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The Evolution Of The Genome

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.

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 efficienc


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