ADDENDUM: I now recall, and it’s been a while since 2017 when most of the paper was written, that the absence of PR.C in the database could also mean that the sequence just didn’t enter the database! After all, we have only a tiny fraction of all bacterial sequences. So, like trying to disprove the existence of chocolate cakes orbiting Neptune, it was thus hard to say PR.C didn’t exist. We could only show it didn’t exist in the database.
It seemed rather compelling that bacteria digested a man-made chemical that never existed before 1935. Something as radical as a frame shift in Ohno’s time seemed like the appropriate level of change needed to create the requisite enzyme.
Finding things like mammalian Trypsin and plant Papain that could degrade nylon, at least made the case that a nylonase didn’t have to evolve after nylon was invented. Hence, at least the perceived need of a radical change was shown as incorrect.
Further, finding homologs of NylB would suggest NylB existed before 1935, and therefore the most parsimonious explanation for the NylB sequence after 1935 was not a frame shift after 1935 but that NylB existed in much of its present form prior to 1935. This was the case that was challenging to make.
It is worth mentioning, but it wasn’t in the paper, a nylonase is a necessary but not sufficient condition for bacteria to digest nylon and live purely off of nylon since the nylonase only made nylon-6 monomers from nylon-6 polymers. Nylonase alone didn’t provide the full metabolic pathway for the monomers to be digested. There had to be a capacity for the bacteria to digest nylon-6 monomers , and to my knowledge, that metabolic pathway has never been characterized. Hence, even if many bacteria have nylonases, they may not necessarily be able to digest nylons.