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Chapter 1 : Mobile DNA: an Introduction

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Abstract:

The once revolutionary idea that genomes contain segments of mobile DNA was actually first conceptualized before the discovery of the structure of DNA. Mobile DNA was first suggested by McClintock when she described "controlling elements" in maize. A notable feature of the work presented in this volume is that our understanding of many of these recombination reactions has moved to the biochemical and structural level. It is appropriate to begin a discussion of site-specific recombination reactions by considering conservative site-specific recombination. Genetic studies of these reactions in the 1950s provided one of the earliest examples of genome modification by a mobile DNA. Transposition is the recombination reaction that mediates the movement of discrete DNA segments between many nonhomologous sites. These segments are variously called insertion sequences, transposons, and transposable elements. There are two large classes of transposable elements: (i) those in which DNA is the actual substrate for recombination and (ii) those in which RNA is the actual substrate for recombination. Several recombination systems mediate the alternate expression of multiple alleles of a gene by moving alternative gene copies or gene segments from a ‘‘silent’’ position to an active ‘‘expression site’’. The continued study of genomes will lead us to more mobile DNAs to identify and understand, and further investigation into mobile DNAs will help us to understand the structure and function of genomes.

Citation: Craig N. 2002. Mobile DNA: an Introduction, p 3-11. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch1

Key Concept Ranking

Genetic Elements
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Group II Introns
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DNA Synthesis
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Figures

Image of Figure 1
Figure 1

Mechanism of conservative site-specific recombination. (A) Conservative site-specific recombination between two sites that share a region of homology (arrow) and related flanking sequences. Recombination within the region of homology results in the reciprocal exchange of the segments that flank the region of homology. (B) Conservative site-specific recombination at higher resolution. There is a short region of homology between the two recombination sites that is flanked by recombinase binding sites (arrows) in inverted orientation at each edge of the core region. When the recombinase (ovals) binds to these sites, it is symmetrically positioned on each side of the core. The recombinase executes breakage, exchange, and rejoining reaction within the core to generate recombinants containing a region of heteroduplex resulting from the staggered positions of breakage and rejoining.

Citation: Craig N. 2002. Mobile DNA: an Introduction, p 3-11. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch1
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Image of Figure 2
Figure 2

Different outcomes of conservative site-specific recombination are possible. Different relative orientations of the recombination sites in conservative site-specific recombination lead to different outcomes, although in all cases, the same breakage and joining events occur within the region of homology. When the recombination sites lie on different DNAs, recombination between them results in integration or fusion. When the two sites lie on the same DNA, two different outcomes are possible depending on the relative orientation of the sites. When the recombination sites are in direct orientation, excision/deletion/resolution of the material between the sites occurs to form an excised circle. When the sites are present in inverted orientation, the DNA segment between the two sites is inverted.

Citation: Craig N. 2002. Mobile DNA: an Introduction, p 3-11. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch1
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Image of Figure 3
Figure 3

Assembly of genes from gene segments. Genes encoding proteins of the immunoglobulin superfamily are assembled by recombination. Multiple copies of different gene segments (V1 to V3, J1, and J2) exist. These segments are flanked by recombination signal sequences (open and filled triangles); recombination occurs only between a site of the open type and the filled type. The recombination reaction shown leads to the joining of the gene encoding segments, V3 and D1, to form a new hybrid gene.

Citation: Craig N. 2002. Mobile DNA: an Introduction, p 3-11. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch1
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Image of Figure 4
Figure 4

Transposition. (Left) The transposable element (white box) is a discrete DNA segment flanked by terminal inverted repeats (gray triangles) which are the binding sites for the transposase (gray circles). The transposase makes double-strand breaks at the termini of the element which separate it from the flanking donor DNA (thin lines). Each transposon 3′ end then attacks one strand of the target DNA (thick line) at staggered positions (arrows), generating a structure in which the transposon is flanked by short gaps. These gaps are then repaired by host functions, generating the target sequence duplications characteristic of transposon insertion. (Right) Transposition of a retrovirus-like element. The single-stranded RNA genome is converted to double-stranded DNA through the action of the element-encoded reverse transcriptase. The resulting DNA is functionally equivalent to the DNA intermediate that has been excised from the donor DNA during cut-and-paste transposition of elements whose life cycle involves only DNA. The transposase, called an integrase for these retrovirus-like elements, then joins the transposable element to the target DNA as described above. Repair of the resulting gaps again occurs by host functions.

Citation: Craig N. 2002. Mobile DNA: an Introduction, p 3-11. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch1
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Image of Figure 5
Figure 5

Transposition of a LINE element. Recombination is initiated by a single-stranded nick in the target DNA by an element-encoded endonuclease. The 3′-OH exposed by this nick acts as a primer for reverse transcription of the LINE element RNA by an element-encoded reverse transcriptase, resulting in one DNA strand of the LINE element joined to the target DNA. The next steps which join the 5′ end of the element to the target DNA and result in the synthesis of the second strand of the element into the target DNA are not yet understood.

Citation: Craig N. 2002. Mobile DNA: an Introduction, p 3-11. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch1
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Image of Figure 6
Figure 6

Yeast mating-type switching by directed gene conversion. Three different loci encode the transcription factors whose expression can determine the yeast mating type of or α. Two of these loci are silent, i.e., the transcription factors are not expressed, whereas one site (center) is active and expresses the transcription factors. An α cell contains the information for the α cell transcription factors at the center expression site as well as at the silent right site (white boxes). Expression of the HO endonuclease leads to cleavage of the DNA at the expression site. The broken DNA invades homologous sequences bounding the mating-type information at the silent site (gray box), allowing double-strand break repair to copy information from the silent site into the expression site. At each switch, the transfer of information is such that alternation between the left and right α silent information occurs.

Citation: Craig N. 2002. Mobile DNA: an Introduction, p 3-11. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch1
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