14.6: The Structure of Eukaryotic DNA (Class II) Transposons
- Page ID
- 88987
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Active eukaryotic DNA transposons share structural features with bacterial mobile elements, including genes required for transposition, flanking inverted repeats, and flanking insertion site direct repeats of host-cell DNA. As we’ll see, Class II transposons can “jump” by cut-and paste or replicative mechanisms. Figure 14.17 illustrates the characteristic structure of a eukaryotic DNA transposon, including its “all-purpose” transposase gene.
14.6.1 Cut-and-Paste Transposition
This mechanism moves a copy from one location and transposes it to another location. As its name suggests, replicative transposition leaves a copy of the original transposon in place, while inserting a new copy elsewhere in the genome (Figure 14.18, below).
Transposase excises the transposon, trims its 3’ OH ends to create a staggered cut, joins the transposon ends, and mediates its insertion at a new DNA site. After ligating the 3′ OH transposon ends to the 5′ OH at the insertion site, replication replaces missing bases to generate the direct repeats of host-cell genomic DNA. Ligation completes the transposition.
14.6.2 Replicative Transposition
Figure 14.19 details the steps of replicative transposition. Like the cut-and-paste mechanism, the transposon is nicked and trimmed at its source (i.e., original) insertion site.
Unlike the cut-and-paste mechanism, transposons are not excised. Its transposase nicks the transposon’s 3′ ends at the insertion site, holding the transposon ends together while it cuts (hydrolyzes) DNA at a new insertion site. Replication from the 3′ OH ends of the insertion-site DNA strands forms a cointegrate structure containing transposon copies. The cointegrate is resolved by one of two recombinational mechanisms, leaving transposon copies at the original site and the new insertion site.
Let’s compare and contrast features of cut-and-paste and replicative transposition. The common features are that (first) a transposon-encoded transposase binds, brings transposon ends together, and catalyzes single-stranded cleavage (hydrolysis), leaving “staggered ends,” and (second) that the transposase holds the transposon ends together for the remaining steps. The differences between the two mechanisms are that in cut-and-paste transposition, the transposon is completely excised and then transposed to a new site in genomic DNA. In contrast, after single-stranded cleavage in replicative transposition, the transposase-bound free 3′ ends of the transposon hydrolyze both strands of double-stranded DNA at a new insertion site. After ligation of the 3’ ends of transposon strands to the 5′ ends of cut genomic DNA insertion-site ends, the remaining 3’ ends of the insertion-site DNA will prime the replication of the transposon to form the cointegrate, the which is then resolved by one of two recombination pathways