Evolutionary dynamics of new enzymes and metabolic pathways

Synopsis

Microbes have exhibited a remarkable ability to evolve new enzymes and metabolic pathways. To respond to environmental changes, microbes recruit the promiscuous function of existing enzymes and further modify them to make new, efficient, and specific enzymes. Such a cycle of recruitment and evolution of enzymes expanded a massive repertoire of enzymes observed in nature. Our laboratory has studied diverse aspects of evolutionary and molecular mechanisms underlying the evolution of novel enzymes, including enzymes evolved against the use of xenobiotics such as organophosphate pesticides. In this talk, I will present the evolutionary mechanisms underlying organophosphate-degrading enzymes and metabolic pathways. First, I will show the key evolutionary mechanisms of two newly evolved organophosphate-degrading enzymes, called methyl-parathion hydrolase (MPH) and phosphotriesterase (PTE). Our molecular and evolutionary studies using ancestral sequence reconstruction unveiled that the evolution of those enzymes was highly contingent on the sequence of ancestral enzymes. Especially three seemingly neutral mutations were required to open the pathway to allow the accumulation of five key adaptive mutations from ancestral lactonase enzymes to MPH. Second, I will present how the evolution of PTE, the gradual development of catalytic efficiency (kcat/KM), is correlated to the cellular ability to grow (fitness). We established an organophosphate degrading bacteria fitness assay using E. coli, where the growth of the E. coli is highly dependent on the degradation of organophosphate (paraoxon) as paraoxon is the sole phosphorous source. Interestingly, the E. coli strains exhibited the ability to grow with a broad range of PTE variants with more than >10,000-fold catalytic efficiency. I will show the mechanisms of how E. coli respond and overcome a low efficiency of the enzyme to grow while degrading the organophosphate. At last, I will discuss the potential evolutionary dynamics of how multi-enzyme metabolic pathways can evolved quickly, especially from a microbial community.