Recent from talks
Enzyme promiscuity
Knowledge base stats:
Talk channels stats:
Members stats:
Enzyme promiscuity
Enzyme promiscuity is the ability of an enzyme to catalyze an unexpected side reaction in addition to its main reaction. Although enzymes are remarkably specific catalysts, they can often perform side reactions in addition to their main, native catalytic activity. These wild activities are usually slow relative to the main activity and are under neutral selection. Despite ordinarily being physiologically irrelevant, under new selective pressures, these activities may confer a fitness benefit therefore prompting the evolution of the formerly promiscuous activity to become the new main activity. An example of this is the atrazine chlorohydrolase (atzA encoded) from Pseudomonas sp. ADP evolved from melamine deaminase (triA encoded), which has very small promiscuous activity toward atrazine, a man-made chemical.
Enzymes are evolved to catalyze a particular reaction on a particular substrate with high catalytic efficiency (kcat/KM, cf. Michaelis–Menten kinetics). However, in addition to this main activity, they possess other activities that are generally several orders of magnitude lower, and that are not a result of evolutionary selection and therefore do not partake in the physiology of the organism. This phenomenon allows new functions to be gained as the promiscuous activity could confer a fitness benefit under a new selective pressure leading to its duplication and selection as a new main activity.
Several theoretical models exist to predict the order of duplication and specialisation events, but the actual process is more intertwined and fuzzy (§ Reconstructed enzymes below). On one hand, gene amplification results in an increase in enzyme concentration, and potentially freedom from a restrictive regulation, therefore increasing the reaction rate (v) of the promiscuous activity of the enzyme making its effects more pronounced physiologically ("gene dosage effect"). On the other, enzymes may evolve an increased secondary activity with little loss to the primary activity ("robustness") with little adaptive conflict (§ Robustness and plasticity below).
A study of four distinct hydrolases (human serum paraoxonase (PON1), pseudomonads phosphotriesterase (PTE), Protein tyrosine phosphatase(PTP) and human carbonic anhydrase II (CAII)) has shown the main activity is "robust" towards change, whereas the promiscuous activities are weak and more "plastic". Specifically, selecting for an activity that is not the main activity (via directed evolution), does not initially diminish the main activity (hence its robustness), but greatly affects the non-selected activities (hence their plasticity).
The phosphotriesterase (PTE) from Pseudomonas diminuta was evolved to become an arylesterase (P–O to C–O hydrolase) in eighteen rounds gaining a 109 shift in specificity (ratio of KM), however most of the change occurred in the initial rounds, where the unselected vestigial PTE activity was retained and the evolved arylesterase activity grew, while in the latter rounds there was a little trade-off for the loss of the vestigial PTE activity in favour of the arylesterase activity.
This means firstly that a specialist enzyme (monofunctional) when evolved goes through a generalist stage (multifunctional), before becoming a specialist again—presumably after gene duplication according to the IAD model—and secondly that promiscuous activities are more plastic than the main activity.
The most recent and most clear cut example of enzyme evolution is the rise of bioremediating enzymes in the past 60 years. Due to the very low number of amino acid changes, these provide an excellent model to investigate enzyme evolution in nature. However, using extant enzymes to determine how the family of enzymes evolved has the drawback that the newly evolved enzyme is compared to paralogues without knowing the true identity of the ancestor before the two genes diverged. This issue can be resolved thanks to ancestral reconstruction. First proposed in 1963 by Linus Pauling and Emile Zuckerkandl, ancestral sequence reconstruction is the inference and synthesis of a gene from the ancestral form of a group of genes, which has had a recent revival thanks to improved inference techniques and low-cost artificial gene synthesis, resulting in several ancestral enzymes—dubbed "stemzymes" by some—to be studied.
Evidence gained from reconstructed enzyme suggests that the order of the events where the novel activity is improved and the gene is duplication is not clear cut, unlike what the theoretical models of gene evolution suggest.
