More complex species evolve by adding new gene functions

KEY CONCEPTS:

• Comparisons of different genomes show a steady increase in gene number as additional genes are added to make eukaryotes, make multicellular organisms, make animals, and make vertebrates.
• Most of the genes that are unique to vertebrates are concerned with the immune or nervous systems.

Comparison of the human genome sequence with sequences found in other species is revealing about the process of evolution. Figure 3.26 analyzes human genes according to the breadth of their distribution in Nature. Starting with the most generally distributed (top right corner of the figure), 21% of genes are common to eukaryotes and prokaryotes. These tend to code for proteins that are essential for all living forms—typically basic metabolism, replication, transcription, and translation. Moving clockwise, another 32% of genes are added in eukaryotes in general —for example, they may be found in yeast. These tend to code for proteins involved in functions that are general to eukaryotic cells but not to bacteria—for example, they may be concerned with specifying organelles or cytoskeletal components. Another 24% of genes are needed to specify animals. These include genes necessary for multicellularity and for development of different tissue types. And 22% of genes are unique to vertebrates. These mostly code for proteins of the immune and nervous systems; they code for very few enzymes, consistent with the idea that enzymes have ancient origins, and that metabolic pathways originated early in evolution. We see, therefore, that the progression from bacteria to vertebrates requires addition of groups of genes representing the necessary new functions at each stage.

One way to define commonly needed proteins is to identify the proteins present in all proteomes. Comparing the human proteome in more detail with the proteomes of other organisms, 46% of the yeast proteome, 43% of the worm proteome, and 61% of the fly proteome is represented in the human proteome. A key group of ~1300 proteins is present in all four proteomes. The common proteins are basic housekeeping proteins required for essential functions, falling into the types summarized in Figure 3.27. The main functions are concerned with transcription and translation (35%), metabolism (22%), transport (12%), DNA replication and modification (10%), protein folding and degradation (8%), and cellular processes (6%).

One of the striking features of the human proteome is that it has many new proteins compared with other eukaryotes, but it has relatively few new protein domains. Most protein domains appear to be common to the animal kingdom. However, there are many new protein architectures, defined as new combinations of domains. Figure 3.28 shows that the greatest increase occurs in transmembrane and extracellular proteins. In yeast, the vast majority of architectures are concerned with intracellular proteins. About twice as many intracellular architectures are found in fly (or worm), but there is a very striking increase in transmembrane and extracellular proteins, as might be expected from the addition of functions required for the interactions between the cells of a multicellular organism. The increase in intracellular architectures required to make a vertebrate (Man) is relatively small, but there is again a large increase in transmembrane and extracellular architectures.