14.7: The Structure of Eukaryotic RNA (Class I) Transposons
- Page ID
- 88988
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Like DNA transposons, all RNA transposons leave insert-site footprints (i.e., direct repeats of genomic DNA flanking the element). Unlike DNA transposons, active eukaryotic Class I transposons move via an RNA intermediate. Also unlike DNA transposons, RNA transposons lack terminal inverted repeats.
The mobility of the RNA intermediate of all retrotransposons requires a promoter, which recognizes a reverse transcriptase enzyme as well as endonuclease and integrase enzymes (to be described later). Autonomous Class I RNA transposons are characterized by Long Terminal Repeats (LTRs) as well as Non-LTR retrotransposons (that lack LTRs). NonLTR retrotransposons include the autonomous Long Interspersed Nuclear Elements (LINEs) and the non-autonomous Short Interspersed Nuclear Elements (SINEs). Both the autonomous LTR and non-LTR LINEs contain and express genes needed for the enzymes required for transposition. On the other hand, the nonautonomous SINEs (a subclass of non-LTR retrotransposons) lack genes for the enzymes required for transposition and therefore cannot transpose independently. Nonautonomous retrotransposons thus rely on “true” (autonomous) retrotransposon activity for mobility. SINEs are sometimes called retroposons to distinguish them from the autonomous retrotransposons.
249 Introduction to Features of Retrotransposition
14.7.1 LTR retrotransposons: The Yeast Ty element
Here we look at structures, genes, and enzyme activities required for retrotransposition. The Ty LTR retrotransposon in Figure 14.20 is an autonomous retrotransposon.
The Ty retroposon encodes several genes needed for transposition:
- Gag encodes group-specific antigen, a protein that forms a virus-like particle that will contain reverse-transcribed transposon DNA.
- RT, encodes reverse transcriptase to reverse-transcribe retrotransposon RNAs.
- Prt encodes a protease to break down the virus-like particle as the retrotransposon enters the nucleus.
- Int encodes integrase, needed to integrate the retrotransposon into a new insertion site. In fact, many of the events in Ty transposition occur in the cytoplasmic “virus-like particle” in yeast cells. To see more, see Virus-Like Particles in Ty Transposition. Note that the Pol region in Figure 14.20 consists of overlapping open reading frames (ORFs) that encode the Prt, RT, and Int genes. The ready-to-move transposon consists only of the bracketed region of DNA, including the long terminal repeat sequences.
14.7.2 Non-LTR Retrotransposons: LINEs
Like LTR retrotransposons, LINEs (long interspersed nuclear elements) encode the enzymes needed for transposition. They also generate target-site direct repeats flanking the inserted element (Figure 14.21). But they do not have long terminal repeats! Instead, their ORFs (genes) are flanked by 5′ and 3′ untranslated regions (UTRs).
The 5′ UTR contains a promoter from which cellular RNA polymerase II can transcribe the downstream genes (see chapter 10 on transcription). The second of these (ORF2) encodes the reverse transcriptase and an integrase activity that are essential for transposition of the LINE. All autonomous Class I (RNA-intermediate) retrotransposons share the following features:
- A promoter in the 5′ UTR from which they can be transcribed
- A reverse transcriptase that generates a cDNA copy of the transposable element
- An RNAse H (an endonuclease) that degrades the transcript after reverse transcription
- An integrase (like a transposase) that catalyzes insertion of the retrotransposon copy at insertion sites
14.7.3 Non-LTR Retrotransposons: SINEs
Non-LTR SINE retrotransposons are non-autonomous, typically lacking genes. However their nongenic DNA is flanked by 5’ and 3’ UTRs. RNA polymerase III can transcribe SINEs, but to transpose, SINEs rely on the concurrent activity of an autonomous, non-LTR transposon (a LINE) to provide the requisite enzymatic activities. The human Alu element in Figure 14.22 is a typical SINE (short interspersed nuclear element).
