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BOX 19-1 FIGURE 1 Comparison of the Gooseberry and laired proteins. The two diagrams summarize and compare the structures of the genes encoding the Gooseberry (Gsb) and Paired (Prd) proteins. Both proteins contain Ri\X and homeobox DNA-binding domains, and the regions in the DNA encoding these are indicated The rule under these structures indicates the approximate locations of these domains within the proteins

BOX 19-1 FIGURE 2 The Prd protein can rescue gsb mutants, (a) The gooseberry-paired fusion gene. The fusion gene contains about 6 kb of 5* flanking sequence from the gsb gene attached to the Pid protein coding region, thereby bringing the Prd coding sequence under the control of the gsb 5' regulatory DW The gsb regulatory DNA contains two enhancers, GFE and GLE, that control the initiation and maintenance of expression in the ectoderm of developing embryos, respectively, (b) The gsb mutant that contains the gsb-prd transgene. The fusion gene completely rescues the mutant phenotype of gsb mutants, indicating that the Prd protein can fulfill Gsb function. Note that the embryo displays a completely normal pattern of denticles, (c) The gsb mutant that lacks the gsb-prd transgene In the gsb mutant (without the transgene) the pattern of denticle hairs s abnormal and there is very Me naked cuticle separating neighboring segments. (Source: Courtesy of Markus Noll; Li X and NoB M. 1994 Nature 357: 83-87, figure 3.)

the organism, in some cases both mechanisms operate. In Box 19-2, Duplication of Glob in Genes Produces New Expression Patterns and Diverse Protein Functions, we describe the cluster of human globin genes. These arose by gene duplication, and, while the different protein products all bind oxygen as part of hemoglobin, they show subtly different affinities for their ligand. The different genes are expressed at different times during development as well.

The high degree of conservation of the genes found in different animals has recently focused attention on the role of changes in gene expression as a general mechanism in generating evolutionary diversity. The importance of this mechanism is highlighted by the striking changes in morphology caused by misexpressing genes in new places during the development of the fruit fly. In this chapter, we emphasize how evolutionary diversity can be generated by expressing a fixed set of genes in different patterns.

61B Comparative Genomics and the Evolution of Animal Diversity Box 1H Duplication of Globin Genes Produces New Expression Patterns and Diverse Protein Functions

Gene duplication events offer the opportunity to expand the repertoire of protein functions and expression profiles. Both forms of evolution are seen for the 0-globin genes in mammals (see Chapter 17). Four related globins have arisen from gene duplication events in humans: e, -y, and p (Box 19-2 Figure 1). All four genes are linked within a common "complex." Tlie four genes exhibit subtle changes in their expression profiles and protein structures. The t- and

■y-giobins bind oxygen more tightly than do & and p. They are used by the fetus, which lacks functioning lungs and must obtain oxygen by exchange from its mother's blood. The &- and p-gicbins bind oxygen with tower affinity, and are used by newborns and adults, which contain higher levels of oxygen. In this example, the evolution of both the protein coding genes and associated regulatory DNAs lead to the specialization of globin function.

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BOX 19-2 FIGURE. 1 Duplication of p-gfobin gene family in the evolution of vertebrates.

(Source: Adapted from Griffiths el at. 2000. An introduction to genetic analysis, 7th edition, p. 787, fig 26-15. Copyright © 2000 W H Freeman. Used i/vith permission.)

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Box 19-3 Creation of New Cenes Drives Bacterial Evolution

Simple bacteria appeared more than three billion years ago, while animals have been around for just over haif a billion years. The rapid evolution of bacteria, along with their extended evolutionary history, have created different forms of metabolism so that they can live in highly diverse and extreme environments. Some live wrthin thermal vents beneath the sea, while others live in sulfur hot springs on land.

There is tremendous variation in both the number and types of genes present in different bacterial genomes. The simplest bacteria such as mycoplasma contain as few as 500 genes, while the most sophisticated bacteria such as Strepto-myces encode over 7,000 genes. This huge range in gene number sharply contrasts with the modest, twofold variation seen among different animals. The genetic content is also highly divergent among even closely related species of bacteria. For example, Staphoccxxus and E. coli last shared a common ancestor about 50 million years ago, which is comparable to the time of divergence of mice and humans. Nonetheless, only approximately 75% of the protein coding genes are shared by the two bacteria. A stunning 25% of the genes are unique and have no dear counterpart in the other species.

In contrast, all animals inhabit similar, and far more temperate, environments. They employ similar metabolic pathways, but exhibit distinctive morphologies. As we wilt see in the course of this chapter, these diverse morphologies depend on changing the activities of a fixed set of genes rather than inventing new ones.

Before beginning that discussion, however, it is worth noting that evolution need not work by redeploying the same genes to generate diversity as seen for animals. For example, bacteria possess the most highly diverse genomes among all living organisms. They contain more than a tenfold range in the number of genes, and live in remarkably diverse environments (Box 19-3, Creation of New Genes Drives Bacterial Evolution).

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