Due to their properties as catalysts producing highly enantio- and regioselective compounds from target substrates under mild reaction conditions, the use of enzymes in biotechnological processes is rising. However, their often insufficient activity on non-natural compounds and narrow substrate ranges still limit their use in industrial setups. To obtain enzymes with enhanced activities, methods of directed evolution are available, involving mutant gene library generation and high throughput testing of individual variants in a cellular context. Linking of the targeted enzymatic activity to cell growth by constructing strains conditionally auxotrophic for essential metabolites or for energy carriers have significantly enlarged the application range of directed evolution (Chen et al., 2022). To achieve spatial and temporal connection between mutagenesis and variant screening, in vivo mutagenesis approaches have recently been developed. Among them are inducible systems employing different deaminase base editors tethered to T7 RNA polymerase (T7 RNAP), provoking base substitutions concomitant to transcription depending on the deaminase used (Cravens et al., 2021; (https://2021.igem.org/ Team:Evry_Paris-Saclay). However, these techniques have not yet been applied for the amelioration of industrial biocatalysts.
The components of the systems, i.e. target genes, T7 RNAP-deaminase fusion proteins and regulatory modules, are plasmid borne. The PhD student will further develop this method by inserting the T7 RNAP editor and the target gene into the E. coli chromosome, thus stabilizing the system and opening the possibility of multiple rounds of mutagenesis and selection steps in GM3 automated continuous culture devices available in the laboratory. He/she will establish a mutagenesis and selection protocol, using a native gene enabling conditional metabolic selection as reporter. The validated protocol will subsequently be applied to heterologous NADPH-dependent dehydrogenases using a generic NADPH sensor selection strain constructed and used in the lab (Lindner et al., 2018). These will include the screening for alcohol and amine dehydrogenases, activities already studied by our group (Ducrot et al., 2020), to obtain variants with broadened substrate specificity. Their potential for synthetic applications will be assessed in laboratory scale, using targets chosen in collaboration with national and international partners. In vitro characterization of the enzymatic activity of enhanced variants will also be undertaken. The PhD student will benefit from multiple expertise and equipment of the UMR Génomique Métabolique, covering molecular genetics, synthetic biology, directed evolution, chemical analytics and enzymology.