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  I’m not trying to cry revolution. There is nothing exceptional about these arguments, and symbiosis is part of the standard evolutionary canon, even if it is played down as a mechanism of generating novelty. For example, the late, great John Maynard Smith and Eörs Szathmáry, in their stimulating book The Origins of Life, argue that biological symbiosis is analogous to a motorbike, which is a symbiosis between a bicycle and the internal combustion engine. Even if we view this symbiosis as an advance, they say, with rather crusty humour, someone still had to invent the bicycle and the internal combustion engine first. Likewise in life, natural selection must invent the parts first, and symbiosis just makes creative use of the available parts. Thus symbiosis is best explained in Darwinian terms.

  All this is true, but it obscures the fact that some of the most profound evolutionary novelties are made possible only by symbiosis. Presumably, if we follow Maynard Smith and Szathmáry, if a bicycle and an internal combustion engine can evolve independently by natural selection, then so too, in principle, could the motorcycle. No doubt it’s faster to evolve a motorcycle by shuffling existing components, but there is no fundamental reason why it should not have evolved anyway, given enough time, in the absence of symbiosis. In the case of the eukaryotic cell, I disagree. Left to themselves, I will argue, bacteria could not evolve into eukaryotes by natural selection alone: symbiosis was needed to bridge the gulf between bacteria and eukaryotes, and in particular a mitochondrial merger was necessary to sow the seeds of complexity. Without mitochondria, complex life is simply not possible, and without symbiosis, mitochondria are not possible—without the mitochondrial merger we would be left with bacteria and nothing but. Regardless of whether we consider symbiosis Darwinian or not, an understanding of why symbiotic mitochondria are necessary is paramount to an understanding of our own past, and our place in the universe.1

  9 Merezhkovskii’s inverted tree of life, showing fusion of branches. The standard ‘Darwinian’ tree of life is strictly bifurcating: branches branch but do not fuse. The origin of the eukaryotic cell was endosymbiotic. On the tree of life, this is represented as bifurcation backwards: branches fuse together, inverting part of the tree of life.

  In Part 3, we will see why there is such a yawning chasm between the prokaryotes and the eukaryotes, and why this deep divide can only be bridged by symbiosis—it is next to impossible, given the mechanism of chemiosmotic energy production (discussed in Part 2) for eukaryotes to evolve by natural selection from prokaryotes. This is why bacteria are still bacteria, and why it is unlikely that life as we know it, based on cells, carbon chemistry, and chemiosmosis, will progress beyond the bacterial level of complexity anywhere else in the universe. In Part 3, we’ll see why mitochondria seeded complexity in the eukaryotes, placing them at the beginning of the ramp of ascending complexity; and in Part 4, we’ll see why mitochondria impelled the eukaryotes onwards up the ramp.

  7

  Why Bacteria are Simple

  The great French molecular biologist François Jacob once remarked that the dream of every cell is to become two cells. In our own bodies, this dream is held very carefully in check; otherwise the result would be cancer. But Jacob was trained as a microbiologist, and for bacteria, one cell becoming two is more than a dream. Bacteria replicate at colossal speed. When well fed, E. coli bacteria divide once every 20 minutes, or 72 times a day. A single E. coli bacterium weighs about a trillionth of a gram (10–12 g). Seventy-two cell divisions in a day corresponds to an amplification of 272 (= 1072 × log2 = 1021.6), which is an increase in weight from 10–12 grams to 4000 metric tons. In two days, the mass of exponentially doubling E. coli would be 2664 times larger than the mass of the Earth (which weighs 5.977 × 1021 metric tons)!

  Luckily this does not happen, and the reason is that bacteria are normally half starved. They swiftly consume all available food, whereupon their growth is limited once again by the lack of nutrients. Most bacteria spend most of their lives in stasis, waiting for a meal. Nonetheless, the speed at which bacteria do mobilize themselves to replicate upon feeding illustrates the overwhelming strength of the selection pressures at work. Amazingly, E. coli cells divide in two faster than they can actually replicate their own DNA, which takes about 40 minutes (or twice the time required for cell division). They can do this because they begin a new round of DNA replication well before the previous round is finished. During rapid cell division, several copies of the full bacterial genome are produced simultaneously in any one cell.

