Archaea and the Tree of Life

Transcript of Part 1: Archaea and the Tree of Life

00:00:01.11	I think archaea represent to some extent
00:00:05.01	a blind spot in our understanding
00:00:07.13	of natural diversity.
00:00:09.19	You hear a lot of people talk, in many different contexts,
00:00:13.00	about diversity,
00:00:14.15	and they’ll bring up viruses,
00:00:15.27	they’ll bring up eukaryotic cells,
00:00:17.18	and they’ll bring up bacteria.
00:00:19.05	But the archaea are often never even mentioned.
00:00:22.17	What I want people to acknowledge
00:00:24.11	when they hear about archaea
00:00:25.27	is that this is a completely distinct domain of life
00:00:28.06	that we should recognize for what it is,
00:00:30.06	rather than blend it in with some other domain.
00:00:34.18	Understanding the tree of life,
00:00:36.28	trying to figure out what the evolutionary relationships
00:00:39.01	of all life forms on our planet…
00:00:42.02	you know, it’s a point of curiosity.
00:00:43.12	We all want to know where we came from.
00:00:47.00	For the longest time,
00:00:48.07	we’ve kind of had this belief in biology
00:00:50.09	that there’s these two different and extremely distinct
00:00:54.23	forms of life on our planet.
00:00:56.06	One is everything that we can see,
00:00:58.09	you know, right?,
00:01:00.04	from the insects, to the trees,
00:01:01.21	human beings, other mammals,
00:01:03.21	fishes, and so on and so forth…
00:01:05.06	you know, the eukaryotes.
00:01:06.27	And then there’s everything that’s invisible,
00:01:08.26	and they were called the microorganisms or prokaryotes.
00:01:12.20	So, “prokaryote” was this all-encompassing term
00:01:15.01	that was used for unicellular microorganisms
00:01:17.24	that did not have organelles within the cells.
00:01:22.07	So, their chromosome essentially just floats around in their cytosol.
00:01:25.25	In contrast, the eukaryotes are organisms
00:01:28.09	that have kind of evolved these complex organelles,
00:01:30.24	one of which is the nucleus,
00:01:33.05	which encapsulates all of their chromosomal material.
00:01:36.11	And so, that distinction was what was used
00:01:38.28	to kind of make evolutionary relationships
00:01:41.09	between everything that does have a nucleus
00:01:43.16	and everything that doesn’t.
00:01:46.04	It turns out that it’s not as simple as that anymore.
00:01:52.05	In 1977, Carl Woese at the University of Illinois
00:01:55.18	wanted to use not just how organisms look
00:01:59.03	— their morphology —
00:02:01.03	as a way to understand how they relate to each other,
00:02:03.03	but looking at parts of their genetic material,
00:02:07.17	their DNA,
00:02:09.06	to make these evolutionary connections.
00:02:14.10	The evolution of new species
00:02:16.28	begin with mutations in DNA.
00:02:19.18	These mutations can change genes,
00:02:22.23	which in turn can change the physical traits of organisms.
00:02:27.27	Sometimes, when an organism passes
00:02:30.18	these genetic changes to their offspring,
00:02:32.17	it can cause a new species to emerge.
00:02:37.20	In the 1960s,
00:02:40.04	scientists began to wonder if they could
00:02:43.00	determine the evolutionary relationship
00:02:45.09	between different species
00:02:47.14	by comparing their DNA sequences.
00:02:51.12	The more similar the DNA sequences of two organisms,
00:02:54.16	the more closely related they must be.
00:02:58.28	Less shared DNA suggests
00:03:01.12	a more distant relationship.
00:03:07.11	To build a tree of life using this approach,
00:03:10.00	Carl Woese needed to find a gene
00:03:11.28	that he could compare across all life forms.
00:03:16.26	He chose one that is needed for cells
00:03:18.22	to perform one of their most essential functions:
00:03:21.26	making proteins.
00:03:24.26	By comparing the sequence of this gene
00:03:26.28	between different types of organisms,
00:03:29.24	he was able to infer the tree of life.
00:03:35.07	This particular molecule that he narrowed in on
00:03:37.23	is called the 16S ribosomal RNA.
00:03:41.29	By looking at just this one particular molecule
00:03:44.05	he was able to glean kind of the evolutionary relationships
00:03:47.13	of these organisms without even having to look at them.
00:03:51.10	So, the story goes that Woese was looking for
00:03:54.04	microbial samples to do 16S ribosomal RNA sequencing for.
00:03:59.04	He went up to one of his colleagues
00:04:01.14	and asked him for these weird methane-producing microorganisms
00:04:03.28	that his lab was studying.
00:04:06.04	This colleague was Ralph Wolfe,
00:04:08.20	who pioneered the study of these methane-producing microbes.
00:04:12.03	And Ralph then handed him a vial of these methane producers
00:04:15.06	and said, yeah, take these bacteria
00:04:17.21	if you want to look at their 16S ribosomal RNA.
