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Background The demand for biobased polymers is increasing steadily worldwide. Microbial hosts for production of their monomeric precursors such as glutarate are developed. To meet the market demand, production hosts have to be improved constantly with respect to product titers and yields, but also shortening bioprocess duration is important. Results In this study, adaptive laboratory evolution was used to improve a C. glutamicum strain engineered for production of the C5-dicarboxylic acid glutarate by flux enforcement. Deletion of the l-glutamic acid dehydrogenase gene gdh coupled growth to glutarate production since two transaminases in the glutarate pathway are crucial for nitrogen assimilation. The hypothesis that strains selected for faster glutarate-coupled growth by adaptive laboratory evolution show improved glutarate production was tested. A serial dilution growth experiment allowed isolating faster growing mutants with growth rates increasing from 0.10 h−1 by the parental strain to 0.17 h−1 by the fastest mutant. Indeed, the fastest growing mutant produced glutarate with a twofold higher volumetric productivity of 0.18 g L−1 h−1 than the parental strain. Genome sequencing of the evolved strain revealed candidate mutations for improved production. Reverse genetic engineering revealed that an amino acid exchange in the large subunit of l-glutamic acid-2-oxoglutarate aminotransferase was causal for accelerated glutarate production and its beneficial effect was dependent on flux enforcement due to deletion of gdh. Performance of the evolved mutant was stable at the 2 L bioreactor-scale operated in batch and fed-batch mode in a mineral salts medium and reached a titer of 22.7 g L−1, a yield of 0.23 g g−1 and a volumetric productivity of 0.35 g L−1 h−1. Reactive extraction of glutarate directly from the fermentation broth was optimized leading to yields of 58% and 99% in the reactive extraction and reactive re-extraction step, respectively. The fermentation medium was adapted according to the downstream processing results. Conclusion Flux enforcement to couple growth to operation of a product biosynthesis pathway provides a basis to select strains growing and producing faster by adaptive laboratory evolution. After identifying candidate mutations by genome sequencing causal mutations can be identified by reverse genetics. As exemplified here for glutarate production by C. glutamicum, this approach allowed deducing rational metabolic engineering strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01586-3.

Additional file 1: Figure S1. (A) DNA region of the plasmid pEC-XT99A-gabTDP134L with the 21 bp sequence deleted in ALE strain GluA T7 (boxed in red). (B) Determination of the minimum inhibitory concentration for tetracycline for strain GluA T0 with the orginal plasmid pEC-XT99A-gabTDP134L and GluA RG1 carrying this plasmid with the 21 bp deletion. Cells were grown in Duetz cultivation system using BHIS supplemented with increasing concentrations of tetracycline (0–80 µg µL−1). The ΔOD600 values were determined after 48 hours and are shown as means with standard deviations (n = 3 cultivations). Figure S2. Dependence of the specific acitvity of GOGAT on the glutamine concentration determined for GRLys1ΔgltB overexpressing the native version of gltBD (A) or the mutated gltBE686QD (B). Crude extracts of GRLys1ΔgltB (pEKEx3-gltBD) and GRLys1ΔgltB (pEKEx3-gltBE686QD) were assayed for specific activity of the glutamate synthase (GOGAT) in the presence of increasing glutamine concentrations (0 mM, 0.1 mM, 0.25 mM, 0.5 mM, 0.75 mM, 1 mM, 2 mM, 5 mM, 10 mM). Values represent means and standard deviations of triplicate measurements. Figure S3. Glutarate production by GluA T7 in chloride-free medium. Cells were grown in Duetz cultivation system using either standard CGXII minimal medium or CGXII minimal medium without chloride supplemented with 40 g L−1 glucose, induced with 1 mM IPTG, and harvested after 48 h. Values and error bars represent means and standard deviations of glutarate (green) and 5AVA concentrations (red) in the culture supernatants (n = 3 cultivations).