Integrated rational and evolutionary engineering of genome-reduced Pseudomonas putida strains empowers synthetic formate assimilation

Abstract

AbstractFormate is a promising, water-soluble C1 feedstock for biotechnology since it can be efficiently produced from CO2—but very few industrially-relevant hosts have been engineered towards formatotrophy. Here, the non-pathogenic soil bacterium Pseudomonas putida was adopted as a platform for synthetic formate assimilation. The metabolism of genome-reduced variants of P. putida was rewired to establish synthetic auxotrophies that could be functionally complemented by expressing components of the reductive glycine (rGly) pathway. The rGly pathway mediates the formate → glycine → serine transformations that yield pyruvate, ultimately assimilated into biomass. We adopted a modular engineering approach, dividing C1 assimilation in segments composed of both heterologous activities (sourced from Methylorubrum extorquens) and native reactions. Promoter engineering of chromosomally-encoded functions coupled to modular expression of rGly pathway elements enabled growth on formate as carbon source and acetate for energy supply. Adaptive laboratory evolution of two lineages of engineered P. putida formatotrophs significantly reduced doubling times to ca. 15 h. During evolution, two catabolic regimes became predominant in independently evolved clones, either via glycine hydroxymethylation (GlyA) or oxidation (ThiO). Taken together, our results expand the landscape of microbial platforms for C1-based biotechnological production towards supporting a formate bioeconomy.Graphical Abstract