It has been widely advertised that nylon eating genes evolved after 1940. I have no problem with that claim in principle since new antibiotic and malaria resistances have evolved since 1940. Even though I can easily accept the possibility of post-1940 nylon-eating evolution in principle, where is the slam dunk evidence that this is actually the case? Did a significant portion of the ability for bacteria to digest nylon take place after 1940 (or 1935 when nylon was first created)?
In an NCSE article New Proteins Without God’s Help we read:
Since nylon first came into commercial production in 1940, we know that the new enzymes have formed since that time.
A similar line of thinking was argued at BioLogos in Biological Information and Intelligent Design, De Novo or Ex Nihilo.
Three nylon eating genes NylA, NylB, NylC were discovered on the Flavobacteria plasmid pOAD2 from 1977-1992, but the researchers concede none of the three have significant sequence homology. Worse, in papers published in 2007, they reported other bacteria contain those same genes in their chromosomes. Unless the researchers have access to pre-1935 bacteria sitting in lab refrigerators, the claim that the genes actually evolved new proteins via mutation is dubious since we have no pre-1935 bacterial samples to actually do a comparison with, especially in the case of NylC. The claim that NylB’s nylon eating ability evolved by gene duplication from a non-functional NylB-prime gene could just as well be interpreted that a functionless NylB-prime gene is a defective copy of a functioning NylB gene!
What’s the proof new nylon eating genes actually evolved after 1940, or is it just speculation? Slam dunk proof would entail having strains of pre-1935 bacteria and then comparing it with the strains after 1935 that supposedly evolved new genes. Is that the case? No. Just speculation which began in 1977 but got less defensible over the next 40 years as more bacteria and non-sequence-homologous genes were discovered to have nylon eating capability.
At least we can credit Richard Lenski who can back up his claims of evolution because he has samples of bacteria in his lab before and after his creatures evolved, whereas the guys promoting the claim the nylon-eaters are new don’t have pre-1935 physical samples of the bacteria. The only pre-1935 samples of the bacteria they have are samples from their imagination.
Incidentally, it is worth pointing out the bacteria that is the centerpiece of the controversy has been mis-classified or misidentified, and thus the name of the bacteria has itself gone through some sort of macro evolution. It was first called Acromobacter gattatus, then renamed as Flavobacterium sp., but then renamed Arthrobacter sp. after it was realized it had been put in the wrong taxonomic category all along.
But anyway, here is the 1977 speculation that became uncritically accepted and exaggerated as fact for the last 40 years:
There are two possible mechanisms for an enzyme to be active towards unnatural synthetic substance such as 6-aminohexanoic acid cyclic dimer; one is that an unnatural compound is hydrolyzed as an analogue of the physiological substrate, and the other is that the compound is hydrolyzed by an evolved enzyme which originally had an activity on a physiological substrate but lost it by the evolutionary mutation. The data obtained in this experiment indicate that this enzyme did not hydrolyze any physiological substrates tested including peptides, cyclic amides, and amides. In addition to the lack of activity on natural compounds, its low turnover number (8 SKcI) compared to other cyclic amide hydrolases (35 – 260 s ~ for penicillinase [12]) supports the possibility that the enzyme has evolved by adaptation to a new synthetic substance which is a waste product of nylon-6 production.
I have no problem if they say “the enzyme has evolved by adaptation to a new synthetic substance which is a waste product of nylon-6 production” when they mean an existing enzyme has changed its pre-existing function to a different one. That is to say, it acquires a new function while also losing its previous one. However, I would have serious issue with the NCSE’s insinuation that this was such a spectacular change that it illustrates how to solve the origin things on the order of the spliceosome or ribosome.
They don’t have strains sitting in a refrigerator from which to compare the “newly evolved” genes with do they? They just guessed, and then 30 years later one of the same team (Negoro) found nylon eating genes on other bacteria, plus reasonable nylon-eating homologues on other bacteria to boot.
Worse, the claim that these are post-1935 genes is weakened by some facts that require a little elaboration. First there is the basic nylon monomer that forms the components of nylon oligomers. NylA, NylB, NylC have different specialties of which nylon oligomer they can degrade. These three enzymes provide what looks like a digestive cascade where N-oligomer substrates are degraded by NylC to dimers which can be further degraded by NylB (and even NylC but to lesser extent). The cascade is described in: Biodegradation of nylon oligomers.
