Metabolomic changes and metabolic responses to expression of heterologous biosynthetic genes for lycopene production in Yarrowia lipolytica

•Metebolome changes were studied for Y. lipolytica engineered for lycopene production.•Metabolome data was converted to pathway abundance to simplify data interpretation.•Pathway abundance alterations were visualized by a pathway relationship network.•Comprehensive analysis revealed metabolic changes associated with crt genes. The metabolomic studies were conducted for both the engineered lycopene-producing Yarrowia lipolytica strain and the control strain. The changes in metabolome profiling and main pathway abundance of Y. lipolytica with the introduction of heterologous crt genes were investigated by multiple analytical and statistical methods More importantly, the metabolome data were transformed into pathway abundances visualized by a pathway relationship network using Cytoscape software. This network provided a simple way to present the statistical results of pathway abundance and interpret the effects of the crt genes in a metabolic view, and the results highlighted the up-regulation of eight pathways and the down-regulation of three pathways in the lycopene fast production phase. The comprehensive analysis suggested that the synthesis of lycopene has remarkable effects on fructose and mannose metabolism, citrate cycle, glyoxylate and dicarboxylate metabolism, glycerophospholipid metabolism as well as the biosynthesis and metabolism of some amino acids including valine, leucine and isoleucine in Y. lipolytica.