The Evolution Of The Genome
Mutation and recombination provide the genome with the means to evolve, but we learn very little about the evolutionary histories of genomes simply by studying these events in living cells. Instead we must combine our understanding of mutation and recombination with comparisons between the genomes of different organisms in order to infer the patterns of genome evolution that have occurred. Clearly, this approach is imprecise and uncertain but, as we will see, it is based on a surprisingly large amount of hard data and we can be reasonably confident that, at least in outline, the picture that emerges is not too far from the truth.
The Evolution of the Genome
In this chapter we will explore the evolution of genomes from the very origins of biochemical systems through to the present day. We will look at ideas regarding the RNA world, prior to the appearance of the first DNA molecules, and then examine how DNA genomes have gradually become more complex. Finally, in Section 15.4 we will compare the human genome with the genomes of other primates in order to identify the evolutionary changes that have occurred during the last five million years and which must, somehow, make us what we are.
Progress was initially stalled by the apparent requirement that polynucleotides and polypeptides must work in harness in order to produce a self-reproducing biochemical system. This is because proteins are required to catalyze biochemical reactions but cannot carry out their own self-replication. Polynucleotides can specify the synthesis of proteins and self-replicate, but it was thought that they could do neither without the aid of proteins. It appeared that the biochemical system would have to spring fully formed from the random collection of biomolecules because any intermediate stage could not be perpetuated. The major breakthrough came in the mid-1980s when it was discovered that RNA can have catalytic activity. Those ribozymes that are known today carry out three types of biochemical reaction:Self-cleavage, as displayed by the self-splicing Group I, II and III introns and by some virus genomes (Table 10.4 and Section 10.2.3);Cleavage of other RNAs (as carried out by, for example, RNase P; Table 10.4 and Section 10.2.2);Synthesis of peptide bonds, by the rRNA component of the ribosome (Section 11.2.3 and Research Briefing 11.1).
How did the RNA world develop into the DNA world? The first major change was probably the development of protein enzymes, which supplemented, and eventually replaced, most of the catalytic activities of ribozymes (Freeland et al., 1999). There are several unanswered questions relating to this stage of biochemical evolution, including the reason why the transition from RNA to protein occurred in the first place. Originally, it was assumed that the 20 amino acids in polypeptides provided proteins with greater chemical variability than the four ribonucleotides in RNA, enabling protein enzymes to catalyze a broader range of biochemical reactions, but this explanation has become less attractive as more and more ribozyme-catalyzed reactions have been demonstrated in the test tube. A more recent suggestion is that protein catalysis is more efficient because of the inherent flexibility of folded polypeptides compared with the greater rigidity of base-paired RNAs (Csermely, 1997). Alternatively, enclosure of RNA protogenomes within membrane vesicles could have prompted the evolution of the first proteins, because RNA molecules are hydrophilic and must be given a hydrophobic coat, for instance by attachment to peptide molecules, before being able to pass through or become integrated into a membrane (Walter et al., 2000).
According to this scenario, the first DNA genomes comprised many separate molecules, each specifying a single protein and each therefore equivalent to a single gene. The linking together of these genes into the first chromosomes, which could have occurred either before or after the transition to DNA, would have improved the efficiency of gene distribution during cell division, as it is easier to organize the equal distribution of a few large chromosomes than many separate genes. As with most stages in early genome evolution, several different mechanisms by which genes might have become linked have been proposed (Szathmáry and Maynard Smith, 1993).
If multiple origins are possible, but modern life is derived from just one, then at what stage did this particular biochemical system begin to predominate? The question cannot be answered precisely, but the most likely scenario is that the predominant system was the first to develop the means to synthesize protein enzymes and therefore probably also the first to adopt a DNA genome. The greater catalytic potential and more accurate replication conferred by protein enzymes and DNA genomes would have given these cells a significant advantage compared with those still containing RNA protogenomes. The DNA-RNA-protein cells would have multiplied more rapidly, enabling them to out-compete the RNA cells for nutrients which, before long, would have included the RNA cells themselves.
