Article Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis

小寺, 正明  ,  Kotera, Masaaki  ,  五斗, 進  ,  Goto, Susumu

13pp.195 - 205 , 2016-07 , Biophysics and Physicobiology
Description
Metabolic pathway reconstruction presents a challenge for understanding metabolic pathways in organisms of interest. Different strategies, i.e., reference-based vs. de novo, must be used for pathway reconstruction depending on the availability of well-characterized enzymatic reactions. If at least one enzyme is already known to catalyze a reaction, its amino acid sequence can be used as a reference for identifying homologous enzymes in the genome of an organism of interest. Where there is no known enzyme able to catalyze a corresponding reaction, however, the reaction and the corresponding enzyme must be predicted de novo from chemical transformations of the putative substrate-product pair. This review summarizes studies involving reference-based and de novo metabolic pathway reconstruction and discusses the importance of the classification and structure-function relationships of enzymes.

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