But important to note: NylA, NylB, NylC are not sequence homologous. In A New Nylon Oligomer Degradation Gene (nylC) on Plasmid pOAD2 from a Flavobactenium sp we read:
Sequence alignment by the method of Wirbur and Lipman (21) showed no significant homology among the
nylA, nylB, and nylC genes. These results suggest that the three nylon oligomer-degradative enzymes evolved independently.
There is no pre-1935 bacteria from which to compare with to establish NylC’s true history, much less anything beyond speculation about the nature of NylC’s ancestor. So how can anyone claim it is new (as in post-1935-new)? Just guesses. They’d have to argue these the genes evolved independently since 1935, and in the case of NylC, the ancestor is almost totally without detailed description.
They however argue, a functional NylB arose from a non-functioning NylB-prime gene via gene duplication in a 1991 paper entitled: Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers.
But for all we know NylB’ is a defective copy of a functioning NylB! Where is a Ken-Miller-pseudo-gene-like argument when you need it?
In fairness, another bacteria called Pseudomonas was shown in lab conditions to acquire enzymatic nylon-eating function after a few months. The gene however in Pseudomonas, according to BLASTN, has no sequence homology with Flavobacteria. However, the protein according to BLASTP can align 91% at 37% homology. But even the researchers were astonishingly vague about what actually changed in the bacteria that enabled nylon degredation. The two relevant papers are: Characterization of the 6-aminohexanoate-dimer hydrolase from Pseudomonas sp. NK87 and Emergence of Nylon Oligomer Degradation Enzymes in Pseudomonas aeruginosa PAO through Experimental Evolution.
Unless we have strains sitting in a refrigerator of pre-1935 bacteria, how do we know that the genes actually evolved to digest bacteria? For all we know, it had that capability already or very close to it. And unless we have genes from all existing bacteria in 1935 and can prove all the bacteria on the globe do not have horizontally-transferrable nylon eating genes which could end up on the plasmids of Flavobacteria, we can’t unequivocally argue the three nylon eating genes (NylA, NylB, NylC) in Flavobacteria didn’t already exist pre-1935.
Even if the capability of nylon eating evolved, it is also not necessarily because of a new gene, but new regulation. A mini-example of this possibility had to be raised because even in their lab, they had bacteria with identical nylon eating genes but which could not digest nylon.
it is conceivable that expression of the nylC gene is enhanced in these strains and the elevated enzyme activities made the cells Nom+. However, the following possibilities could not be ignored: (i) KI725R strains may possess an additional nylon oligomer-degrading enzyme which is active
toward a substrate included in Noml, but K1725 has no degradative ability toward the substrate; (ii) nylon oligomer transport proteins are activated in K1725R strains; or (iii) the EIII proteins were altered by mutations in the coding region of the nylC gene by which the specific activities and/or
substrate specificity of the enzyme were changed. The last possibility should be negligible,
So my question is, if we ignore the NCSE hype, does the scientific literature really even prove unequivocally a significant part of nylon eating genes evolved after 1935 and absolutely rule out these genes pre-existed? Maybe yes, maybe no, but the NCSE can’t now brag that any significant evolution (like say compared to evolution of antibiotic resistance) bacteria definitely evolved after 1940 without God’s help. We simply don’t know.
NOTES:
Here are some accession numbers:
NylB (protein) in Flavobacteria: WP_012476894.1
which generates a BLASTP hit on Agromyces accession number: BAE97621.1
NylC (protein) in Flavobacteria: BAA01528
which generates a BLASTP hit also on Agromyces accession number: BAE97629.1
in Pseudomonas, the nylon eating gene accession numbers are : BAA01524 (protein), D10678.1 (DNA)
which generates BLAST hits on a variety of organisms as well
ERRATA:
should read
[Citation Needed]
[Citation Needed]
I’d like to read those papers. You should supply some references so one can read up on the matter before trying to answer your questions.
Who the hell even says this? Nobody has said this. Where does the NCSE say this?
Oh wait, you said their “insinuation”, so now you’re going to tell us that you somehow mysteriously got that impression from something completely tangential, so that you can now pretend they are acting unreasonably.
Sal,
So your god helps antibiotic resistant bacteria to develop does it?
A) Why?
B) How do you know?
Can you design an experiment that demonstrates that antibiotic resistant bacteria need god’s help to evolve?
And, finally, this is stupid even for you Sal.
