Transposable elements that move via DNA intermediates
Among the most thoroughly characterized transposable elements are those that move by DNA intermediates. In bacteria, these are either short insertion sequences or longer transposons.
An insertion sequences, or IS, is a short DNA sequence that moves from one location to another. They were first recognized by the mutations they cause by inserting into bacterial genes. Different insertion sequences range in size from about 800 bp to 2000 bp. The DNA sequence of an IS has inverted repeats (about 10 to 40 bp) at its termini (Fig. 9.10A.). Note that this is different from the FDRs, which are duplications of the target site. The inverted repeats are part of the IS element itself. The sequences of the inverted repeats at each end of the IS are very similar but not necessarily identical. Each family of insertion sequence in a species is named IS followed by a number, e.g. IS1, IS10, etc.
An insertion sequence encodes a transposase enzyme that catalyzes the transposition. The amount of transposase is well regulated and is the primary determinant of the rate of transposition. Transposons are larger transposable elements, ranging in size from 2500 to 21,000 bp. They usually encode a drug resistance gene or other markerbesides the functions required for transposition (Fig. 9.10.B.). One type of transposon, called a composite transposon, has an IS element at each end (Fig. 9.10.C.). One or both IS elements may be functional; these encode the transposition function for this class of transposons. The IS elements flank the drug resistance gene (or other selectable marker). It is likely that the composite transposon evolved when two IS elements inserted on both sides of a gene. The IS elements at the end could either move by themselves or they can recognize the ends of the closely spaced IS elements and move them together with the DNA between them. If the DNA between the IS elements confers a selective advantage when transposed, then it will become fixed in a population.
Question 9.3.What are the predictions of this model for formation of a composite transposon for the situation in which a transposon in a small circular replicon, such as a plasmid?
Figure 9.10. General structure of insertion sequences and transposons. Flanking direct repeats (FDRs) are shown as green triangles, inverted repeats (IRs) are red or purple triangles, insertion sequences (ISs) are yellow boxes with red triangles at the end, and other genes are boxes of different colors. The boxes and triangles include both strands of duplex DNA. DNA outside the FDRs is shown as one thick blue line for each strand. Tn5 has an IS50 element on each side, in an inverted orientation. Transcripts are shown as curly lines with an arrowhead pointing in the direction of transcription. The neoR gene for Tn5 is composed partly of the leftward IS (ISL) and partly of other sequences (included in the blue box). The transposase for Tn5 is encoded in the rightward IS (ISR).
The TnA family of transposons has been intensively studied for the mechanism of transposition. Members of the TnA family have terminal inverted repeats, but lack terminal IS elements (Fig. 9.10). The tnpAgene of the TnA transposon encodes a transposase, and the tnpRgene encodes a resolvase. TnA also has a selectable marker, ApR, which encodes a beta-lactamase and makes the bacteria resistance to ampicillin.
Transposable elements that move via DNA intermediates are not limited to bacteria, but rather they are found in many species. The P elements and copiafamily of repeats are examples of such transposable elements in Drosophila, as are marinerelements in mammals and the controlling elements in plants. Indeed, the general structure of controlling elements in maize is similar to that of bacterial transposons. In particular, they end in inverted repeats and encode a transposase. As illustrated in Fig. 9.11, the DNA sequences at the ends of an Ac element are very similar to those of a Dselement. However, internal regions, which normally encode the transposase, have been deleted. This is why Dselements cannot transpose by themselves, but rather they require the presence of the intact transposon, Ac, in the cell to provide the transposase. Since transposase works in trans, the Acelement can be anywhere in the genome, but it can act on Dselements at a variety of sites. Note that Ac is an autonomous transposon because it provides its own transposase and it has the inverted repeats needed to act as the substrate for transposase.
Figure 9.11. Structure of Ac and Dscontrolling elements in maize is similar to that of an intact (Ac) or defective (Ds) transposon.