Bacteria dine out on plastic

Plastics are choking our oceans and decimating marine ecosystems, and so people are desperately searching for solutions. Most plastics can't be broken down by naturally occuring substances, but some bacteria do carry enzymes, which are biological catalysts, that are capable of attacking them. And a couple of years ago scientists in Japan discovered bacteria carrying a mutated form of one of these enzymes that was enabling them to degrade PET, one of the commonest forms of man-made plastic. Now John McGeehan, at the University of Portsmouth, has assembled a 3D-model of this mutant plastic-eating enzyme to understand how it works, and to help him to discover how to make the enzyme work even better. Chris Smith heard about the scale of the issue.

John - Everyone’s very aware of the problem, thanks to things like David Attenborough and Blue Planet, really horrific images of plastic leaking into our oceans and residing there for a long time.

Chris - Why are plastics particularly resilient?

John - Without going into too much detail, we need to understand how plastic is made in the first place. It’s basically two building blocks that are pulled together to form a very strong bond; it’s called an ester bond. And if you look at the label on your jacket or your fleece you’ll see the word polyester, and all that means is a long chain full of all these bonds.

Now, these sorts of bonds exist in nature and plant leaves are covered in a material call Cutin that protects them from invading bacteria. That is also a natural polyester and enzymes have evolved over millions of years to eat that material.

Plastics’ are a bit wider because they contain an aromatic compound called terephthalate acid - that gives us PET, that’s where it comes from. Those things don’t fit into natural enzymes very easily.

Chris - But in this paper you’re describing one particular class of microorganism that does appear to be able, or at least taken some steps to begin to degrade these things?

John - It’s fascinating what’s happened. When we looked at the 3D structure of this enzyme, we were stunned to see how similar it was to a natural enzyme called a cutinase that’s the type of enzyme bacteria use to invade a leaf cell, for example. The only difference is that the active site, the bit that does the chemistry, is opened up to be wider in order to accommodate this man-made substance.

Chris - This was first described by the Japanese, this class of microorganisms, as Ideonella sakaiensis.

John - Yes.

Chris - Where did they get it?

John - They actually found it in the soil and waste water runoff of a plastic recycling plant in Japan.

Chris - And it was there why?

John - Because bacteria are incredible organisms. If there’s a community of bacteria and one bacterium makes a mutation to allow it to survive on a new substrate, a new food that no-one else is eating, it’ll grow exponentially very quickly and outgrow the other bacteria. So there’s a massive selection pressure within a recycling plant, for example, for anything that can eat that substrate, in this case PET.

Chris - So you decided to ask: well how have they endowed their biochemistry with this ability and you found that they have altered their enzymes subtly. Is the change that they’ve made as good as it’s going to get or do you models predict that with some further tweeks they could become a lot more efficient?

John - Once you get a 3D structure, the first thing you do is compare it to the ancestral - in this case cutinase enzyme - to see what’s changed; how has it evolved? What we’re doing now is to see if we can unpick what are the important parts of the enzyme and how to make it better, but the potential for doing that is now huge.

Chris - How are you going about trying to optimise the enzyme in that way?

John - We use the 3D structure as a kind of starting point and what we do is nowadays it’s very easy to make synthetic DNA. So we can go in and make very specific changes, which changes the shape of the enzyme, particularly around the parts of the enzyme that recognise and bind the plastic, so that’s what we’re currently engaged with.