  Bacteria are gripped by the naked tyranny of natural selection. Speed is paramount, and herein lies the secret to why bacteria are still bacteria. Imagine a population of bacteria whose growth is restricted by nutrient availability. Feed it. The bacterial cells proliferate. The cells that replicate fastest swiftly dominate the population, whilst those that replicate more slowly are displaced. When the nutrient supply runs out, we are left with a new population held in limbo, at least until the next meal comes along. As long as the fastest replicators are robust, and so able to survive in the wild, the new population mix inevitably comprises mostly the fastest replicators. This is as plain as the fact that the Chinese will come to dominate the world’s population unless their stringent birth-control laws succeed in limiting families to one or two children.

  Because cell division is faster than DNA replication, the speed at which bacteria can possibly divide is limited by the speed at which they can replicate their DNA. Even though bacteria can speed up their DNA replication by making more than one copy per cell division, there is a limit to the number of copies that can be made at once. In principle, the speed of DNA replication depends on the size of the genome, and the resources available for copying it. A suitable energy reserve in the form of ATP is necessary, if not sufficient, for replication. Cells that are not energetically efficient, or starved of resources, make less ATP and so tend to be slower to copy their genome. In other words, to thrive, bacteria must replicate their genome faster than the competition, and to do so requires either a smaller genome or more effective energy production. If two bacterial cells generate ATP at the same speed, then the cell with the smallest genome will tend to replicate fastest, and will eventually come to dominate the population.

  A bacterial cell can tolerate a larger genome if the extra genes enable it to produce ATP more effectively than its competitors during times of lean resources. In a fascinating study, Konstantinos Konstantinidis and James Tiedje, at Michigan State University, examined all 115 fully sequenced bacterial genomes. They found that the bacteria with the largest genomes (about 9 or 10 million letters, encoding 9000 genes) dominate in environments where resources are scarce but diverse, and where there is little penalty for slow growth, in particular the soil. Many soil bacteria only manage to produce about three generations in a year, so there is less selection for speed than for any replication whatsoever. Under these conditions, an ability to take advantage of scant resources is important—and this in turn requires more genes to code for the extra metabolic flexibility needed. So versatility pays dividends if it offers a clear advantage in terms of reproductive speed. It is no accident that bacteria such as Streptomyces avermitilis, which are ubiquitous in the soil, are metabolically versatile with big genomes to match.

  Thus, in bacteria, larger genomes can be tolerated when growth is slow, and versatility is at a premium. Even so, there is still selection for small size in relation to other versatile bacteria, and this apparently sets a bacterial genome ‘ceiling’ of about 10 million DNA letters. These are the largest genomes among bacteria, and most have far fewer genes. In general, it is probably fair to say that bacterial genomes are small in size because larger genomes take more time and energy to replicate, and so are selected against. Yet even the most versatile bacteria have small genomes in comparison with the eukaryotic cells living in the same environment. How the eukaryotes were released from a selection pressure that stifles even the most versatile bacteria is the subject of this chapter.

  Gene loss as
an evolutionary trajectory

  To maintain a small genome, bacteria could either remain passively unchanging, always with the same hand of genes, like a gambler with cold feet, or they could be more dynamic, constantly losing and winning genes—playing their hand and taking another. Perhaps surprisingly, at least for anyone who likes to think of evolution as a steady progression towards greater sophistication (and so more genes), bacteria are quick to gamble with their genes. They lose as often as not: gene loss is common in bacteria.

  One of the most extreme examples of gene loss is Rickettsia prowazekii, the cause of typhus, a terrible epidemic that preys on overcrowded populations in filthy conditions, rife with rats and lice. Over history, epidemic typhus has wiped out whole armies, including Napoleon’s armies in Russia, the vestiges of which escaped from Russia in 1812 ridden with typhus, along with many refugees from Poland and Lithuania. Rickettsia prowazekii is named after two pioneering investigators in the early years of the twentieth century, the American Howard Ricketts and the Czech Stanislaus von Prowazek. Along with the French Tunisian Charles Nicolle, Ricketts and Prowazek discovered that the disease is transmitted through the faeces of the human body louse. Sadly, by the time a vaccine had finally been developed in 1930, almost all these early pioneers had died of typhus, including both Ricketts and Prowazek. The sole survivor, Nicolle, received the Nobel Prize for his dedicated work in 1928. Nicolle’s discoveries were put to use in the First and Second World Wars, when hygienic measures, such as shaving, washing, and burning clothes, helped limit the spread of the disease.