Hiya Rumraket, so nice to see your smiling face on a Saturday morning. . Actually I already provided the links, but here you go…
The first report in 1977 was:
6-Aminohexanoic Acid Cyclic Dimer Hydrolase. A New Cyclic Amide Hydrolase Produced by Acromobacter guttatus KI 72. And I linked to it. You’ll see 1977 as the publication date.
Now I guess I could amend what I said from::
to
I provided the link to NylC here:
A New Nylon Oligomer Degradation Gene (nylC) on Plasmid pOAD2 from a Flavobactenium sp
which says:
By the time NylC was reported, NylA had already been named as evidenced by the NylC paper.
Do you still have issues with my time line?
Thanks for reading and responding.
Here you go.
http://www.sciencedirect.com/science/article/pii/S1389172308700148
Thanks for pointing out my oversight. Hugs.
Now it could be they discovered it a little earlier than 2007 (obviously), but that was the report that was returned doing BLAST searches on Flavobacteria NylC which pointed to Agromyces NylC.
Hope you enjoy. Thanks for reading and responding.
Hiya Rumraket again. I hope you had a safe and blessed St. Patrick’s day.
I provided a link two the essays earlier:
https://ncse.com/cej/5/2/new-proteins-without-gods-help
and
http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-de-novo-or-ex-nihilo
Where they put these forward as examples of solving the problem of protein evolution. It seems to me they want to give the impression one can extrapolate these unproven claims of any post-1935 evolution of Flavobacteria (and even if true, miniscule changes) to suggest the problem of protein evolution is solved.
The NCSE article was written by a biology professor:
Well gee, even though we don’t have pre-1935 bacterial samples it didn’t prevent a lot of speculation. In the case of NylB two speculations, one even by Ohno (Oh No!) and the researchers who discovered NylB.
Ohno proposed 1 frame shift mutation. Which I find surprising since I don’t have proof of the segment he claims was supposedly shifted even existed. Did he like take NylB (in RS-IIA) and unshift it and declare it an ancestor? Anyway, here is OhNo!’s paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC345072/
I couldn’t make heads or tails of it. Can you? It was helpful, nonetheless since I found the sequences in question and manually lifted them from Ohno’s paper the old fashioned way by typing them into BLAST (gasp!). That paper was in 1983, and everyone cites it, but the researchers themselves gave their version in a 1991 papers, which I already also linked to.
But just to repeat, here it is again:
https://www.ncbi.nlm.nih.gov/pubmed/6646204
The supposed substitutions were on a mere 2 residues where they claim NylB was an altered copy of a non-functioning NylB-prime. Now, I want to know, how can they be sure of this since they have no pre-1935 samples. For all we know, NylB-prime is a defective copy from a functioning NylB! I mean, don’t we have things like pseudogenes that do this so much worse. Why is that interpretation not considered? Is that because they just assume NylB evolved to eat Nylon after 1935? And even if that were the case, when did the duplication happen?
If you’re going to say “recently” since it’s only 2 amino acid residues, and claim NylB-prime is non-functional, how long was NylB-prime non-functional. Why then don’t we have more inTRA-species variation on NylB-prime if that’s the case. If NylB-prime had been around a several million years, the inTRA-species divergence should be gynormous by now. One solution is to suppose the bacteria is young, like say….let’s not go there in this discussion. 🙂
No, just a question. At what point on the time line did god intervene?
WIth respect to Flavobacteria, maybe not anytime after 1935, since my OP raises the possibility, the genes pre-existed 1935 so there is possibly no evolution (or at least significant evolution) or no divine intervention need since there was no change post 1935.
So nice to hear from you. I hope you had a nice St. Patrick’s day.
Is there a way to tell the difference between divine intervention and evolution?
There was some green tinsel around the Guinness pump in the pub. Other then that, it went unmarked. However I hope you enjoyed it yourself.
A further thought….
When I first heard of this “new” nylon eating ability, I had wrongly assumed there were at least circumstantially credible examples of pre-1935 bacteria lying around, like say outside the nylon plant. Granted we don’t have the refrigerated true pre-1935 bacteria anywhere, but I just realized, we don’t seem to have anything in the databases of ANY Flavobacteria that isn’t nylon eating!
Given they had mis classified the critter at least twice already, who knows what creature we are really dealing with. Understandably the researchers were just glad to find a nylon eater and weren’t really motivated to find non-nylon eating strains of the creature.
