Scientists have wondered for years how the very first life form may have evolved. How did the Earth go from an environment of simple molecules to primitive cells? Dr. Szostak presents evidence for the “RNA world” hypothesis and explains how lipids, nucleotides and amino acids could all have formed from molecules in the early atmosphere if energy (for example lightening) was added. Once formed, these molecules could have been enclosed in a membrane to form a primitive, self-replicating protocell. After several billion years of evolution, prokaryotes ruled the Earth. In a short video clip, Newman explains how ancient rock formations provide insights into the critical role that photosynthesizing bacteria played in the evolution of the Earth’s atmosphere and modern life.
00:00:00.00 My name is Jack Szostak,
00:00:01.25 I'm a Professor of Genetics at Harvard Medical School,
00:00:05.22 I'm an Investigator at Massachusetts General Hospital, where my labs are,
00:00:09.18 and I'm also an Investigator of the Howard Hughes Medical Institute.
00:00:14.17 In this lecture, what I'd like to tell you about is recent advances
00:00:21.06 in work from my lab on the origin of cellular life on the early Earth.
00:00:26.22 But before I get into those experiments,
00:00:29.08 I'd like to step back from the origin of life per se,
00:00:33.08 and talk a little bit about some insights from modern biology
00:00:39.00 that bear on this question,
00:00:41.01 in particular why the question has attracted so much interest and attention recently.
00:00:46.16 So, this is one of the iconic images of hydrothermal deep sea vents.
00:00:56.02 This is an environment characterized by very high temperature and pressure,
00:01:01.21 and of course the surrounding area is just teeming with life.
00:01:07.04 Here's another example: an image from Norm Pace.
00:01:12.04 You can see a layer of green cells growing inside the rock.
00:01:18.07 These are photosynthetic cyanobacteria,
00:01:21.29 and they're living in the pores of the rock at very low pH.
00:01:28.23 This is one of the famous hot springs in Yellowstone National Park.
00:01:34.26 Again, a very high-temperature environment; again, full of life.
00:01:43.29 And here's yet another distinct kind of extreme environment,
00:01:48.21 another very low pH environment.
00:01:50.14 This is the Rio Tinto in Spain.
00:01:53.27 Very acidic water, but again teeming with life:
00:01:59.00 microbial, eukaryotic life.
00:02:04.17 There are even more extreme examples of this kind of environment in acid mine drainage sites,
00:02:12.00 where the water that's flowing out is basically sulfuric acid at a pH close to zero.
00:02:18.24 And again there is microbial life.
00:02:21.11 So with all of these examples,
00:02:22.22 what it's telling us is just the remarkable extent which our planet
00:02:27.21 has been colonized by life.
00:02:31.17 And even environments that we would've considered incredibly hostile and extreme
00:02:38.20 are apparently easily adapted to by life.
00:02:43.10 And of course, this is a consequence of the power of Darwinian evolution,
00:02:48.10 to lead to adaptations to diverse environments.
00:02:53.16 So, if you put this together with recent observations
00:03:00.01 from our astronomy colleagues, in terms of the discovery of extrasolar planets,
00:03:06.02 it really puts into focus the question of whether there is life out there,
00:03:13.13 apart from our planet.
00:03:16.07 So this is an image of the Milky Way, of course.
00:03:22.20 Up to a couple of years ago,
00:03:24.21 astronomers had discovered on the order of 500 extrasolar planets,
00:03:29.04 planets orbiting other stars.
00:03:32.08 But more recently, as a result of the Kepler mission,
00:03:36.00 a space telescope that is just pointed continuously at a very dense starfield,
00:03:45.22 a large number of additional planets have been found,
00:03:48.24 about 1200 candidates at the last count.
00:03:52.28 And these are detected as the planets orbit around their star,
00:03:57.29 and if they eclipse the star, if they transit in front of it,
00:04:00.27 they block out some of the light, and you can detect that little dip in the intensity of the light.
00:04:06.23 So this has given us a big enough sample to actually make extrapolations,
00:04:12.02 and what I've heard from scientists associated with the Kepler mission
00:04:17.17 is that those extrapolations suggest that there could be roughly on the order of
00:04:23.06 500 million, perhaps even a billion, Earth-like planets
00:04:27.00 orbiting sun-like stars out there in our galaxy.
00:04:32.13 And so, if you put that together with the fact that we know,
00:04:37.03 on our planet, that at least microbial life can live in incredibly harsh and diverse environments,
00:04:44.28 it's pretty clear that there will environments out there on
00:04:49.12 these other planets that could support life.
00:04:52.03 So the question is, and the thing we all really want to know is:
00:04:56.01 Is there life out there?
00:04:58.01 Are we alone, or is the universe, is our galaxy, full of life?
00:05:03.15 So this really comes down to the question you see here.
00:05:07.25 Is it easy or hard for life to emerge from the chemistry of early planets?
00:05:14.13 And, unfortunately, it's going to be a long time before we can answer that question
00:05:18.28 in the most satisfying way, by direct observation.
00:05:23.16 Even to get indirect evidence from spectroscopy of planetary atmospheres
00:05:30.27 may take 10, 20, 50 years, to look at Earth-like planets.
00:05:38.28 So what can we do in the meantime to try to get some clues to answer this question?
00:05:46.27 So, what we've been doing, and other people have been doing,
00:05:49.29 is to go into the lab and do simple, chemical experiments
00:05:54.29 and try to work out a complete, step-by-step, plausible pathway,
00:06:02.17 all the way from simple chemistry to more complex chemistry to simple biology.
00:06:08.02 And if we can actually show that there's a continuous pathway
00:06:13.26 with no super-hard steps along the way,
00:06:17.20 then I think we can conclude that it's likely that there is abundant life
00:06:22.14 out there in our galaxy.
00:06:25.03 On the other hand, it could be that our experiments show
00:06:29.14 that there are some steps in that pathway that are extremely difficult,
00:06:35.01 there are bottlenecks that might be very hard to overcome,
00:06:38.29 in which case the emergence of life might actually be a very rare phenomenon.
00:06:44.04 And in the extreme, we could be it.
00:06:47.23 This could be the only place in our galaxy or even the universe where life has emerged.
00:06:53.28 So we would like to try to get some insight into these questions
00:06:58.11 by doing simple laboratory experiments.
00:07:00.20 Now, there's a related question, which is shown down here.
00:07:06.03 If there is life out there,
00:07:07.25 is it likely to be pretty similar to what we're familiar with on our planet?
00:07:16.12 Will life that evolved independently elsewhere have the same
00:07:23.25 fundamental kind of biochemistry?
00:07:25.24 Will it be cells that are living in water,
00:07:29.00 using if not RNA and DNA, some nucleic acid to mediate heredity?
00:07:35.20 Will they use protein-like molecules to carry out biochemical functions?
00:07:41.18 Or could there be forms of life that are actually much different, much more diverse,
00:07:49.14 maybe using completely different kinds of molecules to mediate heredity
00:07:52.25 and to mediate function?
00:07:55.04 Or even forms of life that live in very different environments,
00:08:00.06 for example, in solvents other than water.
00:08:03.23 Again, this is the kind of thing that we can address by going into the lab
00:08:09.17 and doing simple experiments, and trying to build structures,
00:08:12.26 and assess the possibility of having living systems in
00:08:18.09 different kinds of environments and with different molecular bases.
00:08:25.16 So, let's try to think, then,
00:08:30.21 about how we can deduce something about early forms of life.
00:08:37.04 After all, if we want to experimentally investigate the beginnings of life,
00:08:41.26 we have to have some idea, some kind of conceptual model,
00:08:45.22 of what very primitive forms of life looked like.
00:08:50.17 And this has been a very difficult thing for people to think about,
00:08:55.03 because we're so biased by our view and our understanding of modern life.
00:09:00.25 So if we look at modern cells, they're incredibly complicated:
00:09:05.16 Just a lot of moving parts, very elaborate structures,
00:09:09.14 such as you can see here in this elaborate structure in a eukaryotic cell,
00:09:15.15 all the machinery involved in cell division.
00:09:19.00 If you go deeper and look at the underlying biochemistry,
00:09:23.09 if anything, it's even more complicated.
00:09:26.17 And this is just a small section of the chart of central metabolism,
00:09:32.09 so there are hundreds or thousands of enzymes that catalyze
00:09:36.22 all of the metabolic reactions that are required for cells to grow and divide.
00:09:43.10 Even the general organizational structure of modern cells is very complicated,
00:09:51.10 in the sense that it's highly self-referential.
00:09:54.24 So every aspect of this process,
00:09:59.03 this central dogma (the transmission of information from DNA to RNA
00:10:03.10 to proteins and then down to building structures with function),
00:10:08.21 every part of that depends on all the other parts.
00:10:12.12 So for example, the replication of DNA requires DNA,
00:10:16.14 but it also requires RNA and proteins, the polymerases.
00:10:20.11 The transcription of RNA requires DNA,
00:10:25.11 which is where the information's stored, but it also requires many proteins,
00:10:29.21 and it also requires many other RNA molecules.
00:10:33.02 And similarly, the formation of proteins occurs on a remarkably complex machine,
00:10:38.24 the ribosome, which is itself composed of RNA and proteins.
00:10:44.02 So, for decades, it was very hard for people to think of any reasonable way
00:10:51.07 in which such an internally self-referential system could emerge
00:10:57.25 spontaneously from a chemical environment.
00:11:01.16 And the answer to that really came from thinking about RNA
00:11:08.27 and the different things that it can do.
00:11:10.21 So this simplification in thinking came from the realization that RNA can not just
00:11:18.04 carry information but can also catalyze chemical reactions.
00:11:23.15 And that realization led immediately to the hypothesis that,
00:11:29.01 in primitive cells, RNA might be able to catalyze its own replication,
00:11:34.05 also carry out biochemical functions for the primitive cell.
00:11:39.10 And so then all you really need to think about is a cell with RNA molecules
00:11:45.14 encapsulated within some kind of primitive cell membrane
00:11:48.25 that itself could be a self-replicating structure.
00:11:52.08 So, the history of this idea actually goes back to the 1960s,
00:11:58.24 and three very smart people, Leslie Orgel, Carl Woese, Francis Crick,
00:12:05.05 hypothesized in part on the basis on the complex folded structure of tRNA,
00:12:13.01 that an early stage of life might've evolved RNA as the
00:12:19.01 sole macromolecular basis of evolved machinery.
00:12:24.25 And so, this lets you think of simple cells emerging with just a single biopolymer,
00:12:31.19 RNA, and that later on, as evolution
00:12:38.03 developed more complex cellular structures, information storage
00:12:42.14 became specialized in DNA,
00:12:44.18 and most functional activities because specialized as the job of proteins.
00:12:51.06 Now, although these ideas were put forth in rather elementary form in the 60s,
00:12:56.14 of course nobody took them seriously at the time,
00:12:59.21 because there was absolutely no experimental evidence for the idea
00:13:04.08 that RNA could catalyze chemical reactions.
00:13:06.23 At the time, people had just started to get very detailed,
00:13:11.19 high-resolution information about how proteins catalyzed reactions,
00:13:16.13 and the idea that a molecule like RNA could do the same thing seemed ludicrous.
00:13:22.26 So it wasn't until almost 20 years later,
00:13:25.05 with the work of Tom Cech and Sid Altman,
00:13:29.10 and the experimental demonstration that RNA molecules could actually
00:13:34.02 very effectively catalyze at least certain types of chemical reactions,
00:13:38.14 that people took this whole idea of an RNA-based early stage of life seriously.
00:13:45.00 And so that hypothesis, the "RNA world hypothesis,"
00:13:48.23 was really summarized by Walter Gilbert in an article in 1986,
00:13:57.18 and this has really become the foundation of a lot of thinking
00:14:02.12 about early stages in the emergence of life.
00:14:08.01 So, apart from the basic facts,
00:14:11.20 that RNA does and can catalyze chemical reactions,
00:14:15.04 is there any other evidence that early life might have been
00:14:19.17 based more exclusively on nucleic acids?
00:14:24.21 And in fact, there are several lines of circumstantial evidence.
00:14:28.24 So one of them is the structure of many cofactors.
00:14:33.07 So here you see acetyl-CoA, just one example.
00:14:39.03 But the working part of the molecule is the thioester out here,
00:14:43.27 and for no obvious reason, there's a nucleotide at the other end.