  Rickettsia is a tiny bacterium, almost as small as a virus, which lives as a parasite inside other cells. It is so well adapted to this lifestyle that it can no longer survive outside its host cells. Its genome was first sequenced by Siv Andersson and her colleagues at the University of Uppsala in Sweden, and was published in Nature in 1998 to great clamour. The genome of Rickettsia has been streamlined by its intracellular lifestyle in a similar manner to our own mitochondria—and its remaining genes also share many sequence similarities, prompting Andersson and colleagues to declare Rickettsia the closest living relative to mitochondria, though as we saw in Part 1, others disagree.

  Here it is Rickettsia’s propensity to lose genes that concerns us. Over evolutionary time Rickettsia has lost most of its genes, and now has a mere 834 protein-coding genes left. While this is an order of magnitude more than the mitochondria of most species, Rickettsia has barely a quarter of the number of genes of its closest relatives in the wild. It was able to lose most of its genes in this way simply because they were not needed: life inside other cells, if you can survive there at all, is a spoon-fed existence. The parasites live in the kitchen of a lavish chef, and need make little for themselves. Ironically, instead of becoming fatter, they lose weight: they throw away superfluous genes.

  Let’s pause here for a moment, and think about the pressure to lose genes. Genetic damage is random, and might happen to any gene at any time; but gene loss is not random. Any cell or organism that loses an essential gene (or has it damaged such that its function is lost) will perish: it can no longer survive in the wild, and so will be eliminated by natural selection. On the other hand, if a gene is not essential, then its loss or damage, by definition, cannot be catastrophic. In our own case, our primate ancestors lost the gene for making vitamin C a few million years ago, but did not perish because their diet was rich in fruit, which provided them with plenty of vitamin C. They survived and prospered. We know because most of the gene is still there in our ‘junk’ DNA, as eloquent as the wreck of a ship with a hole beneath the waterline. The remaining sequence corresponds closely to the functional gene in other species.

  At a biochemical level Rickettsia is an extreme equivalent of our primate ancestors. It doesn’t need the genes for making many essential cellular chemicals (such as amino acids and nucleotides) from scratch any more than we need a gene for making vitamin C: it can simply import them all from its host cell. If the genes for making such chemicals in Rickettsia happen to be damaged, so what?—they can be lost with impunity. Unusually among bacteria, nearly a quarter of the total genome of Rickettsia is composed of ‘junk’ DNA. This ‘junk’ is the recognizable relic of recently sunken genes. These shipwrecked genes lie broken, their memory not yet obliterated: their hulks are still rotting in the genome. Such junk DNA will almost certainly be lost altogether in time, as it slows the replication of Rickettsia. Mutations that delete unnecessary DNA will be selected for when they happen, as they speed up replication. So damage is a first step, followed by the complete loss of genes. Rickettsia has already lost four-fifths of its genome in this way and the process is continuing today. As Siv Andersson put it: ‘genome sequences are only snapshots in evolutionary time and space.’ Here the snapshot is a moment in the evolutionary degeneration of a parasite that is losing its unnecessary genes.

  Balancing gene loss and gain in bacteria

  Most bacteria, of course, are not intracellular parasites, but live in the outside world. They need many more genes than Rickettsia. Nonetheless, they face a similar pressure to lose superfluous genes—they just can’t afford to lose as many. The tendency of free-living bacteria to lose genes can be measured in the laboratory. In 1998, the Hungarian researchers Tibor Vellai, Krisztina Takács, and Gábor Vida, then all at the Eötvös Loránd University in Budapest, reported some simple (conceptually if not technically) but revealing experiments. They engineered three bacterial gene ‘rings’, or plasmids (the genetic ‘loose change’ we met in Chapter 1). Each plasmid contained a gene conferring resistance to an antibiotic, and the only important difference between them was their size—each plasmid contained different amounts of non-coding DNA. The plasmids were then added to cultures of E. coli bacteria, which were allowed to grow. The bacteria take up the plasmid—they are transfected—and can call upon the gene if necessary.