If they find non-nylon eating strains somewhere and then do a lab evolution, we could at least nail down what mutations are involved in evolving the nylon eating ability. Right now, it’s all guessing in a vacuum.
Sal, there has to be something wrong with your searches. I just checked NCBI and found 90 Flavobacterium genome assemblies. It isn’t possible that they’re all from nylon-heavy environments, is it? You don’t need 1935 bacteria, just a little comparative biology.
John,
The latest classification of the bug is no longer Flavobacterium, but I use that term since that’s the one most represented in the literature. This is already the 3rd name that’s affixed to this bug, whatever it is!
The gene banks still call the plasmid “Flavobacterium” even though now the authors insist it’s not a Flavobacterium but Arthrobacter sp.
Were the GenBank, Uniprot, the BLAST databases (or whatever) updated? Has the change of name reflected? Nope. Not my problem.
Who knows where the plasmid should really be assigned.
But if there was only a 2 residue change as the authors argue in NylB, that should emerge in a BLAST hit if other Flavobacteria have a homologous plasmid.
Now, do you really want to argue that three 1200 base genes suddenly evolved from nothing after 1935, and appear only on 1 strain of Flavobacteria? It would seem to me we have a horizontal transfer onto the plasmid, and we don’t know where that thing came from. So what was the pre-1935 ancestor to what we find on the Plasmid. Was it ever in a Flavobacteria to begin with?
Why do the best homology hits for the “Flavobacteria” plasmid appear on the chromosomes of Agromyces? Uh, well what do you think? HGT, but we don’t know what direction, and we still don’t know what the pre-1935 ancestor looks like.
Thanks for looking up the stuff on the Flavobacteria.
ADDENDUM:
I was describing a Flavobacteirum with a plasmid homologus to the nylon eater, but with no nylon eating ability. If we had lots of these we could actually estimate the real evolutionary change (or lack thereof) post 1935.
Well since there are three genes for those three enzymes (NylA, B and C), at least one of them might have originated by that putative frame shift mutation Ohno speaks about in his 1984 paper.
“6-AHA LOH” he calls it, which is the NylC enzyme(?) as far as I can gather.
The shifting nomenclature is confusing as hell, (not your fault of course) but it does make trying to trace through the literature laborious and frustrating.
Assuming Ohno is correct and NylC originated by a frameshift mutation inside some other larger gene in the plasmid, given there is no sequence homology between them, the other two had to come from somewhere else.
Actually re-reading the paper now, he says that TWO of the three originated by that same mechanism:
6-ALA LOH (NylA) and 6-AHA LOH (NylC) if I follow the shifting nomenclature correctly.
That leaves NylB without a history unless I’m missing something. Is that also thought to have originated by a frameshift mutation?
What part of the plasmid is homologous to the Agromyces chromosome? This might not even have any bearing on the actual origin of the three enzymes NylA, B and C. The plasmid is apparently about 45.000 bp in total. It could have all sorts of other genes on that plasmid, homologous to the Agromyces chromosome at some locus, but with little or no relevance to nylon metabolism and the three enzymes or their origin.
Sal,
In investigating the origins of the nylonase genes, it would be helpful to have alternative hypotheses to test. Do you have any such alternatives, and if so what are they?
The fact that nylonases have so far been found only in association with nylon waste is to me good evidence that they arose in association with nylon, even in the absence of comparative evidence.
What other genes are on the plasmid, and have you searched for any of those sequences?
This paper might shed light on the evolution of at least NylB: Okada H et a. 1983. Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers. Nature 306:203-206. All I can see is the abstract, but it discusses some relevant features of the whole plasmid, including a homolog of NylB, NylB’, from which they conclude that NylB arose from sequence duplication in a repetitive sequence. Comparative methods can work within genomes as well a between them.
So, not god then?
John,
Stupid atheist. God didn’t want those bacteria to starve, so he tweaked their genes to produce nylonase.
It’s obvious.
Just to be clear, god created a universe that generated bacteria but could not generate a universe that generated bacteria that generated nylonase without additional work/tweaking?
Makes sense….
OMagain:
Nah, he’s been tweaking from the get-go. Screw those theistic evolutionists. They are the spawn of Satan.
I’m not denying they bacteria evolved nylonase capability from some pre-cursor. I’m simply saying there is ambiguity of the timeline whether the nylon-eating evolution happened before 1935 or after 1935.
