sb6b00054_si_001.xlsx (485.35 kB)
ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies
dataset
posted on 2016-07-12, 00:00 authored by Noushin Hadadi, Jasmin Hafner, Adrian Shajkofci, Aikaterini Zisaki, Vassily HatzimanikatisBecause
the complexity of metabolism cannot be intuitively understood
or analyzed, computational methods are indispensable for studying
biochemistry and deepening our understanding of cellular metabolism
to promote new discoveries. We used the computational framework BNICE.ch
along with cheminformatic tools to assemble the whole theoretical
reactome from the known metabolome through
expansion of the known biochemistry presented in the Kyoto Encyclopedia
of Genes and Genomes (KEGG) database. We constructed the ATLAS of
Biochemistry, a database of all theoretical biochemical reactions
based on known biochemical principles and compounds. ATLAS includes
more than 130 000 hypothetical enzymatic reactions that connect
two or more KEGG metabolites through novel enzymatic reactions that
have never been reported to occur in living organisms. Moreover, ATLAS
reactions integrate 42% of KEGG metabolites that are not currently
present in any KEGG reaction into one or more novel enzymatic reactions.
The generated repository of information is organized in a Web-based
database (http://lcsb-databases.epfl.ch/atlas/) that allows
the user to search for all possible routes from any substrate compound
to any product. The resulting pathways involve known and novel enzymatic
steps that may indicate unidentified enzymatic activities and provide
potential targets for protein engineering. Our approach of introducing
novel biochemistry into pathway design and associated databases will
be important for synthetic biology and metabolic engineering.