  In the first set of experiments, the Hungarian investigators grew the three transfected cultures in the presence of the antibiotic. Any bacterium that lost its plasmid would thereby lose its resistance to the antibiotic, and so be killed. Under this selection pressure, the colonies with the largest plasmids grew the slowest, because they had to spend more time and effort copying their DNA. After only 12 hours in culture the cells with the smallest plasmids had outgrown their lumbering cousins tenfold. In the second set of experiments, bacteria were cultured without antibiotic. Now all three cultures grew at similar speeds, regardless of the size of the plasmid. How so? When the cultures were double-checked for the presence of the plasmids, it turned out that the superfluous plasmids were being lost. All three cultures of bacteria were able to grow at a similar rate because they jettisoned the genes for antibiotic resistance, which are not essential when bacteria are cultured in the absence of the antibiotic. The bacteria simply threw away the unnecessary genes in their rush to replicate faster—a case of ‘use it or lose it!’

  These studies show that bacteria can lose superfluous genes in a matter of hours or days. Such fast gene loss means that bacterial species tend to retain the smallest number of genes compatible with viability at any one moment. Natural selection is like an ostrich with its head buried in the sand—it doesn’t matter how stupid an action might be in the long term, so long as it provides some momentary respite. In this case, if the gene for antibiotic resistance is not necessary, it is lost from most cells in a population even if it may turn out to be needed again at some point in the future. Just as bacteria lose the genes for antibiotic resistance, they also lose other genes that are not essential at a particular moment. Such genes are more easily lost from a portable chromosome such as a plasmid, but bacteria can also lose genes that are part of their main chromosome, albeit more slowly. Any gene that is not used regularly will tend to be lost as a result of random mutations and selection for faster replication. The efficiency of these mechanisms acting on the main bacterial chromosome is illustrated by their low amount of ‘junk’ DNA, as well as the low number o
f genes in relation to eukaryotes. Bacteria are small and streamlined because they bin any excess baggage at the first opportunity.

  Throwing away genes is not as foolhardy as it may sound, however, for bacteria can also pick up the same genes again, as well as others. The existence of lateral gene transfer—the uptake of DNA from the surroundings (from dead cells) or other bacteria, by a form of copulation known as bacterial conjugation—shows that bacteria can and do accumulate new genes. Active gain of genes compensates for gene loss. In a fluctuating environment, it is unlikely that all redundant genes will be lost from all bacteria in a population before the conditions change again (for example, with changing seasons), as gene loss is a random process. At least a fraction of the bacterial population is likely to have retained the redundant genes in full working order, and when the conditions change again they can pass them around the population by lateral gene transfer. Such open-handedness with genes explains how antibiotic resistance can spread so swiftly through an entire population of bacteria.

  Although the importance of lateral gene transfer in bacteria has been recognized since the 1970s, we have only recently begun to appreciate the degree to which it can confound evolutionary trees. In some bacterial species, more than 90 per cent of observed variation in a population comes from lateral gene transfer, rather than the conventional selection of cells in clones or colonies. The transfer of genes between different species, genera, and even domains means that bacteria do not pass on a consistent core of genes by vertical inheritance, as we do to our children. This makes it embarrassingly difficult to define the term ‘species’ in bacteria. In plants and animals, a species is defined as a population of individuals that can interbreed to produce fertile offspring. This definition does not apply to bacteria, which divide asexually to form clones of supposedly identical cells. In theory, the clones drift apart over time as a result of mutations, leading to genetic and morphological differences sufficient to call ‘speciation’. But lateral gene transfer often confounds this outcome. Genes can be switched so quickly and so comprehensively that the cacophony obliterates all traces of ancestry—no gene is passed on to daughter cells for more than a few generations before being replaced by an equivalent gene from another cell with a different ancestry. The current champion is Neisseria gonorrhoeae: this recombines genes so quickly that it is impossible to detect any clonal groups at all: even the gene for ribosomal RNA, often claimed to represent the true phylogeny (lineage) of bacteria, is swapped so often that it gives no indication of ancestry.