CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an l-proline exporter for l-proline hyperproduction

• Published in: Nature communications Vol. 13; no. 1; pp. 891 - 16
• Main Authors: Liu, Jiao, Liu, Moshi, Shi, Tuo, Sun, Guannan, Gao, Ning, Zhao, Xiaojia, Guo, Xuan, Ni, Xiaomeng, Yuan, Qianqian, Feng, Jinhui, Liu, Zhemin, Guo, Yanmei, Chen, Jiuzhou, Wang, Yu, Zheng, Ping, Sun, Jibin
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16.02.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 38/35; 38/43; 38/56; 49/22; 49/23; 49/47; 631/326/2522; 631/61/252/318; 631/92/577; Amino acids; Antibiotics; Base Sequence; Bioengineering - methods; Biofuels; Bioreactors - microbiology; Biosynthesis; Biotechnology; Carrier Proteins - genetics; Corynebacterium glutamicum; Corynebacterium glutamicum - genetics; Corynebacterium glutamicum - metabolism; CRISPR; CRISPR-Cas Systems - genetics; Deregulation; Development strategies; Fluctuations; Gene Editing - methods; Humanities and Social Sciences; Kinases; multidisciplinary; Phosphotransferases (Carboxyl Group Acceptor) - genetics; Predictive control; Proline; Proline - biosynthesis; Protein Transport - genetics; Science; Science (multidisciplinary); Screening; Single-stranded DNA; Tuning
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-28501-7

Development of hyperproducing strains is important for biomanufacturing of biochemicals and biofuels but requires extensive efforts to engineer cellular metabolism and discover functional components. Herein, we optimize and use the CRISPR-assisted editing and CRISPRi screening methods to convert a wild-type Corynebacterium glutamicum to a hyperproducer of l -proline, an amino acid with medicine, feed, and food applications. To facilitate l -proline production, feedback-deregulated variants of key biosynthetic enzyme γ-glutamyl kinase are screened using CRISPR-assisted single-stranded DNA recombineering. To increase the carbon flux towards l -proline biosynthesis, flux-control genes predicted by in silico analysis are fine-tuned using tailored promoter libraries. Finally, an arrayed CRISPRi library targeting all 397 transporters is constructed to discover an l -proline exporter Cgl2622. The final plasmid-, antibiotic-, and inducer-free strain produces l -proline at the level of 142.4 g/L, 2.90 g/L/h, and 0.31 g/g. The CRISPR-assisted strain development strategy can be used for engineering industrial-strength strains for efficient biomanufacturing. Corynebacterium glutamicum is a major workhorse in industrial biomanufacturing of amino acids. Here, the authors employ CRISPR-assisted rational flux-tuning and CRISPRi screening of a L-proline exporter to covert a wild-type C. glutamicum to a hyperproducer of L-proline.