Short Wave - In The Club, We All ... Archaea?

Episode Date: December 11, 2024

Thor. Loki. Heimdall. They're not just Norse gods or Marvel characters. They're also the names of various Asgard archaea. These microscopic organisms are found all over the world, from marine sediment to mud volcanoes to hydrothermal vents. A growing body of research suggests we owe them an evolutionary debt. This episode, Emily and guest host Jon Hamilton explore the wild world of archaea: Where are they from? What do they do? And what can they tell us about the origins of life on earth? Interested in more stories about life's origins? Email us at [e-mail]. We'd love to hear from you!See pcm.adswizz.com for information about our collection and use of personal data for sponsorship and to manage your podcast sponsorship preferences.NPR Privacy Policy

You're listening to Shortwave from NPR. Hey, shortwavers, it's Emily Kwong here. And John Hamilton. With a story that kind of picks up where Regina and I left off in November. So, John, do you remember the episode we did about hydrothermal vents and the origins of life? Oh, well, could I forget the two of you were getting at this idea that maybe the building blocks for life, you know, nucleotides, amino acids, were created around those super hot vents on the ocean floor. DNA and RNA, for example, are extremely vulnerable to like UV light. So maybe they first form deep in the ocean where they'd be protected from those rays.

That's amazing. I mean, sounds plausible to me. Right? And it left me with so many questions. Like, where did life go from there? You know, what's the next chapter, the moment where that molecular bath gave rise to discrete life forms, to single-celled organisms, prokaryotes, and eventually to complex multicellular organisms like you and me, You carriotes.

And there's this one type of life form that I think is key to telling that story, John. Have you heard of Archaia? Or Arquia as some say. Both pronunciations are fine. But do you know what they are? I do. But only because years ago I happened to run into a biologist who studies them. I have never seen Archaia in the wild.

It's not your fault. There you are tiny. Even under a high-powered microscope, the largest Archaeans look like tiny dots. But if you zoom in closer, you'll see they possess all kinds of shapes. They're spheres, their rods, their spirals. They look like bacteria, but they're not. And despite having no nucleus, no organelles,

I think these overlooked microbes have main character energy. So today on the show, we're going to give archaea their due. How our microbial ancestors gave us our mighty immune system, are at the center of one of the biggest ideological battles in biology, and are connected to the legendary, of Thor? Bring it on, Quang. You're listening to Shortwave, the science podcast from NPR. Hey, sure we're. Emily Kwong here. Before we get back to the show, I have an update about planet Earth. It's almost completed. It's 365 day, six hour, and nine minute orbit around the sun.

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Emily, so it seems like Archaia has sort of come into their own in the scientific world in the past few decades. So walk me through that. Yes, we're living in the Archaeosants. There's been this big debate in science. Like, I remember it from high school biology. For a long time, microbiologists divided the world into two domains. Eukaryotes, animals, plants, fungi, and prokaryotes, bacteria, which are single-celled organisms. And Archaea went undetected for a long time until Carl Woz came along.

Okay, so who is he? Okay, so Carl Woz was a microbiologist, most recently based at University of Illinois Urbana-Champaign. He passed away in 2012, but I spoke with someone who's become a torchbearer of his legacy, someone who knew him. Microbiologist Rachel Whitaker, also at Urbana Champagne, remembers Woes as someone with a big picture brain, someone willing to take on a question as intimidating as the origin of life. The way evolutionary biology had been done in the organismal side of this world was to look at traits that change over time, you know, butterfly wings, and plant leaves and seed colors and the beaks of the Darwin's finches and things like that. And that's really hard to study when you're looking at microbes because there's no traits.

I mean, they do have different shapes and they do have different surface structures and stuff. But back in the day when we were just discovering, you know, microbes, that was really hard to even say how they were related to each other. Wos said that physical properties are not a reliable way to tell those relationships. He really pushed for a molecular approach. This was back in the 1970s. People were starting to use molecules, amino acids, and RNA. They were starting to use those as signatures of evolution. For him, one molecule that was found all over the map was the ribosome.

That's the machine that turns RNA into proteins. He began to study RNA sequences using these giant films of gel. and cataloging their differences, tracing how they evolved over time. He had these notebooks and notebooks and notebooks, and I've seen these notebooks. There's like shelves of them, which are basically saying the size of each of these little bands and these two-dimensional gels. And based on that, he was finding relationships. And then right down the hall, his colleague Ralph Wolfe found these weird microbes at the bottom of the food web, responsible for the greenhouse gases and cows.

These microbes, they were a single cell, the can't. look like bacteria, but also kind of not? Until he walked down the hall and said to Carl, Woos, you should really look at these guys. They're very different. I don't know what they are. And because Woos had developed this molecular tool for comparing RNA sequences, he could use it on these mystery microbes. And he determined they were not bacteria.

They had different cell walls. Their RNA was more similar to eukaryotic RNA. Weird. So, I mean, what were they? Something new. Something never before seen by science. And he gave them a name. Archaia, which means ancient things.

