How tardigrades defend DNA from radiation

20 December 2019

Interview with 

Jim Kadonaga, UCSD

TARDIGRADE.jpg

A tardigrade

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They’re only about half a millimetre long, and they resemble a scrawny maggot with claws, but these animals are biologically bombproof: they can be frozen to -272 Celsius; you can remove 99% of the water they contain; boil them in alcohol; put them under pressure six times greater than the ocean floor; zap them with cosmic rays and expose them to the void of space for 10 days… and they don’t die! These microscopic marvels are “tardigrades”. And, as he explains to Chris Smith, a suitably intrigued Jim Kadonaga set about discovering the basis of at least part of this story: how these creatures protect their DNA from lethal doses of radiation...

Jim - The reason we got into this project as I was reading Chemical and Engineering News and I read a fascinating article on tardigrades. They described a protein that made cells more resistant to x rays. And I looked at that protein and I thought well this looks like a protein that's related to chromatin which is a subject that we work on. I kind of filed that away in the back of my mind. A couple of months later a student Carolyn Chavez expressed an interest in working in my lab and so I suggested her that she try out that project. And so that's how we got started on it.

Chris - When you say that the protein that you saw in the magazine was very similar to the structure of chromatic.

Jim - In what way was similar chromatin as the natural form of DNA in our cells. DNA is a long molecular chain and it gets wound around these protein spores in a form that's called chromatin. And so I've worked on chromatin for 30 years. And when I looked at the actual components of the protein I thought, "this protein looks like it's going to bind to chromatin!" Of course it was just an idea, but that's what we first tested.

Chris - And your idea is that it binds because the DNA - for want of a better analogy - looks a bit like a hand, and the protein looks like a glove, and one would fit "hand in glove" with the other, which is why you think that they would stick together? 

Jim - Something like that. They had complementary properties.

Chris - So what was the project you embarked upon?

Jim - This project actually had four phases. And the first phase was testing whether or not this protein - called Dsup - binds the chromatin. And in fact it did bind to chromatin.

Chris - So you literally mix the two up together in a tube and ask "does one stick to the other?"

Jim - That's pretty much what we did. And we actually did it like a couple of different ways to show that they bind to each other, just to make we're absolutely sure that we were correct about that.

Chris - And when you look in the tardigrades themselves, do you find this Dsup protein glued onto chromatin in the same way that it appears to be gluing onto the chromatin in your experiments?

Jim - Our experiments were done all biochemically. So these are all done in the test tube. So we actually never looked in the tardigrades themselves, but that's something of a presumption at this point. But the fact that it binds in the test tube very well, we're pretty confident that that's how it binds in the organism. The next phase was that this Dsup protein was found in one tardigrade, but people had looked at a second tardigrade and said it's not there. So that kind of made Dsup seem uninteresting and unimportant if it's present in one tardigrade, but not another. But what we did find was that actually that second tardigrade also did have a Dsup protein.

Chris - Oh, so it had been missed!

Jim - It was missed.  The second tardigrade had a protein that kind of looked like Dsup, but people didn't think that was really Dsup. We confirmed that that second Dsup protein really is Dsup by doing the same experiments that we did with the first one and got the same results.

Chris - So you've basically got the smoking gun at the scene of the crime. Now you can prove this protein walks the walk and it talks the talk. You've got a protein that looks right; it binds the way you think it does; it's found in other tardidegrades which share this behaviour of being very resistant organisms. So that's looking pretty promising. What did you do next?

Jim - Now phase 3 was we asked the question how does this protein make cells resistant to X-rays? Tardigrades themselves of course live on Earth. And so they don't normally get exposed to high levels of X-rays, but they are still resistant to high levels of X-rays. And so then we realised that X-rays, when they strike water molecules, they generate highly reactive molecules called hydroxide radicals, and these hydroxide radicals degrade the DNA. So what we ended up doing was testing whether or not this Dsup protein protects DNA from hydroxide radicals. And, in fact, yes it does. Somewhat remarkably Dsup protects DNA from hydroxide radicals. So we kind of solved the mystery of how Dsup protects tardigrades from X-ray radiation.

Chris - And of course X-ray radiation is not the only reason why you would end up with hydroxide radicals inside cells; other things, like hydrogen peroxide, would lead to that as well wouldn't it? So this is a general defense mechanism against oxidative stress then isn't it?

Jim - Exactly. That's correct. And the Dsup protein serves to protect tardigrades from hydroxide radicals that are formed, especially when they're in this kind of dried dormant state.

Chris - And do you know how the Dsup protein does that protection?

Jim - It goes back to the Phase 1 of our project, that it protects it by binding to the chromatin. After it binds a chromatin, the rest of the protein appears to be unstructured. And so kind of like a cloud, that protects the chromatin from the hydroxide radical molecules.

Chris - So the hydroxyls would jump on to the Dsup protein and do things to these fairly amorphous chunks of the protein rather than unleashing their energy on the DNA?

Jim - That's it!

Chris - And you're saying that the tardigrades do this because they have to exist in particularly fierce environments. Do they therefore turn this stuff on, and apply it to their DNA only when they need it? Because, obviously, if they've got something like a giant protein stuck on to their DNA, it's going to get in the way of other important proteins that need to interact with the DNA - things like these chemicals called transcription factors, that turn genes on and off, and also the enzymes that read the DNA signature - this would be in the way wouldn't it?

Jim - It is kind of an interesting question, and that's in fact one of the things that we're investigating now - how can tardigrades protect DNA yet allow everything else on their DNA to still happen correctly? We don't know the answer, but that's probably going to be very interesting.

Chris - Now, when this paper came out in eLife, you got quite a bit of attention didn't you?

Jim - Yes we sure did!

Chris - Did you go to "overnight celebrity status"?!

Jim - Well I know about that, but it did impress my relatives!

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