Are life forms based on informational molecules other than DNA and RNA possible? Orgel (2000) has reviewed the possibility that RNA was preceded by some other informational molecule at the very earliest period of biochemical evolution and concluded that a pyranosyl version of RNA, in which the sugar takes on a slightly different structure, might be a better choice than normal RNA for an early protogenome because the base-paired molecules that it forms are more stable (Beier et al., 1999; Eschenmoser, 1999). The same is true of peptide nucleic acid (PNA), a polynucleotide analog in which the sugar-phosphate backbone is replaced by amide bonds (Figure 15.5). PNAs have been synthesized in the test tube and have been shown to form base pairs with normal polynucleotides. However, there are no indications that either pyranosyl RNA or PNA were more likely than RNA to have evolved in the prebiotic soup.
Although the very old fossil record is difficult to interpret, there is reasonably convincing evidence that by 3.5 billion years ago biochemical systems had evolved into cells similar in appearance to modern bacteria. We cannot tell from the fossils what kinds of genomes these first real cells had, but from the preceding section we can infer that they were made of double-stranded DNA and consisted of a small number of chromosomes, possibly just one, each containing many linked genes.
If we follow the fossil record forwards in time we see the first evidence for eukaryotic cells - structures resembling single-celled algae - about 1.4 billion years ago (Figure 15.6), and the first multicellular algae by 0.9 billion years ago. Multicellular animals appeared around 640 million years ago, although there are enigmatic burrows suggesting that animals lived earlier than this. The Cambrian Revolution, when invertebrate life proliferated into many novel forms, occurred 530 million years ago and ended with the disappearance of many of the novel forms in a mass extinction 500 million years ago. Since then, evolution has continued apace and with increasing diversification: the first terrestrial insects, animals and plants were established by 350 million years ago, the dinosaurs had been and gone by the end of the Cretaceous, 65 million years ago, and the first hominoids appeared a mere 4.5 million years ago.
There are two ways in which new genes could be acquired by a genome:By duplicating some or all of the existing genes in the genome (Section 15.2.1);By acquiring genes from other species (Section 15.2.2).
The duplication of existing genes is almost certainly the most important process for the generation of new genes during genome evolution. There are several ways in which it could occur:By duplication of the entire genome;By duplication of a single chromosome or part of a chromosome;By duplication of a single gene or group of genes.
The second of these possibilities can probably be discounted as a major cause of gene number expansions based on our knowledge of the effects of chromosome duplications in modern organisms. Duplication of individual human chromosomes, resulting in a cell that contains three copies of one chromosome and two copies of all the others (the condition called trisomy), is either lethal or results in a genetic disease such as Down syndrome, and similar effects have been observed in artificially generated trisomic mutants of Drosophila. Probably, the resulting increase in copy numbers for some genes leads to an imbalance of the gene products and disruption of the cellular biochemistry (Ohno, 1970). The other two ways of generating new genes - whole-genome duplication and duplication of a single or small number of genes - have probably been much more important.
The most rapid means of increasing gene number is by duplicating the entire genome. This can occur if an error during meiosis leads to the production of gametes that are diploid rather than haploid (Figure 15.7). If two diploid gametes fuse then the result will be a type of autopolyploid, in this case a tetraploid cell whose nucleus contains four copies of each chromosome.
Autopolyploidy does not lead directly to gene expansion because the initial product is an organism that simply has extra copies of every gene, rather than any new genes. It does, however, provide the potential for gene expansion because the extra genes are not essential to the functioning of the cell and so can undergo mutational change without harming the viability of the organism. With many genes, the resulting changes in nucleotide sequence will be deleterious and the end result will be an inactive pseudogene, but occasionally the mutations will lead to a new gene function that is useful to the cell. This aspect of genome evolution is more clearly illustrated by considering duplications of single genes rather than of entire genomes, so we will postpone a full discussion of it until the next section. 041b061a72