Some of the hypotheses are:
1. Framshift (Ohno) after duplication
2. 2-residue mutaition (Segoro ) after duplication of NylB-prime
3. nothing much on NylC, but it evolved from something unknown
I linked to the Segoro paper earlier:
https://link.springer.com/article/10.1007/s002530000434
Let’s assume one of the hypotheses is true. The question is why don’t we see samples of the un-evolved pre-1935 like genes in bacteria? If Segoro is right, then we could reasonably expect “Flavobacteria sp.” plasmids that don’t have nylon eating ability somewhere. Why haven’t we found them? This would be consistent with yet another hypothesis that supposes coincidental nylon-eating ability evolved pre-1935 to catalyze a reaction other than nylon, and it was just a side benefit NylB and NylC could also catalyze nylon degredation. So basically the nylon eating capability pre-existed 1935 even before nylon existed in order to catalyze another reaction which we haven’t figured out yet.
If the evolution were observed like Lenski’s LTEE, there would be no question what actually happened and when.
First, the name is “Negoro”.
Second, are the scenarios mutually exclusive? Suppose a proto-NylB evolves by frameshift in a repetitive sequence, followed by gene duplication to produce NylB and NylB’ precursors. I don’t think anyone actually knows the function of NylB’, but lets suppose it does have one and resembles the ancestral gene. It has weak nylonase activity, which could well be a spandrel. Then when nylon comes along, any bacterium with that plasmid would be pre-adapted to digest nylon, and the two mutations that make NylB would have been selected for when they occurred in that environment.
Is that explanation consistent with existing data? I don’t know. I don’t know if that plasmid has been sequenced for strains that don’t digest nylon. I don’t know if the genes even originated in that plasmid. In short, I don’t know where to look for homologs of NylA or NylC, or even to NylB, other than NylB’. Different names for the same organism, plasmid, and genes complicate any search too.
Yup. Thanks for looking into this anyway. I hope there was something of value there to you.
I’m pretty sure it is NylB that Ohno is talking about, not NylC. I’ll state the reason why I believe that to be the case. First, I did the brute method and entered the sequence in the paper by hand into BLAST! I only needed about 40 letters starting with the start codon. It provided a pretty much unique hit to NylB even though what I typed in was only a fragment. I was ready to type the whole dang thing, it, but I was lazy.
Second, Ohno references Okada’s paper in Nature and mentions the transcript in question by the name R-IIA:
The identity of R-IIA is associated with NylB!
So NylB is in R-IIA and is also called 6-AHA LOH (or the gene that code 6-AHA LOH). Yikes!
http://www.nature.com/nature/journal/v306/n5939/abs/306203a0.html
And then it all got renamed to 6-Aminohexanoic Acid Cyclic Dimer Hydrolase, but even then sometimes they drop the “dimer” and sometimes they insert “oligomer”. 🙂
I thought that your point was actually this:
Should you have not mentioned that in your list?
stcordova,
Yes, Ohno is talking about NylB.
Thanks John.
You want to know what’s wrong with TSZ? I’ll tell you what’s wrong. The bullshit (literally, figuratively) thread gets longer and longer while this one died a quick death.
That’s pretty much what’s wrong with the Internet. And it was much the same on the old usenet.
I guess it is easier to participate in a BS thread, because you don’t have to actually know anything.
Neil,
There is a difference between “a BS thread” and a thread about people’s susceptibility to BS, but that point may be too subtle for you.
John,
What more is there to say? Sal tried to smuggle God into nylonase and failed.
If you think there’s more to be said, please say it. I read your comments with interest.
I think the bullshit thread passed it’s sell by date a while back. Take a vote.
Sorry for the delay in re-visiting this thread.
Rumraket was asking about my mention of Agromyces.
Agromyces has on its chromosomes both NylB and NylC that have 99% homology with the “flavobacteria” plasmid pOAD2. I haven’t checked out NylA yet, but the coincidence of 2 genes on the plasmid of one bacteria appearing in the chromosome of another seems too strong to be coincidental.
A few scenarios are possible which maybe a microbiologists can help sort out.
One possibility is the genes on the “flavobacteria” plasmid pOAD2 integrated into the Agromyces genome…
Or, the Agromyces genome got its genes on plasmid and it gave rise to plasmid pOAD2 that appeared ont eh “flavobacterai”….
Or, a plasmid from yet another bacteria invaded both Agromyces and the “flavobacteria” (renamed Arthrobacter sp.).