00:14:48.13 And really the only way to make sense of that is the nucleotide is a "handle,"
00:14:53.11 either a relic of a primitive ribozyme
00:14:56.24 or something that was easy for primitive ribozymes to grab hold of and thereby,
00:15:04.10 using this cofactor, catalyze reactions in a thioester-mediated way.
00:15:11.14 Now there are other examples.
00:15:14.21 Here is vitamin B12, another very important catalyst.
00:15:20.24 Its working part is this complex corrin ring,
00:15:25.07 but down here you see, again, a nucleotide.
00:15:29.22 What's it doing there?
00:15:30.28 It's probably another relic of the RNA world,
00:15:34.02 when all of this complicated biochemistry was being catalyzed by RNA enzymes.
00:15:40.12 Yet another example is the very way that the substrates for
00:15:45.25 DNA synthesis are made, and they're not made de novo,
00:15:50.29 as you might expect if DNA came first.
00:15:53.27 They're actually made from preexisting ribonucleotides,
00:15:58.02 and so the transformation of ribonucleotides to deoxynucleotides
00:16:03.17 is catalyzed by the enzyme ribonucleotide reductase.
00:16:08.13 And this unusual synthetic pathway can be viewed as the relic of the fact that,
00:16:17.04 early in time, metabolism and RNA synthesis used ribonucleotides,
00:16:23.25 and only later when DNA was invented or evolved,
00:16:29.10 was there was requirement to make deoxynucleotides,
00:16:32.15 and so they're from the closest available substrate.
00:16:38.03 Finally, perhaps the most important and dramatic piece of evidence
00:16:44.14 for the early role of RNA in primitive forms of life
00:16:50.06 is the actual structure of the ribosome.
00:16:53.21 And so this is a slide from Tom Steitz showing a
00:16:57.27 view into the active site of the large subunit.
00:17:02.23 So this is the peptidyl transferase center,
00:17:05.06 and this little green structure in here is a transition state analogue
00:17:09.17 that marks it at the place in this giant machine where the chemistry is happening.
00:17:14.28 And what you can see is that it's these gray squiggles,
00:17:17.29 which are the RNA, that completely make up that active site.
00:17:23.23 So all proteins are generated by an RNA machine,
00:17:29.19 the RNA central region of the ribosome itself.
00:17:34.25 So again, this only makes sense in terms of an early stage of biochemistry
00:17:40.00 dominated by RNA functions, which then over time evolved the ability
00:17:45.15 to make proteins, which are now so important in all modern biochemistry.
00:17:52.05 So, if we want to understand the origin of life,
00:17:57.03 what we need to think about is not simply how to make
00:18:02.14 these incredibly complex modern cells, but we need to think about how to go from chemistry
00:18:07.23 to very simple, RNA-based cellular structures.
00:18:13.08 So, what would the process look like?
00:18:16.04 What's the broader picture?
00:18:17.17 When did this all happen on the early Earth?
00:18:20.17 So, what was the timeframe in which these events took place?
00:18:25.07 This is a slide from a review by Gerald Joyce, and it summarizes
00:18:30.02 the broad sweep of events that were important in the origin of life.
00:18:34.20 So we actually need to think of everything from planet formation,
00:18:38.14 the beginning of the Earth itself around 4.5 billion years ago;
00:18:44.07 over time as the Earth cooled, water could condense,
00:18:48.01 we have a stable hydrosphere, we have liquid water on the surface;
00:18:52.06 following that, increasingly complicated organic chemistry going on,
00:18:57.08 probably in many different environments on the early planet;
00:19:01.00 and then somehow that led up to the synthesis of RNA
00:19:06.09 or RNA-like molecules on the Earth,
00:19:09.13 which could start to carry out biochemical functions inside primitive cells;
00:19:14.24 and then eventually lead to the emergence of much more complicated cells
00:19:19.29 that would be biochemically similar to modern life.
00:19:23.14 Now, the first really good evidence we have about
00:19:27.04 the appearance of modern microbial life is roughly 3.5 billion years ago,
00:19:33.17 so there's a billion-year interval between the formation
00:19:38.17 and cooling of the planet and the first good evidence for life.
00:19:43.21 And basically, we have very little hard evidence about
00:19:48.00 where all of these important events that led up to life emerging from chemistry,
00:19:53.01 when they actually happened.
00:19:55.03 And that goes along with the fact that we have very little concrete evidence
00:19:59.25 concerning the environments in which those transitions took place.
00:20:04.27 So, this is one of the difficult aspects of studying this question.
00:20:09.12 We can't actually go back,
00:20:10.28 we can't know for sure what the early environments were really like,
00:20:16.13 we'll never know exactly what really happened.
00:20:19.15 So what's our goal in studying these questions?
00:20:23.00 What we're trying to do is really come up with a plausibly realistic
00:20:29.16 sequence of events so that we understand all of the transitions
00:20:35.00 throughout this whole pathway,
00:20:37.05 and we'd like to understand a complete pathway,
00:20:38.29 from planet formation through early chemistry,
00:20:41.28 more complicated organic chemistry,
00:20:44.05 up to the assembly of those building blocks into the first cells,
00:20:48.29 the emergence of Darwinian evolution,
00:20:51.04 and then the gradual complexification of early life leading up to what we see now.
00:20:58.10 So, let's look a little bit more closely at the chemical steps.
00:21:03.23 So in broad outline, what we think happened is that you
00:21:07.17 start off with very simple molecules such as shown up here.
00:21:14.02 There's still a lot of debate about the nature of the early atmosphere.
00:21:20.00 Scientific opinions have gone back and forth in terms of
00:21:23.09 the structure and how reducing that atmosphere was.
00:21:27.26 But it's also been recognized that there could be very important local variation,
00:21:32.22 so even if the atmosphere was globally fairly neutral
00:21:38.20 or perhaps mildly reducing or mildly oxidizing,
00:21:41.16 there could be local environments that were more reducing.
00:21:46.14 That, together with the input of various forms of energy
00:21:51.21 (for example, from electric discharges, lightning,
00:21:56.06 high-energy ultraviolet radiation, ionizing radiation)
00:22:01.08 these are all forms of very energetic processes that can basically
00:22:06.15 rip these small starting molecules apart into atoms,
00:22:11.26 which can then recombine to generate high-energy intermediates
00:22:15.17 with multiple bonds, molecules like cyanide and acetylene,
00:22:20.19 formaldehyde and so on.
00:22:22.18 And these molecules can then start to interact with each other
00:22:26.20 and gradually build up more complex intermediates,
00:22:29.13 ultimately leading to the things we really care about:
00:22:33.10 the lipids that will make membranes and vesicles,
00:22:37.25 the nucleotides that will assemble into genetic molecules like RNA,
00:22:42.16 amino acids that can assemble into peptides,
00:22:45.29 which may also play roles in primitive cells.
00:22:49.10 And somehow, and this is the question that my lab has really been focused on,
00:22:53.12 somehow all of these molecules come together
00:22:56.17 and assemble into larger structures that look and act like cells
00:23:01.10 that can grow and divide.
00:23:04.04 So how could that possibly happen,
00:23:06.17 and what would such a primitive cell look like?
00:23:09.24 So here is a schematic version of the way that we're thinking
00:23:13.21 about a primitive cell, or "protocell."
00:23:17.11 So what we think are the important components of a primitive cell
00:23:22.14 are basically two things:
00:23:25.01 a cell membrane and inside,
00:23:28.10 some kind of genetic material, maybe RNA, maybe DNA,
00:23:32.05 maybe something simpler, something more stable, we're not really sure.
00:23:37.12 So the first question is how could you assemble such composite structures?
00:23:43.23 So we want to be have a membrane boundary
00:23:46.13 that can keep important molecules encapsulated within
00:23:51.06 and essentially provide a distinction between the cell itself
00:23:54.22 and the rest of the universe.
00:23:57.05 We need to understand how these two components self-assemble,
00:24:02.09 how they come together.
00:24:04.07 And it actually turns out that that part is all fairly straightforward.
00:24:09.26 Self-assembly processes are critical in thinking about all of the steps,
00:24:15.12 and there are multiple different ways in which these components
00:24:19.06 can be made and can come together.
00:24:22.08 A much harder question and more interesting is:
00:24:28.08 Once you have structures like this,
00:24:30.16 how can they grow and then divide without any of the
00:24:34.17 complicated biochemical machinery that's present in all of modern life?
00:24:40.25 So since we're talking about the origin of life,
00:24:43.00 then by definition we didn't have highly evolved biochemical machinery around.
00:24:48.21 So it's sometimes hard to think about these problems
00:24:51.17 because modern cells use so much biochemical machinery
00:24:56.11 to mediate the process of cell growth and cell division.
00:25:00.12 It's almost hard to think of how could that be driven
00:25:06.04 by simple chemical and physical processes.
00:25:10.07 But that's in essence what we need to figure out
00:25:13.00 in order to understand this process.
00:25:15.07 There's no machinery around,
00:25:16.18 so we have to identify the chemical and physical processes
00:25:20.14 that will drive growth and then mediate cell division.
00:25:25.11 So that applies not only to the membrane,
00:25:27.11 but also the genetic material, whether it's RNA or something else.
00:25:31.13 There have to be simple chemical processes
00:25:35.16 that will drive the copying of that information,
00:25:38.12 that will allow the strands to separate
00:25:41.06 so that another round of copying can take place,
00:25:44.05 and that will allow that replicated material to be distributed into daughter cells.
00:25:50.10 So if we can identify chemical and physical processes that do all of that,
00:25:56.25 we would have a situation where essentially the environment
00:26:00.03 is driving a cycle of growth and division
00:26:04.15 that brings us back to this stage,
00:26:07.05 and you can go around and around that cycle again and again,
00:26:12.05 and that would be just very similar to the way in which
00:26:16.22 modern cells grow and divide.
00:26:18.23 The information within would be propagated and transmitted
00:26:22.23 from generation to generation,
00:26:25.08 and the important thing in terms of the emergence of Darwinian evolution is that,
00:26:31.00 during that continuous process of replication,
00:26:35.07 of course mistakes would be made.
00:26:38.18 Over time, more and more of sequence space would be surveyed,
00:26:43.28 and eventually we think, some sequence would emerge that did something
00:26:48.03 useful for the cell as a whole.
00:26:50.14 As soon as that happened, that sequence,
00:26:54.00 by conveying an advantage to its own cell,
00:26:57.24 whether in terms of growth rate or the efficiency of cell division
00:27:03.00 or the efficiency of survival,
00:27:05.22 it would have an advantage and it would gradually over generations
00:27:08.28 take over the population.
00:27:11.09 And so that is really the essence of Darwinian evolution.
00:27:15.05 You have a change in the genetic structure of the population as a result of natural selection.
00:27:21.01 And that is precisely what we would like to see
00:27:24.03 emerge spontaneously in our laboratory experiments.
00:27:27.17 We want to start with a chemical system
00:27:30.18 and watch it transition into the emergence of real Darwinian
00:27:35.18 evolution at a very simple level.
00:27:39.20 So, let's step back again and think about how all of these
00:27:43.25 molecules would be made in the environment of a primitive planet.
00:27:49.02 And of course, the first breakthrough in this research program
00:27:54.03 was the famous Miller-Urey experiment,
00:27:57.23 in which a mixture of reducing gases was subjected to an electric spark discharge,
00:28:02.10 and the products were analyzed.
00:28:04.12 And amazingly, in that mix of products were many of the amino acids,
00:28:11.19 which are major components of the proteins of modern cells.
00:28:16.28 So that was really a revelation.
00:28:19.29 It really took people by surprise that the building blocks of biological structures
00:28:28.05 could be generated in such an easy manner.
00:28:33.01 Now, in fact that result was so powerful
00:28:36.08 that it might have actually been a little bit distracting.
00:28:40.15 Probably the really important thing that's made
00:28:43.19 in this kind of experiment is not amino acids per se,
00:28:48.03 but high-energy intermediates like cyanide and acetylene.
00:28:53.06 Those are the kinds of molecules that can assemble in
00:28:57.25 subsequent steps into nucleotides, the building blocks of genetic materials.
00:29:07.16 Those molecules are thought to have been made in primitive environments,
00:29:14.11 so that was an electric discharge experiment,
00:29:16.08 which is very analogous to the kinds of lightning displays
00:29:21.12 that you get in volcanic scenarios.
00:29:24.12 So this is the lightning that's going on in the ash cloud
00:29:29.14 of a currently erupting volcano in southern Chile.
