14.5: Overview of Eukaryotic Transposable Elements
- Page ID
- 88986
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)There are two classes of transposons in eukaryotes. Class I (RNA) transposons move (i.e., jump) by transcription of RNA at one locus, followed by reverse transcription and integration of the cDNA back into genomic DNA at a different location. Called retrotransposons, they may be derived from (or be the source of) retroviruses, since active retroviruses excise from and integrate into DNA much like retrotransposons. Retroposons are a subclass of retrotransposons (see Table 14.2).
Class II (DNA) transposons move by either of two mechanisms. In the cut-and-paste pathway, the transposon leaves one locus and integrates at another. In the replicative pathway, the original transposon remains in place, but new copies are mobile. Table 14.2 summarizes the distribution and proportion of genomes represented by different classes and types of transposable elements.
The table confirms that bacteria contain relatively few transposons, in contrast to eukaryotes, which vary widely in transposon load (transposons as a percentage of genomic DNA). Transposon load can range from as low as 4% to more than 70% in different organisms.
Table 14.3 summarizes transposable elements by class, subtype, size, genomic distribution, mechanism of transposition, where they are found in nature, and other unique characteristics.
* DNA transposons move from one place to another in one of two ways. In Cut & Paste Transposition, the element excises and moves to another location in the genome. In Replicative Transposition, DNA transposons are copied and the copy transposes to a new location, leaving the original element in place. Retrotransposons are active if their transcripts are reverse transcribed into cDNAs as well as translated into the enzymes required to integrate their cDNA copies into genomic DNA.
** Many transposons are inactive, having been silenced by mutation or other factors. Active eukaryotic Class I or Class II transposons are either autonomous or non-autonomous. Autonomous transposons have all the structural features necessary for transposition (e.g., the maize Ac element). Non-Autonomous transposons can have all the structural elements of autonomous transposons (e.g., inverted repeats and other DNA necessary for transposition), except they lack or can’t transcribe one or more of the genes for enzymes needed for mobility (e.g., the maize Ds element). Nevertheless, they can be mobilized with the assistance of an actively transposing autonomous element that can provide the missing enzymes.
Between the two tables above, we can conclude the following:
- Transposon load is not correlated with the evolutionary complexity of organisms.
- Shared transposons have different evolutionary histories in different organisms.
- Where transposons remain active, they continue to shape genomic landscapes, especially in organisms with a high transposons load.
We will revisit some of these conclusions later, after looking at the structure and mechanism of mobility of different eukaryotic transposable elements.
Speculate on why some species (i.e., a flatworm, a fruit fly and rice!) have so few transposable elements.