As we noted in the introduction to this chapter, transposition provides an alternative survival strategy that almost certainly has ancient roots. Evolution has given rise to many types of transposons, which have colonized the genomes of all extant organisms, and it has also given rise to other, more complex pathogens, such as viruses. Although the need to adapt to their hosts has affected transposon evolution, transposons have not always remained separate entities. Some transposable elements, and the enzymes they encode, have been appropriated by host cells and adapted to new biological tasks. The movements of transposons have driven genomic changes that have contributed in important ways to evolution.

Many well-characterized eukaryotic retrotransposons, from sources as diverse as yeast and fruit flies, have a structure very similar to that of retroviruses. Based on studies of reverse transcriptase genes, researchers hypothesize that retrotransposons probably gave rise to retroviruses.

The evolution of virtually all retrotransposons and retroviruses can be traced through their reverse transcriptase genes. Similarly, the evolution of an even broader range of transposable elements can be linked to the evolution of retrotransposons and retroviruses through their integrase and transposase genes. Integrases and transposases catalyze very similar reactions (Figure 14-20). The most widespread class of both types of enzymes uses a set of three active-site amino acids, two aspartates and one glutamate, to promote the hydrolytic cleavage and transesterification of phosphodiester bonds. These three residues (D, D, and E) are not adjacent in the primary sequence of these enzymes, but they come together in the active site and constitute a well-recognized motif called the DDE motif (Figure 14-21). The close relationship between these enzymes, regardless of source, can have practical benefits. For example, the transposase of the bacterial transposon Tn5 can be used as a model to study the function of the HIV integrase, and even as a rapid test for drugs that might be used to inhibit the HIV enzyme.

Transposons have a long and complex history. Their dispersal may include rare events in which DNA was transferred by some means (such as bacterial conjugation, cellular fusion, viral infection, or accidental DNA uptake) among the cells of different species. When a transposon is introduced into a new species’ genome, there is often a period of many host generations during which the element transposes more or less freely. The number of inserted transposons may increase, with the resulting genomic changes being passed on whenever they do not have a deleterious effect on the host. As time passes, the transposons become subject to silencing processes, including the introduction of mutations in their transposase or integrase genes that inactivate the gene products. Alternatively, the host may find a way to shut down transposition. One common silencing mechanism involves RNA interference (RNAi, a process described in Chapter 22). In brief, the cell produces short RNA molecules that are complementary to the transcripts of the transposase-encoding gene. The RNA hybridizes to the gene transcripts, preventing their translation and effectively blocking the synthesis of an enzyme required for transposition of an entire class of transposons.

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Linear transmission of transposons from one host generation to the next is predominant, with transfer between species occurring rarely. Thus, many transposon families are found only in certain classes of organisms. In eukaryotes, ongoing genomic sequencing efforts have revealed 12 superfamilies of DNA transposons, including Tc1/mariner (Table 14-1). Many of these superfamilies are found in more than one eukaryotic type. Seven are closely related to transposons found in bacteria, suggesting that they appeared before the divergence of bacteria and eukaryotes.

Sometimes transposons benefit their hosts. As we have seen, the antibiotic-resistance genes encoded by the transposon Tn5 have contributed greatly to the development of bacterial pathogens that are resistant to those antibiotics. In human cells, there are more than 1 million copies of the Alu transposon (a 300 bp SINE element) in the DNA, accounting for nearly 10% of the genome. These elements are so widespread that a typical human gene includes several copies in the introns of its primary transcript. Host cells use these elements as target sites for RNA editing (see Chapter 16). Other transposon genes are appropriated by the host for other purposes. Efforts to trace the evolution of mammalian genes have identified several dozen that are derived from transposons. A dramatic case of transposon domestication—occurring in immunoglobulin formation—is described shortly.

Perhaps more important is the overall impact of transposons on the evolution of the host. Genomic changes promoted by transposons come in many forms. Transposons are set up to bring their ends together in a complex prior to any cleavage event, but this control mechanism can go awry. If transposase subunits form a complex involving two ends derived from different copies of the same transposon, on the same or different chromosomes, large genomic rearrangements can result. Genes may be captured between two transposable elements and moved to different genomic locations. If the genes are duplicated in the process, the new gene copies may evolve and acquire new functions. Transposition is not always precise; the insertion of a transposon into a gene, followed by its later excision, can add or subtract base pairs in the gene and create new alleles. Also, the insertion or excision of transposons at particular genomic sites can alter the expression of genes or sets of genes.

