Gene editing creates new organisms -a hope for mitigating climate change?

文:楊燕菱 / 聚和國際 R&D

攝影師：Pixabay: https://www.pexels.com/zh-tw/photo/221012/

Two of the largest factors contributing to climate change are the increase in carbon dioxide (CO2) and methane (CH4), both of which are compounds containing carbon. Methanol can be derived from CO2 and methane. Methanol is currently being widely used as an industrial raw material. If methanol can be used as a biological raw material in the future, it may help slow down the deterioration of the climate (Figure 1).

(Figure 1)
 

Methylotrophs in the natural world convert and utilize methanol through the ribulose monophosphate pathway (RuMP) or the serine cycle. The enzymes involved in RuMP, including methanol dehydrogenase (Medh), hexulose-6-phosphate synthase (Hps), and 6-phospho-3-hexuloisomerase (Phi), are similar to those involved in the typical sugar metabolism of heterotrophs, but are only found in the RuMP pathway. Therefore, it may be possible to create synthetic methylotrophs by expressing these three enzymes in heterotrophs.

With the aim of creating synthetic methylotrophs, the research team led by Academia Sinica President Dr. James Liao used gene editing to modify E. coli into a methylotrophic organism. First, the team introduced the genes encoding the three enzymes mentioned above into E. coli via viral infection. After 20 generations of culture, the evolved CFC381.20 E. coli strain was able to grow from an OD600 of 0.1 to 1.0 within 48 hours in a minimal medium containing 400mM methanol and 20mM xylose. However, the strain was unable to grow on methanol alone.

To address this issue, the team used Ensemble Modeling for Robustness Analysis (EMRA) to compare the natural and engineered metabolic pathways and test the robustness of the enzymes in the synthetic strain. In addition, this analysis also helped to address issues related to DNA-Protein Crosslinking (DPC) that caused cell death during the earlier, longer cultures.

Through the regulation of key enzymes, the authors ultimately succeeded in cultivating the methylotrophic E. coli strain SM1. The SM1 strain not only maintained intracellular metabolic balance but also utilized methanol as its sole carbon source, achieving optimal growth at a concentration of 400mM and a doubling time of 8 hours. The main products of methanol consumption were formate and acetate (Figure 2).

(Figure 2)

Finally, the authors stated that due to the easy manipulability of E. coli genetics, there is great potential for various changes to be made through gene editing technology, resulting in the production of high-value carbon-containing compounds. For example, changing the sole carbon source required for E. coli growth to methane.

 

Source:

Chen et. al., Converting escherichia coli to a synthetic methylotroph growing solely on methanol. Cell. Retrieved September 27, 2022, from https://pubmed.ncbi.nlm.nih.gov/32780992/

Definition：

1. Heterotrophs: organisms that cannot utilize carbon dioxide as a carbon source and require organic compounds as a carbon source.
2. Methylotrophs: also known as methyl utilizing bacteria, are a group of Gram-negative bacteria that can use one-carbon methylated compounds as a carbon source and energy source for growth.