00:04:20.15	And when Carl Woese and his students
00:04:22.05	took a look at those samples,
00:04:24.09	they found that they were nothing like
00:04:26.14	any of the others that they’d looked at,
00:04:28.19	to the point that I think they had to repeat the study
00:04:31.04	at least two or three times to validate the fact
00:04:33.19	that the 16S ribosomal RNA was in fact that different.
00:04:37.04	And so, when you look at them under a microscope,
00:04:39.12	they might look similar.
00:04:41.02	But if you look deeper into the cell, into the DNA,
00:04:43.14	you see that they’re actually
00:04:44.27	a very different group of organisms.
00:04:47.07	So, he knew that… he knew that he was on
00:04:49.21	to something really, really big.
00:04:51.24	The microbes that we all thought were
00:04:54.03	just this one big pool of prokaryotes
00:04:55.22	were not that.
00:04:57.15	There were the bacteria
00:04:59.22	that are very well established and studied.
00:05:01.21	But then there were these archaea,
00:05:04.01	this, you know, enigmatic third domain of life.
00:05:08.00	Woese got so excited that as soon as he, like,
00:05:11.00	made that first three-domain tree of life,
00:05:12.28	he called up the New York Times,
00:05:15.04	and it became the front page article the next day.
00:05:19.28	It was this interesting moment of serendipity.
00:05:22.04	You know, the reason why we discovered archaea
00:05:24.18	was this person, Carl Woese,
00:05:26.13	who had this pioneering technology,
00:05:28.23	but also the fact that, you know,
00:05:30.26	his lab was situated next to that of someone
00:05:32.25	who was studying an archaea.
00:05:34.15	And then, it was those two things coming together
00:05:36.25	that, you know, gave rise to this…
00:05:38.25	this paradigm-shifting concept in biology.
00:05:43.11	So, archaea initially, when they were discovered,
00:05:46.02	were found in extreme environments.
00:05:48.25	So, one of the first archaea
00:05:50.28	that was sequenced
00:05:53.02	was isolated from a hydrothermal vent at the bottom of the ocean.
00:05:56.09	Now, we’ve essentially found archaea
00:05:59.12	everywhere in the environment around us,
00:06:01.09	as well as within us.
00:06:03.05	So, there’s archaea on our skin.
00:06:04.26	There’s archaea in our oral cavity.
00:06:07.07	We have archaea in our guts.
00:06:09.12	And every other place that you can think of,
00:06:11.01	there are archaea.
00:06:12.13	So, often, they’re around us,
00:06:14.02	and we can even see them sometimes.
00:06:15.16	We just don’t know them for who they are.
00:06:18.25	For instance, if you are flying into the San Francisco airport,
00:06:22.07	you’ll see these salt flats that have bright colors as you land.
00:06:26.20	And that’s just a visual cue to you saying,
00:06:29.18	here are archaea.
00:06:31.11	You know, you don’t have to go too far to find them;
00:06:33.11	they’re everywhere.
00:06:35.06	So, the methanogenic archaea that my lab studies…
00:06:37.21	they produce 80% of the methane
00:06:40.22	that’s being released to the atmosphere annually,
00:06:43.15	which has a significant impact on climate change.
00:06:46.17	They also have a very direct impact
00:06:48.22	on human health sometimes,
00:06:50.08	because these methanogens in our distal gut
00:06:53.27	can be up to 10% of the microbial population,
00:06:56.25	which is substantial.
00:06:59.03	So, the amount of calories that you get from your food,
00:07:02.02	and also how you digest your food…
00:07:04.02	what kinds of components come from it…
00:07:07.14	some of those factors also depend
00:07:09.29	on these archaea in your gut.
00:07:12.12	These archaea are actually a lot like us.
00:07:14.20	So, the way the cells replicate…
00:07:16.21	or the way one cell becomes two cells,
00:07:20.12	the way the cells make their proteins…
00:07:22.15	a lot of those things are very similar
00:07:24.29	to the way we do them,
00:07:26.13	compared to the bacteria that are also unicellular.
00:07:29.16	And that’s… and what that’s leading to
00:07:31.24	is this theory, now, that,
00:07:34.22	you know, the last common ancestor to all modern day eukaryotes
00:07:37.29	came from an archaeon.
00:07:41.13	There’s kind of been a revolution in the field of archaea
00:07:43.24	in the last five years.
00:07:47.04	So, people went and found these samples
00:07:49.08	in different marine sediments.
00:07:52.10	And when they sequenced the organisms that lived there,
00:07:55.14	they found this very evolutionarily distant group of archaea
00:08:00.25	called the Asgard archaea.
00:08:03.10	So, the Asgard essentially is a group.
00:08:05.10	Within the Asgard, you have the Lokis
00:08:08.07	and then a bunch of other archaea that are named after Norse gods.
00:08:11.15	These Asgard archaea…
00:08:13.29	they have proteins in their cell
00:08:16.06	that are called eukaryotic signature proteins or ESPs.
00:08:19.21	And the reason why I’m highlighting this
00:08:22.13	is because they’re typically proteins
00:08:25.13	that are only associated with eukaryotes.
