Session 6: From Prokaryotes to Multicellular Organisms

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
06:58.1 #NAME?
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
21:50.2 #NAME?
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; that’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 It’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
00:09:19.08 independently.
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.