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The transposons that seem to clutter mammalian genomes have been referred to as “selfish” or “junk” DNA, but these labels are being shed as our understanding broadens. Transposon DNA may play a key role in chromosomal structure and packaging. And far from being dormant, transposon DNA is actively transcribed in at least some cells. As new classes of functional RNAs are being discovered at a rapid pace, the RNAs produced by transposons may prove to have unexpected cellular roles.

Humans have a complex immune system capable of generating millions of different immunoglobulins (antibody proteins) with distinct binding specificities. But the human genome contains only about 25,000 genes, and just a few hundred of these are immune system genes. Somehow, the millions of different immunoglobulins are generated from these several hundred genes. As B lymphocytes (B cells) differentiate, their immunoglobulin genes recombine so that each cell will express an antibody with a unique binding specificity. Studies of the recombination mechanism reveal a close relationship to DNA transposition and suggest that this system for generating antibody diversity evolved from an ancient cellular invasion by transposons.

Immunoglobulins consist of two heavy and two light polypeptide chains (Figure 14-22 shows the general structure of the IgG class of immunoglobulins). Each chain has two regions: a variable region, with a sequence that differs greatly from one immunoglobulin to another, and a constant region, which is virtually unchanging within a class of immunoglobulins. There are two distinct families of light chains, kappa and lambda, which differ somewhat in the sequence of their constant regions. For all three types of polypeptide chain (heavy chain, and kappa and lambda light chains), diversity in the variable regions is generated by a similar mechanism. The genes for these polypeptides are divided into segments, and the genome contains clusters with multiple versions of each segment. The joining of one version of each gene segment creates a complete gene.

Figure 14-23 depicts the organization of the DNA encoding the kappa light chain and shows how a mature kappa light chain is generated. In undifferentiated cells, the coding information for this polypeptide is separated into three segments. The V (variable) segment encodes the first 95 amino acid residues of the variable region, the J (joining) segment encodes the remaining 12 residues of the variable region, and the C (constant) segment encodes the constant region. For kappa light chains, the genome contains ∽300 different V segments, 5 different J segments, and 1 type of C segment.

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As a stem cell in the bone marrow differentiates to form a mature B cell, one V segment and one J segment are brought together by a specialized recombination system (Figure 14-24). During this programmed DNA deletion, the intervening DNA is discarded. There are about 300 × 5 = 1,500 possible V-J combinations. Additional variation in the sequence at the V-J junction is introduced by imprecision in the recombination reaction, as an enzyme called terminal deoxynucleotide transferase adds a few nucleotides at random to 3′ ends exposed during the recombination process. This increases the overall variation considerably. The final joining of the V-J combination to the C region is accomplished by an RNA-splicing reaction after transcription (see Chapter 16). The assembly of light chains with similarly randomized heavy chains increases diversity still further.

The recombination mechanism for joining the V and J segments is facilitated by recombination signal sequences (RSS) that lie just downstream of each V segment and just before each J segment. These sequences are bound by proteins called RAG1 and RAG2 (products of the recombination activating gene). The RAG proteins catalyze the formation of a double-strand break between the RSS and the V (or J) segments to be joined. The V and J segments are then joined with the aid of a second complex of proteins.

The genes for the heavy chains and the lambda light chains form by similar processes. Heavy chains have more gene segments than light chains, with thousands of possible combinations. Because any heavy chain can combine with any light chain to generate an immunoglobulin, each human can produce at least 10⁷ possible immunoglobulins. And additional diversity is generated by high mutation rates (of unknown mechanism) in the V segments during B-cell differentiation. Each individual mature B cell produces only one type of antibody, but the range of antibodies produced by the many B cells of an individual organism is clearly enormous.

The mechanism of the DNA recombination events required to generate an expressed immunoglobulin gene suggests that the immune system evolved, in part, from ancient transposons. The mechanism for generation of the double-strand breaks by RAG1 and RAG2 closely resembles several reaction steps in transposition (see Figure 14-24). The double-strand breaks that initiate the process are generated by single protein active sites and feature transient hairpin intermediates at each of the ends to be joined, as in the reaction promoted by the Tn5 transposase (see Figure 14-11). In addition, the deleted DNA, with its terminal RSS, has a sequence structure found in most transposons. In the test tube, RAG1 and RAG2 can associate with this deleted DNA and insert it, transposon like, into other DNA molecules (probably a rare reaction in vivo). In fact, a subtle rearrangement of the RSS, coupled with placement of the genes encoding the RAG proteins between the RSS ends, creates a DNA element that functions exactly like a transposon. The RAG1 protein is closely related in sequence to the transposases encoded by the Transib superfamily of eukaryotic transposons (see Table 14-1). The properties of the immunoglobulin gene rearrangement system point to an intriguing origin, in which the distinction between host and parasite has become blurred by evolution.

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