Power, Sex, Suicide

by Nick Lane

  This was the approach employed by Maria Rivera and her colleagues at the University of California, Los Angeles, published in 1998 and in more detail in Nature in 2004. This team compared complete genome sequences from representatives of each of the three domains of life, and found that eukaryotes possess two distinct classes of genes, which they referred to as informational and operational genes. The informational genes encoded all the fundamental inheritance machinery of the cell, enabling it to copy and transcribe DNA, to replicate itself, and to build proteins. The operational genes encoded the workaday proteins involved in cellular metabolism—in other words, the proteins responsible for generating energy and manufacturing the basic building blocks of life, such as lipids and amino acids. Interestingly, almost all the operational genes came from the α-proteobacteria, presumably by way of the mitochondria, and the only real surprise was how many more of these genes there were than expected—it seems the genetic contribution of the ancestor of the mitochondria was greater than anticipated. But the biggest surprise was the allegiance of the informational genes. These genes lined up with the archaea, as anticipated, but they bore a strong resemblance to the genes in a completely unexpected group of archaea: they were most similar to methanogens, those swamp lovers that shun oxygen and produce the marsh gas methane.

  This is not the only piece of evidence to point a suspicious finger at the methanogens. John Reeve and his colleagues at Ohio State University, Columbus, have shown that the structure of eukaryotic histones (the proteins that wrap DNA) is closely related to methanogen histones. This similarity is surely no coincidence. Not only are the structures of the histones themselves closely related, but also the three-dimensional conformation of the whole DNA-protein package is amazingly similar. The chances of finding exactly the same structure in two organisms that are supposedly unrelated, like the methanogens and the eukaryotes, is equivalent to finding the same jet engine in two aeroplanes produced independently by two competing companies. Of course, we might well find the same engine, but we’d be incredulous if told that it had been ‘invented’ twice, without any knowledge of the rival company’s version, or of the prototype: we would assume that the engine had been bought or stolen from another company. In the same way, the packaging of DNA with histones is so similar in the methanogens and the eukaryotes that the most likely explanation is that they derived the full package from a common ancestor—both were developed from the same prototype.

  All this adds up to quite a package. Two tell-tale wisps of smoke curl out of the same smoking gun. If these wisps are believable, it seems we inherited both our informational genes and our histone proteins from the methanogens. Suddenly our most venerable ancestor is no longer the vile parasite that we suspected, but an even more alien entity, which survives today in stagnant swamps and the intestinal tract of animals. The original host in the eukaryotic merger was a methanogen.

  We are now in a position to see what kind of a hopeful monster the first eukaryotic cell might have been—the product of a merger between a methanogen (which gained its energy by generating methane gas) and an α-proteo-bacterium, for example a parasite like Rickettsia. This is a startling paradox. Few organisms hate oxygen more than the methanogens do—they can only be found living in the stagnant, oxygen-free pits of the world. Conversely, few organisms depend more on oxygen than Rickettsia—they are tiny parasites living inside other cells, and have streamlined themselves to their specialist niche by throwing away redundant genes, leaving them with only the genes needed to reproduce themselves—and the genes needed for oxygen respiration. Everything else has gone. So the paradox is this: if the eukaryotic cell was supposedly born of a symbiosis between an oxygen-hating methanogen and an oxygen-loving bacterium, how could the methanogen possibly benefit from having α-proteobacteria inside it? For that matter, how did the α-proteobacteria benefit from being inside? Indeed, if the host was incapable of phagocytosis—and methanogens are certainly not able to change shape and eat other cells—how on earth did it get inside?

