Once prokaryotic life emerged on earth, how did it evolve into larger, more complex eukaryotic organisms? Three scientists help us understand how this may have happened. Dr. Julie Theriot speculates about the important role that cytoskeleton-associated proteins may have played in that transition (and she challenges you to prove her speculation wrong!). Dr. Miller explains how endosymbionts such as mitochondria and chloroplasts came to be the power organelles of eukaryotes. And Dr. Nicole King addresses the fascinating question of how the first multicellular animals may have evolved from our unicellular ancestors.
00:08.0 Hello. I'm Julie Theriot from Stanford University,
00:11.1 and I am back for the third part of my iBio Seminars presentation.
00:15.0 Now, in the first two parts,
00:16.3 I focused on well-understood systems
00:18.3 with strong experimental evidence
00:20.2 supporting all of the conclusions that I was telling you.
00:22.3 For the third part,
00:24.1 I'm going to venture into the field of wild speculation,
00:27.1 and in fact I'm going to wildly speculate
00:28.3 about the biggest questions of all
00:31.1 in the context of biology,
00:33.1 which is how things evolve.
00:35.1 And in particular what I'd like to discuss
00:38.1 is some big picture ideas
00:40.2 about how the dynamic cytoskeleton
00:42.2 has evolved throughout the history of life on Earth
00:45.0 in order to give us such an incredibly diverse array
00:48.1 of cell types, of structures,
00:50.1 and of behaviors of cells.
00:52.2 And just to illustrate that,
00:54.1 here on the left I have an image
00:56.2 of one of the most fabulous of protozoa,
00:58.2 called Stentor,
00:59.3 which is an absolutely enormous cell
01:02.0 with, as you see, a great deal of very detailed subcellular specialization
01:04.1 in terms of its structure.
01:06.1 And then on the right,
01:08.0 a luridly colored electron micrograph
01:09.1 of some bacteria,
01:10.3 which are quite diverse in terms of their
01:13.3 molecular components,
01:15.2 but fairly similar and fairly simple
01:17.2 in terms of their shape.
01:20.0 Now, one of the things that's become very clear
01:22.0 in the modern era of sequencing
01:25.2 is confirming something that of course Darwin had
01:29.1 originally speculated about some time ago,
01:31.2 which is the proposition that
01:33.2 all of the organisms that are currently living on our planet
01:35.1 are descended from a common cellular ancestor
01:38.0 or a common pool of cellular ancestors.
01:41.1 And certainly, one of the most undeniable pieces of evidence
01:44.0 in support of that hypothesis
01:45.1 is the observation that there's
01:47.1 a tremendous number of molecular components
01:49.3 that are found highly conserved
01:51.2 throughout all branches of life.
01:54.1 This particular illustration
01:56.3 shows the sequence similarity among ribosomal RNA
02:00.1 for bacteria,
02:02.2 for archaea,
02:03.2 and for eucaryotes (eukaryotes).
02:05.1 And the fact that it is possible
02:07.1 to arrange all of the known living cells on Earth
02:09.2 in this sort of tree,
02:11.3 where everything looks related to everything else
02:13.2 is a very good indication that in fact
02:17.0 all of the ribosomal RNAs
02:18.2 that exist in cells on the modern Earth
02:20.2 all came from some common ancestor
02:22.3 back at some distant point in the past.
02:25.2 The common ancestor on this diagram
02:27.1 is indicated with the green circle,
02:28.3 and it's fondly called "LUCA",
02:30.1 which stands for the last universal common ancestor.
02:32.2 Now, this was not the first cell,
02:34.1 this was just the last cell
02:36.1 that gave rise to everything that's living today,
02:38.1 and it was already very complex.
02:40.0 It already had ribosomes, it already had DNA,
02:42.2 it already had most of the components of central metabolism,
02:45.1 including, for example,
02:46.2 all of the enzymes involved in glycolysis,
02:48.2 and it also had cytoskeletal components.
02:51.1 And we know this because
02:53.1 those common components
02:54.2 are found in every single branch
02:57.2 of currently living organisms.
02:59.3 Now, given that everybody started off
03:02.0 as part of the same family,
03:03.1 it is interesting, I think,
03:05.1 to speculate about why it is that
03:08.1 some parts of this tree of life
03:10.0 have ended up behaving so differently
03:12.1 from other parts of the tree of life,
03:14.0 and in particular I'd like to draw the distinction
03:16.3 between what I will loosely call the prokaryotes,
03:19.2 which are on the top part of the tree,
03:21.1 and that includes the bacteria and the archaea,
03:24.1 which are very distinct branches,
03:26.0 versus the eukaryotes on the bottom part of the tree.
03:28.3 Now, although bacteria and archaea
03:31.0 are no more closely related to each other
03:33.1 than they are to the eukaryotes,
03:34.3 they nonetheless are quite similar morphologically,
03:38.1 and in fact we didn't even know that the archaea
03:41.1 existed as a separate kingdom until sequencing data started coming along,
03:44.0 because if you just look down a microscope,
03:45.2 it's very hard to tell the difference
03:47.0 between a bacterium and an archaeon.
03:49.2 Whereas the morphology is very simple
03:51.3 in those prokaryotes, the metabolism is extremely diverse,
03:55.0 so almost any interesting chemistry
03:57.2 that's done in living organisms
03:59.1 was first invented by the prokaryotes.
04:02.1 So, what we got going for us down on the eukaryotic side of the tree?
04:05.2 Well, although our chemistry is not
04:07.3 necessarily as interesting or as complex
04:09.1 as what's going on with the little guys,
04:11.1 we have morphology.
04:12.2 We get very big,
04:13.2 we get very complicated,
04:15.0 and we get very multicellular.
04:16.2 So, within this context of everybody
04:18.3 being related to everybody else,
04:20.1 and in fact all of these different organisms
04:23.0 having something that looks like cytoskeletal proteins,
04:25.1 I think it becomes a very interesting question to ask,
04:28.0 well, what is it really then that makes eukaryotes different from prokaryotes?
04:31.0 Specifically, what is it that gives eukaryotes
04:33.0 the ability to have such extremely diverse
04:35.1 and complicated cellular morphologies,
04:37.0 based on cytoskeletal structures?
04:41.0 Just to, again,
04:42.3 give you a little bit of a taste
04:44.2 of the kind of diversity you find
04:46.1 even within a very closely related group of eukaryotes,
04:48.2 these are some illustrations
04:50.0 from one of the great microscopists of the 19th century,
04:52.3 just showing a group of fairly closely related
04:55.1 ciliates and flagellates.
04:56.2 Each of these are unicellular organisms...
04:58.1 they're not all drawn to scale with each other...
05:00.0 this is Stentor,
05:01.2 that I showed you a photograph of on the very first slide,
05:03.1 and a number of other familiar organisms,
05:06.0 including, for example, Paramecium, here,
05:08.3 and Giardia.
05:10.3 And all of these cells,
05:12.2 to a first approximation,
05:14.0 have the same components.
05:15.1 If you look at the protein components of these cells,
05:17.2 there certainly are things that are a little bit different between them,
05:20.0 but the major components,
05:21.1 certainly the major structural components,
05:22.3 are pretty well conserved,
05:24.0 and yet somehow all these different organisms
05:25.3 are able to make drastically different cell shapes
05:28.0 with very different motile behaviors,
05:29.2 very different kinds of division behaviors,
05:31.1 simply by rearranging this common set
05:33.2 of molecular components.
05:37.0 Now, if we contrast that to the bacteria,
05:39.2 you certainly will hear
05:41.2 proponents of the prokaryotic side of the tree
05:45.0 claiming that there is a lot of morphological diversity among bacteria...
05:48.2 and to a small extent that's true.
05:50.1 So, if we look at this illustration
05:54.1 from a really enchanting review by Kevin Young that came out a few years ago,
05:57.3 this shows essentially the diversity
06:00.2 of the different kinds of shapes
06:02.1 that have been described for isolated bacterial species.
06:04.3 And here in the zoomed-in version,
06:07.1 we find a couple of the fairly familiar shapes,
06:09.2 so we see things like E. coli here,
06:11.3 which is a rod shape,
06:13.2 there are some crescent-shaped bacteria here like Caulobacter,
06:17.1 there are helical-shaped bacteria,
06:19.2 but they're all sort of fairly simple variations on a theme.
06:24.2 And then all of those guys are also quite small.
06:27.2 And then we zoom out to higher magnification...
06:29.1 there's really very few bacterial species
06:30.3 that get much bigger than just a few microns
06:33.1 in characteristic size.
06:34.2 One interesting exception
06:36.2 is illustrated here by this yellow dome
06:39.0 that stretches across this drawing,
06:40.3 and this is actually to scale
06:42.2 with the other bacteria here,
06:44.1 an illustration of an organism called Thiomargarita,
06:47.0 which is one of the largest bacteria know,
06:49.0 and these guys actually can be almost a millimeter across.
06:52.2 And this shows a photograph
06:54.3 of Thiomargarita next to a Drosophila
06:59.2 and you can see its absolutely enormous size.
07:02.0 But the trick here is that
07:04.1 even though the cell itself is very large,
07:06.0 its cytoplasm is very small.
07:07.2 Thiomargarita is basically
07:09.1 just a hollow shell of a very thin layer,
07:11.3 a couple of microns thick of cytoplasm,
07:13.3 that's stretched an enormous vacuole.
07:16.1 So, even when bacteria get to be pretty large
07:18.2 and, relative for bacteria,
07:20.0 morphologically complex,
07:21.2 they still have diffusion-limited dimensions.
07:24.1 And it is obviously observable that,
07:28.0 overall, if you take a random eukaryote
07:29.2 and compare it to a random prokaryote,
07:31.0 the eukaryotic cell is bigger
07:33.0 and is much more structurally complex.
07:35.2 So, this just pulls out a couple of those things
07:39.0 as examples.
07:40.1 Here's Paramecium compared to a bacterium to scale,
07:43.0 and then that bacterium blown up,
07:44.2 and here I've chose Vibrio cholerae.
07:46.2 And you can see, again, there is subcellular localization,
07:49.1 subcellular specialization
07:51.0 in the context of Vibrio cholerae.
07:52.1 It's got its flagellum growing out of one pole, for example,
07:55.1 so it somehow is able to know
07:57.1 which end is which
07:58.3 and know the difference between the poles and the sides,
08:00.1 but even at that level the complexity
08:02.2 is just vastly less than what you see in something like Paramecium.
08:06.1 So, if you think about,
08:08.1 what are all the observable differences
08:10.0 between eukaryotes and prokaryotes,
08:11.2 there's a pretty long list that is...
08:14.0 you know, there are some exceptions,
08:15.1 but this is reasonable typical,
08:17.0 reasonably representative of these different kinds of life.
08:19.3 Eukaryotes have, of course,
08:21.1 a membrane-enclosed nucleus,
08:22.3 that's the definition.
08:24.1 And so that means they have separated,
08:25.3 spatially and temporally,
08:27.1 the process of transcription
08:28.3 from the process of translation,
08:30.1 which gives rise to many options
08:32.1 for very complicated regulation
08:33.3 that basically can't be present
08:35.1 in bacteria or archaea.
08:38.0 Along with the membrane...
08:41.1 err, sorry, the nuclear membrane,
08:43.2 the eukaryotes of course also have lots of other internal membranes
08:45.2 making things like the Golgi apparatus
08:47.1 and the endoplasmic reticulum.
08:48.2 They typically have much, much larger genomes
08:51.1 than our bacterial friends,
08:53.0 with often with multiple chromosomes that can be very large.
08:56.2 As I mentioned, they have much larger cell size.
08:58.1 Instead of being characteristically
09:00.1 just a few microns long,
09:01.2 they're usually a few tens to even hundreds of microns in size,
09:05.1 and they have a very high degree of subcellular compartmentalization.
09:08.2 In addition, eukaryotes have endosymbionts,
09:11.3 so they have mitochondria and chloroplasts
09:13.1 that used to be bacteria
09:15.2 that have now been captured and domesticated
09:17.2 by the eukaryotic cells
09:19.1 in order to perform energy functions.
