1. ‘mobile’ DNA: transposable elements
Pretty much everyone who has ever had an address will have come across "spam", that trickle (or flood) of unsolicited junk offering to sell you anything from viagra to a share in a dead dictator's fortune. Most of us just delete them with a touch of irritation at their clogging up of our mailboxes, and promptly get on with whatever we were doing.
But looking inside ourselves, we discover that this phenomenon pre-dates the internet, and even cave drawings and flint axes. Each cell in our bodies contains thousands of copies of "biological junk mail", except this kind is made of DNA instead of words and data packets. Indeed, while only 2% of our genome directly codes for the proteins that make up our bodies, over 40% of the remaining 'non-coding' DNA is filled with spam! What are these biological "junk mails"?
They are called transposable elements, or transposons, and are ubiquitous throughout life

2. Transposable elements
Discrete sequences in the genome that have the ability to translocate or copy itself across to other parts of the genome without any requirement for sequence homology by using a self-encoded recombinase called transposase

3. Transposable elements move from place to place in the genome
1930s Marcus Rhoades and 1950s Barbara McClintock – transposable elements in corn
1983 McClintock received Nobel Prize
Found in all organisms
Most 50 – 10,000 bp
May be present hundreds of times in a genome

4. TEs can generate mutations in adjacent genes
TEs in Maize
Figure 13.25Figure 2 : Colour variations in maize caused by DNA transposons. A normal gene (Bz) gives maize kernels a dark colour (left), whereas a mutant version (bz) confers an orange colour (middle). If the gene is disrupted by a transposon (bz-m) this also results in an orange colour, but in some of the cells in the kernel the transposon has jumped back out of the gene, restoring its function, producing dark spots where this has happened (right).
Fig Genes VII by B. Lewin

5. Classes of transposable elements
Classes of mobile elements. DNA transposons, e.g., Tc-1/mariner, have inverted terminal inverted repeats (ITRs) and a single open reading frame (ORF) that encodes a transposase. They are flanked by short direct repeats (DRs). Retrotransposons are divided into autonomous and nonautonomous classes depending on whether they have ORFs that encode proteins required for retrotransposition. Common autonomous retrotransposons are (i) LTRs or (ii) non-LTRs (see text for a discussion of other retrotransposons that do not fall into either class). Examples of LTR retrotransposons are human endogenous retroviruses (HERV) (shown) and various Ty elements of S. cerevisiae (not shown). These elements have terminal LTRs and slightly overlapping ORFs for their group-specific antigen (gag), protease (prt), polymerase (pol), and envelope (env) genes. They produce target site duplications (TSDs) upon insertion. Also shown are the reverse transcriptase (RT) and endonuclease (EN) domains. Other LTR retrotransposons that are responsible for most mobile-element insertions in mice are the intracisternal A-particles (IAPs), early transposons (Etns), and mammalian LTR-retrotransposons (MaLRs). These elements are not present in humans, and essentially all are defective, so the source of their RT in trans remains unknown. L1 is an example of a non-LTR retrotransposon. L1s consist of a 5'-untranslated region (5'UTR) containing an internal promoter, two ORFs, a 3'UTR, and a poly(A) signal followed by a poly(A) tail (An). L1s are usually flanked by 7- to 20-bp target site duplications (TSDs). The RT, EN, and a conserved cysteine-rich domain (C) are shown. An Alu element is an example of a nonautonomous retrotransposon. Alus contain two similar monomers, the left (L) and the right (R), and end in a poly(A) tail. Approximate full-length element sizes are given in parentheses
Science 12 March 2004: Vol no. 5664, pp

