1. Molecular Evolution 2 Recombination & Transposition

2. Recombination larger scale chromosome rearrangements
Recombination is an integral part of evolution which allows favourable & unfavourable mutations to be separated by shuffling the genes

3. Outline Recombination Homologous recombination
Non-homologous recombination
Site-specific recombination
Transposition
DNA transposition
RNA trnasposition

4. Recombination Homologous recombination
exchange between homologous DNA sequences; accomplished by a set of enzymes
function: meiosis I of eukaryotic cell division, double-strand break repair, telomere maintenance
replication is an integral part of the reaction, allowing reformation of functional replication forks after any fork blocking event

5. Homologous recombination

8. Outline Non-homologous recombination
strand exchange between DNA sequences with very little homology
Site-specific recombination
Transposition

9. Site-specific recombination
accomplished by specific recombinases that catalyse the breaking and rejoining of DNA segments
function: controlling gene expression, increase genetic diversity
replication is NOT part of the reaction

10. Site-specific recombination (SSR)
Important distinguishing Feature
Conservative SSR process involves
Protein-DNA covalent intermediates

11. Site-specific recombination
Fig1 from Site-specific recombination by Anca Segall [

12. Site-specific recombination (SSR)
2 structurally unrelated families
Tyrosine recombinases (l integrase family)
Serine recombinases (resolvase-DNA invertase recombinases)
Site-specific recombination by David J Sherratt [

13. Site-specific recombination
Recombination core sites of S and Y recombinases
FIG 1: Site-specific recombination by David J Sherratt [

14. Site-specific recombination
Serine recombinase
tyrosine recombinase
FIG 3: Site-specific recombination by David J Sherratt [

15. Transposition
Discrete sequences (transposable elements or TEs) 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

16. 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

17. TEs can generate mutations in adjacent genes
TE in Maize
Figure 13.25
Fig Genes VII by B. Lewin

18. Transposition can occur via
RNA intermediate
Class I TEs - transpose via a RNA intermediate
Retroposons
retrotransposons
DNA intermediate - transpose via a DNA intermediate
Class II TEs - catalysed by the enzyme transposase

19. DNA intermediate Class II TEs IS elements and transposons
bounded by terminal inverted repeats (TIR)
Prokaryotic IS elements (e.g. IS10, Ac/Ds, mariner) encode only transposase sequences
eukaryotic transposons encode additional genes such as antibiotic resistance genes

20. DNA intermediate

21. Transposons encode transposase enzymes that catalyze events of transposition
Figure a
Fig a

22. RNA intermediate Class I TEs – transpose via a RNA intermediate
Retroposons are structurally similar to mRNA
retrotransposons are structurally similar to retroviruses and are bound by long terminal repeats (LTR)

23. Class I TEs encode a reverse transciptase-like enzyme
Retroposon
Poly-A tail at 3’ end of RNA-like DNA strand
retrotransposon Long terminal repeat (LTRs) oriented in same direction on either end of element
Figure a
Fig a

24. Figure b
Fig b

25. Transposons are now classified into 5 families
On the basis of their transposase proteins
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)

26. DDE-transposases
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

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

28. Tyrosine (Y) transposases
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

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

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

31. Common mechanism of transposition
Transposase required
Regulation of transposase expression controls transposition
Catalytic domain of transposase involved in transphosphorylation step that initiates DNA cleavage & strand transfer.

32. Common mechanism of transposition
2 sequential steps
  Site specific cleavage of DNA at the end of TE
Complex of transposase-element ends brought to DNA target where strand transfer is carried out by covalent joining of 3’end of TE to target DNA

33. Figure b

34. Common mechanism of transposition
Fig 15.14
Fig 15.10