Natural selection has evidently favored mitochondria with small genomes. By contrast, the nuclear genomes of most eukaryotes seem to have been free to enlarge. Perhaps the eukaryotic way of life has made large size an advantage: predators typically need to be bigger than their prey, and cell size generally increases in proportion to genome size. Whatever the reason, aided by a massive accumulation of DNA segments derived from parasitic transposable elements (discussed in Chapter 5), the genomes of most eukaryotes have become orders of magnitude larger than those of bacteria and archaea (Figure 1–32).
The freedom to be extravagant with DNA has had profound implications. Eukaryotes not only have more genes than prokaryotes; they also have vastly more DNA that does not code for protein. The human genome contains 1000 times as many nucleotide pairs as the genome of a typical bacterium, perhaps 10 times as
Figure 1–31 The origin of chloroplasts.
An early eukaryotic cell, already possessing mitochondria, engulfed a photosynthetic bacterium (a cyanobacterium) and retained it in symbiosis. Present-day chloroplasts are thought to trace their ancestry back to a single species of cyanobacterium that was adopted as an internal symbiont (an endosymbiont) over a billion years ago.
Figure 1–32 Genome sizes compared.
Genome size is measured in nucleotide pairs of dnA per haploid genome, that is, per single copy of the genome. (The cells of sexually reproducing organisms such as ourselves are generally diploid: they contain two copies of the genome, one inherited from the mother, the other from the father.) closely related organisms can vary widely in the quantity of dnA in their genomes, even though they contain similar numbers of functionally distinct genes. (data from
W.h. li, molecular evolution, pp. 380–383. sunderland, mA: sinauer, 1997.) many genes, and a great deal more noncoding DNA (~98.5% of the genome for a human does not code for proteins, as opposed to 11% of the genome for the bacterium E. coli). The estimated genome sizes and gene numbers for some eukaryotes are compiled for easy comparison with E. coli in Table 1–2; we shall discuss how each of these eukaryotes serves as a model organism shortly.
Much of our noncoding DNA is almost certainly dispensable junk, retained like a mass of old papers because, when there is little pressure to keep an archive small, it is easier to retain everything than to sort out the valuable information and discard the rest. Certain exceptional eukaryotic species, such as the puffer fish, bear witness to the profligacy of their relatives; they have somehow managed to rid themselves of large quantities of noncoding DNA. Yet they appear similar in structure, behavior, and fitness to related species that have vastly more such DNA (see Figure 4–71).
Even in compact eukaryotic genomes such as that of puffer fish, there is more noncoding DNA than coding DNA, and at least some of the noncoding DNA certainly has important functions. In particular, it regulates the expression of adjacent genes. With this regulatory DNA, eukaryotes have evolved distinctive ways of controlling when and where a gene is brought into play. This sophisticated gene regulation is crucial for the formation of complex multicellular organisms.
The Genome defines the Program of multicellular development
The cells in an individual animal or plant are extraordinarily varied. Fat cells, skin cells, bone cells, nerve cells—they seem as dissimilar as any cells could be (Figure 1–33). Yet all these cell types are the descendants of a single fertilized egg cell, and all (with minor exceptions) contain identical copies of the genome of the species.