Newly discovered deep-sea enzyme breaks down PET plastic | Hacker News Reader

Newly discovered deep-sea enzyme breaks down PET plastic

phys.org

175 pointshanniabu74 comments

Slightly misleading headline, as PET (polyethylene terephthalate) hydrolases were already known - see https://www.chm.bris.ac.uk/motm/PETase/PETaseh.htm

This is a study of an archaeal enzyme (from the deep-sea) that can degrade both long-chain and short-chain polymers that is more efficient at 70 deg C than other enzymes.

The details are that this is a feruloyl esterase with a conserved alpha/beta-hydrolase fold but with an additional flexible 'lid' domain that covers the active site. The authors suggest this lid domain replaces the conserved Trp that is an Ala in the archaeal enzyme.

"this is a feruloyl esterase with a conserved alpha/beta-hydrolase fold but with an additional flexible 'lid' domain that covers the active site"

As educated as I think I am, it is always humbling to read a hacker news comment that I cannot understand.

ELI5?

Apologies, that was meant for the specialists :) It is mostly just technical jargon so do not feel too humble ...

So I'll break it down:

- "feruloyl esterase" : an 'esterase' is an enzyme that makes or breaks ester bonds. In this case, 'feruloyl' which I've never heard of but apparently is some small molecule that is normally attached to a sugar. https://en.wikipedia.org/wiki/Feruloyl_esterase

- "conserved alpha/beta-hydrolase fold" : a structural pattern (fold) that is shared (conserved) between a set of structures. In other words, these enzymes all have roughly the same shape. https://www.cathdb.info/version/v4_3_0/superfamily/3.40.50.1...

- "additional flexible 'lid' domain that covers the active site" : a 'domain' is just a compact part of a protein, without going into too much detail. They are calling it a 'flexible lid' as the idea is that it moves out of the way to bind the substrate to the active site (where the reaction is carried out) and back again when fully bound.

Thank you.

I've been using ChatGPT4 for this situtations, with excellent results. Check out this conversation about it (I used a PDF reader plugin, also): https://chat.openai.com/share/a682c5a7-f2c5-4849-a999-5a7218...

Enzymes are kind of like a tool for breaking apart lego blocks, or a jig for assembling them. This sounds like a moving part that covers the "teeth" and makes it more effective (or less likely to get jammed by the wrong molecules?).

Two things.

Lot of reactions are energetically favorable. But the reactants are stuck in a local minima. So either doesn't happen or is too slow. Enzymes mediate the reaction so it can happen or happen faster.

Lot of reactions there are side reactions that produce stuff you don't want. Resulting a terrible yield or maybe none. Enzymes can promote the reaction you want increasing the yield.

Interesting thing to watch for is eletrocatalysts. Where you use electricity and a catalist to push a reaction that is energetically unfavorable. Like CO2 + H2O --> methanol. These may become very important as we stop pumping oil and gas out of the ground.

I don't think there's much to say besides "slightly different chemical structure makes it better". At some point you hit jargon rock bottom.

Yeah, it's not bad news at all but it appears to be one of many that still require considerable heat, industrial infra, etc.

Has anyone attempted to put these enzymes to the test in at some scale in an industrial setting, I wonder?

I was recently at a party and spent some time talking with someone who has a stealth startup working on this exact problem. He said that they aren't the first, but getting the scale right (in an industrial setting) and finances right enough that someone is willing to spend the money to set it up is far harder than just finding an enzyme that can break down PET / similar polymers.

No idea. From skimming some university press releases, I see a lot of "potential for!" and similar wording.

This https://news.utexas.edu/2022/04/27/plastic-eating-enzyme-cou... has "Up next, the team plans to work on scaling up enzyme production to prepare for industrial and environmental application. " which is more promising.

As far as I understand, yes it is a very different challenge to make a bioreactor for actually using some random new enzyme than the (also hard) problem of getting the structure in the first place. How to immobilize it on some surface, how to pre-process the material to pass it through the reactor (?) I guess ...

Feels like it's always "potential for"... sigh

I mean my processor hits 70° and has for a decade or more, and my car engine thinks 87° is the happy temperature.

70° is maybe a little out of the reach of a home system but nothing for a municipal system. Right?

A hot water tank is not far from 70C

Should work well in landfills since there's heat buildup

https://www.purecycle.com/who-we-are. ?

> Slightly misleading headline, as PET (polyethylene terephthalate) hydrolases were already known

It doesn't say it was the only one, just a newly discovered one

Sure, fair enough. I just thought people might read it as "Enzyme with new ability (to break down PET) discovered", but maybe I was being pessimistic.

It's also mentioned in the article body:

> Until now, about 80 different PET-degrading enzymes were known, most of which were found in bacteria or fungi.

Most of us aren't reading the body though.

The way to understand the origin of fossil fuel deposits is that hundreds of millions of years ago trees were made of plastic.