Or, the Arthrobacter and Agromyces have a common ancestor pre-1935.
Or…..
If we could find non-nylon eating homologous NylB genes on some bacteria (like say another strain of Agromyecs or Arthrobacter sp., or some bacteria on the planet), we might have a slightly better picture of what is going on. If supposing we did, then we might be able to estimate what actually evolved after 1935. Right now we don’t know.
petrushka,
That’s fine. You’re free to ignore it.
What you read and what you ignore is your responsibility.
Well I’m at work now so I can finally access some of the papers, so now I can at least read up on this a bit.
Just out of curiosity. Nylons are polyamides; they are linear polymers with the subunits linked by peptide bonds. Nylon was first developed as a replacement for silk. Silk is digestible – some spider sps eat and recycle their web daily. Why is it considered such a jump from proteases that evolved to digest peptide bonds in natural silk to an enzyme that can hydrolyse nylon?
The fact that they have tested the nylonase enzymes on hundreds of natural amides and found they are active on none of them. Only the nylon degradation products. Weirdly enough.
From Biodegradation of nylon oligomers:
Of course one can still reason that, since they haven’t tested all the known natural amides, it’s still technically possible there’s some obscure ones out there the enzymes “used” to work on. That just seems very unlikely given they have no cross-reactivity (they also can’t catalyze each other’s reactions). So if they evolved from previous amide hydrolases, there would probably have to be three of them, also with no or very little cross-reactivity.
That would mean all three nylonases would have to have evolved from some three unknown amide hydrolases, active on natural amides none of which are similar enough to hundreds of other known natural amides that the hydrolases have even weak activity on them, but are just by chance quite similar to the degradation products of nylon manufacture.
And then there’s the evidence for the frameshift -> duplication -> point mutation, origin of NylB (Ohno 1984). So I think at least that one can’t be reasonably said to have any homologous precursor protein.
In the Biodegradation of nylon oligomers they write something strange at the end I don’t understand:
That #2 thing makes no sense to me. I guess I have to read Yomo et al. 1992 next.
I will say though, that looking at figure 1, nylonase evolution only really requires the evolution of EII. The top three compounds are all individual waste products of nylon manufacture, and all the bacterium needs is to metabolize one of them, the middle one. The total degradation of that product, all three steps, is catalyzed by NylB. The additional enzymes, EI and EIII, just make it possible for the organism to utilize other waste products too. And if EII originated in a frameshift mutation, that’s really not that far fetched.
Regarding the timing of nylonase evolution and NylB, as far as I can gather, the nucleotide divergence between NylB and NylB’ (the sub-optimal duplicate of the enzyme) is what implies it evolved concomitantly with the invention of nylon manufacture, back in 1935-1940.
But then it gets confusing, because according to Yomo et al 1992:
But this seems to argue against the frameshift scenario? In this view, the entire NylB gene family in both Flavobacterium and Pseudomonas, due to their high divergence but still statistically significant similarity, evolved from a common ancestral genes some 140 million years ago.
Or, are they saying that there was an original gene, that got copied to so it existed both Flavobacteria and Pseudomonas plasmids, 140 million years ago. This gene then diverged a lot during the ensuing 140 million years, until some time around 1935-1940, independently in both species, an idential frameshift mutation in these highly divergent genes, produced two very divergent NylB enzymes? The way I read this they are suggesting the latter scenario.
Regardless, that still leaves open the question of how (and when?) NylA and NylC evolved of course. Though my guess here would be subsequently to NylB, because the products of NylA and NylC still need to be used as a substrate by NylB (according to figure 1, above), so there’d be no benefit to evolving NylA and NylC without NylB. So we’re left with the how?-question for NylA and NylC.
Are they duplications divergent from enzymes from some prior, as-yet unknown amide hydrolase, horizontally transferred to the pOAD2 plasmid? I wonder how thoroughly homologous DNA sequences have been searched for, and how much data they had in 1992 or before, compared to how much we have today. Might be worth looking into.
Or did NylA and NylC also originate by frameshift mutation in other genes, already present on pOAD2?