09:21.0 And then, finally, you know,
09:23.0 the reason we're even able to talk about this
09:25.0 is because eukaryotes make multicellular organisms.
09:27.1 Now again,
09:29.1 just as in the context of the shape,
09:30.3 it's not the case that bacteria
09:32.2 never make multicellular organisms,
09:34.0 it's just that they're not very complicated.
09:35.2 So, for example,
09:37.3 the best understood multicellular bacterial organism
09:39.3 is this thing called a stromatolite.
09:42.1 We see a bunch of stromatolies here,
09:43.3 growing in an ocean next to Australia,
09:45.2 and these are basically big piles of colonial cyanobacteria.
09:50.2 They grow and deposit
09:52.0 some extracellular matrix,
09:53.2 and then the next generation will grow on top of it,
09:55.1 making these very characteristic layer cake patterns
09:58.2 that are seen not only in the kinds of stromatolites
10:00.2 we have growing today
10:02.0 but also are found in stromatolites
10:03.2 that are several billion years old in the fossil record.
10:06.2 And in all that time,
10:08.1 look how far eukaryotes have come,
10:09.3 but bacteria are basically still making the same structures.
10:12.2 Eukaryotes have been able to make things like Redwood trees,
10:15.2 they're been able to make things like coral reefs,
10:17.2 with this extraordinarily morphological diversification.
10:21.1 Okay, so this very fundamental question of,
10:23.3 what is the difference between eukaryotes and prokaryotes
10:26.0 that gives us such extraordinary morphological complexity,
10:30.1 is a question that I would say, today,
10:31.2 we don't know the answer to,
10:33.1 but a few decades ago
10:34.3 we thought we did know the answer to it,
10:36.1 and before 1990 or so
10:38.2 the nearly universally accepted explanation
10:41.2 for why there's such big morphological differences
10:43.1 came down to the eukaryotic cytoskeleton.
10:45.2 If we go through all of those characteristics I described
10:49.1 about what's special about eukaryotes
10:50.2 as compared to bacteria or archaea,
10:52.0 all of those things can be attributed
10:54.0 to functions of the cytoskeleton.
10:55.2 So, for example,
10:57.1 the existence of the membrane-enclosed nucleus
10:59.1 and all of the complex internal membrane systems
11:01.1 can be ascribed as being due to
11:03.3 intracellular membrane transport
11:05.3 with motor proteins, for example,
11:07.2 pulling vesicles along microtubules.
11:10.1 Nuclear lamins,
11:11.3 which are essentially a form of intermediate filaments,
11:13.2 stabilize the nuclear membrane.
11:16.2 The expanded genome in eukaryotes
11:18.3 of course divided by the extraordinary machine
11:21.1 of the mitotic spindle,
11:22.2 which with all of its self-organized microtubules,
11:25.2 and its massive amount of flux
11:28.2 and force generated by motor proteins
11:31.0 such as kinesins and dyneins,
11:32.2 is able to divide a lot of chromosomes,
11:34.2 and it's no big deal for a eukaryote
11:36.2 to generate an extra chromosome,
11:38.0 split a chromosome in half,
11:39.2 vastly expand the size of its genome,
11:41.2 because the mitotic spindle
11:43.1 is able to handle a lot of capacity
11:46.0 in terms of segregating chromosomes.
11:48.2 The much larger cell size of eukaryotes
11:51.1 can be attributed to the fact
11:53.0 that they're no longer diffusion-limited.
11:54.2 Because of the direct action of motor proteins,
11:56.2 you can actually have transport and mixing
11:58.2 within the cytoplasmic compartment.
12:01.2 Similarly, the subcellular compartmentalization,
12:03.3 the existence of endosymbionts,
12:05.2 and even the ability to have cells come together
12:08.2 and make multicellular organisms
12:09.3 with very complex extracellular matrices,
12:12.2 largely involves coupling between microtubules, actin, intermediate filaments,
12:17.3 and other components within the cell
12:21.2 or from one cell to another.
12:22.3 Endosymbionts, for example,
12:25.0 are thought to be the product of a phagocytic event,
12:27.2 where an ancient eukaryotic ancestor
12:29.2 ate a cyanobacterium
12:31.2 and turned it into a chloroplast.
12:35.1 Now, the reason I say we don't know the answer today,
12:37.0 even though we did know the answer in 1990,
12:39.1 was because it became clear in the 1990s
12:41.3 that bacteria actually do have a cytoskeleton
12:44.1 that in many ways is remarkably similar to that
12:46.3 of eukaryotes.
12:48.1 And so the first real nail in this coffin
12:50.1 was the discovery of
12:52.1 a tubulin homologue in bacteria
12:53.3 that goes by the name of FtsZ.
12:56.1 FtsZ had been originally identified genetically
12:59.2 as being a protein that was required for cell division,
13:01.2 and some beautiful work in the 1990s,
13:03.2 combining biochemistry and cell biology of this protein,
13:07.0 has established that it really acts as
13:09.2 a legitimate cytoskeletal protein in bacteria
13:11.2 that's involved in cell division.
13:13.1 It forms a ring right around the middle of a bacterium
13:15.2 that's about to divide,
13:17.0 and as the bacterium divides,
13:18.1 that ring actually becomes smaller.
13:20.2 Furthermore, the purified protein
13:22.1 is able to self-assemble into filaments
13:24.0 in a manner that depends on the presence of hydrolyzable GTP,
13:27.2 which again is a very cytoskeletal behavior.
13:30.1 And any remaining doubt
13:32.1 had to be squashed
13:34.0 when the crystal structures came out
13:35.2 for both tubulin and FtsZ
13:38.1 at about the same time,
13:39.2 back to back in the same issue of Nature,
13:41.3 and it was clear that the structure of one
13:43.3 could be almost perfectly superimposed
13:45.3 on the structure of the other.
13:47.2 So, it's clear that these are not only sort of analogous proteins,
13:50.1 but in fact true homologues,
13:51.3 in the sense that they are descended from a common ancestor,
13:53.3 and by far the simplest explanation for that
13:56.1 is that the LUCA, the last universal common ancestor,
13:59.2 also had a protein like tubulin or FtsZ.
14:04.1 Okay, so bacteria have something like tubulin...
14:06.2 then it turned out a couple of years later,
14:08.2 bacteria also have something like actin,
14:11.1 and just like with FtsZ,
14:13.1 these proteins
14:15.0 -- they go by several names, there's MreB and Mbl
14:17.1 and a few other family members --
14:18.3 were originally described as being genes that are necessary
14:21.0 for some aspect of bacterial shape,
14:23.1 a fundamental cytoskeletal-type function.
14:26.0 And so, for example in Bacillus subtilis,
14:28.0 disruption of any of these actin homologues
14:30.0 causes really abnormal, overall,
14:32.2 types of cell shapes.
14:34.3 And these proteins, when purified,
14:36.3 can assemble into filaments,
14:38.1 again like FtsZ or like any of the eukaryotic cytoskeletal proteins.
14:42.2 Now, one thing that's I think been particularly amusing
14:45.2 in the context of the bacterial actin homologues,
14:48.1 has been the proliferation
14:50.1 of such a large number of them
14:52.0 that appear to have slightly different specialized functions.
14:54.3 So, for example,
14:56.1 one of my favorite examples
14:58.0 is in magnetotactic bacteria
14:59.2 that are able to orient themselves with respect to the Earth's magnetic field.
15:03.0 They do so my lining up these little crystals of magnetite
15:05.3 along a structural element inside the cell
15:10.1 that is in fact made up of an actin-like filament.
15:14.0 Now, this is not the same actin-like filament
15:16.2 that is contributing to cell shape,
15:18.0 it's actually a copy of the gene
15:20.1 that was historically duplicated,
15:22.1 and then diverged for this specialized function.
15:25.0 So, bacteria not only have actin,
15:26.2 they have a bunch of different actins,
15:28.0 but they can use them both to determine their overall shape
15:30.2 and to determine the distribution
15:33.0 of intracellular organelles.
15:35.2 So now I think we're set up to ask ourselves
15:37.2 a slightly different question.
15:38.2 It's clear that bacteria do have a cytoskeleton,
15:41.1 so the existence of the cytoskeleton
15:42.3 cannot be the thing
15:45.0 that distinguishes eukaryotes from prokaryotes.
15:46.2 So, we might ask then, well,
15:48.0 if bacteria do have a cytoskeleton,
15:49.2 then why don't they do something more interesting with it?
15:51.1 And by that I mean in this very eukaryotic-centric world view,
15:54.2 why don't they have morphological complexity
15:57.0 and why don't they make
15:59.0 big, fancy multicellular organisms?
16:01.0 So, here we get to the point of wild speculation,
16:03.2 and my specific hypothesis is that
16:07.2 the thing that all of the cytoskeletons have in common
16:10.0 is the ability to perform large-scale cell organization
16:13.1 based on self-assembly of helical filaments
16:15.2 that are highly dynamic.
16:17.0 That's true among all the different branches of life.
16:21.3 I am proposing that was is special about eukaryotes
16:24.2 is not the cytoskeletal filaments per se,
16:26.3 but rather two specific classes
16:29.0 of cytoskeletal associated proteins:
16:31.1 the nucleators and the molecular motors.
16:35.1 And I'll go into some detail about why I think these are the things
16:38.2 most likely to really be different,
16:40.0 but so far there is no strong positive evidence
16:43.0 that prokaryotes have
16:45.2 any classical molecular motor proteins
16:47.0 or any regulated nucleators for cytoskeletal filaments,
16:50.0 which raises a second question.
16:52.1 You know, if the prokaryotes don't have them,
16:53.3 why don't they have them?
16:55.0 That's something even I'm not going to be able to speculate about,
16:57.3 but as far as why I think these two things
17:00.0 are really the key to this morphological difference,
17:02.1 I'll give you some of the information
17:04.2 that has led me to that proposition,
17:06.2 and suggest a few very specific ways
17:10.0 that these ideas could be tested.
17:13.2 Okay, so the overall basis for this hypothesis,
17:17.2 that you need nucleators and molecular motor proteins
17:19.2 in order to get morphological diversity,
17:22.2 comes from a series of observations
17:24.2 about the kinds of structures
17:26.2 that can be made by cytoskeletal filaments
17:28.0 in bacteria versus in eukaryotes.
17:32.1 In particular,
17:34.1 any self-assembling helical filament
17:37.0 can make either a structure with a single filament
17:40.1 or it can make a bundle or a raft of filaments,
17:44.1 where the filaments are oriented in random directions
17:46.1 with respect to each other.
17:47.2 All that requires is helical self-assembly,
17:49.2 which as we'll see is a very universal feature
17:52.0 of proteins that are able to interact with themselves.
17:56.1 On the other hand, the kinds of structures that really require localized nucleation
18:00.1 or localized motor activity
18:01.2 are illustrated here on the bottom.
18:03.0 These include things like microtubule asters,
18:04.3 which are familiar from the organization
18:07.0 of overall organelles inside of a cell.
18:10.2 These include things like parallel bundles,
18:12.1 which we find inside of eukaryotes flagella,
18:13.3 or we find in muscle...
18:16.0 you know, the sarcomeres that are able to give large-scale muscle contraction...
18:19.3 and also things that have bipolar morphology,
18:23.0 like this mitotic spindle shown here.
18:25.1 We know enough about how these different structures are formed
18:27.1 that I feel fairly confident in stating
18:30.3 that the easiest way to make these kinds of structures
18:32.3 is either by localizing nucleation of filament growth,
18:36.1 or having molecular motor proteins
18:38.2 that are able to sort of filaments of different orientations,
18:41.1 or some combination of both things.
18:43.2 And what I will assert is that
18:46.2 no structures of the type shown under here in class B
18:49.2 have yet been found in bacteria,
18:51.3 specifically have yet been found in the cytoplasm of bacteria,
18:54.2 with perhaps one or two interesting exceptions
18:57.0 that I think actually sort of prove this rule.
18:59.3 So, if nucleators and molecular motor proteins
19:02.1 essentially enable you to take your
19:05.0 helical, self-polymerizing, self-assembling
19:07.2 cytoskeletal filaments
19:08.2 and make large structures out of them,
19:10.2 you might ask, well,
19:12.1 what evidence is there that eukaryotes can do this
19:14.2 but prokaryotes cannot?