00:29:34.02 So since the early Earth was thought to be highly volcanically active,
00:29:38.15 this seems like a very reasonable scenario.
00:29:42.13 What about some of the other molecules that we need
00:29:44.22 to build our primitive early cell?
00:29:50.29 We need to have lipid-like molecules, amphiphilic molecules
00:29:55.29 that can self-assemble into membranes and generate compartments spontaneously.
00:30:00.16 So these are molecules that are amphiphilic:
00:30:03.07 They have one part that likes to be in water,
00:30:05.26 and another part that doesn't like to be in water.
00:30:09.11 And the way that those preferences are balanced
00:30:12.29 is by forming membranes in which the nonpolar parts are on the inside
00:30:17.29 and the polar parts of the molecule face out into the water.
00:30:21.16 So it turns out that it's actually, again,
00:30:24.19 very easy to make molecules like that in a variety of different scenarios.
00:30:30.02 In fact, Dave Deamer and his colleagues showed that you can
00:30:34.08 extract molecules from the Murchison meteorite
00:30:37.11 (it's one of these carbonaceous chondrite meteorites that's rich in organic materials),
00:30:41.23 you can extract molecules that will self-assemble into a vesicle,
00:30:46.10 as you can see here.
00:30:48.04 So they spontaneously make membrane sheets that close up into small vesicles.
00:30:53.19 Here's another example.
00:30:56.00 This is an experiment that was done to
00:31:00.11 mimic processes going on in interstellar molecular clouds,
00:31:05.03 where you have various gasses that have condensed
00:31:07.22 on the surface of silica particles.
00:31:10.11 They're subjected to irradiation by ultraviolet light and ionizing radiation.
00:31:16.03 So if you make ices like that in the laboratory,
00:31:19.18 subject them to ultraviolet radiation,
00:31:22.29 you get a lot of complicated chemistry going on,
00:31:25.01 and then in that vast mix of products,
00:31:28.28 you can extract molecules which again will form membranes
00:31:32.01 and self-assemble into these vesicle compartments.
00:31:37.10 Here is yet another scenario.
00:31:39.03 This is a hydrothermal synthesis done by Bob Hazen and Dave Deamer.
00:31:46.05 Again, in hydrothermal processing,
00:31:50.00 you can grow carbon chains with oxygenated groups
00:31:55.05 such as carboxylates at the end,
00:31:57.05 and these self-assemble into membranes and make many compartments,
00:32:02.03 as you can see in this beautiful image.
00:32:05.29 So, what would be an example of an early Earth
00:32:09.29 environment where something like this could take place?
00:32:14.03 There are a series of experiments from the Simoneit Lab that
00:32:19.14 suggest that hydrothermal synthesis could happen deep down
00:32:24.28 in regions with high temperature and high pressure,
00:32:29.25 on the surface of catalytic minerals such as transition metal sulfides or oxides,
00:32:35.27 and those reactions would basically turn hydrogen and carbon monoxide
00:32:40.27 into fatty acids and related compounds.
00:32:45.05 So the next slide here is a movie that was prepared by Janet Iwasa,
00:32:50.29 that illustrates this process.
00:32:52.15 So we're going deep into the Earth,
00:32:54.23 down through the water channels of a geyser,
00:32:59.00 and here we're looking at the surface of these catalytic transition
00:33:03.28 metal minerals, and you can see hydrogen and carbon monoxide molecules
00:33:08.24 bouncing around the surface, and the mineral is catalyzing
00:33:13.11 their assembly into chains, which eventually will be released and float up,
00:33:21.00 and they'll be caught up in the flow of water
00:33:23.02 and thereby brought to the surface, where you can imagine these fatty acids,
00:33:28.15 fatty alcohols, and related molecules being aerosolized
00:33:32.22 and concentrated in droplets and perhaps even
00:33:35.20 building up into large deposits on the land surface.
00:33:41.05 So it doesn't seem like the prebiotic assembly of molecules
00:33:46.07 that could spontaneously form membrane vesicles is all that difficult.
00:33:53.03 It's definitely an understudied area of prebiotic chemistry, it needs more work,
00:33:57.16 but it looks, I think, reasonably plausible.
00:34:01.13 So the most prebiotically likely molecules
00:34:04.15 would be things like capric acid that you see down here.
00:34:08.24 Short chain, saturated fatty acids.
00:34:12.15 So we do experiments in the lab with molecules like this,
00:34:16.28 but we also use longer chain, unsaturated molecules
00:34:22.07 like myristoleic acid and oleic acid,
00:34:25.05 as model systems because they're just generally easier to work with.
00:34:29.16 So what happens if you just take one of these fatty acids
00:34:34.20 and shake it up in water with some salt and buffer?
00:34:38.06 Is it hard to make membranes? No.
00:34:40.20 What you can see if that you just spontaneously make vesicles
00:34:47.27 in a huge variety of complex structures, a huge range of sizes,
00:34:53.25 all the way from 30 microns (this large vesicle)
00:34:57.19 to many, many smaller vesicles ranging down to 30 nanometers.
00:35:02.29 Many of these vesicles are composed of multiple sheets of membrane,
00:35:08.04 so stacks of membranes.
00:35:10.04 You can see some of these vesicles have smaller vesicles inside them.
00:35:14.17 So it's a very heterogeneous, complex mixture.
00:35:19.29 Now, the other thing that's really important about this is that these vesicles,
00:35:25.25 these membranes, have very, very different properties
00:35:29.02 from modern biological membranes.
00:35:31.26 Modern membranes are basically evolved to be good barriers,
00:35:37.09 so that cells can control the flow of all molecules in and out
00:35:42.04 using complicated protein machines.
00:35:47.26 For a primitive cell, you wouldn't want a situation like that...
00:35:51.03 that would be suicidal.
00:35:52.15 These molecules have to let stuff get across,
00:35:55.03 they have to have dynamic properties
00:35:56.26 that can let them grow and equilibrate.
00:36:00.16 So the next slide is actually a movie, again prepared by Janet Iwasa,
00:36:05.13 to illustrate the dynamic properties of these vesicles,
00:36:09.29 which are so different from modern membranes.
00:36:13.06 And so what you can see here is, first of all,
00:36:15.08 the motion on the surface, a lot of oscillations, diffusion.
00:36:20.27 In the membrane itself, these molecules, the individual molecules
00:36:25.05 are rapidly flip-flopping back and forth from inside to outside,
00:36:29.23 they're constantly entering the membrane, leaving the membrane,
00:36:34.16 so there's a lot of exchange reactions that are
00:36:37.29 going on on very rapid timescales, on the order of a second or less.
00:36:42.23 So they're very dynamic structures.
00:36:44.23 And these dynamic motions are also probably
00:36:49.09 very important in terms of permeability.
00:36:51.26 They allow the formation of transient defects in the membrane,
00:36:55.20 which let molecules get across spontaneously
00:36:58.21 without any complicated machinery.
00:37:02.19 There's another property of these vesicles which I find quite fascinating.
00:37:09.02 So as you saw in the illustration, the molecules that make up
00:37:12.28 any given vesicle come and go and therefore exchange between vesicles
00:37:19.07 on the timescale of roughly a second.
00:37:22.09 In this slide what you see are two populations of vesicles
00:37:25.16 that were labeled with phospholipid dyes,
00:37:28.18 so they're not exchanging between vesicles.
00:37:31.18 The picture here was taken after about a day,
00:37:35.18 and so you can see that they haven't all just fused and mixed up,
00:37:39.01 there are still red vesicles and green vesicles.
00:37:42.11 And yet we know from our other experiments that the molecules
00:37:45.27 that make up any one of these vesicles are changing
00:37:50.29 on a very rapid timescale, yet the structures themselves
00:37:54.23 maintain their identity on the timescale of weeks or months.
00:38:02.03 What about the nucleic acids then?
00:38:05.05 We've talked a lot about the building blocks of membranes,
00:38:07.27 the way they self-assemble,
00:38:09.12 and the properties of the membranes that they assemble into...
00:38:12.27 let's go back to the genetic materials and think about
00:38:15.21 what kinds of building blocks we need to assemble molecules like RNA.
00:38:22.06 Now, again, we have a difference between the molecules used in modern life...
00:38:28.12 so these of course are nucleoside triphosphates,
00:38:32.11 they're almost ideal substrates for a highly evolved cell
00:38:37.13 with very, very powerful catalysts.
00:38:41.15 These molecules are kinetically trapped in a high-energy state.
00:38:47.13 They don't spontaneously act very well at all,
00:38:51.29 so it takes a very sophisticated catalyst to
00:38:54.27 use molecules like this as a substrate.
00:38:57.26 They're also of course very polar, the triphosphate group is highly charged,
00:39:02.16 and that prevents these molecules from leaking out of the cell,
00:39:06.23 which would be a bad thing.
00:39:08.14 On the other hand, in a primitive cell,
00:39:11.19 if you imagine that substrates, food molecules,
00:39:15.05 are being made in chemical processes out in environment,
00:39:19.15 it needs to be possible for those molecules to get across the membrane
00:39:23.17 spontaneously and get into the interior of the cell.
00:39:27.18 So then we to think about different kinds of substrates,
00:39:31.19 molecules that are less polar so they can get into the cell,
00:39:36.25 and more chemically reactive, so that they can polymerize without the need
00:39:43.15 for very sophisticated, advanced, highly evolved catalysts.
00:39:47.24 And so molecules like this were first made by Leslie Orgel
00:39:52.20 and his students and colleagues 20-30 years ago,
00:39:57.13 and studied in quite a bit of detail as models for the early replication of RNA.
00:40:06.17 So, this brings us back to the question of
00:40:12.02 what was the first genetic material?
00:40:14.17 Was it RNA, in fact?
00:40:17.14 Or is RNA so complicated,
00:40:19.24 or its building blocks so hard to make,
00:40:23.03 that life more likely began with something simpler,
00:40:27.18 something easier to make,
00:40:29.12 maybe something more stable that could accumulate,
00:40:31.24 like DNA for example?
00:40:34.16 So this is an area of active debate and investigation,
00:40:39.10 we really don't know the answer to this question,
00:40:43.13 but lots of people are doing experiments and trying
00:40:45.22 to work out chemical pathways leading up to RNA,
00:40:49.09 for example, the Sutherland Lab in the UK has made a lot of progress in this area.
00:40:55.16 We're studying how these molecules could be assembled and replicated.
00:41:01.27 So one of the satisfying thinks about thinking about RNA
00:41:04.22 as the first genetic material,
00:41:06.10 is that we actually have two different chemical physical processes
00:41:12.29 that can lead to the polymerization of activated building block
00:41:17.01 into long RNA chains.
00:41:19.16 The first of these was discovered by Jim Ferris, working with Leslie Orgel,
00:41:26.27 and that was the discovery that a common clay mineral
00:41:30.20 known as montmorillonite can catalyze the assembly of
00:41:34.19 nucleotides into RNA chains.
00:41:37.04 So this illustrates the structure of this clay,
00:41:39.25 it's a layered hydroxide mineral.
00:41:43.03 In between the layer, the aluminum silicate layers,
00:41:47.21 there's water, and in these inner layers,
00:41:50.27 organic molecules can accumulate, and when they're brought close together,
00:41:54.23 they can react each other and start to polymerize.
00:41:58.25 So here is some of the experimental data.
00:42:01.29 So over a period of days, you start off with small chains,
00:42:07.08 and then gradually they get longer and longer, up to lengths of roughly 40,
00:42:12.18 and in more recent experiments up to 50 or 60, nucleotides long.
00:42:17.27 So I wanted to illustrate that with this movie,
00:42:20.16 another one of Janet Iwasa's animations,
00:42:24.16 to show roughly how we think this works.
00:42:27.15 So these chemically activated building blocks like to stick to the
00:42:31.13 surface of the clay mineral,
00:42:33.20 and when they stick in such a way that they're lined up with each other,
00:42:38.05 they can react and assemble a chemically linked backbone,
00:42:43.16 as you see here.
00:42:47.28 Now, there is another process that can do that same thing,
00:42:51.05 which is very interesting because it's so counterintuitive.
00:42:54.05 It turns out if you take these same building blocks and just have them
00:42:57.29 in a dilute solution and put that on your bench, nothing happens.
00:43:03.10 But if you take that same solution and put it in the freezer
00:43:07.08 and then come back the next day, you'll find RNA chains.