Thats not quite literally true but it gives the right sense. In the Carboniferous period trees grew abundently but there were not yet bacteria that could break down the lignins composing the woody structure. Its very similar to what you'd get with plastic trees today: they would fall and pile up like junk in a landfill. Then eventually this would be buried and result in the many-meters-thick coal deposits we find today.

Lessons? I don't know. But piles of un-decomposable hydrocarbons is not a new thing for the planet.

When I searched for this, I found there to be some debate on it (isn't there always?): https://www.pnas.org/doi/10.1073/pnas.1517943113 https://arstechnica.com/science/2016/01/why-was-most-of-the-...

Thanks! Your newer research is pretty convincing. Makes me a bit sad: I really like the 'plastic tree' analogy. Ah, well.

I wonder what forests looked back then. Trees going through and on piles of dead trees?

It's interesting to read about thomas gold's theories about hydrocarbons.

https://en.wikipedia.org/wiki/Abiogenic_petroleum_origin

To me it makes sense that some or all hydrocarbons are or at least started like the hydrocarbons found on other planets in our solar system.

As much plastic as we dump into nature now, we increase the chance for a mutation of a microbe being able to digest it.

If that microbe manage to multiply and spread, plastic can start to rot, just like wood is doing now. On a long term basis, that might be a good thing, but in the short term it would be a catastrophy. We are using plastic as a long lasting material, often with no surface treatment. Imagine if wire insulation, waterproof encapsulation, gaskets and other important parts of our infrastructure starts to rapidly degrade!

That alone should be motivation for cleaning up and stop spreading plastic waste in nature.

Wood doesn’t spontaneously rot at a rate that is problematic. This new enzyme requires temperatures of around 70C to operate. Any microbe that does evolve to eat plastic will probably need some specific living conditions. They are unlikely to be so efficient and universal that we see plastic rotting while we are using it.

IIRC, “plastic eater” was one of the mutations of The Andromeda Strain in the eponymous Crichton novel.

Not to undermine your point about cleaning up plastic, but following your logic: isn't this similar to the antibiotics situation, just maybe on a longer time scale? The more you use it the less effective it is. What's the ultimate solution?

Walls and ladders. There isn't a solution to evolution, you just have to keep adapting.

Is it feasible for something like, e.g., teflon to be decomposed biologically?

So dumping all our plastic in the sea will work out! /s

It seems like these discoveries are coming quickly and in higher numbers. Maybe there's hope in recycling/processing plastics down simpler molecules after all. Currently, recycling plastic is a bit of a lie -- very little of it is actually recycled.

"Currently, recycling plastic is a bit of a lie -- very little of it is actually recycled."

Depends where you live and what you consider recycling. If you mean, making new plastics out of the old, than the challenge is, that there are many, many different plastics you cannot just melt in and reuse if mixed together. A annoying, but working solution here in germany is a mandated bottle bill. Meaning you pay 25 cent extra per bottle, and get it back, if you return that bottle into a machine: but this results in actual reusable plastics as they are all of the same kind.

And for the rest, the most pragmatic solution is burning it for energy. If you use filters, it is not so bad and it is recycling, but it is the same as burning fossil fuels, so not a good long term solution.

>And for the rest, the most pragmatic solution is burning it for energy.

No, burying is better because it sequesters the carbon rather than releasing it into the atmosphere.

If it means not burning coal, oil or gas instead and there are good filters, I think burning plastic makes sense. But if you can actually get all the needed energy from non fossil sources, then yes, burying makes more sense. But I think only some rare places on earth are that far.

> And for the rest, the most pragmatic solution is burning it for energy.

I really wish we'd do more of this. I know it's not ideal, but we in the US need to treat plastic like the trash that it (mostly) is. And trash is just fuel. Instead we have convenient single-stream recycling which means all our actual recyclables also end up in the trash and/or oceans.

We actually do a fair amount of this in the US. Marion County in Oregon burns 90% of their trash. It's much better than landfills, anyways.

How is burning better than landfilling it? If the landfill is lined the garbage isn't going anywhere, and leaving the plastic in the ground is much better than releasing its co2 into the atmosphere. Land use might be an issue in some places, but I doubt that's the case in Oregon.

> Land use might be an issue in some places

It really isn't the land that's the problem, there is absolutely plenty of land to support the entire earth's population of trash in landfills. Just like with food, the problem is moving it to the places you want it to be.

I recognize the sarcasm in your first sentence, but I am not super hopeful. The question is always, "so now it breaks down...into what? And what happens to that?". If that gives rise to the equivalent of some kind of algal bloom that then kills off other life, it might actually be worse than the microplastics themselves.

I for one do not hold out hope for recycling plastics. We had more sustainable materials in the past, and in places we still do that. For example, reusing beer bottles with the Pfand system in Germany, or milk bottles, crates, durable packaging. We're still going backwards with this consumerist throwaway culture.

Here here.

Unfortunately the government has teamed up with the corporations to continue to push it for decades:

https://magarshak.com/blog/?p=362

The recycling was a scam to keep the public distracted so their impulse to “do something” would lead to individuan action rather than lead to organizing to demand reforms!