19:16.2 So, I'd like to now again take a step back
19:19.0 and say, if we are willing to accept the premise
19:21.3 that something about the activity
19:23.2 of the eukaryotic cytoskeleton
19:24.3 is the key difference,
19:26.2 then the question is, what is so special
19:28.1 about the eukaryotic cytoskeleton?
19:30.0 And if you look at the most abundant
19:32.0 and most studied eukaryotic cytoskeletal proteins
19:34.3 -- we have tubulin making microtubules,
19:36.2 actin monomers making actin filaments,
19:39.2 and then intermediate filaments
19:40.3 made up of their own subunits --
19:42.1 and what you immediately see,
19:44.0 looking at all these things,
19:45.1 is that they're all basically helical self-assembled structures,
19:49.3 but I would argue that helicity
19:52.2 of a self-assembled structure
19:54.1 is not something that's particularly difficult to evolve.
19:56.2 And in fact there is a very strong argument
19:58.2 made first by Crane
20:01.1 and then by Pauling, back in the 1950s,
20:03.1 that pretty much any protein
20:05.1 that has any tendency to associate with itself
20:08.1 is more likely to form a helix than it is to form anything else.
20:12.0 And the argument is pretty simple:
20:13.3 if you have a globular protein
20:16.2 where every aspect of that protein's surface
20:18.0 has slightly different physical attributes
20:20.2 -- slightly different charge distribution,
20:22.1 slightly different shape --
20:24.2 and that protein has some tendency
20:28.0 to interact with a second copy of itself
20:30.0 in some particular orientation
20:31.2 where, you know, part A of one protein
20:33.2 binds to part B of another protein...
20:36.0 if the protein is going to make a dimer,
20:37.2 you know, those two things that interact with each other
20:40.2 have to be distributed symmetrically on the protein.
20:42.2 But if the part A and part B
20:44.2 are in any orientation
20:46.2 other than just directly opposite each other,
20:49.0 then essentially what's going to happen
20:50.2 is those two subunits will come together
20:52.2 and there will be an interaction between the two
20:55.1 that will give a dimer that's got,
20:57.1 you know, some slightly off-center asymmetrical structure
21:00.1 where, if part A and part B are engaged here,
21:03.1 this subunit still has a part B available
21:05.1 and this subunit still have a part A available.
21:08.1 Now, if you think that through, as these guys did,
21:10.1 what you see is that you can then
21:12.1 add another subunit on this side,
21:13.3 you can add another subunit on that side,
21:15.2 and you're able to make helices
21:17.1 out of this very simple binary interaction rule.
21:20.2 And in this really creative
21:23.0 and beautiful illustration
21:24.1 done in this original paper
21:26.3 using little matchboxes,
21:28.0 you can see you can actually build all sorts of different kinds of helices
21:30.2 just by slightly changing
21:32.2 the orientation of the interaction between those two subunits.
21:36.1 So, making a helix is not a big deal,
21:39.0 and in fact a really great piece of evidence
21:41.3 to show that that's true
21:44.0 is the effect of the sickle cell mutation on hemoglobin.
21:47.0 Now, hemoglobin is highly selected to be very, very soluble
21:52.2 can get up to on the order of 300 mg/mL --
21:55.2 but just one mutation in hemoglobin
21:58.1 can give it the tendency to precipitate.
22:00.3 And when it precipitates
22:03.0 it forms these incredible looking
22:05.1 helical filaments that look, really,
22:07.2 almost exactly like microtubules.
22:09.2 If I told you this was a microtubule,
22:11.0 you would probably even believe me,
22:12.1 but it's actually a polymer of sickle cell hemoglobin.
22:15.2 So, when you take a very soluble protein
22:18.1 and you make something go just a little bit wrong
22:20.1 with one part of its surface
22:21.3 so that it has a very minor tendency to self-associate,
22:24.1 the consequence is you get a helix.
22:27.2 Okay, so forming a helix
22:29.1 is not a special property...
22:31.1 what is it about cytoskeletal filaments
22:32.2 that gives them their ability to give us morphology?
22:35.2 Well, one other important thing
22:37.3 that is true of all of the eukaryotic cytoskeletal filaments
22:40.3 is that they have this very interesting dichotomy
22:44.3 that they have to be stable in order to have physical strength,
22:48.0 but they also have to be unstable
22:50.1 in order to allow the cell to change shape
22:52.1 or to move or to rearrange its elements
22:54.2 as it's dividing.
22:56.0 And at least for actin
22:58.1 and for tubulin,
23:00.0 part of the reason that they're able to
23:02.0 exhibit this dichotomy
23:04.0 is because those subunits are also able to bind and hydrolyze nucleotide --
23:07.2 ATP in the case of actin,
23:09.1 GTP in the case of tubulin.
23:11.2 And as you see in this illustration here,
23:13.3 the fact that you can have
23:15.3 different conformational states of a protein
23:17.1 based on the identity of the nucleotide that's bound to it,
23:21.1 can set up a situation where you can have one conformational state,
23:24.3 in this case illustrated as being the thing binding ATP,
23:27.3 which is a conformation appropriate
23:30.2 for forming one of these helical filaments,
23:32.2 and you can have an alternative conformational state,
23:35.1 which is shown here in this case
23:36.3 as being the nucleotide free state,
23:39.0 but it could also be the ADP state,
23:40.2 that will tend to disassemble.
23:42.2 And so having that switch
23:44.2 between an assembly-competent form
23:46.2 and an assembly-incompetent form
23:49.0 can enable the dynamics
23:51.0 that are characteristic of eukaryotic cytoskeletal filaments,
23:53.1 and in fact it's very interesting
23:55.1 that actin itself
23:57.1 is a close structural relative of hexokinase,
24:00.0 the glycolytic enzyme which is best characterized
24:02.0 with respect to its very large conformational change
24:04.1 on binding and hydrolysis of substrate.
24:09.1 And in fact it's true
24:11.3 that if you look at the cytoskeletal elements of eukaryotic cell,
24:15.0 they're all highly dynamic,
24:16.2 and this is something that's been appreciated
24:18.1 for many decades in the context of microtubules,
24:20.2 actin, and intermediate filaments...
24:22.1 all of them turn over very fast inside of cells.
24:24.2 And in fact for things that require
24:28.2 the cytoskeletal filaments, like for example forming the mitotic spindle,
24:31.1 if you inhibit either the assembly
24:34.2 or the disassembly of the microtubules
24:37.3 in a mitotic spindle,
24:39.1 the net effect is the same in both cases,
24:41.1 which is that the cell fails to divide.
24:43.3 So it's not just the helical structure,
24:45.2 but also the turnover is clearly key.
24:47.3 Okay, well let's turn back to the prokaryotes --
24:51.2 do they have dynamics associated with their cytoskeletal filaments?
24:54.3 Well, actually, as it turns out, they do.
24:56.2 So, as I mentioned FtsZ,
24:58.2 that's a close structural homolog of tubulin,
25:00.1 also binds and hydrolyzes GTP,
25:02.3 and in vivo turns over very, very rapidly,
25:05.2 as can be seen in this photobleaching study.
25:08.2 So, here there are two cells
25:10.1 that have assembled FtsZ rings.
25:12.2 Here, one half of one of these rings
25:14.1 has been bleached out,
25:15.2 and you can see, actually within just a few seconds,
25:18.1 the ring is able to come back.
25:20.1 And this particular experiment
25:23.2 also had a really, really nice direct demonstration
25:28.2 that those dynamics are associated with nucleotide hydrolysis,
25:31.3 which was they were able to compare the dynamics of wild type FtsZ protein
25:34.1 with an FtsZ protein
25:36.1 that had a point mutation that slowed down GTP hydrolysis,
25:39.0 and looking at the turnover of the wild type protein
25:41.2 versus the turnover of the slower protein,
25:45.1 in vivo,
25:46.1 they were able to see that there's this direct correlation
25:48.1 between how fast the filaments turn over
25:50.2 and their ability to hydrolyze GTP.
25:53.2 Okay, so the prokaryotic filaments,
25:55.1 they do the same kinds of dynamics
25:57.1 as the eukaryotic ones do,
25:58.2 so it's not the helical structure,
26:00.0 it's not the dynamics in terms of turnover,
26:01.2 and it's not even fancy dynamics.
26:03.3 So, microtubules, for example,
26:05.1 famously do this dynamic instability,
26:07.1 where even in a uniform chemical environment
26:10.1 an individual microtubule end will grow for a while
26:12.0 and then shrink for a while,
26:13.1 and then grow for a while and then shrink for a while,
26:15.3 and it's not at all obvious why this should be possible.
26:18.1 This is something that people have been studying for many years
26:21.1 and we have a pretty good overall chemical understanding
26:23.1 of how this can happen,
26:25.0 but it's definitely dependent on
26:28.1 the ability of the structures to hydrolyze nucleotide
26:30.2 and change their conformational states.
26:33.2 So, this illustration up top
26:36.0 shows the classic direct demonstration
26:37.3 of this dynamic instability on microtubules,
26:39.3 it was done in 1986,
26:41.2 and then almost 20 years later
26:44.1 another group was able to show with one of the bacterial actin homologs,
26:47.0 this one called ParM,
26:49.0 that they were able to see exactly the same kinds of behaviors
26:51.0 of these filaments growing for a while
26:52.2 and then shrinking for a while,
26:54.1 even when the chemical environment is uniform.
26:57.0 Okay, so it's not the helicity,
26:58.2 it's not the ability to hydrolyze nucleotide,
27:00.3 it's not the ability to turnover rapidly in vivo,
27:03.1 and it's not even the ability to do fancy things
27:06.1 like dynamic instability.
27:08.2 What it is, then, that's different?
27:10.1 Well, looking at bacterial cells,
27:12.1 it's clear that the way they're able
27:14.2 to get some sort of overall cellular organization
27:16.1 definitely depends
27:18.1 on this tendency of proteins
27:19.3 to make helical filaments.
27:21.1 And in fact if you look at bacteria
27:22.2 and you look at different aspects of their structures,
27:24.2 what you see is the helices are all over the place,
27:27.2 and you can make lots of different kinds of helices,
27:29.2 ranging from different things like the overall helical pattern of a spirochete
27:32.3 to the twisting helices associated with bacterial flagella,
27:36.2 to even the much more, sort of uniform helix
27:42.0 associated with something like a bacterial pilus.
27:45.2 So, it's clear it's not just the classical cytoskeletal proteins in bacteria
27:49.2 that are able to do this helical self-assembly trick,
27:51.1 but in fact lots of other proteins as well.
27:55.2 And looking specifically at the cytoskeletal proteins,
27:59.1 I think one interesting example
28:01.1 is the bacterium Caulobacter crescentus,
28:03.0 which is this very cute little banana shape
28:05.1 with structural differentiation on its two ends.
28:08.1 It's got not just actin and tubulin,
28:10.3 but it also has something that looks very much like
28:13.3 an intermediate filament,
28:14.3 and each of those things assumes slightly different helical patterns
28:17.2 inside of a growing cell.
28:19.1 And mutations in either the actin homolog,
28:21.1 the tubulin homolog,
28:22.2 or the thing that looks like an intermediate filament
28:24.1 will affect the overall shape of the cell
28:26.2 in very different ways.
28:28.1 So, lots of helical organization,
28:30.3 lots of function associated with helical organization,
28:33.2 but still no great morphological diversification.
28:37.3 Now, like everything else in biology,
28:39.3 there's going to be some exceptions,
28:41.1 and there are some bacteria that have really,
28:42.3 particularly spectacular shapes,
28:44.0 and this just shows a couple of my favorites.
28:45.2 This is a star-shaped bacteria called Stella humosa.
28:48.3 It's flat, but it has either five or six points
28:51.1 depending on what stage of its cell cycle it's at.
28:54.2 This is another weird-looking flat prokaryote
28:58.1 that in this case is an archaeon.
29:00.2 This is called Haloquadratu walsbyii
29:02.3 and it was first cultured in pure form
29:05.1 only a few years ago,
29:06.3 and this is actually flat like a floor tile,
29:08.3 and when it divides
29:11.0 it divides across the middle and then again like that,
29:13.0 so you have one floor tile going into four smaller ones.
