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cover of episode In The Club, We All ... Archaea?

In The Club, We All ... Archaea?

2024/12/11
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Emily Kwong
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John Hamilton
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Emily Kwong: 本节目探讨了古菌在生命起源和演化中的作用,以及其与免疫系统进化的关系。古菌的发现改变了我们对生命三域的理解,阿斯加德古菌的基因与真核生物的相似性,暗示了真核生物可能起源于古菌。 John Hamilton: 古菌虽然微小,但形态多样,且在生命演化中扮演着重要角色。它们在极端环境中生存,为我们理解生命起源提供了线索。 Carl Woese: 通过对核糖体RNA序列的研究,Woese 发现了古菌,并提出了生命三域系统,彻底改变了生物学对生命演化的认知。 Rachel Whitaker: Whitaker 回忆了Woese 的研究工作,以及他如何通过分子方法来研究微生物的进化关系。 Brett Baker: Baker 的团队发现了阿斯加德古菌,并以北欧神话中的神明为其命名。这些古菌的基因与真核生物非常相似,支持了真核生物起源于古菌的理论。 Pedro Leal: Leal 的研究发现,阿斯加德古菌中存在与真核生物免疫系统蛋白相似的蛋白质,这表明古菌可能在真核生物免疫系统的进化中发挥了重要作用。 Emily Kwong: 本节目探讨了古菌在生命起源和演化中的作用,以及其与免疫系统进化的关系。古菌的发现改变了我们对生命三域的理解,阿斯加德古菌的基因与真核生物的相似性,暗示了真核生物可能起源于古菌。对阿斯加德古菌的研究不仅能帮助我们理解生命起源和免疫系统进化,还有可能带来新的医疗应用,例如开发新型抗病毒药物。

Deep Dive

Key Insights

What are archaea and why are they significant in the study of life's origins?

Archaea are microscopic single-celled organisms that resemble bacteria but have distinct characteristics. They are found in extreme environments like hydrothermal vents and are crucial in understanding the evolutionary history of life, particularly the origins of eukaryotes.

Who discovered archaea and how did they classify them?

Carl Woese discovered archaea in the 1970s by using RNA sequences to trace evolutionary relationships. He classified them as a third domain of life, alongside bacteria and eukaryotes, based on their unique molecular signatures.

What are Asgard archaea and why are they named after Norse gods?

Asgard archaea are a special type of archaea found in hydrothermal vents, named after Norse gods like Loki and Thor. Their discovery has challenged the traditional view of life's origins by suggesting that eukaryotes may have evolved from an ancient Asgardian ancestor.

How do Asgard archaea challenge the traditional view of life's origins?

Asgard archaea have genes and proteins similar to eukaryotes, suggesting that eukaryotes may have evolved from an ancient Asgardian ancestor rather than branching off independently. This challenges the traditional three-domain model of life proposed by Carl Woese.

What role do archaea play in the evolution of the human immune system?

Archaea may have contributed to the evolution of the human immune system through the transfer of defense proteins. Research suggests that these proteins, which help combat viral infections, are more prevalent in archaea and eukaryotes than in bacteria, indicating a possible ancestral link.

How did Pedro Leal's research contribute to understanding the immune system's origins?

Pedro Leal used AI tools to predict protein structures in Asgard archaea that are similar to those in the human immune system. His findings support the idea that archaea, not just bacteria, played a key role in the evolution of our immune defenses.

What potential applications could archaea research have for human health?

Archaea research could lead to the development of new antiviral therapies by leveraging the defense systems found in archaea. These systems could provide insights into how to combat viruses more effectively.

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Hey, short wavers. 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, how 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 UV light. So maybe they first formed deep in the ocean where they'd be protected from those rays. That's amazing. I mean, it sounds plausible to me. Right? And it left me with so many questions.

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, eukaryotes. And there's this one type of life form that I think is key to telling that story, John. Have you heard of archaea? Or archaea, as some say. Tomatoes, tomatoes, tomatoes.

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 archaea in the wild. It's not your fault. They 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, they're rods, they're 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 legend of Thor? Bring it on, Kwong. You're listening to Shortwave, the science podcast from NPR.

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Emily, so it seems like archaea 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 archaea-sance. 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 Arkea went undetected for a long time until Carl Woese came along. Okay, so who is he? Okay, so Carl Woese 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-Champaign, remembers Woese 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 things.

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. And Woese 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 RNAs

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 in these two-dimensional gels is

And based on that, he was finding relationships. And then, right down the hall, his colleague Ralph Wolf found these weird microbes at the bottom of the food web responsible for the greenhouse gases in cows.

These microbes, they were single-celled. They kind of looked like bacteria, but also kind of not. Until he walked down the hall and said to Carl, Woese, you should really look at these guys. They're very different. I don't know what they are. And because Woese 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. Archaea, which means ancient things. Oh, I get it. Archaea. Archaeologist. And he 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 azothrax.

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 archaeota 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 more groups and Odin and Heimdall. 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 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've started finding all these proteins in the Asgards that are like, they've only even seen eukaryotes before. Which suggested something that went beyond Woese's work. It suggested that eukaryotes, like trees, mushrooms, birds, us... All the cool kids. May have in fact...

come from archaea 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. Eukaryotes actually fall within the archaea. We are literally...

Asgardian. 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. So a few years ago, another microbiologist, Pedro Leal, who's from Brazil, came to work in Brett's lab at UT 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 in the archaeal side of the origin of eukaryotes, I was like, why someone is focusing one in one player that formed the eukaryote and not a second one?

I know archaea play a role in this. He was like, why are they not looking at archaea? Why 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 Archaea 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

Using an AI tool called CollabFold, 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 less than, I don't know, a couple of weeks. The research he and Brad 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 Archaea because it is way more prevalent there. Meaning there was a symbiotic relationship between bacteria, which had these original immune systems, and Asgards. And Pedro 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 and 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 therapeutic 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 Asgards 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 a way, 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 too, check out our episode on AlphaFold. We'll link to it in our episode notes.

This episode was produced by Hannah Jin. It was edited by our showrunner, Rebecca Ramirez. Tyler Jones checked the facts. Jimmy Keeley 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.

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