Repair of DNA and protein damages caused by formaldehyde improves methanol assimilation

Methanol is regarded as a next-generation feedstock. However, the efficiency of synthetic methylotrophs remains suboptimal compared to their preferred carbon sources. In this study, we conducted a comprehensive investigation into the microbial assimilation of methanol, revealing that this process is impeded by formaldehyde toxicity. By utilizing DNA-protein cross-links (DPC) protease GCNA1 from Caenorhabditis elegans and thioproline aminopeptidase PepP from Escherichia coli, we effectively mitigated the formaldehyde-causing DNA and protein damages. Integration of these damage-repair enzymes in methanol-assimilating E. coli strains led to a substantial improvement in methanol consumption. Specifically, the engineered E. coli strain demonstrated a methanol consumption amount of up to 440 mM (∼14.1 g/L), with an average consumption rate of 0.229 mM/h. This represents a remarkable 50-fold increase compared to the control strain. Notably, this achievement stands out as the highest methanol consumption level observed among all methanol-assimilating E. coli strains, highlighting the pivotal role of alleviating formaldehyde cytotoxicity in enhancing methanol assimilation efficiency.