Parts-Prospecting for the Methanol Economy: Yhbo and Formaldehyde Resilience

Formaldehyde (HCHO) is a highly reactive carbonyl compound that cross-links and formylates proteins, DNA, and small molecules, making it both cytotoxic and genotoxic. The mechanism of HCHO damage, and the enzyme systems that repair or prevent it, are critical to natural and synthetic methylotrophy – and hence to the proposed methanol economy. Methanol produced in various ways is a potential cheap and sustainable carbon source for biofuel production and other SynBio applications. As the oxidation of methanol to HCHO is the first step in methanol metabolism, HCHO production is an unavoidable facet of methylotrophy. The accumulation of HCHO can damage the metabolic machinery in platform cells and increase their mutation rate, leading to rapid loss of engineered production traits. Little is known about whether or how cells repair HCHO-damage to proteins, DNA, and small molecules. Comparative genomic analysis indicates that the enzyme YhbO is associated with HCHO-related proteins. YhbO belongs to the DJ-1 protein family, which is implicated in carbonyl damage repair. Deletion of yhbO in Escherichia coli strain BW25113 increases sensitivity to exogenous HCHO; this phenotype is specific to HCHO and is independent of carbon source. Interestingly, deleting yhbO in other E. coli K12 backgrounds (e.g., MG1655) does not lead to HCHO-sensitivity. YhbO thus has potential as a damage-repair part in engineering synthetic methylotrophy. We are now testing possible mechanisms by which YhbO confers HCHO resilience, (e.g., by deformylating proteins) using genetic and biochemical approaches and investigating the gene(s) responsible for the difference between the BW25113 and MG1655 strains.