00:08:27.14	These ESPs have not been found in other archaea
00:08:29.14	or in bacteria.
00:08:30.24	But now, we’re seeing the presence of these proteins
00:08:33.15	in archaea as well.
00:08:35.00	So, these organisms…
00:08:36.24	when you put them back on the tree of life
00:08:38.22	to figure out where they are,
00:08:40.12	they’ve essentially changed the topology
00:08:42.19	or the way the tree looks now.
00:08:44.28	Previously, there were three domains,
00:08:46.19	and there was a shared ancestor
00:08:48.13	between the archaea and all of modern day eukaryotes.
00:08:52.08	There was a last common ancestor that we shared,
00:08:55.19	and then the archaea split off and the eukaryotes split off.
00:08:57.29	But now, what we’re seeing is that
00:09:01.15	there is an archaeal ancestor
00:09:03.09	that gave rise to the eukaryotes.
00:09:05.02	What this seems to indicate is that these eukaryotes
00:09:07.25	are branching from within the archaea
00:09:09.16	and are closely related to these distant groups
00:09:12.12	that we’ve recently found.
00:09:15.08	So, that essentially makes archaea
00:09:17.18	even more closely related to us, now,
00:09:19.29	than we’d initially believed.
00:09:21.24	And that’s kind of changing
00:09:23.24	that view of the three-domain tree of life
00:09:26.10	back to maybe a two-domain tree of life —
00:09:28.26	but the two domains are different.
00:09:30.10	The two domains are both actually unicellular organisms,
00:09:32.15	and the eukaryotes are branching from one group
00:09:35.26	of these unicellular organisms.
00:09:39.29	So, now that you’re thinking about the tree of life
00:09:43.09	slightly differently,
00:09:45.00	one question that arises as a result is,
00:09:47.05	how did that unicellular archaeal ancestor
00:09:49.10	give rise to this complex eukaryotic cell?
00:09:52.18	Now, one key evolutionary step
00:09:55.09	that happened along the way
00:09:57.16	to becoming a eukaryote
00:09:59.09	was the fact that these cells had to acquire
00:10:01.22	the mitochondrion.
00:10:03.22	What one hypothesis out there is
00:10:07.11	is that an archaeal cell engulfed a bacterial cell,
00:10:09.17	a free-living bacterial cell,
00:10:11.15	and eventually that particular bacterial cell
00:10:14.00	living inside the archaeon
00:10:16.08	went on to become the mitochondria as we know it today.
00:10:19.19	So, these Loki archaea
00:10:23.25	encode these eukaryotic signature proteins.
00:10:25.23	And when we look a little closer into what these…
00:10:28.09	what these proteins do,
00:10:30.08	they also provide us a hint as to how
00:10:33.10	the complex eukaryotic cell may have arisen.
00:10:36.07	A lot of these proteins encode for
00:10:38.19	interesting cytoskeletal features,
00:10:40.23	the features that make up the body of the cell.
00:10:46.13	They produce these appendages outside the cell,
00:10:49.09	and these appendages look like they could be used to engulf
00:10:52.18	another organism
00:10:54.28	that would eventually become the mitochondria
00:10:56.23	for the eukaryotic cell.
00:10:58.24	There are also proteins that confer the cell
00:11:02.12	the ability to engulf other cells through endocytosis.
00:11:05.07	All of these proteins have functions
00:11:07.10	that we can use to kind of make sense
00:11:10.03	of how that engulfment of a mitochondria
00:11:12.27	may have occurred.
00:11:14.18	It almost seems like these Asgard archaea
00:11:16.18	are primed for some of the functions
00:11:19.10	that we ascribe to have happened
00:11:21.03	for the first eukaryotic cell to have arisen.
00:11:26.09	It’s an interesting time to be an archaeal biologist
00:11:28.27	because we’re kind of in this… this…
00:11:31.27	you know, major transition in thinking about archaea
00:11:34.15	from an evolutionary standpoint.
00:11:36.29	Right now, we’re in this phase that we’re gathering a lot of information,
00:11:40.27	and that information is kind of letting us
00:11:43.11	build new hypotheses about the tree of life.
00:11:45.29	As more information is revealed to us,
00:11:47.25	we’ll kind of keep refining the tree of life.
00:11:50.02	It is extremely likely that in the future
00:11:51.27	we’ll find something else,
00:11:53.26	and that might make us want to revisit the tree of life again.
00:11:56.23	They’re such an understudied group of organisms
00:11:59.01	that I don’t think there’s one right question to ask.
00:12:02.00	I think there’s so many things that we can look at.
00:12:05.19	We know what’s unique about eukaryotes,
00:12:08.06	and similarly with the bacteria.
00:12:09.29	But very little is known about what it means to be an archaea.
00:12:12.12	What is kind of unique and distinctive about them?
00:12:15.06	We have a few things that we know,
00:12:17.15	but we don’t really know their deep, dark secrets, so to say.
00:12:20.04	It’s a good time to go learn more about that.