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

IF 3.7 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS ACS Synthetic Biology Pub Date : 2025-01-19 DOI:10.1021/acssynbio.4c00769

Lu Liu, Xiangjun Zhang, Tengteng Zhu, Tong Ye, Wei Ding, Huiyan Liu, Haitian Fang

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Abstract

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.

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结合转录组学和13C代谢组学分析发现pgi和edd基因参与大肠杆菌胞苷高效合成的调控

高效生产胞苷的工程菌株的开发具有重要的研究和工业应用价值。在这项研究中，pgi和edd基因被敲除，以揭示它们在大肠杆菌中参与有效胞苷合成调控的作用。结果表明，摇瓶发酵36 h后，pgi敲除菌株大肠杆菌NXBG-14产生胞苷浓度为2.57±0.04 g/L， pgi和edd双敲除菌株大肠杆菌NXBG-15产生胞苷滴度为2.68±0.03 g/L，分别比启动菌株提高了1.68和1.75倍。转录组分析显示，NXBG-14菌株的差异表达基因（DEGs）主要富集在糖酵解途径和三羧酸（TCA）循环中。此外，13C代谢流分布表明NXBG-15的戊糖磷酸途径（PPP）中6-磷酸葡萄糖酸显著增加。这些发现表明pgi和edd基因的修饰改变了中心碳代谢，促进了胞苷的积累。

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来源期刊

ACS Synthetic Biology 生物-

CiteScore

8.00

自引率

10.60%

发文量

380

审稿时长

6-12 weeks

期刊介绍： The journal is particularly interested in studies on the design and synthesis of new genetic circuits and gene products; computational methods in the design of systems; and integrative applied approaches to understanding disease and metabolism. Topics may include, but are not limited to: Design and optimization of genetic systems Genetic circuit design and their principles for their organization into programs Computational methods to aid the design of genetic systems Experimental methods to quantify genetic parts, circuits, and metabolic fluxes Genetic parts libraries: their creation, analysis, and ontological representation Protein engineering including computational design Metabolic engineering and cellular manufacturing, including biomass conversion Natural product access, engineering, and production Creative and innovative applications of cellular programming Medical applications, tissue engineering, and the programming of therapeutic cells Minimal cell design and construction Genomics and genome replacement strategies Viral engineering Automated and robotic assembly platforms for synthetic biology DNA synthesis methodologies Metagenomics and synthetic metagenomic analysis Bioinformatics applied to gene discovery, chemoinformatics, and pathway construction Gene optimization Methods for genome-scale measurements of transcription and metabolomics Systems biology and methods to integrate multiple data sources in vitro and cell-free synthetic biology and molecular programming Nucleic acid engineering.