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As we saw in Chapter 12, a major effort of molecular genetics is directed toward determining the complete DNA sequence of a variety of different species. At the time at which this paragraph was written, the genomes had been sequenced from more than forty species of bacteria; two species of yeast; the fungus Neurospora crassa; the nematode, Caenorhabditis elegans; two species of Drosophila; two plants, Arabidopsis and rice; the mouse; and humans. By the time you read these lines, many more genomes of many more species will have been sequenced. The availability of such data makes it possible to reconstruct the evolution of the genomes of widely diverse species from their common ancestors. Moreover, it is now possible to infer the similarities and differences in the proteomes of these species by comparing the gene sequences in various species with gene sequences that code for the amino acid sequences of proteins with known function.

With our current state of knowledge, we can suggest functions for about half the proteins in the proteome of each of the eukaryotes whose genomes have been sequenced, by using the similarity of their sequences with proteins of known function. Figure 21-17 depicts the distribution of this half of each proteome into general functional categories. Strikingly, the group of proteins engaged in defence and immunity have expanded greatly in humans compared with the other species. For other functional categories, though there are greater numbers of proteins in the human lineage, there is no case in which the differences between humans and all other eukaryotes are as pronounced.

As discussed in Chapter 10, gene expression is often controlled through the regulation of transcription by proteins called transcription factors. Perhaps as a manifestation of the many cell types that differentiate in humans, the size and distribution of the families of specific transcription factors in humans far exceed the numbers for the other sequenced eukaryotes, with the exception of mustard weed (Arabidopsis thaliana, see Figure 21-17). The distribution of proteins described in the pre- ceding paragraph is a description of only half of each proteome. What about the other half? It can be broken down into two components. One component, comprising about 30 per cent of each proteome, consists of proteins that have relatives among the different genomes, but none have had a function ascribed to them. The other component, comprising the remaining 20 per cent or so of each proteome, consists of proteins that are un-related by amino acid sequence to any protein known in another branch of the eukaryotic evolutionary tree. We can imagine two possible explanations for these novel polypeptides. 

One possibility is that some of these polypeptides first evolved after the sequenced species having a common ancestor diverged from one another. Because none of these species is evolutionarily closer than a few hundred million years, it is per- haps not surprising to find this frequency of newly evolved proteins. The other possibility is that some of these proteins are very rapidly evolving, and so their ancestry has been essentially erased by the overlay of new mutations that have accumulated. It is almost certain that both possibilities are correct for a subset of these novel polypeptides. Finally, we can ask, Where do the protein-coding genes in the human genome come from? Figure 21-18 depicts the distribution of human genes in other species. 

About a fifth of the known human genes have been found only invertebrates. Another fifth seem to be ubiquitous in eukaryotes and prokaryotes. About a third are found throughout eukaryotes but not in bacteria. Curiously, a few hundred genes (less than 1 per cent) appear to be found only in humans and in prokaryotes. Either these genes were present in a common ancestor of prokaryotes and eukaryotes and have disappeared from most other eukaryotes in the course of their evolution or else these genes that we and prokaryotes have uniquely in common have been passed on to us from prokaryotes through horizontal gene transfer. 

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