What happens to the genes that are transferred? According to Bill Martin, whom we met in both Parts 1 and 2, such a process might account for the origin of the eukaryotic nucleus. To understand how, we need to recall two points that we have discussed in earlier chapters. First, recall that Martin's hydrogen hypothesis argues that the eukaryotic cell was first forged from the union of an archaeon and a bacterium. And second, recall from Chapter 6 (page 98) that archaea and bacteria have different types of lipid in their cell membranes. The details don't matter here, but consider the kind of membranes we would expect to find in that first, chimeric eukaryote. The host cell, being an archaeon, should have had archaeal membranes. The mitochondria, being bacterial, should have had bacterial membranes. So what do we actually see today? Eukaryotic membranes are uniformly bacterial in nature—both in their lipid structure and in many details of their embedded proteins (like the proteins that make up the respiratory chain, and similar proteins found in the nuclear membrane). The bacterial-style membranes of the eukaryotes include the cell membrane, the mitochondrial membranes, other internal membrane structures, and the double nuclear membrane. In fact there is no trace of the original archaeal membranes in the eukaryotes, despite the fact that other features make it virtually certain that the original host cell was indeed an archaeon.
Such basic consistency, when we would expect to find disparity, has led some researchers to question the hydrogen hypothesis, but Martin considers the apparent anomaly to be a strength. He suggests that the genes for making bacterial lipids were transferred to the host cell, along with many other genes. Presumably, if functional, the genes went ahead with their normal tasks, such as making lipids; there is no reason why they should not function normally as before. But there may have been one difference—the host cell may have lost the ability to target protein products to particular locations in the cell (protein targeting relies on an 'address' sequence that differs in different species). The host cell may therefore have been able to make bacterial products, such as lipids, but not known exactly what to do with them; in particular, where to send them. Lipids, of course, don't dissolve in water, and so if not targeted to an existing membrane would simply precipitate as lipid vesicles—spherical droplets enclosing a hollow watery space. Such droplets fuse as easily as soap bubbles, extending into vacuoles, tubes, or flattened vesicles. In the first eukaryote, these vesicles might simply have coalesced where they were formed, around the chromosome, to form loose, baggy membrane structures. Now this is exactly the structure of the nuclear membrane today—it is not a continuous double membrane structure like the mitochondria or chloroplasts, but is composed of a series of flattened vesicles, and these are continuous with the other membrane systems within the cell. What's more, when modern eukaryotic cells divide, they dissolve the nuclear membrane, to separate the chromosomes destined for each of the daughter cells; and a fresh nuclear membrane forms around the chromosomes in each of these daughter cells. It does so by coalescing in a manner reminiscent of Martin's proposal, and remains continuous with the other membrane systems of the cell. Thus, in Martin's scenario, gene transfer accounts for the formation of the nuclear membrane, as well as all the other membrane systems of eukaryotic cells. All that was needed was a degree of orientational confusion, a map-reading hiatus.
There is still one step to go: we need to put together a cell with bacterial-style membranes throughout, in other words we need to replace the archaeal lipids of the cell membrane with bacterial lipids. How did this happen? Presumably, if bacterial lipids offered any advantage, such as fluidity, or adaptability to different environments, then any cell that expressed only the bacterial lipids would be at an advantage. Natural selection would ensure that the archaeal lipids were replaced, if such an advantage existed: there was little call for evolutionary 'novelty'; it was merely a matter of playing with existing parts. It remains possible, however, that some eukaryotes did not go the whole hog. It would be interesting to know if there are still any primitive eukaryotic cells that retain vestiges of archaeal lipids in their membranes. In support of the possibility, virtually all eukaryotes, including fungi, plants, and animals like ourselves still possess all the genes for making the basic carbon building blocks of archaeal lipids, the isoprenes (see page 99). We don't use them for building membranes any more, however, but for making an army of isoprenoids, otherwise known as terpenoids or terpenes. These include any structure composed of linked isoprene units, and together make up the single largest family of natural products known, totalling more than 23 000 catalogued structures. These include steroids, vitamins, hormones, fragrances, pigments, and some polymers. Many isoprenoids have potent biological effects, and are being used in pharmaceutical development; the anticancer drug Taxol, for example, a plant metabolite, is an isoprenoid. So we haven't lost the machinery for making archaeal lipids at all; if anything, we have enriched it.
If his theory is correct, then Martin has derived an essentially complete eukaryotic cell via a simple succession of steps: it has a nucleus enveloped by a discontinuous double membrane; it has internal membrane structures; and it has organelles such as mitochondria. The cell is free to lose its cell wall (but not, of course, its external cell membrane), as it no longer needs a periplasm to generate energy. Being derived from a methanogen, it wraps its genes in histone proteins and has a basically eukaryotic system of transcribing its genes and building proteins (see Part 1). On the other hand, this hypothetical progenitor eukaryotic cell probably did not engulf its food whole by phago-cytosis—despite having a cytoskeleton (inherited from the archaea or the bacteria), it has not yet derived the dynamic cytoskeleton characteristic of mobile protozoa like amoeba. Rather, the first eukaryotes may have resembled unicellular fungi, which secrete various digestive enzymes into their surroundings, to break down food externally. This conclusion is corroborated by some recent genetic studies, but we won't look into these here, for too many uncertainties remain.
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