  It is possible that Siv Andersson’s Ox-Tox hypothesis still applies—in other words, the oxygen-guzzling bacterium protected its host from toxic oxygen, enabling the methanogen to venture into pastures new. But there is a big difficulty with this scenario now. Such a relationship makes sense for a primitive archezoon that lives by fermenting organic remains. This will prosper if it is able to migrate to any environment where such remains can be found. Such scavenging cells are the single-celled equivalent of jackals prowling Africa, covering vast distances in the search for a fresh carcass. But this roving existence would kill a methanogen. A methanogen is as tied to a low-oxygen environment as a hippo is to waterholes. The methanogens can tolerate the presence of oxygen, but they can’t generate any energy in its presence, because they depend on hydrogen for fuel, and this is very rarely found in the same environment as oxygen. So if a methanogen does leave its watering hole, it must starve until it gets back: festering organic remains mean nothing to a methanogen—it would do better never to leave. Thus there is a deep tension between the interests of the methanogen, which gains nothing from venturing to pastures new, and those of an oxygen-guzzling parasite, which can’t generate any energy at all in the anoxic environment favoured by methanogens.

  This paradox is heightened because, as we have seen, their relationship could not have depended on energy in the form of exchangeable ATP—bacteria do not have ATP exporters, and never benevolently ‘feed’ each other. The tryst could still have been a parasitic relationship, in which the bacteria consumed the organic products of the methanogen from within—but again, there are problems with this, as an oxygen-dependent bacterium could not generate any energy from the innards of a methanogen unless it could persuade the methanogen to leave its waterhole, those comfortable oxygen-free surroundings. One might picture the α-proteobacteria herding the methanogens and driving them like cattle to an oxygen-rich slaughter field, but for bacteria this is nonsense. In short, the methanogens would starve if they left their waterhole; the oxygen-dependent bacteria would starve if they lived in the waterhole, and the middle ground, a little oxygen, must have been equally disadvantageous to both parties. Such a relationship seems to be mutually insufferable—is this really how the stable symbiotic relationship of the eukaryotic cell began? It is not just improbable, but downright preposterous. Luckily there is another possibility, which until recently seemed fanciful, but is now looking far more persuasive.

  3

  The Hydrogen Hypothesis

  The quest to find the progenitor of the eukaryotic cell has run into dire straits. The idea that there might have been a primitive intermediate, a missing link with a nucleus but no mitochondria, has not been rigorously disproved, but looks more and more unlikely. Every promising example has turned out not to be a missing link at all, but rather to have adapted to a simpler lifestyle at a later date. The ancestors of all these apparently primitive groups did possess mitochondria, and their descendents eventually lost them while adapting to new niches, often as parasites. It seems possible to be a eukaryote without having mitochondria—there are a thousand such species among the protozoa—but it does not seem possible to be a eukaryote without once having had mitochondria, deep in the past. If the only way to be a eukaryotic cell is via the possession of mitochondria, then it might be that the eukaryotic cell itself was originally crafted from a symbiosis between the bacterial ancestors of the mitochondria and their host cells.

  If the eukaryotic cell was born of a merger between two types of cell, the question becomes more pressing—what types of cell? According to the textbook view, the host cell was a primitive eukaryotic cell, without mitochondria, but this obviously can’t be true if there never was a primitive eukaryotic cell that lacked mitochondria. In her endosymbiosis theory, Lynn Margulis had in fact proposed a union between two different types of bacteria, and her hypothesis looked set for a return to prominence after the demise of the missing link. Even so, Margulis and everyone else were thinkin
g along the same lines—the host, they imagined, must have relied on fermentation to produce its energy, in the same way that yeasts do today, and the advantage that the mitochondria brought with them was an ability to deal with oxygen, giving their hosts a more efficient way of generating energy. The exact identity of the host could potentially be traced by comparing the gene sequences of modern eukaryotes with various groups of bacteria and archaea—and modern sequencing technology was just beginning to make that possible. But, as we have just seen, the apparent answer came as another shock: the genes of eukaryotic cells seem to be related most closely to methanogens, those obscure methane-producing archaea that live in swamps and intestines.

