Combined Transcriptomics and 13C Metabolomics Analysis Reveals pgi and edd Genes Involved in the Regulation of Efficient Cytidine Synthesis in Escherichia coli

The development of an engineered strain for efficient cytidine production holds significant value for both research and industrial applications. In this study, the pgi and edd genes were knocked out to reveal their roles involved in the regulation of efficient cytidine synthesis in Escherichia coli. The results showed that after 36 h of shaking flask fermentation, the pgi knockout strain E. coli NXBG-14 produced a cytidine concentration of 2.57 ± 0.04 g/L, and the pgi and edd double knockout strain E. coli NXBG-15 produced a cytidine titer of 2.68 ± 0.03 g/L, which represented enhancements of 1.68 and 1.75 times over the start strain, respectively. Transcriptome analysis revealed that the differentially expressed genes (DEGs) in the NXBG-14 strain were mainly enriched in the glycolytic pathway and the tricarboxylic acid (TCA) cycle. Additionally, 13C metabolic flow distribution indicated a significant increase in 6-phosphogluconate in the pentose phosphate pathway (PPP) for NXBG-15. These findings suggest that modifications of the pgi and edd genes redirect central carbon metabolism and promote cytidine accumulation.