Evolution of Genes

The coding portions of eukaryotic genes, termed "exons," are interrupted by noncoding regions, termed "introns." The evolutionary role of introns has been controversial since their discovery in 1977. Some scientists propose they are just another form of "junk DNA," and may be the relics of transposable elements or other forms of selfish DNA. Others suggest they may have played a central role in protein evolution.

The argument about the evolutionary importance of introns turns on exactly how they divide up the genes in which they are found. Proteins, which are encoded by genes, are not random strings of amino acids, but rather highly organized three-dimensional shapes, with different functions served by discrete parts, known as domains. A protein may contain half a dozen domains; one may bind a signaling molecule from outside the cell, another embeds the protein in a membrane, another binds an internal protein, and so on. It is often the case that each domain in a protein is folded up from a discrete segment of the amino acid chain.

Just as the domain's amino acids occur in sequence in the protein, the nucleotides that code for them occur in sequence in the gene. Those who propose that introns play a vital role in protein evolution suggest that exons correspond to the protein's domains, and that introns serve to divide the gene into these useful little bits of code. In this view, exons serve as "modules," or useful gene segments, that can be shuffled (via gene duplication and transposable elements, for instance) to create genes for new proteins with novel functions. For instance, a module for a membrane-embedding domain could be linked to a module for an oxygen-binding domain, allowing oxygen to be stored on a membrane, or a hormone-binding domain might be joined to a promoter-binding domain, allowing a hormone to control gene transcription.

The validity of this model of protein evolution depends on whether a gene's exons do indeed correspond to its protein's domains, and whether introns do actually separate domain-coding regions. So far the evidence is mixed, with some genes clearly divided this way, but many others showing complex or conflicting structures.

Because of this, scientists do not yet agree on the importance of exon shuffling in protein evolution. While it likely has occurred, it is unknown how widespread it may be. Also at issue is whether introns themselves arose early or late in life's evolution. If early, it may have been central to the development of all forms of life. The absence of introns in bacteria would then presumably be due to a streamlining of their genome by natural selection. If introns arose late, they were probably confined to eukaryotes and were therefore only important in their evolution.

While there is much that remains controversial, there is little disagreement about the importance of a related use of exons that occurs continually in many tissues. This is called alternative splicing. In this case, particular exons may be omitted, or they may be reassembled differently from tissue to tissue, creating tissue-specific variants, called isoforms, of the same protein.