I'm fearing that degradable plastics is also a lie.. is it just turning it into microplastics small enough that the problem visually disappears?

It breaks them down into their atomic components and enables bacteria that can straight up digest plastic. The issue from this is that we rely on plastics not being degradable for a lot of the properties we use it for. Imagine if bugs got this enzyme in their gut bacteria, and started eating the food wrappers instead of just nibbling through them. Plastic used to seal sterile equipment in medical settings or for implants? Useless. The plastic waste would only last a few years relative to the decades+ now, but it would also ruin plastic's ability to seal stuff, which is why we use it.

Overall, probably a good thing to reduce our reliance on plastic, but it will come at a cost, it's not just "we can dump plastic in the ocean now"

It would still be difficult for bugs to gnaw on solid plastic

It's difficult for bugs to gnaw on solid wood, too. Termites still cause billions in damages a year.

And they took millions of years to evolve and depend on microbes living in their gut to digest the wood. They have to keep those microbes in a protected environment to allow them do do the digestion. They aren’t just digesting wood out in the open.

I can follow these goalposts. They're already in gut microbiomes.

https://pubmed.ncbi.nlm.nih.gov/29763555/

https://pubmed.ncbi.nlm.nih.gov/32374590/

AMP-Free link

https://phys.org/news/2023-09-newly-deep-sea-enzyme-pet-plas...

Changed from https://phys.org/news/2023-09-newly-deep-sea-enzyme-pet-plas.... Thanks!

I love the idea of finding enzymes that break down plastics. I also like to imagine the post-apocalyptic Sci-Fi short story possibilities of accidentally releasing something that breaks down _all_ plastic!

Imagine my delight in reading this:

    At the molecular level, PET46 is very similar to another enzyme, ferulic 
    acid esterase. This degrades the natural polymer lignin in plant cell walls
    by breaking down lignin polymers to release sugars from woody plant parts.
    Lignin and PET have many structural similarities, so the PET-degrading
    enzymes found in nature may be important for composting wood in forest
    soils, for example.

Now, join me in imagining the post-apocalyptic Sci-Fi short story possibilities of accidentally releasing something that breaks down all plastic _and_ all plants! I mean, until some of them finally adapt.

Unlike the plastic substrate of modern technological society, plants have survived hundreds of millions of years of efforts by the rest of the biosphere to eat them.

True, although I believe dredging up unusual enzymes from the stygian depths facilitates new and exciting dystopian storylines.

You might enjoy the Rifters trilogy by Peter Watts.

Now splice this into the genome of black mold and release it in a coca-cola bottling plant.

Less fun, PET is heavily used in medical devices including implants. There's a huge cut to life expectancy if it becomes a secondary food source for something like an engineered MSRA strain.

More reason to be furious at plastic peddling billionaires. They made us hostages. We still have to stop them, but it's going to hurt even more.

Eh. Thinking plastic would last forever was probably a reasonable assumption at the time. I doubt it was the billionaires making that design call. Though in hindsight maybe we should have known better, given the history of lignin and natural waxes.

Though especially given the history of lignin, we probably have millions of years before medical devices being eaten by microbes becomes a widespread problem that anyone seriously needs to worry about. There's bigger fish to fry right now.

> Thinking plastic would last forever was probably a reasonable assumption at the time

That's... not what I'm mad about at all.

Don't laugh, someday a terrorist or hacker may engineer a fast-eating critter, and half our stuff will become useless in a year. Termites learned to work with gut microbes to speed up wood munching, a home-owner's biggest nightmare.

That's still kind of funny in a existential hysteria kind of way.

Humans are pretty adaptable. If half our stuff did become useless do you think that might put a damper on rampant consumerism?

It would increase consumerism since everything would need to be replaced on a periodic basis

Everything? I think instead, we'll just stop making most things out of plastics. We have longer-lasting, more durable materials than plastics already, for when you want something that will actually survive decades or generations. They're metals and woods and stones.

Some things, like wire coatings, will still likely need to be plastic and will become disposable. But most uses of plastic for long-lasting goods will just stop using plastics. Goods will get much heavier, but more durable.

Woods? If wood can survive so can plastic in this hypothetical world. Just keep water away from the plastic.

With new plastics full of chemicals that the bugs won't eat.

Sounds like "Mutant 59"

The Andromeda Strain!

Or Peter Watts' Starfish, since it's from the deep sea

There's one significant detail about Behemoth missing...

Thank you phys.org for putting an actual link to the scientific publication, something that is missing far too often these days.

It's really awesome that all our plastic will one day rot.

But we have lots of pipes and cables underground that will need to be replaced - with what I wonder.

Why do we want to break down PET? Why not just re-use it?

Heat, stress, and light will probably break it down mechanically over time no matter how diligent you are about reusing or recycling it.

At the very least, this should hopefully mean that all those scary endocrine-disrupting and bioaccumulating microplastic and nanoplastic particles that are apparently being shed by the millions every time you heat or handle anything plastic aren't necessarily going to keep building up forever.

Most is not reused, or only reused with limited capacity

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