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

Constructing efficient bacterial cell factories to enable one‐carbon utilization based on quantitative biology: A review

“…Next, by strengthening the formate dehydrogenase via adaptive evolution, they ultimately obtained a synthetic formate and carbon dioxide-utilizing E. coli that has the doubling time of 8 h and gives the biomass yield of 2.3 g DCW mol −1 formate. These achievements accompanied by metabolomic analysis of glycine-related metabolic pathways [79] have encouraged the researchers to introduce the rGly pathway to other bacteria such as Cupriavidus necator [80], Pseudomonas putida [81], and Clostridium pasteurianum [82] to create synthetic strains that can assimilate formate. In addition, other novel linear pathways have been designed based on computational reaction thermodynamics, enzyme kinetics, and minimization of reaction steps, which theoretically outperform natural pathways (e.g., the RuMP F I G U R E 4 Quantitatively analyzing the 13 C labeling patterns under different labeled tracers to confirm that the reductive glycine pathway fully support the growth of synthetic non-C1-utilizing bacteria of E. coli on the formate and carbon dioxide.…”

“…coli that has the doubling time of 8 h and gives the biomass yield of 2.3 g DCW mol −1 formate. These achievements accompanied by metabolomic analysis of glycine‐related metabolic pathways [79] have encouraged the researchers to introduce the rGly pathway to other bacteria such as Cupriavidus necator [80], Pseudomonas putida [81], and Clostridium pasteurianum [82] to create synthetic strains that can assimilate formate. In addition, other novel linear pathways have been designed based on computational reaction thermodynamics, enzyme kinetics, and minimization of reaction steps, which theoretically outperform natural pathways (e.g., the RuMP cycle) in various aspects (e.g., ATP and reducing power production, carbon conversion, etc.)…”

Single carbon metabolism – A new paradigm for microbial bioprocesses?

“…Improved versions of formatotrophic E. coli strains were used for production of lactic acid but still reaching only low yields [ 48 ]. Also in P. putida which shows high tolerance against formate, formate assimilation via the reductive glycine pathway was demonstrated [ 49 , 50 ]. Lately a fully functional reductive glycine pathway was demonstrated in engineered S. cerevisiae [ 51 ].…”

Pseudomonas putida as a platform for medium‐chain length α,ω‐diol production: Opportunities and challenges

“…has been found to degrade plastics such as polyethylene (Balasubramanian et al., 2010 ; Gyung Yoon et al., 2012 ), polypropylene (Arkatkar et al., 2010 ), and polyvinyl chloride (Giacomucci et al., 2019 ). Moreover, P. putida is recently engineered to use formate and methanol for cell growth (Bruinsma et al., 2023 ; Turlin et al., 2022 ). The aforementioned traits and pathways enable the wider application of P. putida in bioremediation and industrial biotechnology, such as plant biomass valorization and plastic upcycling (Mohamed et al., 2020 ; Sullivan et al., 2022 ).…”