Emergence of Novel Enzyme Quasi-Species Depends on the Substrate Matrix

Origins of Specificity and Promiscuity in Metabolic Networks

“…Catalytic Efficiency of Promiscuous Enzymes-We used our definition of latent promiscuity in order to investigate the previously reported experimental observation that enhancement of latent catalytic activities does not seem often to trade off with parallel decreases in the original function (16,24), in contradiction with the commonly accepted assumption that broad substrate acceptance generally comes at the price of low reaction turnover numbers (19). In our results, catalytic efficiency, estimated from experimental data as described under "Experimental Procedures," does not seem to be related in general to the latent promiscuity of enzymes because the trend that we observed remains flat for most of the values of latent enzyme promiscuity (r ϭ 0.02, p ϭ 0.27; see supplemental Fig.…”

“…Finally, another mechanism that we want to examine in this study is how the environment influences enzyme evolution. The presence of substrates plays a pivotal role in determining whether latent catalytic abilities become manifest in a novel enzyme (24), as has been observed in recent years with the emergence of enzymes that degrade novel synthetic chemicals and with the alarming evolution of drug resistance.…”

Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism?

“…Secondary activities of promiscuous enzymes are not under selective pressure, and they can accumulate mutations that decrease or increase their catalytic efficiency. The efficiency of promiscuous activities of enzymes may evolve in different degrees in the microbial species, depending on how the environment influences the evolutionary trajectories of enzymes [21] and the ability that promiscuity activity gives to each organism. Therefore, the original question raised in the title of this review, do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism?, seems to have a positive response.…”

“…This repertoire can be modified by the ecological conditions to which the bacteria face, i.e. chemical environment or substrate matrix, could influence the evolutionary trajectories of evolving enzymes; such as the appearance of novel substrates in the biochemical niche in which enzyme activity is expressed may influence the selective advantage that a new activity could provide [21]. In this context, an example of differential evolution in promiscuous enzymes associated to lifestyle is the secondary N-acyl amino acid racemase activity of the o-succinylbenzoate synthases from E. coli found in the gastrointestinal tract of animals, and in the soil bacterium Amycolaptosis sp.…”

A Novel Quasi-Species of Glutathione Transferase with High Activity towards Naturally Occurring Isothiocyanates Evolves from Promiscuous Low-Activity Variants

“…15 The substrate matrix is the array of compounds presented to the enzymes as possible substrates in their physiological niche or by an experimental system in vitro. Catalytic potential with substrates that are never encountered by an enzyme will remain latent.…”