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Flanking direct repeat

Protease, integrase, reverse transcriptase, RNase genes

-Delta sequence (334 bp)-(direct repeat)

Flanking direct repeat also generate direct repeats at the point of insertion. Retrotransposons include the Ty elements in yeast, the copia elements in Drosophila, and the Alu sequences in humans.

Ty elements in yeast Ty (for transposon yeast) elements are a family of common transposable elements found in yeast; many yeast cells have 30 copies of Ty elements. These elements are retrotransposons that are about 6300 nucleotide pairs in length and generate 5-bp flanking direct repeats when they insert into DNA ( Figure 11.25). At each end of a Ty element are direct repeats called delta sequences, which are 334 bp long. The delta sequences are analogous to the long terminal repeats found in retroviruses (see p. 000 in Chapter 8). These delta sequences contain promoters required for the transcription of Ty genes, and the promoters may also stimulate the transcription of genes that lie downstream of the Ty element. Between the delta sequences at each end of a Ty element are two genes (TyA and TyB, which encode several enzymes) that are related to the gag and pol genes found in retroviruses (see p. 000 in Chapter 8). Many Ty elements are defective and no longer capable of undergoing transposition.

Ac and Ds elements in maize Transposable elements were first identified in maize (corn), more than 50 years ago by Barbara McClintock ( FIGURE 11.26). McClintock spent much of her long career studying their properties, and her work stands among the landmark discoveries of genetics. Her results, however, were misunderstood and ignored for many years. Not until molecular techniques were developed in the late 1960s and 1970s did the importance of transpos-able elements become widely accepted.

Born in 1902, Barbara McClintock attended Cornell University as an undergraduate and, later, as a graduate student. She was especially interested in genetics, but the subject was taught in the department of plant breeding, which did not accept women students. So she registered for botany instead and studied maize chromosomes for her Ph.D. dissertation.

After receiving her degree, McClintock remained at Cornell, continuing her cytogenetic analysis of maize chromosomes. Her discoveries in the next 10 years included the identification of all the chromosomes in maize, the assignment of linkage groups to chromosomes, proof of crossing over, mapping genes to chromosomes by using rearrangements, and associating chromosome elements with the nucleolus.

11.26 Barbara McClintock was the first to discover transposable elements. (CSHL Archives/Peter Arnold.)

McClintock's discovery of transposable elements had its genesis in the early work of Rollins A. Emerson on the maize genes that caused variegated (multicolored) kernels. Most corn kernels are either wholly pigmented or colorless (yellow), but Emerson noted that some yellow kernels had spots or streaks of color ( FIGURE 11.27). He proposed that these kernels resulted from an unstable mutation: a muta-

11.27 Variegated (spotted) kernels in corn are caused by mobile genes. The study of variegated corn led Barbara McClintock to discover transposable elements. (Matt Meadows/Peter Arnold.)

tion in the wild-type gene for pigment produced a colorless kernel; but, in some cells, the mutation reverted back to the wild type, causing a spot of pigment. However, Emerson didn't know why these mutations were unstable.

McClintock discovered that the cause of the unstable mutation was a gene that moved. She noticed that chromosome breakage in maize often occurred at a locus that she called Dissociation (Ds) but only if another gene, the Activator (Ac), also was present. Ds and Ac exhibited unusual patterns of inheritance; occasionally, the genes moved together. McClintock called these moving genes controlling elements, because they controlled the expression of other genes.

McClintock published her conclusion that controlling elements moved in 1948. Although her results were not disputed, they were neither understood nor recognized by most geneticists. Of her work, Alfred Sturtevant, then a prominent geneticist remarked, "I didn't understand one word she said, but if she says it is so, it must be so!" He expressed what seems to have been the attitude of many geneticists at the time. McClintock was frustrated by the genetics community's reaction to her research, but she continued to pursue it nonetheless. In the 1960s, bacteria and bacteriophages were shown to possess transposable elements, and the development of recombinant DNA techniques in the 1970s and 1980s demonstrated that transposable elements exist in all organisms. The significance of McClintock's early discoveries was finally recognized in 1983, when she was awarded the Nobel Prize in Physiology or Medicine. A series of links to Barbara McClintock and her work on transposable elements

Ac and Ds elements in maize have now been examined in detail, and their structure and function are similar to those of transposable elements found in bacteria: they possess terminal inverted repeats and generate flanking direct repeats at the points of insertion. Ac elements are about 4500 bp long, including terminal inverted repeats of 11 bp, and the flanking direct repeats that they generate are 8 bp in length ( FIGURE 11.28a). Each Ac element contains a single gene that encodes a transposase enzyme. Thus Ac elements are autonomous — that is, able to transpose. Ds elements are Ac elements with one or more deletions that have inactivated the transposase gene ( FIGURE 11.28b). Unable to transpose on their own, (nonautonomous), Ds elements can transpose in the presence of Ac elements because they still possess terminal inverted repeats recognized by Ac transposase.

Each kernel in an ear of corn is a separate individual, originating as an ovule fertilized by a pollen grain. A kernel's pigment pattern is determined by several loci. A pigment-encoding allele at one of these loci can be designated C, and an allele at the same locus that does not confer pigment is designated as c. A kernel with genotype cc will be colorless — that is, yellow or white ( FIGURE 11.29a); a kernel with genotype CC or Cc will produce pigment and be purple (< Figure 11.29b).

A Ds element, transposing under the influence of a nearby Ac element, may insert into the C allele, destroying its ability to produce pigment ( FIGURE 11.29c). An allele inactivated by a transposable element is designated with a subscript "t"; so in this case it would be designated Ct. After the transposition of Ds into the C allele, the kernel cell has genotype Ctc. This kernel will be colorless (white or yellow), because neither the Ct nor the c allele confers pigment.

(a) Ac element

Ac element (4563 bp)

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