regulate their accumulation. Such a resource will undoubtedly assist in downstream synthetic biology experiments.

Methods & Results

This online resource has two core initial goals.

  1. The first goal is the continuous accumulation of non-redundant information on pathways, genes, proteins involved in the osmoprotection, adapation and/or regulation in response to salt stresses in microorganisms. Our initial endeavour was focused on publicly and commercially-available databases such the MetaCyc online resource and KEGG. Pathways and reactions and their respective genes, proteins, and compounds were extracted from the databases' flatfiles and stored in a relational database for a consistent structure and ease of querying.

  2. However, manual curation of the ever-increasing scientific literature poses a tremendous challenge both time-wise and financially and so we add a text mining layer on top of the database. The text mining facility is similar, in spirit, to the “KAUST Knowledge Exploration System” (KKES) implemented and hosted by CBRC. The KKES-like layer uses keywords and search terms generated from the database tables to text mine and investigate co-occurrences in the literature. The KAUST Knowledge Exploration System discovers associations between biomedical concepts and explores hypotheses which system automatically generates suggesting new topics for research. It integrates text and data mining and applies information retrieved from various sources to construct new knowledge. The system uses various techniques including information retrieval, text analysis, information extraction, visualisation, database technology, machine learning, and data mining.

Publication

DEOP: a database on osmoprotectants and associated pathways. Bougouffa S, Radovanovic A, Essack M, Bajic VB. Database (Oxford). 2014 Oct 17;2014. pii: bau100. doi: 10.1093/database/bau100.