Hub AI
Enzyme promiscuity AI simulator
(@Enzyme promiscuity_simulator)
Enzyme promiscuity
Enzyme promiscuity is the ability of an enzyme to catalyze an unexpected side reaction in addition to its main reaction. Although enzymes are remarkably specific catalysts, they can often perform side reactions in addition to their main, native catalytic activity. These wild activities are usually slow relative to the main activity and are under neutral selection. Despite ordinarily being physiologically irrelevant, under new selective pressures, these activities may confer a fitness benefit therefore prompting the evolution of the formerly promiscuous activity to become the new main activity. An example of this is the atrazine chlorohydrolase (atzA encoded) from Pseudomonas sp. ADP evolved from melamine deaminase (triA encoded), which has very small promiscuous activity toward atrazine, a man-made chemical.
Enzymes are evolved to catalyze a particular reaction on a particular substrate with high catalytic efficiency (kcat/KM, cf. Michaelis–Menten kinetics). However, in addition to this main activity, they possess other activities that are generally several orders of magnitude lower, and that are not a result of evolutionary selection and therefore do not partake in the physiology of the organism. This phenomenon allows new functions to be gained as the promiscuous activity could confer a fitness benefit under a new selective pressure leading to its duplication and selection as a new main activity.
Several theoretical models exist to predict the order of duplication and specialisation events, but the actual process is more intertwined and fuzzy (§ Reconstructed enzymes below). On one hand, gene amplification results in an increase in enzyme concentration, and potentially freedom from a restrictive regulation, therefore increasing the reaction rate (v) of the promiscuous activity of the enzyme making its effects more pronounced physiologically ("gene dosage effect"). On the other, enzymes may evolve an increased secondary activity with little loss to the primary activity ("robustness") with little adaptive conflict (§ Robustness and plasticity below).
A study of four distinct hydrolases (human serum paraoxonase (PON1), pseudomonads phosphotriesterase (PTE), Protein tyrosine phosphatase(PTP) and human carbonic anhydrase II (CAII)) has shown the main activity is "robust" towards change, whereas the promiscuous activities are weak and more "plastic". Specifically, selecting for an activity that is not the main activity (via directed evolution), does not initially diminish the main activity (hence its robustness), but greatly affects the non-selected activities (hence their plasticity).
The phosphotriesterase (PTE) from Pseudomonas diminuta was evolved to become an arylesterase (P–O to C–O hydrolase) in eighteen rounds gaining a 109 shift in specificity (ratio of KM), however most of the change occurred in the initial rounds, where the unselected vestigial PTE activity was retained and the evolved arylesterase activity grew, while in the latter rounds there was a little trade-off for the loss of the vestigial PTE activity in favour of the arylesterase activity.
This means firstly that a specialist enzyme (monofunctional) when evolved goes through a generalist stage (multifunctional), before becoming a specialist again—presumably after gene duplication according to the IAD model—and secondly that promiscuous activities are more plastic than the main activity.
The most recent and most clear cut example of enzyme evolution is the rise of bioremediating enzymes in the past 60 years. Due to the very low number of amino acid changes, these provide an excellent model to investigate enzyme evolution in nature. However, using extant enzymes to determine how the family of enzymes evolved has the drawback that the newly evolved enzyme is compared to paralogues without knowing the true identity of the ancestor before the two genes diverged. This issue can be resolved thanks to ancestral reconstruction. First proposed in 1963 by Linus Pauling and Emile Zuckerkandl, ancestral sequence reconstruction is the inference and synthesis of a gene from the ancestral form of a group of genes, which has had a recent revival thanks to improved inference techniques and low-cost artificial gene synthesis, resulting in several ancestral enzymes—dubbed "stemzymes" by some—to be studied.
Evidence gained from reconstructed enzyme suggests that the order of the events where the novel activity is improved and the gene is duplication is not clear cut, unlike what the theoretical models of gene evolution suggest.