29:16.1 And then there are things like this,
29:17.2 this is Epulopiscium fishelsonii,
29:19.2 which competes with Thiomargarita
29:21.1 as being one of the biggest bacteria known,
29:22.3 and this is absolutely huge,
29:24.1 it can be half a micron long,
29:26.1 and it has many copies of its genome
29:28.0 that are actually distributed
29:29.2 in a very regular pattern
29:31.1 throughout the entire cell,
29:32.2 and it moves its genome around depending on what time of day it is.
29:35.1 So, I think for things like this,
29:36.3 there's gotta be something else going on
29:39.0 besides just our usual bacterial helical self-organization,
29:41.2 and I think it's an interesting challenge
29:43.1 to now try to go into these organisms
29:45.1 and find out what it is that's determining their ability
29:47.2 to have these very specific morphologies.
29:51.2 Okay, but getting back to the main thread,
29:53.2 I've been arguing that
29:56.1 you can have simple helical structures
29:58.1 without motor proteins and nucleators,
30:00.0 and in order to have more complicated things
30:02.1 that make eukaryotes what they are,
30:03.2 we need to have either nucleators or motors.
30:06.0 So, this raises the question,
30:07.3 well, why don't bacteria have them?
30:09.0 Where did they come from in eukaryotes?
30:10.1 And why does it seem like it's so hard for the bacteria
30:12.0 to pick them up?
30:14.1 Well, for the nucleators,
30:15.2 this is a particularly interesting problem
30:17.2 because the way that eukaryotic cells tend to nucleate
30:22.1 their cytoskeletal proteins
30:23.3 is very often by taking the subunit,
30:27.0 copying that gene,
30:28.2 and then having it diverge a little bit
30:30.3 to have it assume a specialized nucleation function.
30:33.1 And we've seen this in two cases,
30:35.1 completely independent cases,
30:36.2 for actin nucleation and for tubulin nucleation.
30:39.1 So, actin nucleation can be performed
30:41.2 by this complex that's called the Arp2/3 complex,
30:44.1 where Arp stands for actin-related protein,
30:46.3 because there are two different proteins
30:48.3 from different genes,
30:50.1 both structural homologs of actin,
30:52.1 that come together to make this regulated nucleation complex.
30:56.1 In the case of microtubules,
30:58.0 the nucleation is often carried out
30:59.3 by what's called the gamma-tubulin ring complex.
31:02.1 Now, the lattice of the microtubule
31:03.3 is made up with alpha-tubulin and beta-tubulin.
31:06.0 Gamma-tubulin is specialized only for nucleation function.
31:10.2 Why can't bacteria do this?
31:12.1 Well, I think they clearly could if they wanted to,
31:14.3 because we do see, as I mentioned,
31:17.2 among the actin homologs in bacteria,
31:19.1 an individual cell may have
31:21.2 several kinds of actin homologs
31:23.1 that are all present within that same genome
31:25.1 that have all been evolved for slightly different functions.
31:28.1 And yet, so far, as far as we know,
31:31.1 none of them have been specialized specifically
31:33.1 for filament nucleation.
31:35.3 I don't know why they don't want to,
31:38.0 but it seems like they could,
31:39.2 and yet they don't.
31:43.1 Turning now to the molecular motor proteins,
31:46.0 this is something where it might be a little more clear
31:48.2 why bacteria don't have them.
31:50.1 If we think about where the really good molecular motor proteins come from in eukaryotes...
31:54.3 there are of course three different classes,
31:56.3 there's the myosins, the kinesin, and the dyneins,
31:58.1 that all hydrolyze nucleotide
32:00.0 in order to undergo a conformational change,
32:01.3 and of these the kinesin and the dyneins move on microtubules.
32:06.2 The myosins move on actin filaments.
32:08.1 Now, these different motor proteins
32:10.0 had all been purified,
32:11.1 had all been studied biochemically,
32:12.2 and sequenced,
32:14.1 and then eventually their structures were determined,
32:16.0 and at the point when the structures were determined,
32:18.0 there was this huge surprise,
32:19.3 and this, again, was back in the 1990s,
32:22.0 where it was found that
32:25.1 the fundamental of the catalytic core of myosin
32:27.1 was almost identical
32:29.1 to the structure of the catalytic core of kinesin.
32:31.3 Even though myosin walks on actin filaments
32:33.2 and kinesin walks on microtubules,
32:35.2 they still seem to be homologs
32:37.2 derived from a common ancestor.
32:39.2 And in both cases, the fundamental way that ATP hydrolysis
32:42.2 at the core of the motor protein
32:44.2 results in the conformational change
32:46.0 that gives you a step
32:49.0 is very similar at the heart of the motor protein,
32:50.3 even though all the details about how it couples to its filaments
32:53.2 are quite different between the two.
32:56.1 So, this gives rise to, you know,
32:58.2 another field ripe for speculation
32:59.3 about where did the motor proteins come from.
33:01.2 Well, if kinesins and myosins are related to each other,
33:04.1 it seems like there must have been some sort of motor precursor,
33:07.2 and we don't know what its substrate was,
33:09.2 if it was actin or microtubules,
33:10.2 or if it might have been something else.
33:12.2 We don't know what the complement of motors was
33:15.2 in the earliest thing that became a eukaryote,
33:18.1 and whether this might have been something
33:20.1 that actually drove it to separation
33:23.1 from the prokaryotic branches of the tree
33:25.1 in terms of morphological diversification.
33:28.1 One thing we do know, though,
33:30.3 is that those motor proteins, kinesin and myosin,
33:33.1 are both derived from a particular branch of
33:37.2 the superfamily of proteins that's called P-loop NTPases,
33:40.1 that includes a lot of ATPases and GTPases.
33:43.1 And this fairly complicated diagram
33:45.2 is a summary of sequence diversification
33:49.1 among many, many different family members
33:51.2 of this large protein superfamily
33:53.2 across the entire tree of life.
33:56.1 And what this group,
33:58.1 this is Eugene Koonin's group that's done this,
34:00.0 has attempted to do
34:02.2 is look at what the distribution of what all these protein types
34:05.1 in currently living cells
34:06.3 and then project backwards in time
34:08.2 to see when they might have evolved.
34:10.3 And so there's some classes of proteins
34:12.3 that you see here with these pink lines
34:14.2 that are present in bacteria, in archaea, and in eukaryotes,
34:17.1 and so they must have been present in LUCA,
34:19.0 in the last universal common ancestor.
34:21.1 But there's one particular protein family, right here,
34:24.1 that's shown in brown,
34:26.0 that has both the myosins and kinesins in it,
34:30.0 and then also has a whole lot of other GTPases
34:32.1 that we associate with specifically eukaryotic functions
34:34.3 -- Ras, the Rab proteins that are involved in membrane trafficking,
34:38.3 the Rho proteins that are involved
34:40.2 in large-scale organization of cell polarity --
34:44.0 all of those things come from
34:46.1 the same relatively narrow branch of the P-loop NTPases.
34:49.2 So, one possible explanation
34:53.2 for why eukaryotes and prokaryotes are different from one another
34:55.3 is because the proteins that are best poised
34:58.1 to become stepper motors
35:00.2 of the kind that are familiar from eukaryotes
35:02.2 happen to be in this branch of proteins
35:05.1 that didn't evolve until the eukaryotic ancestor
35:07.1 had already split off.
35:09.3 It's very tempting to speculate
35:11.1 that this particular class of proteins
35:12.2 that includes not only the myosins and kinesins,
35:15.3 but also all of these regulatory GTPases,
35:19.0 might be part of what makes eukaryotes what we are.
35:22.2 Now, I'd like to point out, of course,
35:24.3 there's plenty of other protein families
35:26.2 that are not shared between eukaryotes and prokaryotes
35:28.1 -- about 50 other classes of proteins
35:30.1 have been identified to date --
35:31.1 however, I think, mechanistically,
35:33.0 this is a particularly intriguing group
35:36.1 for generating specifically morphological diversification
35:37.3 at the level of cells
35:40.1 and at the level of whole organisms.
35:43.1 Now, I don't mean to say that bacteria don't have motors;
35:45.2 bacteria have amazing motors.
35:47.1 Bacteria have the flagellar rotor,
35:49.2 which is a very complicated structure,
35:52.0 it's much more complicated even than dynein,
35:54.1 that's able to spin at 200 Hertz
35:56.0 and is made up of more than 40 different gene products.
36:00.1 Bacteria also have extremely strong motors
36:02.2 like the motor that drives twitching,
36:05.3 by retraction of these type IV pili,
36:08.1 and this is something where a single motor
36:10.1 interacting with a filament
36:12.2 that's extended from the...
36:14.1 that's extended through the bacteria envelope
36:17.1 is able to generate up to 100 picoNewtons of force,
36:20.0 just from movement
36:23.0 of a single extended filament structure.
36:26.0 So, the motors in bacteria can be very powerful,
36:28.1 very efficient,
36:29.3 and very complicated,
36:31.2 and yet all of them seem to do things on the surface of the bacterium.
36:34.2 None of them seem to do anything in the cytoplasm.
36:37.1 So somehow this question of morphological diversification,
36:40.1 about how you get complex intracellular structures,
36:43.1 seems to be at least correlated
36:45.1 with the presence of linear stepper motors for cytoskeletal proteins
36:50.2 in eukaryotes,
36:51.2 and no real equivalent in prokaryotes.
36:54.0 And, you know, again, I can speculate wildly
36:55.3 about why there seems to be this difference,
36:59.0 but nevertheless this is a fairly compelling correlation.
37:02.3 It doesn't come down to complexity or anything like that,
37:05.1 but really only down to the presence or absence
37:07.1 of this one particular protein family.
37:11.1 Okay, so this is, overall, the hypothesis, again,
37:14.0 that we need nucleators and molecular motors
37:15.3 in order to drive things like the mitotic spindle,
37:18.2 or like microtubule asters,
37:19.2 or like parallel bundles of cytoskeletal filaments
37:23.1 that give eukaryotes morphological complexity,
37:25.1 and I've made the claim
37:28.2 that no structures of this kind, again,
37:30.0 with just very minor exceptions,
37:32.0 have yet been found in the cytoplasmic compartment in bacteria.
37:37.3 I'm focused, of course,
37:39.1 on the role of the cytoskeleton in all of this,
37:41.1 but it is worth think about maybe other kinds of explanations
37:43.2 for the difference,
37:45.0 and one thing that might really be connected
37:46.2 is the fact that it's been observed in bacteria,
37:48.2 where of course the chromosome
37:52.0 is just embedded in the cytoplasm
37:53.3 and there's no nuclear membrane separating the chromosome
37:56.2 from the cytoplasm,
37:57.3 in the cases where it's been well documented,
37:59.1 the bacterial chromosome is actually highly organized.
38:02.1 And one of the first hints of that came from these studies in Caulobacter,
38:05.1 showing that a circular bacterial chromosome
38:08.1 that was marked with different fluorophores
38:11.2 at specific locations would actually organize itself
38:14.1 in basically every cell within a bacterial colony
38:17.2 such that those markers on the chromosome
38:19.1 are all found in the same order.
38:20.3 In other words, the bacterial chromosome
38:22.1 is packed into the cell
38:24.1 in a highly structured, highly regular way
38:26.2 that can provide spatial information
38:29.1 for targeting other kinds of subcellular structures,
38:31.2 for example, to the poles
38:33.2 or to the nascent septal zone.
38:36.1 So, you know, one possible way
38:39.1 to bring these two ideas together
38:41.2 is that at some point in the development of the eukaryotic ancestor
38:43.3 something happened
38:46.0 that either enabled the nuclear envelope to come in
38:49.1 or somehow otherwise separated the chromosome
38:51.3 from the cytoplasm,
38:53.1 and if bacterial cells and archaeal cells
38:55.1 primarily rely on their chromosome
38:57.1 as being their major organizing principle
38:59.0 as far as where to put things in the cytoplasm,
39:00.3 then when that separation happened,
39:03.2 the little filaments that were left out in the cytoplasm,
39:06.0 that in bacteria had only been doing
39:08.0 fairly trivial things
39:09.2 of figuring out where to divide
39:11.1 and how to determine the overall shape
39:13.1 of where to lay down the cell wall,
39:14.2 those guys were left by themselves out in the cytoplasm.