00:43:11.20 Why is that?
00:43:13.09 It's because when water freezes and forms ice crystals,
00:43:16.26 that during the growth of the ice crystals,
00:43:19.12 other molecules (solutes) are excluded from the growing crystal,
00:43:23.23 and so they end up concentrated as much as a thousand fold
00:43:27.21 in between the grains of ice,
00:43:31.04 and so when they're so concentrated, again they can react and polymerize.
00:43:35.08 So having two different processes that can lead the assembly of
00:43:38.23 RNA chains is actually a very satisfying thing...
00:43:41.29 that's something we look for in this field,
00:43:43.29 if there's more than one way of solving a problem,
00:43:47.04 it makes the whole solution seem more robust.
00:43:51.15 Now, the hardest problem, perhaps,
00:43:54.07 is once you've got RNA chains like this, how can they be replicated?
00:43:59.16 So much of our early thinking was based on RNA catalysis,
00:44:04.19 and in fact the whole basis of the RNA world is the idea
00:44:07.16 that RNA can act as an enzyme that could catalyze its own replication.
00:44:13.18 And Dave Bartel, when he was a student in my lab many years ago,
00:44:19.17 actually evolved an RNA enzyme with a catalytic activity,
00:44:25.11 that can ligate together pieces of RNA.
00:44:29.04 And Dave subsequently evolved this ribozyme into an even more complex structure
00:44:35.07 that is really an RNA polymerase made out of RNA.
00:44:40.09 Now, that's a very impressive proof of principle,
00:44:43.26 but unfortunately, despite many advances over the years,
00:44:47.26 we're still far from having an RNA molecule that can
00:44:51.09 completely catalyze the copying of its own sequence.
00:44:55.28 So, what we've decided to do is to actually again step back
00:45:01.07 and try to look at the underlying chemistry
00:45:04.03 and see if there might be ways of adjusting or playing
00:45:10.05 with the chemistry of RNA polymerization that would simplify this problem.
00:45:17.04 Ideally, perhaps we will be able to find a complete chemical process
00:45:22.00 that could drive RNA replication.
00:45:25.15 Now, that's a very difficult task,
00:45:28.16 Leslie Orgel and his colleagues worked on that for many years,
00:45:32.17 got partway to a solution,
00:45:34.22 but were never able to have complete cycles of replication.
00:45:39.23 But we have decided to go back and look at some model systems
00:45:44.16 and see if we can get some clues as to how to approach that problem,
00:45:48.24 perhaps in some fresh ways.
00:45:51.13 So, just to illustrate what we're really after,
00:45:53.24 I'm going to show another of Janet Iwasa's movies,
00:45:57.16 and so what you see here is an RNA template, a single-stranded molecule,
00:46:02.00 floating in a solution full of activated monomers,
00:46:05.05 which then find their complementary bases,
00:46:07.26 so they use Watson-Crick base pairing to line up on the template,
00:46:11.06 and then they basically click together to build up a complementary strand,
00:46:16.16 generating a duplex product.
00:46:20.25 So we're after some kind of simple,
00:46:25.03 chemical system that would drive that process very efficiently.
00:46:30.18 So, if we could get to that point,
00:46:33.06 then we would be back to being able to assemble this kind of model system,
00:46:39.10 a model protocell, composed of a membrane compartment boundary
00:46:45.07 and replicating genetic material on the inside.
00:46:50.28 Now, when we're thinking of a complex composite system like this,
00:46:56.13 the question often arises as to,
00:46:58.06 well, why really bother with the membrane compartment?
00:47:01.10 Why not just let the RNA molecules replicate in solution?
00:47:05.17 And one way of thinking about that is that,
00:47:09.22 for Darwinian evolution to emerge,
00:47:12.27 molecules that are in some way better than their neighbors
00:47:15.25 have to have an advantage for themselves.
00:47:19.01 So if we think about RNA replicases floating around in solution,
00:47:24.02 so these would be RNA molecules that catalyze the replication
00:47:27.24 of another RNA molecule,
00:47:30.14 it doesn't really help if you have a mutation which is faster or more accurate,
00:47:37.23 if all it's doing is copying random, other RNAs
00:47:41.01 that it bumps into in solution.
00:47:44.01 It has to have an advantage for itself.
00:47:47.18 And the simplest way to imagine that happening
00:47:50.13 is to encapsulate these molecules within a vesicle,
00:47:54.20 so that they're always copying molecules that are related by descent.
00:48:01.03 Now, the self-assembly of these kinds of complex structures
00:48:06.22 is something that's actually quite simple.
00:48:09.28 So, at the lowest level,
00:48:12.26 the formation of a membrane vesicle can just encapsulate
00:48:16.01 whatever is there in the surrounding solution.
00:48:19.17 However, it's intriguing that there are ways of making the process more efficient,
00:48:24.02 and one of the most interesting ways of doing that is
00:48:28.05 to take advantage of that same clay mineral, montmorillonite,
00:48:31.25 that we've already seen can catalyze the assembly of RNA strands.
00:48:36.24 And so what you can see in this picture,
00:48:39.19 which was generated by Shelly Fujikawa and Martin Hanczyc
00:48:44.11 when they were in my lab about eight years ago...
00:48:47.03 what you can see is that we have here a clay particle,
00:48:51.15 which has RNA molecules bound to its surface,
00:48:55.21 so the orange color is a dye-labeled RNA,
00:48:59.02 and it turns out these clay particles can catalyze the
00:49:01.28 assembly of membrane sheets from fatty acids.
00:49:08.15 And what's happened here is that this clay particle has catalyzed
00:49:11.15 the assembly of this large surrounding vesicle
00:49:15.29 as well as the many smaller vesicles encapsulated within.
00:49:20.03 So what we now can see is that a single very common,
00:49:25.11 abundant mineral can catalyze the assembly of a genetic material,
00:49:30.17 it can catalyze the assembly of compartment boundaries (cell membranes),
00:49:34.08 and it can help bring them together.
00:49:36.13 So very intriguing as a way of simplifying the assembly of
00:49:39.14 cell-like structures on the early Earth.
00:49:43.02 Here's another picture: clay particle inside a vesicle.
00:49:48.01 Here the boundary is quite dramatically evident,
00:49:52.07 so this is a stack of many layers of membrane bilayers.
00:49:56.26 Here's yet another example where the large outer vesicle
00:50:00.15 is filled with hundreds of smaller vesicles, all assembled under
00:50:04.08 the catalytic influence of this clay particle in the middle.
00:50:10.11 So, assembling these things looks fairly simple.
00:50:14.02 What about the process of growth and division?
00:50:16.21 After all, that's what we really need to generate
00:50:19.07 cell-like structures that can propagate.
00:50:22.18 And at this point,
00:50:25.01 what I can say is that we've come up with a process that looks fairly robust.
00:50:31.09 We can start with vesicles and food in the form of fatty acid micelles.
00:50:37.16 They grow remarkably into filamentous structure,
00:50:42.13 which can then divide very easily into daughter cells,
00:50:45.19 and this generates a cycle that can go around and around indefinitely.
00:50:51.08 And in the next part of this lecture,
00:50:53.26 I'll go into much more detail about the nature of this process
00:50:57.09 and the mechanism by which this happens.
00:51:01.02 But, putting this cycle together with our
00:51:06.17 thinking about nucleic acid replication,
00:51:09.13 we can actually start to imagine what a
00:51:12.13 primitive cell cycle would have looked like.
00:51:15.12 And so this is shown in this figure from a Scientific American article
00:51:20.04 that I wrote with Alonso Ricardo from my lab,
00:51:23.03 and it summarizes some of our ideas about the ways in which
00:51:28.28 the early Earth environment might help to drive cell growth and division.
00:51:35.22 So the idea is that the general environment should be rather cold,
00:51:40.15 perhaps even an ice-covered pond,
00:51:44.24 something you might find in an arctic or alpine environment.
00:51:48.29 There are many examples on the modern Earth.
00:51:52.16 The reason for wanting a cold environment in general is that the
00:51:56.08 copying chemistry seems to go better at low temperatures.
00:52:01.06 The low temperature helps the building blocks
00:52:03.10 to bind to the template and facilitates the copying process.
00:52:07.10 But then we know that eventually, once copying is complete,
00:52:10.28 you have to get the strands apart so that you can
00:52:13.09 undergo another round of copying.
00:52:15.21 Simplest way for that to happen is to invoke high temperatures.
00:52:19.23 And so what we like to think about are
00:52:21.21 convection cells driven by geothermal energy;
00:52:26.12 so essentially in a hot spring type of environment,
00:52:30.13 you could have a pond that's mostly cold,
00:52:32.20 but every now and then, these particles would get caught up
00:52:35.01 in a plume of hot water rising from a hot spring.
00:52:39.01 They'd be transiently exposed to high temperatures
00:52:41.24 that would result in strand separation.
00:52:45.02 It also allows for a rapid influx of nutrients from the environment
00:52:50.02 to feed growth and replication through the next round.
00:52:54.08 And then that would generate a cycle in which the
00:52:57.25 entire process of growth and replication and division
00:53:01.07 is driven by fluctuations in the environment.
00:53:04.20 This is driving us to talk to geologists and to search
00:53:09.19 for analogues of this kind of environment on the modern Earth.
00:53:13.13 Here is a beautiful image of an Antarctic lake
00:53:18.19 in which you see stromatolites,
00:53:20.15 these mounds here are microbial growths on the surface,
00:53:25.18 and the reason that it's liquid is of course there is heat rising up from
00:53:29.18 below geothermally, so it's not a perfect analogue
00:53:34.15 of the scenario I described.
00:53:36.05 We'd like to find environments like this where there are hot springs
00:53:39.12 generating convection cells that could drive the whole cycle.
00:53:43.05 So that would be very satisfying if we could identify such environments.
00:53:48.29 So, what I've tried to show in this lecture is basically
00:53:54.13 the context of the environment and the chemistry
00:53:57.10 leading up to the assembly of primitive cells,
00:54:00.25 in a way that's plausible on the early Earth.
00:54:03.17 And what we'll head into in the next two parts
00:54:06.18 are a more detailed look at the chemistry of membrane assembly,
00:54:11.11 growth, and division;
00:54:12.16 and the chemistry of nucleic acid replication.
00:54:15.25 And all of this work is of course has been done through many
00:54:20.17 very talented students and postdocs in the lab
00:54:25.03 who you can see here on this slide.
00:54:28.13 Thank you.
00:00:02.17 Hello, and welcome to iBioSeminars. My name is Dianne Newman, and I'm a professor in the Divisions of Biology
00:00:07.16 and Geology and Planetary Sciences at the California Institute of Technology,
00:00:11.26 and I am also an investigator at the Howard Hughes Medical Institute.
00:00:15.13 So I am going to be giving you a lecture in three parts today,
00:00:19.16 and this is part one, which will be a very general overview on microbial diversity and evolution.
00:00:25.09 In part two, I'll tell a specific story about a modern example of a microbial metabolism
00:00:30.29 that's quite interesting and very important in affecting the geochemistry of the environment with
00:00:36.04 regard to arsenic geochemistry.
00:00:38.06 And in part three, I'll talk about work we've been doing that is more directed
00:00:43.17 at understanding a metabolism that evolved in the past, namely oxygenic photosynthesis.
00:00:49.02 But let's start with an overview now
00:00:52.14 and consider four important points about
00:00:57.00 microorganisms and their history. And I am going to walk you through each of these four points.
00:01:02.14 So the microbial world is really quite remarkable
00:01:06.23 and my goal in this first overview is to leave you with an impression
00:01:10.22 of its diversity, its antiquity, and how abundant and ubiquitous
00:01:16.18 this world is. So let's begin with antiquity.
00:01:20.27 When we think about the evolution of life, oftentimes we think in terms of macroscopic
00:01:25.23 fossils such as the ones that you see here. And it is pretty clear when you look
00:01:30.01 at these rocks, that something living was present on Earth when they formed.
00:01:33.24 In this panel over here you see a fossil of some type of algae. It is not clear
00:01:39.26 exactly what type, but it is inferred to be an alga.
00:01:42.09 And this shape here is known as a trilobite.
00:01:45.06 And this section of rock that you are looking at is one of the most famous fossils on the plane.
00:01:50.12 It is called the Burgess Shale. It's found in Canada, and it dates to what we call the Cambrian explosion,
00:01:57.14 which occurred roughly half a billion years ago around
00:02:00.29 five hundred and sixty million years ago.
