CRISPR interference

Gene

Amino acid

Biotechnology

Biology

Genome editing

Corynebacterium glutamicum

CRISPR

Biochemistry

Computational biology

Genetics

Organic chemistry

Proline

Biomanufacturing

Trehalose

Chemistry

In silico

Metabolic engineering

Flux (metallurgy)

Synthetic biology

Nature Communications

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.

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