39:16.1 They had no landmarks,
39:17.3 they had no chromosome to tell them where anything was,
39:19.1 and so they somehow had to figure out
39:21.2 how to make larger-scale structures
39:23.2 like asters, like bundles, like spindles,
39:26.2 that could help them organize themselves
39:29.1 in the cytoplasm,
39:30.2 in the absence of information from the chromosome.
39:34.0 Okay, like I said, this was wild speculation,
39:36.0 but one of the things that I think is fun about this
39:38.3 is that it's wild speculation that is absolutely disprovable.
39:41.1 So I'd like to give you a personal challenge
39:43.2 to look for and try to find
39:46.2 either a cytoskeletal stepper motor
39:48.1 that walks on a bacterial cytoskeletal filament
39:50.2 in a way analogous to what kinesin or myosin
39:53.1 does in eukaryotic cells,
39:55.0 or else to find a regulated nucleator
39:57.2 of any of these bacterial cytoskeletal filaments.
40:00.0 A lot of very smart people have been looking in various ways
40:02.1 for at least the past 20 years
40:05.0 and, as far as I'm aware,
40:06.3 nobody has yet found any proteins in one of these classes.
40:08.2 Now, that certainly doesn't mean they're not out there,
40:10.2 but it does mean that if either of these things were found,
40:13.0 that would be absolutely definitive proof that my big, crazy hypothesis
40:16.2 is wrong.
40:18.0 So, please try to prove me wrong,
40:20.1 and if you do find one of these classes of proteins,
40:22.1 a bacterial cytoskeletal stepper motor
40:24.1 or a bacterial regulated nucleator,
40:26.0 please send me an email and let me know.
40:28.0 I would love to hear about it.
40:29.2 And if you do, I personally will send you
40:32.0 a large bouquet of flowers
40:33.2 and also hearty congratulations
40:35.1 for taking another step forward
40:37.1 to trying to understand one of these biggest questions
40:39.1 about why cells on Earth look so different
40:41.1 from one another.
40:42.2 Thank you.
00:00:16;05 Hi, my name is Ken Miller, and I want to talk to you today about
00:00:21;01 why evolution matters to biology, not just biology, but all of science.
00:00:25;07 I've got to start right up front by telling you that I'm not an evolutionary biologist.
00:00:29;19 I don't dig for fossils. I'm actually a cell biologist,
00:00:32;07 and most of my career has been spent working on the structure of biological membranes,
00:00:37;28 especially the photosynthetic membrane.
00:00:40;13 I use the electron microscope; thatâ€™s where my training is.
00:00:43;06 I've used a technique called freeze etching to look inside those membranes,
00:00:47;00 and I've also used image analysis and reconstruction to develop things like
00:00:51;14 a 3-dimensional model of a photosynthetic membrane. This ended up on the cover of Nature.
00:00:56;12 And more recently my laboratory has also worked on the translocon,
00:01:00;12 which is a little channel by which proteins leave the ribosome and enter the rough endoplasmic reticulum.
00:01:06;07 So how does a nice cell biologist get interested in evolution?
00:01:09;18 There are actually two answers to that.
00:01:11;29 The first answer came from a student.
00:01:14;05 When I first began to teach at Brown University, where I still am,
00:01:18;11 a student came to me in the spring of 1981 and he challenged me.
00:01:22;21 He asked me if I wanted to debate a scientific creationist.
00:01:28;03 I had actually never heard of scientific creationism before
00:01:32;01 and the more I looked into it, the more I thought, "Yeah, I might like to go ahead and do this."
00:01:35;27 So the students ended up establishing and setting up a debate at my university.
00:01:41;04 To my amazement, an enormous crowd bought tickets to this event,
00:01:45;29 so many that we had to put it in the largest room on our campus
00:01:49;03 which was the ice hockey rink, believe it or not.
00:01:51;21 And I participated that year in another debate as well.
00:01:54;29 And in fact, in the two debates, in that year (1981), more than 3000 people showed up in aggregate.
00:02:02;21 I'd given scientific talks before, but I'd never attracted a crowd even close to that or seen that level of interest.
00:02:09;19 That made an impression on me.
00:02:11;11 That told me this was an important issue; one that people care about in the general public.
00:02:16;01 And also, I was appalled by the amount of scientific distortion
00:02:20;08 and misinformation that was garnished in the name of scientific creationism.
00:02:25;17 A second thing happened. Pretty much the same year, and that is, when the debates were over,
00:02:32;18 a former student of mine came to me with what I thought was an outlandish idea.
00:02:37;14 And that is: how about you and I get together and write a high school biology textbook?
00:02:42;19 Well, after a few debates, I decided that was over.
00:02:45;17 I sat down with my friend Joe Levine,
00:02:48;00 and Joe and I published a series of biology textbooks designed for high school students
00:02:53;25 that have been very successful and have been used through all parts of the country.
00:02:57;19 That's the second part of the story as to how I came to be interested in evolution.
00:03:02;28 Our books, being cutting edge biology, had a very strong treatment of the theory of evolution.
00:03:09;08 In some school districts, they were banned.
00:03:11;28 In other school districts chapters were cut out,
00:03:14;13 and in one, very important school district, a warning label,
00:03:18;06 which you can see right here, was actually placed on the surface of the textbook,
00:03:22;10 warning students that evolution was a theory and not a fact.
00:03:26;08 That brought me, in a way,
00:03:27;27 right back into the issue of whether evolution should be taught as part of mainstream biology.
00:03:33;25 Now a lot of my scientific colleagues ask me from time to time,
00:03:37;21 "Didn't we settle all this in 1925 during the Scopes so-called monkey trial?"
00:03:43;04 And unfortunately, I'm afraid, that what they're thinking of when they talk about this
00:03:47;05 is in fact the movie, Inherit the Wind, which is loosely based on the Scopes trial.
00:03:52;07 The reality is that when William Jennings Bryan and Clarence Darrow squared off
00:03:58;02 in that Tennessee court room, John Scopes was convicted,
00:04:01;27 and evolution basically disappeared from science textbooks in the United States for almost 50 years.
00:04:08;19 It's an extraordinary thing.
00:04:10;08 And even today, the anti-evolution movement in this country is thriving.
00:04:14;26 TIME magazine, several years ago, had a cover story on it. They called it the evolution wars.
00:04:20;16 Books, pamphlets, movies and even a museum have been opened to support the idea
00:04:27;15 that evolution is fundamentally wrong and that evolutionary science is completely mistaken.
00:04:33;06 This sort of activity led to a dramatic confrontation in 2005 in a federal court room
00:04:39;27 in the state of Pennsylvania after a town, Dover, Pennsylvania, decided to
00:04:45;08 order its teachers to prepare a curriculum on an anti-evolution idea called 'intelligent design'.
00:04:51;29 What followed was a dramatic and widely publicized seven week trial.
00:04:57;21 I had the honor, but I'm never sure if that's the right word,
00:05:00;22 of serving as the lead witness in that trial,
00:05:02;24 and what you see right here is actually the NBC TV court room sketch of my cross-examination
00:05:08;22 during the first days of that trial.
00:05:11;13 At the end of the seven weeks, what happened?
00:05:13;02 Well, the judge, actually a conservative republican,
00:05:16;09 appointed by George W. Bush, looked at the evidence and testimony and said,
00:05:20;27 "Intelligent design simply isn't science."
00:05:24;21 In my opinion, of course, exactly the right verdict.
00:05:27;22 And this was big news. It appeared on the nightly news on every one of the major networks,
00:05:32;03 front page of the New York Times, everywhere you can possibly imagine.
00:05:36;06 Now, despite this verdict as it turns out, or perhaps because of the verdict,
00:05:41;08 a lot of us who testified in the trial, and I was just one of several scientists who did that,
00:05:46;04 ended up with some very interesting requests when the trial was over.
00:05:49;21 I appeared on a couple of TV programs, here's a snapshot of one of them.
00:05:53;26 And those TV programs appeared on unlikely networks like Comedy Central.
00:05:58;16 And, yes, I actually appeared as a guest on the Colbert Report,
00:06:02;07 and if any of you listening to this would like to find a clip of that, it's really easy to do.
00:06:06;22 You just go to Google, and you type in my name and Colbert Report
00:06:10;24 and a couple of appearances on Colbert will come up.
00:06:13;14 It was an extraordinary thing.
00:06:15;10 It got, I think, the message of science across to an audience that normally wouldn't get it.
00:06:19;28 But something interesting comes out of that,
00:06:24;03 and that's one of the key points that I want to make.
00:06:26;10 All too many of my colleagues in the biological science community think that
00:06:31;11 evolution's just a story about the past, and therefore defending evolution is the job of
00:06:36;10 paleontologists and fossil hunters and that sort of stuff.
00:06:39;18 But the reality of science today is that evolution is everywhere.
00:06:44;13 It's even in our blood, and because it's in our blood, it's in our genome.
00:06:49;07 Now, what I've put up here is an image showing hemoglobin,
00:06:53;08 the red protein that carries oxygen in our blood stream.
00:06:56;28 We know the exact location of the genes for alpha and beta globin on the human chromosome,
00:07:02;14 and there's something very different and very interesting about their structure and organization.
00:07:08;12 We actually have five copies of the gene for beta globin.
00:07:13;22 We use this at different times in our life cycle.
00:07:16;03 They were all produced, any evolutionary biologist would tell you,
00:07:20;03 by the process of gene duplication, but here's what's really cool.
00:07:23;18 Right in the middle of this collection of genes, and you can see it right there,
00:07:28;14 is in fact a pseudogene. You can see the Greek letter psi above it.
00:07:32;08 That means it's a gene that is broken. Now why do I say it's broken?
00:07:36;26 It means that one of these multiple copies
00:07:39;02 accumulated so many mistakes that it couldn't work anymore.
00:07:43;01 What are the nature of the mistakes? You can see them here.
00:07:45;27 They involve altered control regions, frame shift mutations.
00:07:49;20 Even if this piece of DNA could be transcribed,
00:07:52;21 it could never be translated; it could never be made into a protein.
00:07:56;01 Now, why is all of that significant? It's significant for a very simple reason.
00:08:01;07 Mistakes are unique. They occur only once, and then they're propagated to
00:08:07;06 all of one's descendants, and that's what's happened with the beta globin pseudogene.
00:08:11;09 But, the interesting part is that we share not only the structure of this beta globin locus,
00:08:18;12 but we also share those mistakes with three other organisms.
00:08:23;29 Want to know who they are?
00:08:25;15 They're the gorilla, the chimpanzee and the orangutan.
00:08:28;29 And what does that mean? It means that all four of these species,
00:08:33;04 these three guys and us, share common ancestry.
00:08:36;06 And our genome is testament to that. But, there's even more.
00:08:40;21 As a cell biologist, I've worked prety much my entire career on organelles within cells.
00:08:46;10 Two of the most interesting are chloroplasts and mitochondria.
00:08:50;14 And my lab has done some research on both.
00:08:52;25 These are extraordinary organelles that are involved in the transduction of
00:08:56;28 either chemical or solar energy into a form that the cell can use.
00:09:01;29 Now there are some weird things about these two organelles.
00:09:05;24 One of them is: they both import proteins from the cytoplasm (the rest of the cell).
00:09:10;18 Now, that's not surprising, but they import them, take them inside,
00:09:14;28 and then re-export them into their own membranes.
00:09:18;08 Itâ€™s sort of a roundabout route.
00:09:19;27 It's like going to one side of the shopping center and then the other,
00:09:23;05 and then coming back in and then going back out again.
00:09:25;19 It makes very little sense.
00:09:27;20 It also turns out, they're both surrounded by two membranes.
00:09:31;12 Most organelles of the cell-only one.
00:09:33;29 How come two? It's a bit of a puzzle.
00:09:35;15 Another thing is they are not made by the cell from scratch. They're self-replicating.
00:09:42;00 In other words, they come only from the division of pre-existing mitochondria and chloroplasts.
