Abstract
BackgroundEssential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction is catalyzed by multiple enzymes, then inhibiting the reaction would be a better option than targeting the enzymes or the corresponding enzyme-encoding gene. The existing databases such as BRENDA, BiGG, KEGG, Bio-models, Biosilico, and many others offer useful and comprehensive information on biochemical reactions. But none of these databases especially focus on essential reactions. Therefore, building a centralized repository for this class of reactions would be of great value.DescriptionHere, we present a species-specific essential reactions database (SSER). The current version comprises essential biochemical and transport reactions of twenty-six organisms which are identified via flux balance analysis (FBA) combined with manual curation on experimentally validated metabolic network models. Quantitative data on the number of essential reactions, number of the essential reactions associated with their respective enzyme-encoding genes and shared essential reactions across organisms are the main contents of the database.ConclusionSSER would be a prime source to obtain essential reactions data and related gene and metabolite information and it can significantly facilitate the metabolic network models reconstruction and analysis, and drug target discovery studies. Users can browse, search, compare and download the essential reactions of organisms of their interest through the website http://cefg.uestc.edu.cn/sser.
Highlights
Essential reactions are vital components of cellular networks
If a single reaction is catalyzed by multiple enzymes, inhibiting the reaction would be a better option than targeting the enzymes itself or the corresponding enzyme-coding gene [15] and this was the key driving force for us towards constructing species-specific essential reactions database (SSER)
A reaction is classified as essential if the growth ratio is less than 1% and these reactions were extracted into a separate file for further curation
Summary
The current version of SSER comprises 6077 essential biochemical and transport reactions of twenty-six organisms. The reactions were identified via flux balance analysis (FBA) in conjunction with manual curation on experimentally validated metabolic network models. SSER would be a prime source to obtain essential reactions data and related gene and metabolite information. It can significantly facilitate the metabolic network models reconstruction and analysis, and drug target discovery studies. SSER provides a function for comparing essential reactions across organisms thereby extending its applicability to evolutionary studies. (XLSX 36 kb) Additional file 5: Shared reactions between E.coli and Shigella flexneri 2a str. (XLSX 14 kb) Additional file 7: Shared essential reactions across all organisms.
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