  Methanogens! This answer is an enigma. In Chapter 1, we noted that the methanogens live by reacting hydrogen gas with carbon dioxide, and evanescing methane gas as a waste product. Free hydrogen gas only exists in the absence of oxygen, so the methanogens are restricted to anoxic environments—any marginal places where oxygen is excluded. It’s actually worse than that. Methanogens can tolerate some oxygen in their surroundings, just as we can survive underwater for a short time by holding our breath. The trouble is that methanogens can’t generate any energy in these circumstances—they have to ‘hold their breath’ until they get back to their preferred anoxic surroundings, because the processes by which they generate their energy can only work in the strict absence of oxygen. So if the host cell really was a methanogen, this raises a serious question about the nature of the symbiosis—why on earth would a methanogen form a relationship with any kind of bacteria that relied upon oxygen to live? Today, modern mitochondria certainly depend on oxygen, and if it was ever thus, neither party could make a living in the land of the other. This is a serious paradox and did not seem possible to reconcile in conventional terms.

  Then in 1998, Bill Martin, whom we met in Chapter 1, stepped into the frame, presenting a radical hypothesis in Nature with his long-term collaborator Miklós Müller, from the Rockefeller University in New York. They called their theory the ‘hydrogen hypothesis’, and as the name implies it has little to do with oxygen and much to do with hydrogen. The key, said Martin and Müller, is that hydrogen gas can be generated as a waste product by some strange mitochondria-like organelles called hydrogenosomes. These are found mostly among primitive single-celled eukaryotes, including parasites such as Trichomonas vaginalis, one of the discredited ‘archezoa’. Like mitochondria, hydrogenosomes are responsible for energy generation, but they do this in bizarre fashion by releasing hydrogen gas into their surroundings.

  For a long time the evolutionary origin of hydrogenosomes was shrouded in mystery, but a number of structural similarities prompted Müller and others, notably Martin Embley and colleagues at the Natural History Museum in London, to propose that hydrogenosomes are actually related to mitochondria—they share a common ancestor. This was difficult to prove as most hydrogenosomes have lost their entire genome, but it is now established with some certainty.1 In other words, whatever bacteria entered into a symbiotic relationship in the first eukaryotic cell, its descendents numbered among them both mitochondria and hydrogenosomes. Presumably, said Martin—and this is the crux of the dilemma faced today—the original bacterial ancestor of the mitochondria and hydrogenosomes was able to carry out the metabolic functions of both. If so, then it must have been a versatile bacterium, capable of oxygen respiration as well as hydrogen production. We’ll return to this question in a moment. For now, lets simply note that the ‘hydrogen hypothesis’ of Martin and Müller argues that it was the hydrogen metabolism of this common ancestor, not its oxygen metabolism, which gave the first eukaryote its evolutionary edge.

  Martin and Müller were struck by the fact that eukaryotes containing hydrogenosomes sometimes play host to a number of tiny methanogens, which have gained entry to the cell and live happily inside. The methanogens align themselves with the hydrogenosomes, almost as if feeding (Figure 3). Martin and Müller realized that this was exactly what they were doing—the two entities live together in a kind of metabolic wedlock. Methanogens are unique in that they can generate all the organic compounds they need, as well as all their energy, from nothing more than carbon dioxide and hydrogen. They do this by attaching hydrogen atoms (H) onto carbon dioxide (CO2) to produce the basic building blocks needed to make carbohydrates like glucose (C6H12O6), and from these they can construct the entire repertoire of nucleic acids, proteins, and lipids. They also use hydrogen and carbon dioxide to generate energy, releasing methane in the process.

  While methanogens are uniquely resourceful in their metabolic powers, they nonetheless face a serious obstacle, and we have already noted the reason in Chapter 1. The trouble is that, while carbon dioxide is plentiful, hydrogen is hard to come by in any environment containing oxygen, as hydrogen and oxygen react together to form water. From the point of view of a methanogen, then, anything that provides a little hydrogen is a blessing. Hydrogenosomes are a double boon, because they release both hydrogen gas and carbon dioxide, the very substances that methanogens crave, in the process of generating their own energy. Even more importantly, they don’t need oxygen to do this—quite the contrary, they prefer to avoid oxygen—and so they function in the very low-oxygen conditions required by methanogens. No wonder the methanogens suckle up to hydrogenosomes like greedy piglets! The insight of Martin and Müller was to appreciate that this kind of intimate metabolic union might have been the basis of the original eukaryotic merger.