00:09:46;26 In addition, the ribosomes, the protein synthesizing machines, within these are distinct.
00:09:52;13 They're very different from ribosomes from the rest of the cell.
00:09:55;14 Why should these guys have their own unique ribosomes?
00:09:59;00 And last but not least, they've got their own DNA.
00:10:01;26 They have their own genetic systems.
00:10:04;20 Why is all of this the case?
00:10:06;12 Well, the answer, from evolution, turns out to be very clear and very straightforward.
00:10:10;24 Mitochondria, there's very clear evidence, arose from primitive bacteria
00:10:15;29 that were then taken inside an early eukaryotic cell and then surrounded by a second membrane
00:10:21;11 and eventually formed into the organelles that today we call mitochondria.
00:10:26;15 Chloroplasts are pretty much the same thing,
00:10:28;17 except it was a cyanobacteria (a photosynthetic prokaryotic organism).
00:10:33;14 And once you understand this process, which is called evolution by endosymbiosis,
00:10:38;19 everything makes sense, protein import and re-export, the double membranes,
00:10:43;20 the self-replication and the unique ribosomes, and the fact that these organelles have their own DNA.
00:10:49;01 It all fits together, and it fits together quite beautifully.
00:10:52;03 Today, evolution itself is a research tool.
00:10:57;00 We use evolution to understand the relationships of proteins in the cytoskeleton, for example.
00:11:03;14 We also use evolution to understand the development of body plans
00:11:07;26 in the field of evolutionary developmental biology.
00:11:11;20 If you want to read up on this, pick up Sean Carroll's great book, "Endless Forms Most Beautiful".
00:11:17;29 And in this, Carroll explains the way in which the animal body is modular.
00:11:22;02 It's made up of repeating parts and these repeating parts
00:11:25;16 basically produce the forms and patterns that we look at and appreciate as biologists.
00:11:30;20 Now, one of the problems that I see as a scientist and an educator is
00:11:35;00 that evolution acceptance in this country is near the bottom of the industrialized world.
00:11:40;05 There were 29 countries polled in which a larger proportion of their citizens
00:11:45;17 accepted the theory of evolution than in the United States.
00:11:48;21 We're at the bottom of that list. The only country we beat out in Western Europe is Turkey.
00:11:53;20 Why is that? I think in large measure that's because
00:11:56;22 evolution is presented as a fearful doctrine, as something to be afraid of.
00:12:01;24 And that fear that characterizes, or the induction of fear that characterizes
00:12:06;12 the anti-evolution movement is dangerous.
00:12:09;01 Not just because it might cause people to reject evolution,
00:12:11;20 but rather because it might lead to us raising up a generation of young people
00:12:17;02 who have been taught that science is to be feared and distrusted.
00:12:21;03 And if we do that, this country will give up world scientific leadership,
00:12:25;14 something that we simply cannot afford to do.
00:12:28;03 In fact, in the current year, 2011, anti-evolution measures have actually
00:12:34;11 been introduced and attempted to be made law in no fewer than 7 state legislatures.
00:12:40;15 I'd like to pretend this is in the past, but it is in fact an ongoing problem.
00:12:45;07 So, what do we make of this?
00:12:46;18 Defending evolution is really defending the scientific method.
00:12:50;29 It isn't about Darwin anymore. It's about the science that we do today.
00:12:55;16 And I think every member of the scientific community
00:12:58;09 whether student, post-doctoral researcher, faculty level researcher or independent scientist,
00:13:05;02 owes it to themselves to defend evolution for two reasons.
00:13:08;14 One is, it is the unifying principle that makes sense of everything we do in biology.
00:13:13;14 And number two, acceptance of evolution means acceptance and embrace
00:13:17;28 of science and the scientific method.
00:13:20;08 Nothing could be more important for the scientific enterprise,
00:13:23;15 and in my opinion, nothing could be more important to our country.
00:13:27;05 Thanks for listening.
00:00:07.27 So, animals are incredible!
00:00:10.06 Some of them can fly through the air,
00:00:12.09 some of them can swim.
00:00:14.06 Animals have incredibly diverse body plans,
00:00:16.29 for instance this nudibranch.
00:00:19.13 Some of them can pattern their coloration
00:00:22.02 in different ways,
00:00:23.19 like this moth,
00:00:25.09 and even what we might consider simple organisms,
00:00:27.20 like the jellyfish that we see here
00:00:30.06 or a sponge...
00:00:32.22 these are incredibly interesting organisms as well,
00:00:35.11 and all of these animals share in common
00:00:37.16 something important,
00:00:39.02 which is they are composed of thousands and millions of cells
00:00:41.16 and these cells are working together
00:00:43.19 to make the organism work properly.
00:00:46.11 How did this all come to be?
00:00:48.16 Well, that's the focus of the talk
00:00:50.21 that I'm going to give you today.
00:00:52.12 The work in my laboratory has to do
00:00:54.03 with the origin of multicellularity.
00:00:56.12 My name is Nicole King.
00:00:58.01 I'm an investigator with the Howard Hughes Medical Institute
00:01:00.04 and a professor at the University of California at Berkeley,
00:01:02.23 and I'm excited to be here today
00:01:04.15 to tell you about my research.
00:01:06.18 Now, in the closing line of
00:01:09.25 Darwin's Origin of Species,
00:01:11.17 he remarked on endless forms most beautiful,
00:01:13.19 and he was referring to
00:01:16.28 the incredible diversity of body plans that we can see here,
00:01:19.10 and much of his research and thinking
00:01:22.14 had to do with trying to understand,
00:01:24.22 how do we get this diversity of organisms?
00:01:27.00 And there's been a great deal of progress in this regard,
00:01:29.24 largely from the work of embryologists
00:01:33.07 and evolutionary biologists
00:01:34.22 and geneticists working together
00:01:36.13 to try to understand what are the molecular
00:01:38.20 and mechanistic underpinnings
00:01:40.12 of the diversification of animal body plans.
00:01:43.07 But, in fact, there's something else important
00:01:45.14 that we need to keep in mind,
00:01:46.26 and that is that animals are united
00:01:48.21 by their shared ancestry.
00:01:50.08 They all share a common ancestor
00:01:51.27 that you can see here, indicated by this red dot.
00:01:55.07 And, in fact, we know relatively little
00:01:57.03 about the nature of that organism.
00:01:59.10 We don't know much about what its biology was like
00:02:01.21 or what its genome contained,
00:02:05.00 and we know even less
00:02:06.25 about the organisms from which it evolved,
00:02:09.05 but we can make some reasonable inferences
00:02:12.17 about the prehistory,
00:02:14.07 the pre-metazoan history of animals.
00:02:16.15 What we can reasonably infer
00:02:19.01 is that there some important evolutionary processes
00:02:22.05 that predate animal origins,
00:02:24.16 and these have to do with the origin of multicellularity,
00:02:27.22 the transition from a single-celled lifestyle
00:02:30.09 to one with organisms that were capable
00:02:33.07 of being multicellular
00:02:35.15 and coordinating the activities
00:02:37.07 of their different cells.
00:02:38.28 So, what I'd like to talk to you about today,
00:02:40.23 in this first part of my talk,
00:02:42.29 is what are the big questions that we want to ask
00:02:45.23 when we want to think about reconstructing animal origins,
00:02:49.25 and I think there are some discrete questions
00:02:51.27 that we can start to address.
00:02:53.26 The first is:
00:02:55.24 how did genome evolution contribute to animal origins?
00:02:59.07 It's clearly the case
00:03:01.21 that different groups of organisms on the tree of life
00:03:04.21 have different types of genes in their genomes,
00:03:07.03 and what we're interested in in my lab
00:03:09.10 is trying to understand how changes in gene sequences
00:03:12.17 and the composition of genomes
00:03:15.10 might have contributed to animal origins.
00:03:17.06 In addition, we're interested in understanding
00:03:19.21 how genes that are required for animal development
00:03:22.09 might have functioned before animals first evolved.
00:03:26.13 One of the special things about animals
00:03:28.08 is they have different cell types
00:03:30.15 that are not found in other groups of organisms.
00:03:32.23 These might include neurons
00:03:34.20 or the epithelial cells that make up your skin
00:03:37.01 and the lining of your gut.
00:03:38.28 How did those specialized cell types first evolve?
00:03:42.25 And then, in a topic that
00:03:45.29 we didn't expect to be studying,
00:03:47.20 we find that we're becomingly increasingly interested
00:03:49.24 in how interactions with bacteria
00:03:51.21 might have influenced animal origins,
00:03:53.19 and I'm gonna come back to that topic in part two.
00:03:56.27 And, of course, in the background of all of this
00:04:01.01 we're interested in understanding
00:04:03.23 the evolutionary implications of multicellularity,
00:04:05.21 and this is a topic of research that is ongoing.
00:04:12.00 Now, historically,
00:04:14.12 we've been very interested...
00:04:16.15 evolutionary biologists
00:04:18.29 have approached the evolution of animals
00:04:21.00 and the diversification of body plans
00:04:23.01 by really focusing on the fossil record,
00:04:25.12 and fossils have been great.
00:04:26.26 They tell us about the age of certain animal groups
00:04:29.03 and they can tell us about the shapes
00:04:31.07 of some of their body parts.
00:04:33.24 So, for instance, these beautiful star-shaped objects
00:04:36.21 are actually spicules from an ancient sponge,
00:04:39.27 this is a hypothesized embryo
00:04:43.08 that has recently been recovered,
00:04:45.20 and here we have a fossil of a coral,
00:04:47.17 and so we can see the fossil remnants of animals,
00:04:50.24 but it really doesn't tell us the whole story.
00:04:52.20 It doesn't tell us how animals came to be
00:04:55.02 and it doesn't tell us how cells
00:04:57.23 in those ancient organisms actually interacted.
00:05:01.18 To really understand animal origins,
00:05:03.15 I think we need to be focusing
00:05:05.20 on comparing living organisms,
00:05:07.13 and so what I'm going to tell you in this first part
00:05:09.22 of my iBio seminar
00:05:11.17 is about an unusual group of organisms
00:05:13.15 called the choanoflagellates
00:05:14.29 and how they can give us special insight into animal origins.
00:05:18.21 And then I'm going to tell you about
00:05:20.23 how the study of choanoflagellates,
00:05:22.06 and comparisons with animals,
00:05:24.10 have started to reveal the genome composition
00:05:26.11 and biology of the first animals,
00:05:28.15 organisms that lived and died
00:05:31.04 almost a billion years ago,
00:05:32.27 and yet by studying living organisms
00:05:34.12 we can learn about how they functioned.
00:05:37.01 In Part II, which I will come to later,
00:05:39.08 I will tell you that some choanoflagellates
00:05:41.22 can transition between being single-celled
00:05:43.26 and multi-celled,
00:05:45.16 and I'll tell you about how that happens,
00:05:47.22 and in addition I will tell you
00:05:50.03 about how that's regulated.
00:05:51.26 There are intrinsic and extrinsic influences on this process.
00:05:54.21 But, let me get back to this big question:
00:05:57.21 how did animals first evolve?
00:06:00.01 And in particular, can we focus on multicellularity?
00:06:03.14 So, let me remind you that
00:06:06.05 animals are not the only multicellular organisms out there.
00:06:08.29 We are only one of many
00:06:11.23 diverse multicellular forms out there.
00:06:13.09 So, of course, we have representative animals,
00:06:15.21 but plants are a remarkable example of multicellularity.
00:06:18.28 There are also green algae,
00:06:20.28 the fungi,
00:06:22.11 and, on the far side of the slide,
00:06:24.12 the slime molds,
00:06:25.23 and there are, you know,
00:06:27.13 probably 20 different lineages that are multicellular,
00:06:30.01 and so each of these lineages
00:06:34.01 has an interesting history in terms of multicellularity
00:06:37.04 and you might think that we could compare
00:06:39.01 among all of these lineages
00:06:40.17 and learn something about the origins of multicellularity,
00:06:43.21 but it turns out that that's not possible,
00:06:46.00 and that's not possible for a few reasons.
00:06:48.05 One is that if we look at the cell biology
00:06:50.14 of each of these different multicellular lineages,
00:06:53.01 we see that their multicellularity
00:06:55.08 is set up differently.