6. Common mechanism of transposition
Transposons encode transposases that catalyse transposition events
Regulation of transposase expression essential
Regulation of transposition activity is essential to balance the adaptive advantages provided by transposable elements to their host genome, at the same time limiting the damage they might cause by potentially lethal DNA rearrangements. Indeed, mutant elements with increased transposition activities seem relatively straightforward to isolate, therefore, ‘inactivity’ has been suggested to be an evolutionary strategy of many transposable elements . Transposable elements have provided many examples of judicious regulatory mechanisms. However, regulation in generating the protein–DNA complexes (transpososomes) that are necessary for catalysis of the DNA cleavage and strand transfer reactions at the heart of the transposition process has received little attention.
Regulation of catalysis occurs at various steps: transpososome assembly, catalytic activation, target DNA capture or resolution of the transposition products.
Fig13.24a: Hartwell

7. Common mechanism of transposition

8. Common mechanism of transposition
2 sequential steps
Site specific cleavage of DNA at the end of TE
Complex of transposase-element ends (transpososome) brought to DNA target where strand transfer is carried out by covalent joining of 3’end of TE to target DNA
transpososome
Illustration of Tn10 and Tn5 transposition pathways at the transpososome level. (a) Tn5 and Tn10 are represented by a thick green line with red boxes or arrows representing the reactive ends of the transposons (OE = outside; IE = inside, with respect to the transposon. Tpase (blue) binds and assembles a paired end complex (PEC) by dimerization, a process that might involve divalent metal ions (Me2+). The PEC is then active for the cleavage reactions that remove flanking donor DNA (thin black lines) and transfer of the transposon ends into target DNA (black dotted line). (b) Sequence of Tn5 OE showing interactions with specific Tpase residues and the nucleotide numbering system, described in the text. The ‘flipped-out’ T residue is indicated. The end sequences are shown in red. Abbreviations: NTS, non-transferred strand; TS, transferred strand.

9. Common mechanism of transposition
transposase (blue) binds and assembles a paired end complex (PEC) by dimerization, a process that might involve divalent metal ions (Me2+).
PEC is then active for the cleavage reactions that remove flanking donor DNA (thin black lines) and transfer of the transposon ends into target DNA (black dotted line).
Illustration of Tn10 and Tn5 transposition pathways at the transpososome level. (a) Tn5 and Tn10 are represented by a thick green line with red boxes or arrows representing the reactive ends of the transposons (OE = outside; IE = inside, with respect to the transposon. Tpase (blue) binds and assembles a paired end complex (PEC) by dimerization, a process that might involve divalent metal ions (Me2+). The PEC is then active for the cleavage reactions that remove flanking donor DNA (thin black lines) and transfer of the transposon ends into target DNA (black dotted line). (b) Sequence of Tn5 OE showing interactions with specific Tpase residues and the nucleotide numbering system, described in the text. The ‘flipped-out’ T residue is indicated. The end sequences are shown in red. Abbreviations: NTS, non-transferred strand; TS, transferred strand.
Trends in Microbiology 2005 Vol13(11) pp

10. Catalytic domain of transposase involved in a transphosphorylation reaction that initiates DNA cleavage & strand transfer
Fig 15.14
Fig 15.10
GenesVII Lewin

11. How transposons move
Figure b

12. Transposition can occur via
RNA intermediates
Class I TEs –
Use a ‘copy & paste’ mechanism
DNA intermediates
Class II TEs
Use a ‘cut and paste’ mechanism
Generally short sequences
Structure of the main classes of transposable elements found in human genome. (a) Class I elements: A and B: RNA polymerase
III promoters; Core: conserved region of unknown function; ENDO: endonuclease; gag: capsid gene; pol: polyprotein including reverse
transcriptase, integrase, ribonuclease H and protease domains; LTR: long terminal repeat; PBS: primer-binding site; PTT: polypurine tract;
RT: reverse transcriptase; transposase: protein required for the excision and insertion of class II elements. The gray shading for the envelope
(env) gene indicates that a functional gene is not always found. (b) Class II elements: ITR: inverted terminal repeat; MITEs: miniature
inverted-repeated transposable elements.
See interspersed repeats from the repetitive elements lecture

