Growing fast on a formate diet: A metabolic engineering challenge in E. coli

One of our biggest current challenges is the climate crisis, caused by an excess of greenhouse gas emissions, of which CO₂ is a major contributor. Its devastating effects on the environment, with major impacts on for instance agriculture, food security, and biodiversity, are only expected to increase in the coming years. Therefore, scientists are hard at work on designing new ways of fixating and utilizing CO₂ for the production of valuable products.

Background

Formate is a promising sustainable feedstock for microbial biosynthesis of biobased fuels and chemicals, as it can be produced sustainably by electrochemical reduction of CO₂ (Yishai et al., 2016). Unfortunately, microorganisms naturally capable of utilizing this one-carbon substrate are generally unsuitable for biotechnological applications. Therefore, synthetic biologists started engineering efficient formate assimilation pathways in the biotechnological model organism Escherichia coli, which cannot grow on formate naturally (Cotton et al., 2020).

Recently, Kim et al., (2020) for the first time successfully established growth on formate as sole energy and carbon source in E. coli. This was done by introducing the rationally engineered Reductive Glycine (RG) pathway into the genome of E. coli. The RG pathway appears to be the optimal route for assimilation of formate in an aerobic (oxygen rich) environment. Due to its very low ATP consumption, the RG pathway theoretically allows for high growth and product yields (Satanowski & Bar-Even, 2020). However, currently this engineered E. coli strain is growing far from optimally. In this project, we will use advanced genome editing tools available in E. coli to further develop and optimize the growth on C1 substrates.

Aim

This project aims to use advanced genome editing and metabolic engineering tools available in E. coli to engineer efficient and fast growth on C1 substrates like formate.

-      This project will involve rational selection of suitable target genes for editing through advanced genome editing strategies.

-      Strains with improved growth on the substrate of interest will be selected through competition growth experiments, for instance in bioreactors.

-      The developed strains will be characterized through various techniques (e.g. growth characterization in bioreactors or plate readers, biomass yield analysis, whole genome sequencing, and transcriptome analysis)

Contact

Thesis projects are available for enthusiastic Bsc and Msc students. If you are interested in this project, don’t hesitate to contact me at suzan.yilmaz@wur.nl.

References

Yishai O, Lindner SN, Gonzalez de la Curz J, Tenenboim H, Bar-Even A. The formate bio-economy. Curr. Opin. Chem. Biol. 35 (2016)

Cotton, C. A. R., Claassens, N. J., Benito-Vaquerizo, S. & Bar-even, A. Renewable methanol and formate as microbial feedstocks. Curr. Opin. Biotechnol. 62, 168–180 (2020).

Kim, S. et al. Growth of E. coli on formate and methanol via the reductive glycine pathway. Nat. Chem. Biol. 16, 538–545 (2020).

Satanowski A, Bar-Even A. A one-carbon path for fixing CO2. EMBO reports. 21 (2020)