1. Introduction

15.1 Introduction

Key terms defined in this section

Transposon is a DNA sequence able to insert itself at a new location in the genome (without any sequence relationship with the target locus).

Genomes evolve both by acquiring new sequences and by rearranging existing sequences.

The sudden introduction of new sequences results from the ability of vectors to carry information between genomes. Extrachromosomal elements move information horizontally by mediating the transfer of (usually rather short) lengths of genetic material. In bacteria, plasmids move by conjugation (see 12 The replicon), while phages spread by infection (see 11 Phage strategies). Both plasmids and phages occasionally transfer host genes along with their own replicon. Direct transfer of DNA occurs between some bacteria by means of transformation (see 1 Genes are DNA). In eukaryotes, some viruses (notably the retroviruses discussed in 16 Retroviruses and retroposons) can transfer genetic information during an infective cycle.

Rearrangements are sponsored by processes internal to the genome. One cause is unequal recombination, which results from mispairing by the cellular systems for homologous recombination. Nonreciprocal recombination results in duplication or rearrangement of loci (see 4 Clusters and repeats). Duplication of sequences within a genome provides a major source of new sequences. One copy of the sequence can retain its original function, while the other may evolve into a new function. Furthermore, significant differences between individual genomes are found at the molecular level because of polymorphic variations caused by recombination. We saw in 4 Clusters and repeats that recombination between "minisatellites" adjusts their lengths so that every individual genome is distinct.

Another major cause of variation is provided by transposable elements or transposons: these are discrete sequences in the genome that are mobile-they are able to transport themselves to other locations within the genome. The mark of a transposon is that it does not utilize an independent form of the element (such as phage or plasmid DNA), but moves directly from one site in the genome to another. Unlike most other processes involved in genome restructuring, transposition does not rely on any relationship between the sequences at the donor and recipient sites. Transposons are restricted to moving themselves, and sometimes additional sequences, to new sites elsewhere within the same genome; they are therefore an internal counterpart to the vectors that can transport sequences from one genome to another. They may provide the major source of mutations in the genome.

Transposons fall into two general classes. The groups of transposons reviewed in this chapter exist as sequences of DNA coding for proteins that are able directly to manipulate DNA so as to propagate themselves within the genome. The transposons reviewed in the next chapter are related to retroviruses, and the source of their mobility is the ability to make DNA copies of their RNA transcripts; the DNA copies then become integrated at new sites in the genome.

Transposons that mobilize via DNA are found in both prokaryotes and eukaryotes. Each bacterial transposon carries gene(s) that code for the enzyme activities required for its own transposition, although it may also require ancillary functions of the genome in which it resides (such as DNA polymerase or DNA gyrase). Comparable systems exist in eukaryotes, although their enzymatic functions are not so well characterized. A genome may contain both functional and nonfunctional (defective) elements. Often the majority of elements in a eukaryotic genome are defective, and have lost the ability to transpose independently, although they may still be recognized as substrates for transposition by the enzymes produced by functional transposons (for review see Finnegan, 1985). A eukaryotic genome contains a large number and variety of transposons. The fly genome has >50 types of transposon, with a total of several hundred individual elements.

Transposable elements can promote rearrangements of the genome, directly or indirectly:

• The transposition event itself may cause deletions or inversions or lead to the movement of a host sequence to a new location.
  
• Transposons serve as substrates for cellular recombination systems by functioning as "portable regions of homology"; two copies of a transposon at different locations (even on different chromosomes) may provide sites for reciprocal recombination. Such exchanges result in deletions, insertions, inversions, or translocations.

The intermittent activities of a transposon seem to provide a somewhat nebulous target for natural selection. This concern has prompted suggestions that (at least some) transposable elements confer neither advantage nor disadvantage on the phenotype, but could constitute "selfish DNA," concerned only with their own propagation. Indeed, in considering transposition as an event that is distinct from other cellular recombination systems, we tacitly accept the view that the transposon is an independent entity that resides in the genome.

Such a relationship of the transposon to the genome would resemble that of a parasite with its host. Presumably the propagation of an element by transposition is balanced by the harm done if a transposition event inactivates a necessary gene, or if the number of transposons becomes a burden on cellular systems. Yet we must remember that any transposition event conferring a selective advantage-for example, a genetic rearrangement Vwill lead to preferential survival of the genome carrying the active transposon (for review see Campbell, 1981).

Reviews

Campbell, A. (1981). Evolutionary significance of accessory DNA elements in bacteria. Ann. Rev. Immunol. 35, 55-83.

Finnegan, D. J. (1985). Transposable elements in eukaryotes. Int Rev Cytol 93, 281-326.