How evolution shapes enzyme selectivity – lessons from aminoacyl‐tRNA synthetases and other amino acid utilizing enzymes

Abstract

Aminoacyl‐tRNA synthetases (AARSs) charge tRNA with their cognate amino acids. Many other enzymes use amino acids as substrates, yet discrimination against noncognate amino acids that threaten the accuracy of protein translation is a hallmark of AARSs. Comparing AARSs to these other enzymes allowed us to recognize patterns in molecular recognition and strategies used by evolution for exercising selectivity. Overall, AARSs are 2–3 orders of magnitude more selective than most other amino acid utilizing enzymes. AARSs also reveal the physicochemical limits of molecular discrimination. For example, amino acids smaller by a single methyl moiety present a discrimination ceiling of ~200, while larger ones can be discriminated by up to 105‐fold. In contrast, substrates larger by a hydroxyl group challenge AARS selectivity, due to promiscuous H‐bonding with polar active site groups. This ‘hydroxyl paradox’ is resolved by editing. Indeed, when the physicochemical discrimination limits are reached, post‐transfer editing – hydrolysis of tRNAs charged with noncognate amino acids, evolved. The editing site often selectively recognizes the edited noncognate substrate using the very same feature that the synthetic site could not efficiently discriminate against. Finally, the comparison to other enzymes also reveals that the selectivity of AARSs is an explicitly evolved trait, showing some clear examples of how selection acted not only to optimize catalytic efficiency with the target substrate, but also to abolish activity with noncognate threat substrates (‘negative selection’).

Enzyme promiscuity and evolution in light of cellular metabolism

“…It stems from the physicochemical and evolutionary constraints under which enzymatic active sites are shaped. Ita Gruic and Dan Tawfik [4] analyze these constraints by examining aminoacyl‐tRNA synthetases – an enzyme class that has systematically evolved for high selectivity. In his article, William Atkins [5] reviews the other extreme – detoxifying, drug‐metabolizing enzymes, and transporters that exhibit unusually broad substrate acceptance, as well as high substrate and catalytic promiscuity.…”

Discovery of an ultraspecific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway

“…In addition, TrtA displays exquisite substrate specificity for triuret with other substrates only having several orders of magnitude less activity than for triuret ( Table 2). Discriminating against small substrate molecules is an evolutionary challenge which often requires different structural folds if discrimination between substrates cannot be achieved in the same fold (23). An amidase, not in the IHL protein family, already exists to hydrolyze carboxybiuret, the TrtA reaction product, to dicarboxyurea which is named AtzEG and found in the cyanuric acid mineralization pathway of Pseudomonas sp.…”

On the evolution of chaperones and co-chaperones and the expansion of proteomes across the Tree of Life

“…While corechaperones can exert high-affinity binding to few specific substrates at their native folded state, they generally tend to bind misfolded and aggregated polypeptides that abnormally expose hydrophobic surfaces (Gong et al, 2009;Rudiger et al, 1997;Scheibel et al, 1998). The main driving force for duplication and specialization is a functional tradeoff-optimization of one function comes at the expense of other functions (Tawfik and Gruic-Sovulj, 2020). However, given a 'generalist' mode of function, the quality-control of increasingly large and complex proteomes could be achieved by an increase in abundance of core-chaperones, rather than by the emergence of new core-chaperone families.…”