Rumraket,
Thanks for this, I actually missed it, and wouldn’t have noticed if you had not pointed it out:
and you say:
I have similar thoughts. It seems to me, much of the popularizers, including William Dembski argue for the frame shift scenario! Worse, popularizers usually no distinction about which gene they are talking about NylA, NylB, NylC. To them a 6-aminohexanoate hydrolase codes from the same gene — not true! Several different genes can code for a 6-aminohexanoate hydrolase. NylB and NylC, as far as I can tell have no homology but are technically 6-aminohexanoate hydrolases, though NylB’s specialty is the dimer form.
And not helping matters are YECs like Don Batten who argue God intelligently designed high speed evolution on the plasmid, but Batten didn’t do much to clarify what and how much evolution either!
Looks to me a lot of blame can be passed around for the confusion on all sides, and few people are keeping up-to-date on what’s happening and are actually checking the gene banks and understanding the chemistry and combing through the papers.
The diagram you posted is excellent. It was the diagram I was referring to when I said there appeared to be a digestion cascade involving NylC breaking things down for NylB.
I’m not arguing against the evolution of nylon-eating ability. If it evolved like anti-biotic resistance or like Lenski’s LTEE post 1935, why should I dispute it? What I am pointing out is there is ambiguity when and how much evolution happened, especially post 1935. There is ambiguity based on the data available, and there is ambiguity because the literature isn’t exactly helping clarify matters, and there is ambiguity because of the popularizers and even the creationists who are making a lot of noise but who probably haven’t looked into the matter as carefully as you just did!
Thanks for reading this. I’m really not taking a stand against the evolution of nylon eating anymore than I’m taking a stand against evolution of anti-biotic resistance. I am saying, it’s not clear when and how much evolution happened.
I’ll revisit the papers some more, but it’s reassuring to me that I’m not the only one who looks at the 40-year history of papers on the topic and thinks the matter is rather a confused mess of reporting. I think the lab science and environmental engineering side of their work is pretty good, but some of their inferences aren’t clearly articulated.
I think you both have mistaken the scenario. Here’s my understanding:
1. Ancestral repetitive-sequenced gene, function unknown.
2. Frame shift to produce a new ORF, function unknown.
3. Spread of new ORF to various plasmids in various strains, including what the referenced paper calls P and F.
4. Millions of years pass.
5. Duplication of new ORF in F plasmid to produce precursors to F-NylB and F-NylB’.
6. Millions of years pass.
7. Nylon appears in the environment.
8. Fixation of two new mutations in in the F-NylB precursor that make it a highly effective digester of nylon waste. And changes, so far uncharacterized, in the P-NylB precursor for a similar reason.
The main question I have here is about the “function unknown” bits. Do these precursors need to have a function so that purifying selection keeps them from degrading? I can’t be sure, but it seems so to me. Otherwise we would seem to need some active mechanism to prevent degradation of useless sequences. Starting from a highly repetitive sequence would help, since no codon would be one or two mutations away from a stop codon. But that doesn’t seem adequate here.
Still, as far as I know NylB has been found only in an environment rich in nylon waste, which is indeed evidence that it evolved in that environment, and thus post-1935.
John,
Thanks for your comments.
A data point I should add is that the NylB and NylC gene share a promoter. So if NylB evolved by gene duplication from NylB-prime, it sure was fortuitously duplicated to the same place to share a promoter with the NylC gene which is in the digestion cascade I mentioned earlier and which Rumraket posted (depicted below). The products of NylC’s activity are digested by NylB. NylC and NylB share no sequence homology. So if “flavobacteria” and Agromyces digest nylon, the cascaded nylon digestion ability had to CO-evolve simultaneously (or close to it) in both genes since 1935.
Additionally I heard in passing someone say we’ve only sequenced not even 1% of the bacterial species out there. So it is possible we just don’t have adequate sample sizes yet.
I’m not averse to some sort of evolution of nylon eating like that clearly demonstrated in Pseudomonas after 3 months. The same group that discovered how to evolve Pseudomonas to eat nylon however, don’t know the mechanism. They don’t know what had to change to make it digest nylon. It’s a little frustrating, because if they simply put the controls on the experiment like Richard Lenski did in his LTEE, there would be no ambiguity of what specifically had to evolve in Pseudomonas! It’s worth noting the Pseudomonas nylon eating gene has no nucleotide homology to NylB nor NylC, only slight protein homology (37% which reported above) to NylB.
Note:
E-I = NylA
E-II = NylB
E-III = NylC
You might be right, I just can’t seem to extract why this particular scenario is the one they intend to convey. I have to agree with Sal that they’re not very explicit about their reasoning.