Oh, I get it. Archaeologists. And you made this argument that there were actually three domains of life, bacteria, eukaryotes, and archaea. Now, in the decades since, more types of archaea have been found in the soil, in the ocean, and notably, in some of the most extreme environments on Earth, like hydrothermal vents. I was waiting for that. And the story doesn't end there because, John, in the last decade or so, at these vents, scientists have discovered a special type of archaea, which really complicate the story of life. They're called Asgard's. The first one was found in this hydrothermal vent in the North Atlantic called Loki's Castle.

This is Brett Baker, a marine biologist at the University of Texas at Austin, someone who studies these Asgard archaea. All right, I'm getting the theme here. Asgard's Loki Norse mythology. Correct, yes. And after the discovery of these Loki Archeota in 2015, Brett says... And we found this other group that was related to it. So we called it Thor. We collaborated and found a bunch of more groups than Odin and Heimdahl.

Ever since, Brett's team and others have been sequencing the genes of these Asgard Archaea, found in hot springs, aquifers, freshwater, saltwater environments around the world, and what they've found has challenged the work of Carl Wos and the story of how life began. How so? Okay, so these Asgard Archaea, their genes, are actually really similar to Eukaryotes, and then, Brett told me,

they started finding all these proteins in the Asgardes that are like, they've only been seen eukaryotes before. Which suggested something that went beyond Wose's work. It suggested that eukaryotes, like trees, mushrooms, birds, us, all the cool kids, may have in fact come from Archea that the eukaryotic branch, in fact, sprouted from some ancient Asgardian ancestor. I literally went running into my grad student's office and I said, oh my God, we have something very big. And at the time, this was very controversial. But Brett and other researchers

kept doing the work and standing up to the naysayers saying, no, this is right. You carrots actually fall within the archaea. We are literally as guardian. Obviously, it's two billion years of evolution since we evolved from them, but they are our ancestors. And new research is continuing to bear this out when it comes to the story of how our immune system evolved. So bring us up to date. Give me some specifics here.

a few years ago, another microbiologist, Pedro Liao, who's from Brazil, came to work in Brett's lab at U.T. Austin as a postdoc. And Pedro was reading about how certain proteins that helped our ancient immune system do its job may have come from bacteria. And me, as someone working with in the Archaeos side of the origin of Okaryotes, I was like, why someone is focusing one in one player that formed the Okaryote and not the second one? I know Archaeo player role in this. He was like, why are they not looking at Archao? are people always forgetting about archaea. And he wanted to look for evidence that archaea may bear clues for how our immune system evolved. I'm getting the theme with these Archaia investigators.

So this guy is on a quest now, right? Yeah, they're a tenacious bunch. That's true. Pedro started looking at two classes of proteins found in our ancient immune system. And these proteins basically mess with viral DNA. Mess with it like they stop viruses from spreading? Yeah, they're really important. And Pedro started looking for similar amino acid sequences in these Asgards.

Using an AI tool called CalabFold, he predicted what those proteins would look like, took that work to Brett, and he found those exact protein structures in nature, in those Asgards from the deep sea. Some researchers in my field wait their whole life for someone to prove their predictions were right. I had to wait to last then, I don't know, a couple of weeks. The research he and Brett and a whole team at UT Austin did was published in the journal Nature Communications this summer. I'm going to show you one of the illustrations in the paper.

Super exciting. This compares where the sequences for defense proteins show up. They are way bigger in Asgard and Eukaryotes than they are in bacteria. So what that means is that they are more prevalent in Asgard and Eukaryotes than they are in bacteria. So I was like, okay, if this is coming from a prokaryote, a bacteria or an archaea, it is most likely that they are coming from Marcia because it is way more prevalent there. Meaning there was a symbiotic relationship between bacteria, which had these original immune systems and Asgard's.

And Pedger just did like the Ancestry.com research to prove it. So he's pretty confident. Yeah, he's very confident. I fully believe this is how it happened, but how many times did it happen it did not work? This is something that is a main question in biology still. and we don't know. So that's the thing that keeps me up at night. These archaea scientists are tenacious, so I fully believe they'll get there.

And this work could be beneficial to us someday, too. I mean, we are surrounded by viruses with the potential to infect us. Yeah, always have been and always will be. Yeah, and if our immunity is thanks in part to archaea, we should be looking to them for clues about how to keep us safe and healthy in the future. Perhaps we could use these defense systems in some therapy. way to, you know, fight off viruses. And they've been looking in bacteria, which are very different than us.

Maybe we should be looking at Asgard's for some sort of useful things to come from it. Well, Emily, I look forward to an Asgardian antiviral any day now. Where there's our Kia. There's away, John. For sure. Follow our show on Apple and Spotify. It makes a huge difference. Also, if the AI protein folding sounded cool to you to, check up. out our episode on AlphaFold. We'll link to it in our episode notes.

This episode was produced by Hannah Chin. It was edited by our showrunner, Rebecca Ramirez, Tyler Jones, check the facts. Jimmy Keely was the audio engineer. Beth Donovan is our senior director, and Colin Campbell is our senior vice president of podcasting strategy. I'm Emily Kwong. And I'm John Hamilton. And thank you for listening to Shortwave, the science podcast from NPR.