00:02:04.16 So we can certainly claim when we look at rocks of this age that life was present.
00:02:09.17 But if we want to think about the evolutionary history of life,
00:02:12.22 over a much larger time span of billions of years,
00:02:15.26 given that the Earth is 4.6 billion years old,
00:02:20.02 we need to step back in time and look at more ancient rocks.
00:02:22.12 And when we do this, the shapes suddenly change, and it becomes
00:02:26.03 not quite as evident that we are looking actually at fossilized versions of life,
00:02:30.09 and yet we are. So for instance, take this rock as an example.
00:02:34.07 Here you see these dome-like structures, and these are vestiges of a type of microbial community
00:02:41.29 forming in a shallow marine environment
00:02:44.16 that became lithified and left these domal structures,
00:02:48.07 and we call these structures stromatolites.
00:02:50.08 Now this particular rock that you are looking at
00:02:52.21 is about 3 billion years old and is from South Africa.
00:02:56.19 But these rocks can be found all over the world, and they occur
00:02:59.21 throughout Earth's history, going back as far as 3.4 billion years.
00:03:04.20 However, when we go even further back in time,
00:03:08.04 for example, back to 3.8 billion years,
00:03:10.17 you can see ore deposits that one might not intuit immediately had anything to do with
00:03:16.26 microorganisms, and yet they do. They indeed record a history of microbial activities that was quite profound,
00:03:24.24 so profound that it quite literally transformed the planet.
00:03:27.19 And this is one beautiful example. So what you are looking at here is actually a 2.4 billion year old quarry.
00:03:35.27 This is in Western Australia in the Hamersley formation, and this is known as a banded iron formation.
00:03:41.13 And they're extremely important today because they constitute the world's largest source of iron ore.
00:03:47.03 But they also record a remarkable history of the evolution of metabolism.
00:03:51.13 Now how can this be? How do these massive rock quarries tell us anything about microbial life?
00:03:57.14 Well, when you think about what they actually constitute
00:04:01.00 they are made up of iron minerals, as well as other minerals
00:04:04.21 cherts, which is a type of silicon oxide,
00:04:07.07 intermixed with these iron species, but for now let's just focus on the iron.
00:04:12.02 So how did this iron get into this big deposit that you see here?
00:04:15.12 Well, it began a long time ago in ancient seas, in the form of ferrous iron
00:04:20.23 that's called Fe2+.
00:04:22.17 And then some process, which I'll get to in just a minute, oxidized this ferrous iron to ferric iron,
00:04:29.00 and at that point it could react with constituents in the waters such as hydroxyl species,
00:04:34.26 to form iron minerals, such as this one: ferric oxyhydroxide, rust.
00:04:41.01 And over time this mineral transformed and changed
00:04:44.19 into different types of minerals, became compacted,
00:04:47.17 and mingled with others and wound up in these rocks that we today know as banded iron formations.
00:04:54.14 But this initial step here is the critical one in terms of giving us some insight into microbial
00:05:00.23 activities on the ancient Earth. And let's think about two scenarios where microorganisms
00:05:06.05 might have been involved. The first scenario
00:05:09.03 is one where a very primitive type of photosynthetic organism,
00:05:12.27 well, I should say primitive in quotes, because actually this metabolism is remarkably sophisticated.
00:05:17.16 Nonetheless, this is primitive in the sense that it is a type of photosynthesis
00:05:21.18 that does not generate oxygen. Rather it is called anoxygenic, meaning that there is
00:05:29.09 an electron donor, in this case ferrous iron, that is oxidized to ferric iron
00:05:35.29 and that powers the reduction of inorganic carbon, CO2, to biomass.
00:05:42.18 And you can see this is a very dramatic metabolism
00:05:46.25 when it occurs because all you need is light, microorganisms, and ferrous iron,
00:05:52.21 and a few other things to help them get going, but those are really the three most important ones
00:05:57.22 in a bottle here, with, as I said, a few nutrients added so they can do their thing,
00:06:04.19 and when light is shined on this bottle,
00:06:08.24 these organisms very rapidly are able to oxidize the iron.
00:06:12.19 And they produce rust, and you can see the rusty color here in this bottle.
00:06:16.14 And this rust is exactly the type of iron that is the predecessor of the minerals that constitute
00:06:22.04 these banded iron formations. Now in the middle you see these organism growing on a different
00:06:27.03 electron donor, and I'll get to what I mean by an electron donor and an electron acceptor later in this lecture.
00:06:33.17 And in this case they are utilizing hydrogen as an electron donor, and the pink color you see
00:06:39.13 is due to photosynthetic pigments in their membranes
00:06:42.16 that enable them to harvest light and grow in this way.
00:06:45.07 So this scenario, as I said, is one that is catalyzed by
00:06:51.01 organisms that do not generate oxygen. They are anoxygenic phototrophs
00:06:55.14 capable of oxidizing iron in a photosynthetically mediated
00:06:58.29 process under environments where no oxygen is present whatsoever, and yet these ferric minerals can form.
00:07:07.22 Now scenario two, that is entirely different
00:07:11.02 is one where the organisms that ultimately catalyze the precipitation
00:07:15.11 of these minerals were producers of molecular oxygen, and these are the cyanobacteria
00:07:21.24 that you can see here that were critically important in the history of the evolution of metabolism
00:07:27.08 and quite frankly also in changing the overall chemistry of the Earth including its atmosphere
00:07:33.04 because they evolved the ability, the remarkable ability, to use water as an electron donor in photosynthesis,
00:07:40.05 oxidize it to molecular oxygen, and through this process, power the reduction of CO2 to biomass.
00:07:48.19 Now once they produce this oxygen, the oxygen chemically would have been able to react
00:07:55.09 with ferrous iron, oxidizing it to ferric iron,
00:07:58.25 and then this in turn would go down the pathway to precipitate these rusty minerals I showed you.
00:08:03.06 So here we have two options: one scenario where no oxygen is involved,
00:08:10.11 and a second scenario where oxygen is mandatory.
00:08:12.21 And both of these are biological processes.
00:08:15.22 So how do we distinguish between them if we are interested in understanding
00:08:20.19 the types of organisms that were present on Earth in the remote past?
00:08:23.29 Well this is quite a challenge, indeed, and there will be many years of investigations in the future
00:08:31.07 in order to really pin this down.
00:08:32.29 And it is a great field to get into if you are a beginning student
00:08:36.07 and interested in both biochemistry and evolution,
00:08:39.16 but what I'll say just for now is that we know from a variety of indicators
00:08:43.23 that somewhere between 2 billion and 3 billion years old
00:08:47.26 it is very probable, indeed it is almost certain,
00:08:52.05 that the process of oxygenic photosynthesis arose.
00:08:54.19 But when exactly this happened and how the evolutionary events came together
00:09:00.19 such that these anoxygenic phototrophs that can utilized reduced substrates
00:09:06.05 such as hydrogen, or sulfur species, or iron as electron donors in photosynthesis
00:09:12.13 morphed into a more sophisticated type of phototroph,
00:09:18.00 that was capable of using water as an electron donor,
00:09:20.25 the cyanobacteria, which in turn, are what became the plastids,
00:09:26.22 the chloroplasts that we find in modern marine algae
00:09:30.10 and also of course, in plants that are very well known for their ability to do oxygenic photosynthesis.
00:09:36.09 We do not know. We do not know when this happened.
00:09:39.14 And in my third lecture in this series, I will discuss ways that we can begin to approach this problem.
00:09:44.22 But it's a profound question, and what I would like to leave you with now
00:09:47.27 is just the simple message that these very ancient rocks, such as these banded iron formations,
00:09:52.16 here are holding clues to a mystery that we have to unravel.
00:09:56.22 And it is through tools of modern biology that ultimately we hope to get there.
00:10:01.13 All right, now as I said the history of microbial life
00:10:06.19 extends very far back in time, as far as 3.8 billion years as we currently estimate,
00:10:12.22 but this might have been even earlier for all we know.
00:10:15.22 How do we decipher when particular microbial metabolisms evolved and what types they were?
00:10:22.04 Well, this indeed is extremely challenging.
00:10:24.09 And there are three primary ways that we can gain insight
00:10:28.04 into the microbiology of the past through using either
00:10:31.25 morphological, molecular, or genomic, which is of course a form of molecular biosignatures.
00:10:38.21 And these are very different in what they can tell us.
00:10:41.20 So the first two, morphological and molecular,
00:10:45.01 are important because they can be concretely linked to rocks, old rocks, that we can date.
00:10:51.02 And because of this when we see a particular form,
00:10:55.09 this is being held in the hand a sample of stromatolite.
00:10:58.29 This is at a very different scale here. You are looking at a thin section of a rock,
00:11:03.14 and that is true for these images below
00:11:05.28 where the scale is about 1 millimeter, in this image, and it is even smaller down here.
00:11:12.10 The structures that you observe have been interpreted as being vestiges of ancient life for various reasons.
00:11:19.13 But this interpretation is often ambiguous, and it is a challenge to be able to come up with unambiguous
00:11:25.06 biosignatures simply on the basis of their shape.
00:11:28.12 And so geobiologists, those interested in seeking to understand life in ancient times,
00:11:35.02 have turned recently to what we call molecular biosignatures that come in two forms:
00:11:39.27 either organic biosignatures, or some type of inorganic biosignature,
00:11:46.26 often expressed as a ratio of different isotopes in a sample.
00:11:51.04 Now this in turn is challenging as well,
00:11:54.25 but it may be the best way that we can gain more specific insight into
00:11:59.18 different types of metabolisms, by looking at actually the chemistry what is left in the rock
00:12:04.10 and being able to deduce through finer scale analyses whether or not
00:12:09.14 this chemistry was one that was uniquely imparted by a biological process.
00:12:13.13 Lastly we can think of genes as fossils, and the genomic record has been crucial
00:12:20.03 in establishing the diversity of life on the planet, as I'll get to in a little while in this lecture,
00:12:25.21 but it also helps us understand the relatedness of different enzymatic functions
00:12:30.22 and how they evolved from one another.
00:12:33.19 While this does not give us a concrete date when these metabolisms
00:12:37.14 evolved, it does provide us with an ability to look at
00:12:41.10 the relationship between different metabolisms, and come up with an order in which they likely were invented.
00:12:49.06 So that is all I am going to say right now on the antiquity of microbial life,
00:12:53.22 and if you are interested, tune in for lecture three in this series,
00:12:56.22 where I will spend some more detail talking about how we use a particular compound found in lipids
00:13:02.13 in modern cells as a potential indicator for oxygenic photosynthesis
00:13:06.19 and whether or not this is a valid thing to do.
00:13:10.01 The next point now I want to turn to is just how numerous microbes are.
00:13:14.22 So let's ask a very simple question. How many microbes are there on Earth?
00:13:18.11 And to bring this into a human reference point, let's begin with the number of the human population.
00:13:23.19 So I am from Los Angeles, which at the latest census,
00:13:27.27 was around 10 million people. And in the state of California, we are up to approximately 35 million,
00:13:34.11 and in the United States in general, nearly 300 million.
00:13:39.16 These are large numbers, but overall in the world we are up three orders of magnitude.
00:13:44.18 at 6 billion people. And that's a lot of folks.
00:13:47.27 However, this is nothing in comparison to the microbial population
00:13:51.18 as estimated by a wonderful paper that I am citing here at the bottom of the slide
00:13:55.22 called, "Prokaryotes, the Unseen Majority" that was published in PNAS in 1998.
00:14:01.29 These are very rough numbers, but give or take an order of magnitude
00:14:05.01 here or there, I think you are going to be impressed when you see the number that I am about to show you.
00:14:09.06 So the estimates for the microbial population are just enormous, 5 times 10 to the 30th cells.
00:14:15.08 And this indeed is such a large number that it is very difficult to wrap our minds around it.
00:14:20.21 So to try to make this a bit easier to do,
00:14:22.16 I did a very simple calculation, where I assumed that the length of a given micro-organism
00:14:27.01 was one micron and asked, "how many times would we need to go back and forth between the Earth
00:14:33.11 and the Sun if we lined up all of these organisms end to end in order to account for this number?"
00:14:38.29 And the answer, shockingly, is we would need to go back and forth 200 trillion times.
00:14:45.12 So hopefully that impresses you with just how many of these creatures there are on the planet.
00:14:49.28 Now where are they, if there are so many?
00:14:52.08 How come we don't think about this all the time?
