In contrast to bacterial and archaeal genes, the vast majority of genes in multicellular eukaryotes contain multiple introns. As noted in Chapter 3, many proteins from higher eukaryotes have a multidomain tertiary structure (see Figure 3-11). Individual repeated protein domains are often encoded by one exon or by a small number of exons that are repeated in genomic DNA and encode identical or nearly identical amino acid sequences. Such repeated exons are thought to have evolved from multiple duplications of a length of DNA lying between two sites in introns on either side of an exon, resulting in insertion of a string of repeated exons separated by introns. The presence of multiple introns in many eukaryotic genes permits expression of multiple, related proteins from a single gene by means of alternative splicing. In higher eukaryotes, alternative splicing is an important mechanism for production of different forms of a protein, called isoforms, by different types of cells.

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Fibronectin, a multidomain protein found in mammals, provides a good example of alternative splicing (Figure 5-16). Fibronectin is a long, adhesive protein secreted into the extracellular space that can bind other proteins together. What and where it binds depends on which domains are spliced together. The fibronectin gene contains numerous exons, grouped into several regions corresponding to specific domains of the protein. Fibroblasts produce fibronectin mRNAs that contain exons EIIIA and EIIIB; these exons encode a protein domain that binds tightly to proteins in the fibroblast plasma membrane. Consequently, this fibronectin isoform adheres fibroblasts to the extracellular matrix. Alternative splicing of the fibronectin primary transcript in hepatocytes, the major type of cell in the liver, yields mRNAs that lack the EIIIA and EIIIB exons. As a result, the fibronectin secreted by hepatocytes into the blood does not adhere tightly to fibroblasts or to most other cell types, which allows it to circulate. During formation of blood clots, however, other fibrin-binding domains of hepatocyte fibronectin bind to fibrin, one of the principal constituents of blood clots. Yet another domain of the bound fibronectin then interacts with integrins on the membranes of passing platelets, thereby expanding the clot by addition of platelets.

More than 20 different isoforms of fibronectin have been identified, each encoded by a different, alternatively spliced mRNA composed of a unique combination of fibronectin gene exons. Sequencing of large numbers of mRNAs isolated from various tissues and comparison of their sequences with genomic DNA has revealed that nearly 90 percent of all human genes are expressed as alternatively spliced mRNAs. Clearly alternative RNA splicing greatly expands the number of proteins encoded by the genomes of higher, multicellular organisms.