13. DNA intermediate Class II TEs IS elements and transposons
bounded by terminal inverted repeats (TIR)

14. DNA intermediate Class II TEs
Prokaryotic IS elements (e.g. IS10, Ac/Ds, mariner) encode only transposase sequences
eukaryotic transposons encode additional genes such as antibiotic resistance genes

15. Some types of rearrangements mediated by DNA transposons
Gene (2005)345 pp91-100

16. Class I TEs encode a reverse transcriptase-like enzyme
Retroposon
Retroposons are structurally similar to mRNA
Poly-A tail at 3’ end of RNA-like DNA strand
Retrotransposon are structurally similar to retroviruses and are bound by long terminal repeats (LTR)
Long terminal repeat (LTRs) oriented in same direction on either end of element
retrotransposon
Figure a
Fig a

17. Class 1 TEs
Retroposons
LTR retrotransposons

18. Transposons move in different ways
Classified into 5 families on the basis of their transposition pathways
1)      DDE-transposases
2)      RT/En transposases
(reverse transcriptase/endonuclease)
3)  Tyrosine (Y) transposases
4)      Serine (S) transposases
5) Rolling circle (RC) or Y2 transposases
Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

19. DDE-transposases
Contains invariant DDE motif responsible for excision and integration
DDE motif facilitates catalysis by divalent metal ions
2 step catalysis occurs on transpososome
Characterised by target duplication, the length of which is specific for each transposon
Transposons move in different ways. Five protein families dictate different transposition pathways: DDE-transposases,
reverse transcriptase/endonucleases (RT/En), tyrosine (Y)-transposases, serine (S)-transposases and rolling-circle (RC)- or
Y2-transposases. Transposons (blue) can be either ‘cut-out’ or ‘copied-out’ of the flanking donor DNA (green). a | Most DDEtransposons
excise from the flanking DNA to generate an excised linear transposon, which is the substrate for integration into a
target (orange). b | Retrotransposons copy-out by reverse-transcribing (RT) a full-length copy of their RNA (purple) that is generated
by transcription (Txn). Long-terminal repeat (LTR)-retrotransposons make a full-length cDNA copy (pink represents newly replicated
DNA) from their RNA and integrate this into a target using a DDE-transposase. c | TP-retrotransposons use reverse transcriptase
(RT) to copy their RNA directly into a target that has been nicked by a transposon-encoded nuclease (En). d | Y-retrotransposons are
thought to generate a circular cDNA intermediate by reverse transcription. A Y-transposase integrates the element into the target.
e | and f | Y- and S-transposons encode either a tyrosine or serine transposase, which mediates excision of the transposon to form
a circular intermediate. A reversal of the catalytic steps results in transposon insertion. g | Y2-transposons ‘paste’ one strand of the
transposon into a target and use it as a template for DNA replication. Two models have been proposed for Y2-transposition.
Representatives of each type of transposon are listed below each pathway.
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

20. RT/En transposases (reverse transcriptase/endonuclease)
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

21. Tyrosine (Y) transposases
Related to Y recombinases
Transposon is excised out to generate a circular intermediate
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

22. Serine (S) transposases
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

23. Rolling circle (RC) or Y2 transposases
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

24. Some transposons can encode integrons
Integrons are assembly platforms — DNA elements that acquire open reading frames embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct expression.
e.g. bacterial Tn7 also encodes an integron — a DNA segment containing several cassettes of antibiotic-resistance genes. These cassettes can undergo rearrangements in hosts that express a related recombinase, leading to alternative combinations of antibiotic-resistance genes.

25. Mazel Nature Reviews Microbiology 4, 608–620 (August 2006)
Integrons
Mobile Integrons
Superintegrons
Mazel Nature Reviews Microbiology 4, 608–620 (August 2006)

26. References Chapter 9 pp 265-268 Chapter 10: pp 339-348
HMG 3 by Strachan and Read
Chapter 10: pp
Genetics from genes to genomes by Hartwell et al (2/e)
Nature (2001) 409: pp