00:14:54.27 Why aren't we overwhelmed?
00:14:56.04 Well, one reason is that oftentimes we are shockingly ignorant
00:14:59.19 about the fact that they are all around us, that we ourselves are walking micro-organisms.
00:15:04.04 So one of the first scientists to appreciate this profound fact
00:15:08.10 was the father of microscopy, Antony van Leeuwenhoek.
00:15:11.11 And this is a lovely image that he drew from his observations down his first microscope
00:15:18.01 in 1684, and you can see he drew some nice rods and cocci, and even pictures of probably motility
00:15:26.22 what is meant by these dotted lines from C to D.
00:15:30.29 And he reflected, as he was looking through the microscope about his own teeth, and this is I think a very funny quote.
00:15:37.28 He said, "Though my teeth are kept usually very clean,
00:15:40.24 nevertheless when I view them in a magnifying glass,
00:15:43.25 I find growing between them white matter as thick as a wetted flower.
00:15:47.09 The number of these animals in the scurf of a man's teeth,
00:15:50.05 are so many that I believe they exceed the number of men in a kingdom."
00:15:54.17 Well, this indeed is actually an underestimate.
00:15:58.28 Not only do they exceed the number of men and women in a kingdom,
00:16:02.13 they go far beyond that. So if we actually look at our own bodies...
00:16:06.13 just take a look at your wrist, at one square inch on the surface of your wrist.
00:16:10.23 Right there, we are estimated to have five to fifty thousand bacterial cells.
00:16:16.22 And it just increases in density as we move to other parts of the body, such as the groin and the underarms,
00:16:22.28 in our teeth, and really where it's mainly at in our bodies is in our colon.
00:16:29.06 And the overall total per person is seventy trillion.
00:16:33.25 That is quite a lot.
00:16:35.24 And one thing that I think is really important for you
00:16:38.18 to know about the microbial community within your own body,
00:16:42.16 is that there are ten times the number of microbial cells
00:16:47.04 in our system than there are human cells.
00:16:51.21 And not only that, when we look at the genetic potential of the DNA
00:16:56.09 within these organisms, the genetic potential of only those within our guts
00:17:02.15 is over one hundred times that of the human genome.
00:17:06.21 So you might begin to ask whether or not humans are not merely walking vats of microorganisms,
00:17:11.29 carriers serving their existence.
00:17:14.08 It is something to think about, and there's a great deal of research now emerging
00:17:18.20 that is beginning to illuminate just how crucial these organisms are
00:17:21.25 for human health, not only with regard to being able to help us digest our food,
00:17:27.07 but also interfacing and controlling our immune system,
00:17:30.09 in ways that are fascinating and profound.
00:17:32.29 Now despite the fact that this number, ten to the twelfth, seems really large, and indeed it is,
00:17:38.25 it's peanuts when we compare it to other domains where we find microorganisms.
00:17:44.09 So let's start with the least abundant, up in the air,
00:17:46.24 It is quite amazing to me that they've been detected as high as thirty four to forty six miles up
00:17:53.06 into the sky. But these concentrations are really small relative to other compartments.
00:18:00.00 As I told you, within the human body we have quite a few.
00:18:04.12 And when you add up all of the humans and domestic animals, and then termites,
00:18:08.08 which I'll get back to in just a bit,
00:18:09.20 the order of magnitude jumps up to about ten to the 23rd, to 24th
00:18:14.06 This is superceded by the quantities that you can find in soils,
00:18:20.06 in forests and grasslands, deserts, tundras, swamp environments.
00:18:24.10 These places are very fertile homes for microorganisms and there their activities can transform
00:18:29.23 the chemistry of their environment quite profoundly.
00:18:31.29 And this is of course also true in aquatic domains, where at similar orders of magnitude
00:18:38.08 we find microorganisms in both marine and freshwater environments.
00:18:42.01 But all of these numbers pale in comparison to the numbers that we find in the subsurface,
00:18:46.14 both in terrestrial and oceanic environments, where microorganisms
00:18:51.09 have been detected as deep as two miles.
00:18:54.22 Now, this really is a very interesting frontier area in microbiology
00:18:58.05 It is hard to go down into these depths, and yet nowadays, researchers are equipped with the tools
00:19:05.02 they need in order to access these remote communities.
00:19:07.26 And what remains to be learned is what exactly these organisms are doing in situ.
00:19:12.11 Are they active? And if so, what are their activities?
00:19:15.26 Are these activities affecting in a significant way
00:19:19.05 the physical and chemical properties of these environments?
00:19:22.07 We don't know, and we look forward in the coming decades to finding
00:19:25.04 the answers to these and other interesting questions.
00:19:27.19 So now let me just give you an example, a tour through various parts of the world
00:19:34.05 and other inhabitants of that world where we find these organisms.
00:19:39.17 Just to bring home to you how ubiquitous microbes are on the planet.
00:19:44.07 So to start with what might be a more familiar image, here what you are looking at is pond scum.
00:19:51.09 You are looking at a wonderful assemblage of phototrophs
00:19:54.27 and other microorganisms in this pond. And my favorites of course are these purple phototrophs.
00:20:00.03 These are the ones that I told you about earlier that are what we call the anoxygenic phototrophs
00:20:04.27 that are not utilizing water as a substrate in photosynthesis,
00:20:08.29 but are utilizing other more reduced compounds such as different types of sulfur species, hydrogen, or iron.
00:20:17.15 Now these organisms that we see in modern day ponds, as I told you at the beginning when I was illustrating
00:20:23.20 the antiquity of microbial life with the example of the banded iron formations,
00:20:27.25 are absolutely historically important for their metabolism,
00:20:33.19 and the diversity of their metabolism, and how it's changed the geochemistry of the Earth.
00:20:38.00 Not only has the evolution of photosynthesis contributed to evolving our atmosphere
00:20:43.20 to one that contains oxygen over the course of time,
00:20:46.14 but as I also showed you with the banded iron formations,
00:20:48.29 these types of organisms have likely shaped ore formation as well.
00:20:54.21 And many other important processes have been able to come about
00:21:00.21 thanks to these organisms doing what they do, and it should be noted
00:21:05.15 that this type of metabolic activity, photosynthesis, is one that today we are highly interested in
00:21:12.06 because of our need for coming up with alternative energy sources, and
00:21:16.25 certainly if chemists were able to mimic what these wonderful microbes in this pond do, we would
00:21:22.25 be able to not worry so much about our dependence on foreign oil
00:21:27.02 and our fossil fuel supplies being burnt, but that's a story for another day.
00:21:32.08 The point is, their metabolic diversity is old. We see it all around us, and the biochemistry is really quite fascinating.
00:21:39.18 Continuing on with the chemistry and the metabolism of these organisms
00:21:44.28 not only do they do important things when they are growing,
00:21:48.00 but they also do important things when they start hitting what we call stationary phase.
00:21:51.24 And this is a point in their development where they're not necessarily actively growing,
00:21:56.12 but they are at a higher density and they are just hanging out metabolically.
00:22:00.26 And when this occurs in their lifecycle,
00:22:04.09 sometimes metabolites and pigments begin to be excreted.
00:22:08.08 And these pigments, which are called secondary metabolites,
00:22:12.14 although that name itself may be a bit misleading, because they are only secondary in a temporal sense,
00:22:18.14 in that they are made after a phase of active growth,
00:22:21.21 but by no means are they secondary in terms of the physiology of the organisms that produce them.
00:22:27.00 None the less, these metabolites oftentimes are used today by pharmaceutical companies
00:22:32.14 as natural products that confer antibiotic activity.
00:22:35.13 And a terrific example of this are organisms in the Streptomycetes family that you see here
00:22:40.18 in this Petri dish that are producing a whole host of wonderful antibiotic compounds.
00:22:45.02 Now containing in the environment of the soil of course are roots of plants.
00:22:51.00 And in this part of soil known as the rhizosphere,
00:22:55.04 we can find microorganisms as well that are colonizing in a very beneficial way the plant roots.
00:23:00.28 And here is a tomato root seedling. This is an image taken by Guido Bloemberg.
00:23:06.25 And he showed in experiments in the laboratory that when he took tomato root seedlings
00:23:12.27 and mixed them with an organism called Pseudomonas,
00:23:16.01 that this bacterium was able to colonize the plant and form what we call biofilms on the surface of the root.
00:23:22.18 And this is just one example of organisms that interact with plants.
00:23:26.20 There are many that fall into this category with different names.
00:23:30.12 And the bottom line is that they have a very beneficial relationship with these plants,
00:23:34.11 where sometimes they produce natural products that fend the plant off from fungal predators
00:23:40.05 and so they serve as biocontrol agents.
00:23:42.24 Other times these organisms are capable of fixing molecular nitrogen
00:23:48.14 into a usable form and essentially acting as a natural fertilizer.
00:23:53.14 Now crawling around in not only soil environments,
00:23:58.00 but of course we are very familiar with these from our homes, are termites.
00:24:01.00 And the termites are a terrific source of microbial diversity
00:24:05.17 and one that is becoming an increasingly important micro-environment
00:24:10.07 in which to look because of our desire to understand microbial processes
00:24:16.00 that might be harnessed for lignocellulose degradation.
00:24:19.04 Again, out of a need to develop alternative sources of energy.
00:24:22.22 Now a colleague of mine, Professor Jared Leadbetter at Caltech
00:24:26.14 studies these termites, and he likes to call them "an ecosystem in a microliter".
00:24:31.05 And I think this is really a fantastic description of them because it is within their hindgut that you find a zoo
00:24:38.21 of microorganisms and protozoa that are swimming around
00:24:43.12 doing all sorts of important activities that make it possible for the termites
00:24:47.12 to digest their wood. And in the process they emit methane,
00:24:52.02 and not an insignificant fraction of this methane ultimately makes its way
00:24:55.16 up into the atmosphere and contributes to the overall chemistry on the planet.
00:25:02.17 So speaking of methanogens, here you see
00:25:05.08 a dramatic illustration of them at work.
00:25:07.18 This image that I am standing in front of is taken from Cedar Swamp in Woods Hole, Massachusetts.
00:25:12.15 And it is an image from a group of students from the microbial diversity class,
00:25:18.02 which is a fantastic course for about twenty students, half from the United States and half from overseas,
00:25:24.07 who come together every summer to understand how
00:25:27.00 microorganisms are able to perform these various metabolic activities
00:25:32.08 that I have been describing in these lectures.
00:25:34.26 And what you can see here is that the students have gone waist deep into this swamp
00:25:39.19 and they have stomped around, and as they have done this they have collected the bubbles that come up
00:25:46.03 as they stomp the sediment, and collected them in these inverted funnels.
00:25:51.11 And then some brave individual holds that funnel
00:25:54.14 and removes their hand just at the moment when a friend comes by with a flame,
00:25:59.09 and ignites it, and here you see a lovely illustration of methane at work.
00:26:04.25 So methanogenesis led to the creation of the methane gas that was ignited here.
00:26:10.06 Now in the past the activity of these organisms that generate this methane
00:26:15.23 that are called methanogens, might have been important in shaping the chemistry of the Earth's environment.
00:26:19.27 And the reason we suspect this may be the case is because early in Earth's history the environment
00:26:25.00 contained appreciably more methane than it does today.
00:26:28.18 Now a different example of a habitat where microorganisms are very important
00:26:33.21 is in Chile and in other places on Earth,
00:26:37.19 but this example here is taken from the Andina Copper mine in the Andes in Chile
00:26:44.23 where microorganisms are exploited for their abilities to help
00:26:48.27 with bioleaching. And so what happens is that in these mines there are piles
00:26:54.06 that are built up, and they are fertilized essentially with indigenous microbial populations
00:27:01.08 that are able to live in shockingly low pH levels,
00:27:05.17 down to pH as low as one, and sometimes even lower.
00:27:08.23 And these organisms are essentially eating the minerals in this mine pile
00:27:14.14 and the process of metabolizing it, changing the mineralogy, in such a way
00:27:19.06 that copper is solubilized and leached. So here is another example of an environment
00:27:25.27 that is quite extraordinary and yet microorganisms have been able to adapt and even to thrive in this extreme condition.
00:27:33.04 So on our tour of extreme pHs, we just saw an example of low pH, so let's go to a high pH environment.
00:27:39.24 This one I am showing you is Mono Lake that is in Northern California.
00:27:44.09 And Mono Lake is quite an extraordinary place. It looks almost like it is from another planet.
