Genome-Scale Metabolic Model-Based Reactome-Phenome Map of Synechocystis sp. PCC 6803, A Potential Biofuel Producer
Yik Yew Wee, Xander Kng, Si Xian Sor and Maurice HT Ling*
Published: April 21, 2022
DOI: 10.55162/MCMI.22.021
Abstract
Synechocystis sp. PCC 6803 is a potential producer of lipids, alcohols, and biofuels. Genome-scale models (GSM) has been used to examine potential knockout to optimize specific metabolite (such as, ethanol) production. Besides from a metabolic production perspective, GSMs can also be used examine the effects of genes from the perspective of genotype-phenotype relationship. However, most GSMs are reaction-based rather than gene-based. Hence, GSMs can be used for reactome-phenome mapping where each reaction may be the result of one or more genes. In this study, we examine the reactome-phenome map of Synechocystis sp. PCC 6803 using its GSM model, iJN678, by performing single knockouts to each of its 863 reactions. Our results suggest that 37.3% to 39.7% (322 to 343 reactions) of the knockouts have minimal impact on the phenome as they were clustered together with wildtype phenotype and 53.5% (462 reactions) are essential. The rest of the 58 to 79 reactions can be clustered into 9 to 33 phenotypic clusters. Moreover, the fluxome variation within wildtype cluster is significantly larger than that of essential reaction cluster (t ≥ 3.26, p-value ≤ 1.3E-3). This suggests that individual reaction knockout may have measurable effects on the fluxes; which may be useful in metabolic engineering.
Keywords: Genome-scale model; Genotype-phenotype map; Reactome-phenome map; Fluxome; Cameo; AdvanceSyn Toolkit; Flux-balance analysis