00:06:56.24 So, some organisms like plants and green algae,
00:06:59.19 they have stiff cell walls
00:07:02.20 that mean that a cell is born where it's going to die,
00:07:06.18 they're not able to move around relative to each other,
00:07:08.29 whereas animals and the slime mold
00:07:12.12 don't have a cell wall and the cells are able to move around
00:07:15.09 and resculpt,
00:07:17.05 and that changes their ability to form complex structures
00:07:20.02 and interact with their environment.
00:07:22.17 So, these differences as the cell biological level
00:07:24.23 also help us to understand
00:07:27.03 something that we see at the level of genomes.
00:07:29.15 Now, you might imagine that you could
00:07:32.20 compare the genomes of different multicellular organisms,
00:07:34.26 and the genes they share in common,
00:07:36.22 which are indicated here at the intersection,
00:07:38.17 that these would be the ones involved in multicellularity,
00:07:40.20 but in fact that is not the case.
00:07:42.20 The genes found at the intersection
00:07:44.13 of comparing the genomes
00:07:46.09 of these different multicellular lineages
00:07:48.23 are the genes that are involved
00:07:51.18 in basic housekeeping functions in the cell:
00:07:53.26 DNA replication, translation, repair, etc.
00:07:58.09 The genes that are involved
00:07:59.05 in mediating interactions between cells
00:08:02.04 are actually the genes that are unique
00:08:04.18 within each of these genomes.
00:08:06.11 Why? Why is that the case?
00:08:08.22 Well, to explain why the genes for multicellularity
00:08:12.14 are different in each of these lineages,
00:08:14.07 I need to introduce you to a simple tree.
00:08:17.02 So, what I'm showing you here is
00:08:20.25 a very simple tree depicting the relationships
00:08:23.15 between three different major multicellular lineages
00:08:25.24 -- the animals,
00:08:27.11 which are also called the metazoa,
00:08:29.03 the fungi, which include the mushrooms,
00:08:31.23 and the plants --
00:08:34.04 and what I hope you can see is that
00:08:36.03 there are a few surprises in looking at this tree.
00:08:38.16 First of all, it's only recently been appreciated
00:08:40.27 that the closest living multicellular relatives of animals
00:08:44.23 are the fungi,
00:08:46.15 but the other thing I need to tell you
00:08:49.01 is that, by looking at diverse organisms,
00:08:51.28 it has now become clear that multicellularity
00:08:54.14 evolved independently in each of these lineages,
00:08:57.12 and that's depicted by these yellow bars.
00:08:59.22 So we think, actually,
00:09:01.15 that the last common ancestor,
00:09:03.13 for instance, of the animals and the fungi,
00:09:05.16 was not multicellular.
00:09:07.09 In fact, it was unicellular.
00:09:09.20 So, we have a rich history
00:09:11.19 of unicellular life
00:09:14.00 before the origin of these different multicellular lineages,
00:09:16.19 and then these lineages evolved multicellularity
00:09:21.06 Well, what are we going to do?
00:09:22.28 How do we operate within this framework
00:09:24.24 to learn anything about the nature
00:09:27.06 of the organisms from which animals first evolved?
00:09:30.05 Well, the way we do that
00:09:31.24 is to try to find lineages
00:09:34.00 between this long-extinct unicellular ancestor
00:09:38.06 and the origin of multicellularity, here,
00:09:40.11 in the animals.
00:09:42.04 And we do that using a group of organisms
00:09:44.12 that sits in this sweet spot on the phylogenetic tree,
00:09:47.10 and these are the choanoflagellates.
00:09:49.22 So, choanoflagellates were discovered long ago
00:09:53.03 and I'm going to tell you
00:09:54.09 quite a bit about them in the next few slides,
00:09:56.04 but I want to say that the evidence for them sitting
00:09:59.19 on this spot on the tree, as the sister group of animals, or metazoa,
00:10:03.13 is that they have shared cell biological features with animals
00:10:07.02 that are not seen anywhere else in diversity.
00:10:09.21 Phylogenetic analyses of diverse genes
00:10:12.12 have indicated that choanoflagellates
00:10:14.20 are the closest living relatives of animals,
00:10:16.18 and then I'm going to tell you, very excitingly,
00:10:18.21 that we've sequenced the genomes
00:10:20.25 of diverse choanoflagellates,
00:10:23.18 and when we compare the composition
00:10:26.04 of choanoflagellate genomes to those of animals
00:10:28.15 it's very clear that they share a very close relationship
00:10:32.24 to animals.
00:10:34.29 Let me tell you about these organisms
00:10:36.15 because you may never have heard about them before.
00:10:39.02 Choanoflagellates are single-celled microbial eukaryotes.
00:10:43.11 They're about the size of a yeast cell,
00:10:45.18 and they have some diagnostic features
00:10:49.04 that tell you that you're looking at a choanoflagellate.
00:10:51.24 They have a spherical or ovoid cell body.
00:10:54.10 At the top of the cell,
00:10:56.18 which we call the apical surface of the cell,
00:10:58.12 they have, as you can see in red here,
00:11:00.23 something that's called a collar,
00:11:02.25 and this is actually the source of the name choanoflagellate.
00:11:07.24 The phrase choano- refers to the collar,
00:11:09.29 and the choanoflagellates
00:11:12.19 also have a long flagellum,
00:11:14.06 and you can reasonably think of these cells
00:11:16.08 as resembling sperm cells,
00:11:18.16 with the addition of this collar.
00:11:20.23 Now, choanoflagellates are actually quite diverse.
00:11:23.18 They can come in many different shapes and forms.
00:11:26.19 So, almost all choanoflagellates
00:11:29.08 have a single-celled phase to their life history
00:11:31.23 as you can see here.
00:11:33.28 And, as I said, all choanoflagellates
00:11:36.10 have a flagellum and collar,
00:11:38.03 but some of them can form beautiful colonial structures,
00:11:41.06 such as you can see here.
00:11:42.26 This species can actually
00:11:45.02 fluctuate between colonial and single-celled,
00:11:47.25 and some of them form very ornate extracellular structures,
00:11:52.12 such as this beautiful organism,
00:11:54.24 which can actually biomineralized silica
00:11:57.00 to form a rigid structure that protects the cell
00:11:59.23 and mediates its interactions with other organisms
00:12:02.16 in the open ocean.
00:12:05.26 Why do choanoflagellates
00:12:08.07 have this combination of the flagellum and the collar?
00:12:11.16 What does that do for the choanoflagellate?
00:12:14.07 Well, let me show you.
00:12:16.00 What you're going to see, this is a movie,
00:12:18.04 and the flagellum is undulating back and forth,
00:12:21.15 and what this does is it actually creates fluid flow,
00:12:24.20 indicated by the arrows, that pulls water
00:12:28.14 along the surface of the collar,
00:12:30.22 and the flagellum pushes water out
00:12:33.25 behind the cell,
00:12:35.20 and so this has two consequences.
00:12:37.25 If the choanoflagellate cell is not attached to anything,
00:12:40.28 the movement of flagellum allows it
00:12:43.25 to swim along through the water column,
00:12:46.23 but that fluid flow also has a second important function,
00:12:49.17 and that is it allows the choanoflagellate
00:12:52.01 to pull bacteria up against the surface of the collar,
00:12:55.01 and so you can see in this picture right here
00:12:58.07 a bacterial cell that's been trapped
00:13:00.18 up against the side of the collar,
00:13:02.12 and so choanoflagellates actually have an important
00:13:04.25 and intimate interaction with choanoflagellates that...
00:13:08.16 errr, sorry, with bacteria...
00:13:10.14 that is essential for their viability.
00:13:13.03 Now, choanoflagellates were actually,
00:13:14.28 although they are not widely known,
00:13:17.04 choanoflagellates were actually first discovered
00:13:19.21 a long time ago, in the mid to late 1800s,
00:13:23.21 and people like Ernst Haeckel and William Saville-Kent
00:13:26.18 were obsessed with choanoflagellates.
00:13:28.29 Saville-Kent actually wrote a large monograph
00:13:32.24 called the Manual of Infusoria,
00:13:34.27 and there are many, many plates dedicated to the choanoflagellates,
00:13:38.23 showing their incredible diversity.
00:13:41.07 And, one of the things that excited Saville-Kent
00:13:44.00 about choanoflagellates
00:13:46.03 was that, to his eye,
00:13:48.15 they were completely indistinguishable
00:13:50.25 from another group of cells that he saw
00:13:53.01 in the natural world, and that was in sponges.
00:13:56.03 So, he noticed this similarity
00:13:58.07 between the morphology of choanoflagellates
00:14:00.09 and the morphology of sponges,
00:14:02.23 and from that he made the argument that
00:14:05.04 choanoflagellates and sponges might be closely related,
00:14:07.28 and you can see that similarity, I think,
00:14:10.09 even more clearly in this electron micrograph,
00:14:16.01 in which you can see, again, a choanoflagellate cell
00:14:18.22 with its cell body, its collar, and its flagellum,
00:14:22.06 and here you can see, in SEM,
00:14:25.15 a group of choanocytes,
00:14:27.25 that's the name for the collar cells in sponges,
00:14:30.21 arranged in a circle, and they're doing the same thing.
00:14:33.29 They're actually creating fluid flow to capture bacteria.
00:14:37.26 And, I think the power...
00:14:41.07 or the organization of these choanoflagellates,
00:14:44.00 or sorry choanocytes,
00:14:46.08 into this choanocyte chamber
00:14:48.14 is actually a very nice demonstration
00:14:50.22 of what happens when an organism becomes multicellular.
00:14:54.23 And so, an example of this,
00:14:56.18 I'm going to just show you in this movie,
00:14:59.01 is that the coordinated action of collar cells in sponges
00:15:03.14 allows for tremendous fluid flow.
00:15:06.19 And so, what you're going to see in this movie,
00:15:09.11 taken by PBS,
00:15:12.26 is that a diver comes in
00:15:15.13 and releases a cloud of fluorescent water
00:15:19.17 just near a sponge,
00:15:21.28 and now watch what the sponge can do with this,
00:15:24.04 just through the movement and activity of choanocytes.
00:15:28.06 So, the diver comes in,
00:15:30.12 this fluorescent dye is released near the sponge,
00:15:33.00 and now as the camera pan back you see that the sponge,
00:15:35.22 which we think of as a very simple organism,
00:15:38.17 is creating coordinated fluid flow
00:15:41.19 and sponges, through this action, are able to
00:15:44.10 capture enormous amounts of bacteria out of the water column.
00:15:50.25 So, choanoflagellates and sponges
00:15:53.20 are using an indistinguishable cell type
00:15:56.13 to capture bacteria out of the water column,
00:15:59.12 and it turns out that cells that resemble
00:16:02.12 choanocytes and choanoflagellates
00:16:04.12 are actually also found in other groups of organisms,
00:16:06.20 including in the form of epithelia and sperm.
00:16:10.04 When we map the distribution
00:16:12.14 of these types of cells, the collar cells,
00:16:14.20 onto a phylogenetic tree,
00:16:16.21 we can infer that because collar cells
00:16:19.27 are widespread within animals
00:16:22.01 and they're also found in all choanoflagellates,
00:16:24.17 then we can reasonably make an inference
00:16:26.24 that choanocytes and collar cells
00:16:29.03 were also present in their last common ancestor.
00:16:31.21 And we can also compare other features
00:16:33.21 of the biology of choanoflagellates and animals
00:16:36.11 within the context of a phylogenetic tree
00:16:38.21 and that brings us to a very exciting point,
00:16:41.00 which is that we can start to make
00:16:43.06 specific inferences about the cell biology
00:16:45.10 and life history of the first animals.
00:16:48.01 So, in this schematic,
00:16:49.21 what I'm showing you is what we now infer
00:16:53.01 to have been the case for the biology of the first animals.
00:16:56.18 We think that it had a simple epithelium,
00:17:00.08 this planar sheet of cells.
00:17:02.24 We think those cells were adhering tightly to each other.
00:17:06.21 We think that some of those cells, at least,
00:17:09.03 were capable of differentiating into collar cells
00:17:11.22 and, importantly, that those cells
00:17:14.02 were actually eating bacteria.
