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Molecular Evolution 2
Recombination & Transposition
Recombination


larger scale chromosome
rearrangements
Recombination is an integral part of
evolution which allows favourable &
unfavourable mutations to be
separated by shuffling the genes
Outline

Recombination
 Homologous recombination
 Non-homologous recombination
 Site-specific recombination
 Transposition
 DNA transposition
 RNA trnasposition
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
Homologous
recombination
Outline
Non-homologous recombination
strand exchange between DNA sequences
with very little homology
 Site-specific
recombination
 Transposition
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
Site-specific recombination (SSR)
Important distinguishing Feature
Conservative SSR process involves
Protein-DNA covalent intermediates
Site-specific recombination
Fig1 from Site-specific recombination by Anca Segall [www.els.net]
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 [www.els.net]
Site-specific recombination
Recombination core sites of S and Y recombinases
FIG 1: Site-specific recombination by David J Sherratt [www.els.net]
Site-specific recombination
Serine recombinase tyrosine recombinase
FIG 3: Site-specific recombination by David J Sherratt [www.els.net]
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
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
TEs can generate mutations in adjacent genes
TE in Maize
Fig 15.19 Genes VII by B. Lewin
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
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
DNA intermediate
Transposons encode transposase enzymes that
catalyze events of transposition
Fig. 13.24 a
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)
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
Fig. 13.23 a
Fig. 13.23 b
Transposons are now classified
into 5 families
On the basis of their transposase proteins
1)
2)
3)
4)
5)
DDE-transposases
RT/En transposases
(reverse transcriptase/endonuclease)
Tyrosine (Y) transposases
Serine (S) transposases
Rolling circle (RC) or Y2 transposases
Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)
DDE-transposases
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)
RT/En transposases (reverse transcriptase/endonuclease
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)
Tyrosine (Y) transposases
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)
Serine (S) transposases
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)
Rolling circle (RC) or Y2 transposases
Fig1 from Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)
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.
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
Common mechanism of transposition
Fig 15.14
Fig 15.10