00:27:49.25 You see these beautiful tufa towers that are calcium carbonate minerals forming,
00:27:55.05 and it is because the pH is so high and the alkalinity is so high that they naturally precipitate from these waters.
00:28:01.19 In addition to having these carbonate minerals, contained within this lake environment
00:28:07.09 is a ton of arsenic, and I will get to this in part two of my lecture today.
00:28:11.07 And what I want to point out right now is that in this very high pH environment, and also one
00:28:17.14 that's replete with arsenic, nevertheless we find organisms called alkaliphiles
00:28:21.23 that thrive here, that are able to make a living utilizing arsenic as a terminal electron receptor in respiration.
00:28:30.05 This is the subject of my second lecture. And in so doing account for 14% of the carbon turnover in this system.
00:28:38.23 Now let's go on to another example of an extreme environment.
00:28:42.14 Here now we are looking at an extreme of salt.
00:28:45.26 And there is no better example of this than the Dead Sea in Israel, but
00:28:50.06 you can find organisms such as those that inhabit the Dead Sea also in the Great Salt Lake,
00:28:56.04 and other places on Earth such as salt flats, where you have very high salt content.
00:29:04.19 And the organisms living here are capable of growing despite this high salt
00:29:08.21 and have adapted particular molecular strategies to cope with it.
00:29:12.15 One very elegant example of this is their ability to use special photopigments called rhodopsin
00:29:18.23 and these are colored purple.
00:29:21.24 And these rhodopsins, they have in their membranes, and enable them to generate energy
00:29:27.11 under conditions where they need to use slightly different
00:29:30.02 strategies than organisms that are growing under
00:29:33.28 conditions that we would consider more normal.
00:29:36.27 Now, so approaching the end of our tour through microbial diversity and ubiquity, I want to end with a few other extremes
00:29:44.00 now that are based on temperature and pressure.
00:29:46.04 If we think about the extremes of cold there is no better place to go than Antarctica.
00:29:50.27 And you might be surprised to realize that even in this environment you have microorganisms thriving in the crust.
00:29:57.02 And these organisms are psychrophiles, and they're ability to grow is dependent upon dust
00:30:02.26 from winds carrying nutrients picked up from the continents surrounding Antarctica, South America, Australia, Africa,
00:30:14.24 that reach Antarctica, deposit their dust and fertilize these upper crusts of the ice
00:30:20.14 where we have intrepid pioneer organisms that are able to utilize these nutrients
00:30:26.03 and grow, even in these very cold regimes.
00:30:28.02 So another extreme is that of temperature and pressure, and there is no better environment in which to observe this
00:30:34.24 than at the bottom of the ocean, in environments where we have hydrothermal vents
00:30:39.21 that are releasing nutrients into the deep. And here is an example of one of these vents. It is called a black smoker
00:30:46.17 because the nutrients that it releases, including manganese and iron,
00:30:51.14 often precipitate in the conditions of the oceans at these sites
00:30:57.16 such that they look black.
00:30:59.22 Now around these vents there is abundant life,
00:31:04.07 really extraordinary life, not just microbial life.
00:31:06.08 but giant tube worms, and fish, and other macroscopic organisms.
00:31:10.10 So the ability of all of this abundant life to be in this environment
00:31:15.10 crucially depends upon the activities of microorganisms that are chemosynthetic.
00:31:20.01 that are able to grow by the oxidation of sulfur and other compounds that you have
00:31:25.03 present in this environment, and couple that oxidation of these reduced substrates to
00:31:31.05 the fixation of CO2 into biomass.
00:31:34.15 And this is at the base of the food chain that then sustains the growth of other marine organisms.
00:31:40.12 such as these tube worms. And here you see an example of that
00:31:43.10 in these beautiful tubeworms. If you cut them open and you look at one of their organs,
00:31:50.29 called the trophosome within these organs are bacterial symbionts
00:31:55.27 that are doing the process that I just mentioned.
00:31:58.08 So my final example that I will end with
00:32:01.12 is one that might be the most familiar to you
00:32:04.02 if you have ever done any PCR in molecular biology.
00:32:06.25 So most of you have heard of the enzyme Taq polymerase,
00:32:10.06 and this polymerase is what allows us to do an amplification reaction when we are doing PCR.
00:32:18.21 Now this enzyme, Taq, derives from a bacterium called Thermus aquaticus,
00:32:24.28 that is where the Taq comes from. The "T" is from the Thermus and the "aq" from aquaticus.
00:32:31.05 And this is a thermophile that was isolated in Yellowstone
00:32:35.14 at a hot spring, many decades ago.
00:32:38.03 And it was presciently realized by Kary Mullis
00:32:41.18 and others that the enzymes contained within it could be useful for various biotechnological applications
00:32:47.26 because they wouldn't denature at the temperatures that would kill most other types of cells.
00:32:54.02 So these thermophiles are a very fascinating group of organisms
00:32:57.28 whose molecular adaptations include not only DNA polymerases,
00:33:03.26 but also a wide variety of other enzymes that might be of industrial use.
00:33:10.01 So let's now end with diversity, which is really my favorite part
00:33:14.14 of the microbial world. And I want to cover a few different areas of this.
00:33:18.18 The first is phylogenetic diversity.
00:33:20.03 Now one of the most important lessons to be learned in evolutionary theory
00:33:25.03 was learned several decades ago from work by Carl Woese and his colleagues,
00:33:30.03 including Norman Pace, who applied Carl Woese's fundamental
00:33:34.07 insights into the diversity of life to the natural world.
00:33:38.02 And these individuals together with others were able to demonstrate very clearly
00:33:44.05 that when we think about the diversity of life out there on the planet,
00:33:48.16 we are really talking about a microbial world, whether we call these
00:33:52.22 microorganisms Bacteria or Archaea or even Eucaryotes.
00:33:58.23 What I want you to appreciate is that when you look at the tree of life,
00:34:03.11 that's what this is. It is a tree that is drawn based upon comparing the sequences of a very particular molecule
00:34:11.06 that every living organism has, that is ribosomal RNA, that is necessary for the process of translating
00:34:19.07 messenger RNA into protein.
00:34:21.07 Because this is a very universal and highly conserved molecule
00:34:24.28 Carl Woese and colleagues were able to deduce that it was a beautiful molecular chronometer
00:34:31.01 that we can employ to look at the evolutionary relatedness between different organisms.
00:34:36.16 And when he and his colleagues did this , he recognized that
00:34:39.19 there were three primary domains of life, the Bacteria, the Archaea, and the Eucarya.
00:34:43.16 And moreover, what I want to stress now is that our entire universe of Homo sapiens
00:34:52.12 and humans and plants and animals, the macroscopic eucaryotic world,
00:34:57.12 is only occupying in terms of this space on the tree,
00:35:01.27 which is known as a phylogenetic tree, meaning a tree of evolutionary distances
00:35:06.21 between different types of life forms, a very tiny miniscule branch.
00:35:12.00 And everything else that I am showing here is microbial.
00:35:14.13 So hopefully that impresses you, but before we leave this tree let me point out two more
00:35:19.20 facts that are very important.
00:35:20.29 All of the metabolism on the planet was invented by microorganisms
00:35:26.05 including the metabolism that we perform in our bodies today in our mitochondria.
00:35:31.11 So the mitochondrion is nothing more than an ancient bacterial cell
00:35:36.28 that invented the ability to do oxidative phosphorylation, which I'll tell you about in a little bit,
00:35:42.24 that was engulfed or brought into symbiosis with some other type of cell,
00:35:47.23 and over the course of time involved into the organelle that we call the mitochondrion.
00:35:52.28 But it was a microorganism first, and that is where the beautiful metabolism that it goes through was generated.
00:36:02.14 The same story is true for the chloroplast. This is nothing more
00:36:06.03 than cyanobacteria that over time turned into plastids and became incorporated into other cells.
00:36:11.25 Now the next important point I want to make is that microbial diversity also manifests itself morphologically.
00:36:18.19 And this is something that only recently we are coming to appreciate in its full glory.
00:36:24.02 Back in the days of Leeuwenhoek, when he had a simple microscope, all he could really see were different shapes of microbes,
00:36:30.24 and to be quite honest, that is not terribly spectacular and includes rods and spirals and some cocci.
00:36:37.11 Once in a while you see higher structures forming of communities however,
00:36:41.25 and Leeuwenhouk didn't necessarily know about these,
00:36:44.05 but here is an example of one here. This is a beautiful example
00:36:48.13 of fruiting bodies beginning to form by the soil organism Myxobacteria
00:36:53.10 that does all sorts of interesting things when it comes together in a group
00:36:57.01 that it wouldn't do as any individual cell.
00:37:00.25 This is social behavior. So this is an example of bacteria acting in a multicellular fashion, if you will.
00:37:06.11 Microorganisms, however, can get remarkably large. They are not just on the scale of microns.
00:37:11.21 And here is a good example of this.
00:37:13.20 This is, to my knowledge, one of the largest microbial
00:37:16.28 cells known to date. It is called Thiomargarita namibiensis,
00:37:19.29 which means the sulfur pearl of Namibia.
00:37:22.17 And it is on the same scale as the eye of a fruit fly.
00:37:25.13 And when you look at it in more detail, the reason it is so big is that it contains this huge vacuole
00:37:31.21 filled inside with nitrate, which is one of the substrates it uses to power its metabolism.
00:37:38.02 And it couples the reduction of nitrate to a more reduced form of nitrogen
00:37:43.07 to the oxidation of sulfide, and in this way it powers energy for growth.
00:37:48.00 But let's leave the metabolism aside and stay focused now just on the form.
00:37:52.03 Here is an example of one of my favorite organisms, Rhodopseudonomas palustris,
00:37:57.02 and the reason I am showing you this is simply to illustrate
00:37:59.24 that it has quite an amazing membrane structure within it.
00:38:05.27 One that is reminiscent even of the Golgi in higher organisms.
00:38:09.09 And indeed it might have been the progenitor of that at the cell biological level.
00:38:14.17 And how these various structures form, these are what we call
00:38:18.06 the inner cytoplasmic membranes where the photosynthetic machinery is housed in this case,
00:38:22.19 in terms of the detail of what creates their shape is an open and exciting question
00:38:27.08 that future microbial cell biologists will no doubt solve.
00:38:30.17 But the final example, which is probably my all time favorite, is of an organism called a magnetotactic bacterium.
00:38:38.16 And here you see if you just look at it in a light microscope,
00:38:41.15 although this is actually an image of fluorescence where we have put some GFP into the bug,
00:38:46.04 it looks like just a common spiral.
00:38:48.09 If you take a fancier microscope, a transmission electron micrograph, and cut it
00:38:53.01 open and do a thin section, you can see that it has this beautiful chain of magnetic particles inside it.
00:39:00.00 And now what I am going to show you is, I think, the best advertisement for the beauty of bacterial cell biology
00:39:05.28 that I know, and it is a cryo-electron tomogram of one cell.
00:39:13.10 And this was work done by Arash Komeili who is now a professor at UC Berkeley
00:39:18.26 and his collaborator Zhuo Li in Grant Jensen's lab at Caltech. And together
00:39:23.17 we made this movie showing the internal structure of these organisms.
00:39:27.26 So what you are going to see now is coming up through the bacteria different sections,
00:39:32.11 and here you see the magnetosomes coming into view. Those are the membranes that contain the magnetite.
00:39:39.10 If you missed them, now look, OK.
00:39:41.02 Here they are in red, those magnetosome membranes, and then there is this yellow filament surrounding them.
00:39:46.27 And what we have come to appreciate is that this filament is a protein that is very similar to actin.
00:39:52.11 And it is necessary for these magnetosomes, for these organelle-like,
00:39:58.01 although they never separate from the membrane, so they are not true organelles.
00:40:01.14 Here you see they're attached by a neck that's only 5 nanometers in diameter, which is quite amazing, to this inner membrane.
00:40:10.24 They invaginate and form these vesicles within which a beautiful single domain crystal of magnetite can form.
00:40:19.19 And this order, the fact that they are linear in a chain,
00:40:22.21 is enabled by a cytoskeletal filament, an actin-like protein.
00:40:28.17 OK. So the next to the last point that I want to make on diversity
00:40:33.09 is behavioral diversity, and there is another lecture in this iBioSeminar series
00:40:37.06 by Professor Bonnie Bassler from Princeton that can give you more information about this if you are interested.