  Bill Martin argues that the hydrogenosomes and the mitochondria stand at opposite ends of a little-known spectrum. Rather surprisingly, to anyone who is most familiar with textbook mitochondria, many simple single-celled eukaryotes have mitochondria that operate in the absence of oxygen. Instead of using oxygen to burn up food, these ‘anaerobic’ mitochondria use other simple compounds like nitrate or nitrite. In most other respects, they operate in a very similar fashion to our own mitochondria, and are unquestionably related. So the spectrum stretches from aerobic mitochondria like our own, which are dependent on oxygen, through ‘anaerobic’ mitochondria, which prefer to use other molecules like nitrates, to the hydrogenosomes, which work rather differently but are still related. The existence of such a spectrum focuses attention on the identity of the ancestor that eventually gave rise to the entire spectrum. What, asks Martin, might this common ancestor have looked like?

  3 The image shows methanogens (light grey) and hydrogenosomes (dark grey). All are living inside the cytoplasm of a much larger eukaryotic cell, specifically the marine ciliate Plagiopyla frontata. According to the hydrogen hypothesis, such a close metabolic relationship between methanogens (which need hydrogen to live) and hydrogen-producing bacteria (the ancestor of the mitochondria as well as hydrogenosomes) may have ultimately given rise to the eukaryotic cell itself: the methanogens became larger, to physically engulf the hydrogen-producing bacteria.

  This question has profound significance for the origin of the eukaryotes, and so for all complex life on earth or anywhere else in the universe. The common ancestor could have taken one of two forms. It could have been a sophisticated bacterium with a large bag of metabolic tricks, which were later distributed to its descendents, as they adapted to their own particular niches. If that were the case, then the descendents could be said to have ‘devolved’, rather than ‘evolved’, for they became simpler and more streamlined as they grew specialized. The second possibility is that the common ancestor was a simple oxygen-respiring bacterium, perhaps the free-living ancestor of Rickettsia we discussed in the previous chapter. If that were the case, then its descendents must have become more diverse over evolution—they ‘evolved’ rather than ‘devolved’. The two possibilities generate specific predictions. In the first case, if the ancestral bacterium was metabolically sophisticated, then it was in a position to hand down specialized genes directly to its ancestors, such as those for hydrogen production. Any eukaryotes adapting to hydrogen production could have inherited its genes from this common ancestor,
regardless of how diverse they were to become later. Hydrogenosomes are found in diverse groups of eukaryotes. If they inherited their hydrogen-producing genes from the same ancestor, then these genes should be closely related to each other, regardless of how diverse their host cells became later. On the other hand, if all the diverse groups had originally inherited simple, oxygen-respiring mitochondria, they had to invent all the different forms of anaerobic metabolism independently, whenever they happened to adapt to a low-oxygen environment. In the case of the hydrogenosomes, the hydrogen-producing genes would necessarily have evolved independently in each case (or transferred randomly by lateral gene transfer), and so their evolutionary history would be just as varied as that of their host cells.

  These possibilities give a plain choice. If the ancestor was metabolically sophisticated, then all the hydrogen-producing genes should be related, or at least could be related. On the other hand, if it was metabolically simple, then all these genes should be unrelated. So which is it? The answer is as yet unproved, but with a few exceptions, most evidence seems to favour the former proposition. Several studies published in the first years of the millennium attest to a single origin for at least a few genes in the anaerobic mitochondria and hydrogenosomes, as predicted by the hydrogen hypothesis. For example, the enzyme used by hydrogenosomes to generate hydrogen gas (the pyruvate: ferredoxin oxidoreductase, or PFOR), was almost certainly inherited from a common ancestor. Likewise the membrane pump that transports ATP out of both mitochondria and hydrogenosomes seems to share a similar ancestry; and an enzyme required for the synthesis of a respiratory iron-sulphur protein also appears to derive from a common ancestor. These studies imply that the common ancestor was indeed metabolically versatile and could respire using oxygen or other molecules, or generate hydrogen gas, as the circumstances dictated. Critically, such versatility (which might otherwise sound somewhat hypothetical) does exist today in some groups of α-proteobacteria such as Rhodobacter, which might therefore resemble the ancestral mitochondria better than does Rickettsia.