00:17:16.08 So, the first animals were bacterivorous.
00:17:19.13 We think that the first animal
00:17:22.00 also was capable of undergoing apoptosis,
00:17:24.01 or programmed cell death,
00:17:25.29 and that there were different cell types in the first animal,
00:17:28.18 indicative of cell differentiation within the soma.
00:17:33.01 Moreover, it's become clear,
00:17:35.13 by looking at the distribution
00:17:39.16 of different modes of sexual reproduction,
00:17:41.14 sperm and egg in animals,
00:17:44.02 it's become clear that the first animal
00:17:46.26 from which all living animals evolved
00:17:48.26 was capable of undergoing gametogenesis,
00:17:52.05 and that it produced differentiated eggs and sperm
00:17:55.21 and that these merged, in a process of fertilization,
00:17:58.24 to produce a zygote,
00:18:00.29 and then that zygote underwent multiple rounds of cell division
00:18:03.29 and cell differentiation
00:18:05.28 to produce this adult form that I just told you about.
00:18:08.11 So, I think this is an exciting time in which we're starting
00:18:11.19 to see the power of comparative biology,
00:18:13.27 and we can compare the cell biology of choanoflagellates
00:18:16.22 to animals
00:18:18.19 and start to really make specific inferences
00:18:20.16 about the biology of their last common ancestor.
00:18:24.02 Moreover, with the advent of genomic approaches,
00:18:28.02 we can start to learn something
00:18:30.11 about the genome of this organism.
00:18:34.00 Now, choanoflagellates
00:18:36.11 have really been relatively poorly studied
00:18:38.24 by molecular biologists.
00:18:40.18 There was this flurry in the mid-1800s
00:18:43.01 in which people were spending a lot of time
00:18:45.10 looking at and thinking about choanoflagellates
00:18:47.23 and then they were relatively forgotten
00:18:49.23 within the world of molecular biology,
00:18:52.22 and during the molecular biology revolution.
00:18:56.01 And so, one of the first things I did
00:18:58.13 when I started studying choanoflagellates
00:19:00.27 was to collaborate with the Joint Genome Institute
00:19:03.00 and the Broad Institute
00:19:04.17 to sequence the genomes of two different choanoflagellates,
00:19:06.27 Monosiga brevicollis,
00:19:08.23 which so far we have only seen in unicellular form,
00:19:11.14 and S. rosetta, which can be single-celled or colonial.
00:19:15.12 These genomes have a modest number of genes,
00:19:19.05 between 9-12000 genes in their genomes,
00:19:22.03 and we can compare the composition
00:19:24.08 of those genomes with animal genomes
00:19:26.14 to make inferences about the genome of their last common ancestor.
00:19:29.22 In addition, we've recently started sequencing
00:19:34.16 the transcribed and translated genes
00:19:38.23 in the genomes of twenty other
00:19:42.10 additional choanoflagellates that are in culture,
00:19:45.07 and I just want to make the point that
00:19:47.15 there's a lot of diversity in choanoflagellates,
00:19:49.19 and by surveying the genomes
00:19:52.05 of many, many different choanoflagellates
00:19:53.28 we're starting to get an increasingly complete
00:19:56.01 and complex picture
00:19:58.07 of what the genomic landscape of animal origins
00:20:00.18 might have been.
00:20:02.06 Now, I'm not going to tell you about
00:20:04.03 all of the different genes that are found in that ancestral genome,
00:20:06.14 but I do want to summarize some of the exciting findings.
00:20:10.03 When we analyzed these genomes,
00:20:13.03 we particularly focused on genes
00:20:16.06 whose functions are required for
00:20:19.26 animal multicellularity and animal development,
00:20:22.03 and in particular we focused on genes that are required
00:20:24.18 for cells to adhere to each other,
00:20:26.19 genes that are involved in cell signaling,
00:20:28.13 that is, allowing cells to talk to each other
00:20:30.08 and coordinate their functions,
00:20:32.16 genes that are required for gene regulation,
00:20:34.25 which allows one cell to differentiate
00:20:36.19 its function from the other,
00:20:38.25 and genes that are involved in interactions
00:20:41.07 with what's called the extracellular matrix, the ECM,
00:20:44.08 and these are the genes and proteins
00:20:46.16 whose functions allow cells to create this matrix,
00:20:50.27 this structure that provides a landing spot
00:20:54.27 and scaffold for cell-cell interactions.
00:20:57.21 So, we can think about these as being essential functions
00:21:00.00 for animal multicellularity.
00:21:02.17 Many of the genes that are required for these processes
00:21:04.17 in animals
00:21:06.19 had not previously been found in a non-animal before,
00:21:09.14 and now we can ask, if we look at choanoflagellates,
00:21:12.06 what does that tell us about the ancestry of these genes?
00:21:15.15 Are they really animal-specific?
00:21:17.10 Or, might some of these genes
00:21:19.06 have evolved earlier to serve other functions?
00:21:21.24 Now, remember,
00:21:23.04 we have to do this within a phylogenetic framework,
00:21:25.06 and so we're going to ask two different questions.
00:21:29.00 If we are focused on these classes of genes,
00:21:31.14 what fraction of them seem to be restricted to animals?
00:21:35.04 And, what fraction of them
00:21:37.05 are also in choanoflagellates
00:21:38.22 and therefore, we infer,
00:21:40.15 present in their last common ancestor with animals?
00:21:42.25 Some of these genes might have evolved
00:21:45.02 much earlier in the colonial and unicellular
00:21:48.02 progenitors of animals.
00:21:50.11 So, when we do these types of comparisons,
00:21:53.02 and when we did them, it was really quite exciting.
00:21:56.08 I think it helped to motivate
00:21:58.08 a lot of the future study for choanoflagellates,
00:22:00.15 and that's because choanoflagellates
00:22:03.17 turned out to express many different components of the...
00:22:07.29 or, many different genes that are required
00:22:11.12 for the functions that I was just discussing.
00:22:13.29 So, we can find genes that are required
00:22:16.12 for cell signaling in animals,
00:22:18.08 including things like...
00:22:19.27 it's a bit of a chicken soup,
00:22:21.22 but the GPCRs, these are protein coupled receptors,
00:22:24.02 the receptor tyrosine kinases,
00:22:26.09 proto-oncogenes like Src and Csk.
00:22:29.10 We can also find genes whose functions
00:22:32.07 are both necessary and sufficient for allowing cells
00:22:34.11 to stick together.
00:22:35.28 These include the cadherins and C-type lectins.
00:22:38.01 We can find representatives of various transcription factors
00:22:41.18 that are involved in gene regulation,
00:22:43.03 Myc, p53, and Forkhead,
00:22:45.12 and we even find genes that are involved
00:22:48.13 in forming and coordinating the interactions
00:22:52.24 of animals cells with an extracellular matrix.
00:22:55.13 But, remember,
00:22:57.00 we're finding representatives of these genes
00:22:58.21 in non-animals, the choanoflagellates,
00:23:00.27 and so I think an exciting future area of research
00:23:03.08 is to try to figure out
00:23:05.15 how these genes function in choanoflagellates,
00:23:07.25 and try to make inferences
00:23:10.13 about how they might have functioned
00:23:12.07 in our long-ancient progenitors.
00:23:14.17 Now, it was very exciting to find all these animal genes
00:23:17.06 in choanoflagellates,
00:23:18.29 but I think we all need to agree that choanoflagellates
00:23:21.03 are not animals.
00:23:22.21 So, what makes animals different?
00:23:24.20 And, what is exciting is that these genomic interactions...
00:23:28.22 or, sorry, these genomic comparisons,
00:23:30.24 allow us to learn about
00:23:33.27 what types of genes and genomic innovations
00:23:36.12 might have actually contributed to animal origins.
00:23:38.20 And so, when we look at the gene complement of animals
00:23:42.20 and compare it to choanoflagellates
00:23:44.20 we find that there are some genes
00:23:47.02 that thus far have never been found
00:23:49.13 in a non-animal.
00:23:51.06 And so, these are representatives
00:23:53.11 from each of these different
00:23:56.13 groups of processes as well,
00:23:58.17 and they include important genes involved
00:24:00.17 in developmental signaling,
00:24:02.27 one special class of cadherins,
00:24:05.07 the classical cadherins,
00:24:07.06 that are essential for allowing epithelial cells to interact,
00:24:10.19 important and famous developmental patterning genes
00:24:13.21 like the Hox genes,
00:24:15.17 so far have never been found in a non-animal,
00:24:17.19 and very specialized forms of extracellular matrix components,
00:24:21.00 including the Type IV collagens.
00:24:23.19 So, having genome sequences
00:24:26.22 from living organisms
00:24:28.25 has now allowed us to reconstruct,
00:24:30.28 in increasing detail,
00:24:32.06 the genomic landscape of animal origins.
00:24:36.03 So, what I want to say, then,
00:24:39.17 and what I've tried to say in Part I,
00:24:41.26 is that by studying
00:24:45.07 these previously enigmatic organisms,
00:24:47.27 that had been poorly studied,
00:24:50.16 we're starting to grow and develop
00:24:53.01 a new model for animal origins,
00:24:55.12 and we can study these organisms, now,
00:24:58.15 in a modern context to start to learn
00:25:01.07 about animal origins and details.
00:25:03.14 So, what I've told you in this first section
00:25:06.00 is that choanoflagellates, the study of choanoflagellates,
00:25:08.10 has illuminated the cell biology and genome
00:25:11.14 of the progenitors of animals,
00:25:13.19 and told us that those first animals
00:25:16.09 probably ate bacteria and they had collar cells.
00:25:19.02 And, the second important thing that we've learned
00:25:21.05 by studying choanoflagellates
00:25:23.18 is that a remarkable number of genes
00:25:25.10 required for multicellularity in animals
00:25:27.18 actually evolved before the origin of multicellularity,
00:25:31.19 and an exciting future area of research
00:25:33.25 will be to figure out what those genes were doing
00:25:36.23 before they were required for mediating cell-cell interactions.
00:25:41.23 So, that is the completion of Part I,
00:25:44.20 and in Part II
00:25:47.10 I will tell you about a transition to multicellularity
00:25:49.27 that didn't happen hundreds of millions of years ago,
00:25:52.25 but actually happens every day
00:25:55.25 in one particular choanoflagellate,
00:25:58.00 and I'm going to tell you about how that's regulated.
00:26:01.21 Finally, this work wouldn't have been possible
00:26:04.10 without the help of my past and current lab members,
00:26:07.27 and I'm also very grateful to all the collaborators
00:26:10.20 that made all this work possible.
00:26:13.10 Finally, I'm very grateful
00:26:16.07 for the generous support that's come
00:26:18.13 from the National Institutes of Health,
00:26:20.08 the Gordon and Betty Moore Foundation,
00:26:22.02 the Canadian Institute for Advanced Research,
00:26:24.07 and most recently the Howard Hughes Medical Institute.
00:26:26.10 Thank you very much.
- Julie Theriot iBioSeminar: Cell Motility and the Cytoskeleton
- Kenneth Miller iBioMagazine: Evolution – Why it Matters
- Nicole King iBioSeminar: Choanoflagellates and the origin of animal multicellularity
While fossils sparked Nicole King’s childhood interest in evolution, she realized that the fossil record doesn’t explain fully how animals first evolved from their single celled ancestors. To answer this question, King decided to study modern day choanoflagellates. Choanoflagellates are single celled organisms that can also develop into multicellular assemblages. King first learned about choanoflagellates… Continue Reading
Ken Miller is a Professor of Biology at Brown University where his lab studies membrane structure. Miller is determined to improve the public’s understanding of evolution and he has written numerous articles and spoken widely on this topic. Miller has also written a number of high school and college biology textbooks with co-author Joe Levine. Continue Reading
Julie Theriot attended college at the Massachusetts Institute of Technology, graduating with degrees in Physics and Biology. She pursued graduate training at the University of California, San Francisco, earning her Ph.D. in Cell Biology in 1993. After four years as a Fellow at the Whitehead Institute for Biomedical Research, Theriot moved to Stanford University School… Continue Reading