Nylonase involved the survival of a population of bacteria because of the mutation of one amino acid of a pre-existing protein with an existing function, causing change to allowing the efficient breakdown of nylon. There was nothing new created, nothing to see here.
Ann Gauger writes: "Thus, EII′ and EII did
not have frameshifted new folds. They had pre-existing folds with activity characteristic of their fold type. There was no brand-new protein. No novel protein fold had emerged. And no frameshift mutation was required to produce nylonase.
Where
did the nylon-eating ability come from? Carboxylesterases are enzymes with broad substrate specificities; they can carry out a variety of reactions. Their binding pocket is large and can accommodate a lot of different substrates. They are “promiscuous” enzymes, in other words. Furthermore, the carboxylesterase reaction hydrolyzes a chemical bond similar to the one hydrolyzed by nylonase. Tests revealed that both the EII and EII′ enzymes have carboxylesterase
and nylonase activity. They can hydrolyze both substrates. In fact it is possible both had carboxylesterase activity
and a low level of nylonase activity from the beginning, even
before the appearance of nylon....So. This is not the story of a highly improbable frame-shift producing a new functional enzyme. This is the story of a pre-existing enzyme with a low level of promiscuous nylonase activity, which improved its activity toward nylon by first one, then another selectable mutation. In other words this is a completely plausible case of gene duplication, mutation, and selection operating on a pre-existing enzyme to improve a pre-existing low-level activity, exactly the kind of event that Meyer and Axe specifically acknowledge as a possibility, given the time and probabilistic resources available. Indeed, the origin of nylonase actually provides a nice example of the
optimization of a pre-existing fold’s function, not the
innovation or creation of a novel fold."
"Our studies demonstrated that among the 47 amino acids altered between the EII and EII’ proteins, a single amino acid substitution at position 181 was essential for the activity of 6-aminohexanoate-dimer hydrolase [nylonase] and substitution at position 266 enhanced the effect." Kato et al. (1991)
"Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the β-lactamase fold resulted in the evolution of the nylon oligomer hydrolase."
X-ray Crystallographic Analysis of 6-Aminohexanoate-Dimer Hydrolase
"Let’s put to bed the fable that the nylon oligomer hydrolase EII, colloquially known as nylonase, arose by a frame-shift mutation, leading to the creation of a new functional protein fold. There is absolutely no need to postulate such a highly improbable event, and no justification for making this extravagant claim. Instead, there is a much more parsimonious explanation — that nylonase arose by a gene duplication event some time in the past, followed by a series of two mutations occurring after the introduction of nylon into the environment, which increased the nylon oligomer hydrolase activity of the nylB gene product to current levels. Could this series of events happen in forty years? Most certainly. Probably in much less time. In fact, it has been reported to happen in the lab under the right selective conditions. And most definitely, the evolution of nylonase does not call for the creation of a novel protein fold, nor did one arise. EII’s fold is part of the carboxylesterase fold family. Carboxylesterases serve many functions and have been around much longer than forty years." Anne Gauger
The Nylonase Story: When Imagination and Facts Collide | Evolution News
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g.