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‘mobile’ DNA: transposable elements

‘mobile’ DNA: transposable elements. 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.

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‘mobile’ DNA: transposable elements

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  1. ‘mobile’ DNA: transposable elements

  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 byusing 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 Fig 15.19 Genes VII by B. Lewin

  5. Classes of transposable elements Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632

  6. Common mechanism of transposition • Transposons encode transposases that catalyse transposition events • Regulation of transposase expression essential 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

  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). Trends in Microbiology 2005 Vol13(11) pp 543-549

  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

  12. Transposition can occur via • DNA intermediates • Class II TEs • Use a ‘cut and paste’ mechanism • Generally short sequences • RNA intermediates • Class I TEs – Use a ‘copy & paste’ mechanism See interspersed repeats from the repetitive elements lecture

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

  14. Class II TEs DNA intermediate • 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 Retrotransposonare 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 Fig. 13.23 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 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. Integrons Mobile Integrons Superintegrons Mazel Nature Reviews Microbiology4, 608–620 (August 2006)

  26. References • Chapter 9 pp 265-268 HMG 3 by Strachan and Read • Chapter 10: pp 339-348 Genetics from genes to genomes by Hartwell et al (2/e) • Nature (2001) 409: pp 879-891

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