I’m not sure why you infer there’s a millions of years-step 6. – following step 5. According to Yomo et al 1992:
“The primary structures of the F-EII and F-EII’ enzymes are very similar (88% identity), but the activity of F-EII’ toward 6-aminohexanoate dimer is <1% of that of F-EII (7). Thus these two genes seem to be the descendants that diverged through the duplication of a common ancestral gene (7)."
88% similar of 392 amino acids is a difference of 47 amino acids. If they diverged following duplication, they each evolved somewhere about 23 amino acid substitutions, following the divergence presumably about 1940’ish. It seems reasonable to me that positive selection on NylB for increased catalysis could fix 23 amino acid substitutions in that timeframe (or maybe even more), while the NylB’ homologue just drifted (or even that it didn’t change much at all, because it was maintained by purifying selection for the ancestral function of the original reading frame).
Looking at that (7) reference we get Okada H et al 1983 (which I can’t access from home right now) but at least it says in the abstract: “From comparisons of the nucleotide sequences and gene products of the nylB and nylB’ genes, we now conclude that EII enzyme is newly evolved by gene duplication followed by base substitutions on the same plasmid.”
I agree, the common ancestor must have had a function or it would have not just degraded, I think it would have totally disappeared in 140 million years. Bacteria don’t carry junk around for that long, particularly if it’s located on a plasmid.
Not only that, the fact that it catalyzes only nylon degradation, acts on the linear polymer and acts to reduce it all the way from hexamer to monomer, implies it’s highly specialized towards nylon waste and nothing else.
The NylA and NylC enzymes I would stipulate had to come from something else not yet sequenced (or searched for recently in any database?).
Sal,
Why not stick God into both gaps? There’s no rule that says God can’t muck around in the laboratory.
The more gaps you stick God into, the more likely it is that at least one of them won’t close up and spit God out.
Only in the substances they tested. We don’t know what else might be in the original environment from which the genes came from, wherever they came from.
I also just learned something recently. The Rubisco enzyme in plants catalyzes two different reactions. Rubisco is listed as a carboxylase and an oxygenase. By way of extension, the nylonases aren’t restricted to nylons at least in principle.
I would imagine something like the Pseudonomas in vitro evolution scenario happened for post-1935 nylonase if indeed there was evolutionary adaptation to nylon specifically after 1935. Unfortunately, the researchers of Pseudomonas evolution were astonishingly silent on what changed in the 3 months that it took to evolve in vitro the Pseudomonas version of nylonase (not sequence homologous to either NylB or NylC).
Maybe they just haven’t found the substances in the wild that NylB and/or NylB’ may catalyze other than nylon.
The ancestor of NylB and NylB’, yes, I agree that one probably had a different function. But I don’t believe that function is retained in NylB, it might in NylB’.
True, but Rubisco has two active sites. I think I read that NylB doesn’t (seem to?) in one of the papers. Don’t take my word for it, I have to go back and read it again.
Given how NylB is so effective on linear nylon oligomers, that alone testifies to it being the derived nylon-adapted version. So if the enzyme really is capable of catalyzing other reactions, I’d put my money on NylB’ being better at it.
Rumraket,
The reason I presented that scenario is that it’s the only one that makes sense of the data; I think it’s what at least some of the sources are saying, but I could be wrong.
12% divergence, even given the rates the source allows (which are themselves quite high) would not produce that divergence in much less than 10^7 years. If you invoke selection, and if the duplication is recent, then NylB would have to have experienced all 47 differences, NylB’ none. Just not credible, even with strong selection. Even 23 wouldn’t be credible.
Or perhaps NylB’ is the duplicate. You need to separate the duplication process from the evolution of nylon-digesting activity. Either copy of the gene could have evolved that activity. I would suggest that it’s more likely that NylB is the original copy, and that its precursor and the NylC precursor shared a promoter originally and that both co-evolved because their proximity made that pathway advantageous.
I see what you mean, I didn’t do the numbers. If 37% similarity between the F and P enzymes implies 140 million years ago divergence, 12% can’t be mere decades. I stand corrected.
Not true. NylB alone can digest linear oligomers. NylA and NylC merely render cyclic oligomers linear. If, as seems most reasonable, nylon waste consists of a mixture of cyclic and llinear oligomers, NylA and NylC would most plausibly have evolved after NylB (both versions) and would merely enable NylB to digest the waste more efficiently.