The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia towards sustainable production of the 2 nd generation of biofuels, with Methyl Ethyl Ketone (MEK) being one promising fuel candidate. MEK is a commercially valuable petrochemical with an extensive application as a solvent. However, as of today, a sustainable and economically viable production of MEK has not yet been achieved despite several attempts of introducing biosynthetic pathways in industrial microorganisms. We used BNICE.ch as a retrobiosynthesis tool to discover all novel pathways around MEK. Out of 1'325 identified compounds connecting to MEK with one reaction step, we selected 3oxopentanoate, but-3-en-2-one, but-1-en-2-olate, butylamine, and 2-hydroxy-2methyl-butanenitrile for further study. We reconstructed 3'679'610 novel biosynthetic pathways towards these 5 compounds. We then embedded these pathways into the genome-scale model of E. coli, and a set of 18'622 were found to be most biologically feasible ones based on thermodynamics and their yields. For each novel reaction in the viable pathways, we proposed the most similar KEGG reactions, with their gene and protein sequences, as candidates for either a direct experimental implementation or as a basis for enzyme engineering. Through pathway similarity analysis we classified the pathways and identified the enzymes and precursors that were indispensable for the production of the target molecules. These retrobiosynthesis studies demonstrate the potential of BNICE.ch for discovery, systematic evaluation, and analysis of novel pathways in synthetic biology and metabolic engineering studies.3
Graphical abstract4 Limited reserves of oil and natural gas and the environmental issues associated with their exploitation in the production of chemicals sparked off current developments of processes that can produce the same chemicals from renewable feedstocks using microorganisms. 1-3 A fair amount of these efforts focuses on a sustainable production of the 2 nd generation biofuels.Compared to the currently used fossil fuels and bioethanol, these 2 nd generation biofuels should provide lower carbon emissions, higher energy density, and should be less corrosive to engines and distribution infrastructures. Recently, a large number of potential candidates for the 2 nd generation biofuels has been proposed such as nbutanol 4 , isobutanol 4 , 2-methyl-1-butanol 4 , 3-methyl-1-butanol 4 , C13 to C17 mixtures of alkanes and alkenes 5 , fatty esters, fatty alcohols 1 , and Methyl Ethyl Ketone (MEK) 6 .While some of these compounds were detected in living cells, none was produced by native organisms in appreciable quantities. 7 For chemicals whose natural microbial producers are not known, the feasibility of their bioproduction has to be assessed and potential novel biosynthetic pathways for production of these chemicals are yet to be discovered. 8,9 Even when production pathways for target chemicals are known, it is important to find alternativ...