00:40:41.28 But what I wanted to point out here while we are going through a tour through diversity
00:40:46.13 is simply that microorganisms can act in ways that are quite extraordinary
00:40:51.15 when they are acting as a group.
00:40:53.11 And you can see that illustrated by the activities of the bacterium Vibrio fischeri within the light organ of a squid.
00:41:01.10 And here is an image that is from the beautiful pioneering work of Margaret Mefal-Ngai
00:41:06.18 and Ned Ruby at the University of Wisconsin, Madison where they have been studying for decades the interactions
00:41:12.01 between the microorganisms in the light organ of the squid and the squid,
00:41:16.28 and the ability of these organisms to colonize this environment,
00:41:20.06 and when the lights go out at night, emit a beautiful luminescence. Here you can see pictures of these organisms
00:41:28.12 that have just been streaked out on a plate in the dark.
00:41:30.11 They are glowing. Well, they glow as well here at night in the belly of the squid.
00:41:35.27 And it shields these squids from predators below
00:41:39.00 because the light of the moonlight coming down from the top
00:41:41.28 is roughly of the same luminescence as the light that they are emitting.
00:41:45.26 So it allows them to have a stealth function and glide around in the oceans
00:41:50.19 and be unseen to predators deeper below them.
00:41:56.07 Now, this isn't just a phenomenon that affects the squid. This is a phenomenon that can get quite enormous in its scope.
00:42:03.19 And the best example to illustrate this is this satellite image here taken off of the Somalian coast,
00:42:09.11 where you see an image that quite literally is of milky seas as described by the ancient mariners,
00:42:17.21 but what today we understand as glowing bacteria.
00:42:21.26 In this case an organism, likely called Vibrio harveyi, associating with micro-algae in this environment
00:42:28.22 that for whatever reasons that are not fully understood at this particular point in time
00:42:33.22 when this satellite image was taken, had a bloom and began luminescing like crazy, and filled up a volume the size of Connecticut.
00:42:41.27 All right, so, to end I want to just mention a few rules of microbial diversity
00:42:47.23 because almost everything that I have talked about so far
00:42:51.11 in this lecture ultimately comes back to the ability of organisms to generate energy in ways that are quite amazing.
00:42:59.06 And I would stipulate that microbes are by far the best chemists on the planet.
00:43:02.25 And so if you are a chemist, pay attention, because a lot of lessons can be learned from these guys.
00:43:07.06 All right. Now when we are talking about the phase of active growth,
00:43:11.13 the bottom-line that microbes are facing is they simply want to divide.
00:43:15.12 And to do this they need two things. They need energy, and they need carbon.
00:43:20.08 And beyond that, they are virtually unconstrained, although there are a few constraints,
00:43:26.25 and we will come back to that in a moment.
00:43:29.03 They need substrates, and these substrates can be organic or inorganic compounds.
00:43:36.11 This is now for the part where they are going to be generating energy.
00:43:40.22 Those substrates are converted to products through catabolic reactions, or energy generation, if you will.
00:43:49.09 And often times we think of energy generation in the form of ATP,
00:43:52.20 the most important energy carrying molecule within the cell.
00:43:57.06 Now this part of metabolism, catabolism, is coupled to anabolism,
00:44:03.12 which is the part of metabolism that is concerned with energy consumption, or biosynthesis.
00:44:08.12 And now down here what we are talking about is the conversion of
00:44:12.01 carbon, often in the monomeric form, to biomolecules that are far more complex, so protein, DNA, lipid, for example.
00:44:22.27 Now if we are thinking just about the substrates, as I said they can come from a variety of sources.
00:44:30.06 Always they're chemical, although light can help enable cells
00:44:34.21 to actually utilize those chemicals in ways that they otherwise wouldn't be able to do.
00:44:39.10 But when we are talking about the growth of organisms just purely on chemicals, without needing
00:44:46.15 a boost from light, the name we give to this metabolism is chemotrophy.
00:44:50.18 And that in turn is classified into two different types, inorganic and organic.
00:44:57.06 And when we are talking about inorganic sources of energy like hydrogen, and sulfide, and iron minerals,
00:45:03.18 this is called chemolithotrophy. And when we are talking about growing on organic substrates like glucose, or glycerol, or acetate,
00:45:11.23 this is called chemoorganotrophy.
00:45:14.04 And of course, as I said, while chemistry is always at the basis for any type of metabolism,
00:45:20.20 there is a photochemical boost that is often necessary,
00:45:25.09 when activating a compound that otherwise might not be biologically utilizable
00:45:30.16 for energy, and that is when we call that process a phototrophic one.
00:45:36.10 So the final part of this that I want to just mention is that the carbon source,
00:45:42.02 which is distinct or can be distinct from the energy source...
00:45:44.28 sometimes they are the same thing, but they don't have to be the same thing...
00:45:47.26 is either coming from inorganic carbon, CO2, or organic carbon.
00:45:52.19 And when it is coming from inorganic carbon that is called autotrophy,
00:45:55.21 and when it is coming from organic carbon, that is called heterotrophy.
00:45:58.22 So we are heterotrophs, we need to eat some type of organic carbon whether we are vegetarians
00:46:04.28 or meat eaters, but microorganisms are far more sophisticated.
00:46:09.12 They can eat minerals. They can just take CO2 from the air, and they'll be on their way.
00:46:17.14 So finally the last part I want to mention about metabolic diversity writ quite large
00:46:22.29 is that you can generate ATP through one of two different ways.
00:46:26.13 The first way is through what is called substrate level phosphorylation.
00:46:29.15 And this is also termed fermentation, and essentially is the process
00:46:33.22 where different types of reactions between chemicals within a cell
00:46:39.26 enable transfer of an inorganic phosphate ultimately to ADP to produce ATP.
00:46:49.21 And this process is enabled by chemical rearrangements within the cell
00:46:55.05 and reactions one on one between compounds.
00:46:57.18 The next major way that ATP can be formed in a cell is through the remarkable process of oxidative phosphorylation.
00:47:03.10 Basically this is about electron transport chains in membranes
00:47:07.23 that are coupled to generating a battery around a membrane
00:47:11.08 by extruding protons to one side and polarizing it so that there is an electrochemical potential gradient
00:47:18.00 across this membrane that can be harnessed to do the work of making ATP.
00:47:22.06 Now something that I am not showing you on this diagram,
00:47:25.03 but I want to introduce as terms are an electron donor and an electron acceptor.
00:47:31.00 So in metabolism there is always a substrate that is used as the primary electron donor
00:47:36.14 that can be metabolized through various pathways
00:47:39.08 and reduced to a compound that can donate electrons
00:47:43.17 to the electron transport chain in the membrane.
00:47:45.20 And then there is always something that serves as the acceptor of those electrons at the end of the chain,
00:47:52.10 and that is called the terminal electron acceptor.
00:47:54.28 And it is the path of electron transfer and proton translocation
00:47:58.22 between this electron donor and this terminal electron acceptor that is really harnessed by the membrane to do work.
00:48:05.05 And so that is what you see here pictured very generically without a whole lot of detail
00:48:10.08 in the sense that through this electron transport process,
00:48:13.20 which imagine if you will, is coupled as I said to proton translocation,
00:48:18.00 and that is achieved by different things within this membrane.
00:48:22.15 They can be proteins, or small molecules that are able to simultaneously
00:48:26.25 pass electrons through the membrane to something else
00:48:29.24 in the electron transport chain and push protons, or translocate protons
00:48:34.15 across the membrane so that there is this gradient that arises where there is more positive charge on the outside
00:48:42.07 than on the inside. Now once this happens this gradient can be used to drive ATP synthesis.
00:48:49.21 And this happens through a really amazing molecular machine called the ATP synthase,
00:48:54.09 which allows the traversal through the membrane of a proton,
00:48:58.27 that concomitantly gives the energy to phosphorylate ADP, adding that inorganic phosphate on, and making ATP.
00:49:09.08 And as this happens, the electrochemical potential gradient lessens.
00:49:15.00 And so that is what I am showing here: the energized membrane
00:49:16.25 due to proton transport coupled to electron transfer through the membrane,
00:49:22.10 and then this being expended and used in order to drive ATP synthesis.
00:49:26.12 Now while you can imagine a whole variety of things that can be electron donors
00:49:32.02 and electron acceptors from microbial metabolism,
00:49:34.27 metabolic diversity does have to conform to some rules.
00:49:37.06 And there are three that I want to point out that I think are particularly important.
00:49:41.02 The first is that the amount of energy has to be at a very minimal level,
00:49:47.14 at least in order to sustain the cell, both with regard to active growth, where you need a high level of energy,
00:49:53.27 at some threshold amount in order to double, but also at the level where you are generating enough energy simply to maintain
00:50:01.18 basic cellular processes even if they are not coupled directly to growth.
00:50:05.11 Now what is this number and how do we constrain it?
00:50:09.13 Thermodynamically, this can be expressed in this very straight forward equation here,
00:50:14.20 which is saying that the standard free energy that can be gained
00:50:18.04 from a process where there is electron transfer between the electron donor and the electron acceptor
00:50:23.13 is a function of the number of electrons transferred,
00:50:26.22 multiplied by the Faraday constant, and this in turn multiplied by
00:50:32.21 the difference in redox potential between the electron donor and the electron acceptor.
00:50:37.21 So for example, a common intracellular reductant, is NADH,
00:50:43.09 and in its oxidized state this is NAD+.
00:50:45.10 The redox potential of this redox pair is very low.
00:50:51.07 It is very negative on the electron potential scale that is typically expressed in millivolts.
00:50:57.07 On the other side of this scale are the electron acceptors with very high redox potentials, like oxygen.
00:51:04.20 And so when you couple through the membrane
00:51:09.27 a process of electron transfer from NADH to oxygen, thermodynamically you have the potential to generate
00:51:16.16 a lot of energy, and this is captured through a beautiful sequence of proton carriers and electron
00:51:24.14 transfer biomolecules contained within these membranes.
00:51:28.28 But these electron transport chains need not be between NADH and oxygen,
00:51:33.26 you can have a whole assemblage of things that can interrelate and so the minimum amount of energy
00:51:39.13 that needs to be supplied has been calculated. And this is a very crude estimation,
00:51:45.03 but it is an interesting study, and I refer you to below where you can see the reference.
00:51:49.05 Where for organisms operating in very low energy regime,
00:51:55.03 it was inferred that the minimum free energy required to sustain them and their growth
00:52:00.29 was about -4 kilojoules per mole, and that is about as low as you can go at least as experimentally measured.
00:52:06.21 Finally, regardless of the thermodynamic potential there are two other very important factors to keep in mind.
00:52:14.02 The second point is that the substrates themselves must be bioavailable. And so this is more of a kinetic problem
00:52:21.07 where we need to consider accessibility and transport of substrates
00:52:25.17 across the membrane to the site in the cell where they are used.
00:52:28.21 Or the ability of the cell to figure out a way to access them even if they can't transport them inside.
00:52:34.05 And the final point is that these substrates or the products after the metabolism has done its thing
00:52:42.00 must not themselves be toxic. So in the next couple of sections of this lecture,
00:52:47.26 I am going to give you examples of different microbial metabolisms to illustrate
00:52:52.12 these general points I have been making,
00:52:55.02 but I hope what you will remember from this seminar is the four big points about microbial diversity.
00:53:01.03 One, that it is incredibly ancient and over this long period of Earth history
00:53:06.08 numerous microorganisms in ubiquitous environments
00:53:09.18 have evolved diverse metabolisms that allow them
00:53:13.00 to catalyze fascinating chemical reactions and that these reactions
00:53:16.23 have affected not only the ability of the cells to grow and divide,
00:53:20.07 but in many instances have profoundly affected their environment,
00:53:24.09 be that environment one in an ancient ocean,
00:53:27.05 or today inside the human body.
00:53:30.18 Thank you.
Dr. Newman is a Professor in the Divisions of Biology and Geological and Planetary Sciences at the California Institute of Technology. When Newman began her undergraduate studies at Stanford University she wasn’t sure she was going to be a scientist because she was interested in a variety of different fields. In fact, she received her… Continue Reading
Early in his research career, Dr. Szostak made important contributions to the field of genetics. These included construction of the first yeast artificial chromosome and furthering our understanding of the function of telomeres, work for which he shared the Nobel Prize in Physiology or Medicine in 2009. By the 1990s, however, Szostak had redirected his… Continue Reading