Evolutionary Adaptation of Prephenate Dehydrogenases: A regulatory ACT domain acquisition in ecological niche specialization

Abstract

Bacteria prephenate dehydrogenase (PDH) participates in the metabolic pathway for tyrosine biosynthesis. PDHs within the Bacilaceae phylum contain an ACT domain which enables them to be allosterically regulated by tyrosine. The mechanism via which the ACT domain introduces allostery onto PDH enzymes remains elusive. Furthermore, the evolutionary and biological advantages of ACT domain mediated regulation of metabolic pathways are highly debated. Building on our previous study, in which we solved the crystal structure of a Bacillus antraces ACT-containing PDH and proposed a model for its allosteric regulation by tyrosine, we now present further structural, and functional analyses in support of this model. In this study, we generated truncated PDH protein constructs lacking the ACT domain, determined their crystal structure and evaluated the role of tyrosine in modulating their enzymatic activity. We determined that the truncated PDH remains catalytically active, however, it is no longer allosterically regulated by tyrosine. Comparative structural analysis between the truncated PDH and PDHs naturally lacking the ACT domain that are known to be competitively inhibited by tyrosine revealed only minor changes in a loop region in the prephenate binding site. Attempts to introduce amino acids identified from the competitively inhibited PDH into the truncated construct did not restore tyrosine sensitivity, even at high concentration. This indicates that additional main chain amino acids away from the substrate binding site also contribute competitive inhibition by tyrosine. Analysis of a highly represented phylogenetic tree revealed that ACT containing PDHs are predominantly distributed amongst Firmicute and Actinomycetota. Representative organisms from both groups colonize nutrient limited and extreme environments. This distribution suggests that acquisition of the ACT domain may confer an evolutionary advantage by enabling organisms to efficiently partition chorismate, the end product of the shikimate pathway, for the biosynthesis of tyrosine and other essential aromatic compounds.