Although the carbon assimilation pathway is highly conserved across species, metabolic phenotypes could differ in composition, type, and quantity. To unravel the metabolic complexity and advantage of cassava over other starch crops, in terms of starch production, we investigated the carbon assimilation mechanisms in cassava through genome-based pathway reconstruction and comparative network analysis. First, MeRecon — the carbon assimilation pathway of cassava was reconstructed based upon six plant templates: Arabidopsis, rice, maize, castor bean, potato, and turnip. MeRecon, available at http://bml.sbi.kmutt.ac.th/MeRecon, comprises 259 reactions (199 EC numbers), 1,052 proteins (870 genes) and 259 metabolites in eight sub-metabolisms. Analysis of MeRecon and the carbon assimilation pathways of the plant templates revealed the overall topology is highly conserved, but variations at sub metabolism level were found in relation to complexity underlying each biochemical reaction, such as numbers of responsible enzymatic proteins and their evolved functions, which likely explain the distinct metabolic phenotype. Thus, this study provides insights into the network characteristics and mechanisms that regulate the synthesis of metabolic phenotypes of cassava.
The complexity of the carbon assimilation metabolic pathway of cassava based on association of enzymatic proteins and metabolic enzymes. (a) The distribution of proteins annotated to an enzyme (Complexity: CP/E): CAL - Calvin cycle, SUC - sucrose biosynthesis, STA - starch biosynthesis, RES - respiration, AMI - amino acid biosynthesis, CEL - cell wall biosynthesis, FAT - fatty acid biosynthesis, and NUC - nucleotide biosynthesis; (b) Box-plot of Complexity (CP/E) determined from each sub-metabolism; (c) Complexity (CP/E) of carbohydrate-related sub-metabolisms (black bar: STA, CAL, RES, SUC, and CEL) and non-carbohydrate-related sub-metabolisms (gray bar: NUC, AMI, and FAT) calculated based on the average CP/E value of enzymes in the pathway.