Molecular Evolution 2Molecular Evolution 2

Recombination & TranspositionRecombination & Transposition

RecombinationRecombination larger scale chromosome larger scale chromosome

rearrangementsrearrangements

Recombination is an integral part of Recombination is an integral part of evolution which allows favourable & evolution which allows favourable & unfavourable mutations to be unfavourable mutations to be separated by shuffling the genes separated by shuffling the genes

OutlineOutline

RecombinationRecombination Homologous recombinationHomologous recombination Non-homologous recombinationNon-homologous recombination

Site-specific recombinationSite-specific recombinationTranspositionTransposition

DNA transpositionDNA transpositionRNA trnaspositionRNA trnasposition

RecombinationRecombination

Homologous recombinationHomologous recombination exchange between homologous DNA exchange between homologous DNA

sequences; accomplished by a set of sequences; accomplished by a set of enzymesenzymes

function:function: meiosis I of eukaryotic cell meiosis I of eukaryotic cell division, double-strand break repair, division, double-strand break repair, telomere maintenancetelomere maintenance

replicationreplication is an integral part of the reaction, is an integral part of the reaction, allowing reformation of functional replication allowing reformation of functional replication forks after any fork blocking eventforks after any fork blocking event

Homologous Homologous recombinationrecombination

OutlineOutline

Non-homologous recombinationNon-homologous recombinationstrand exchange between DNA sequences strand exchange between DNA sequences

with very little homologywith very little homology

Site-specific recombinationSite-specific recombination

TranspositionTransposition

Site-specific recombinationSite-specific recombination

accomplished by accomplished by specific recombinasesspecific recombinases that catalyse the breaking and that catalyse the breaking and rejoining of DNA segmentsrejoining of DNA segments

function:function: controlling gene expression, controlling gene expression, increase genetic diversityincrease genetic diversity

replicationreplication is NOT part of the reaction is NOT part of the reaction

Site-specific recombination (SSR)Site-specific recombination (SSR)

Important distinguishing FeatureImportant distinguishing Feature

Conservative SSR process involvesConservative SSR process involvesProtein-DNA covalent intermediatesProtein-DNA covalent intermediates

Site-specific recombinationSite-specific recombination

Fig1 from Site-specific recombination by Anca Segall [www.els.net]

Site-specific recombination (SSR)Site-specific recombination (SSR)

2 structurally unrelated families2 structurally unrelated families

Tyrosine recombinases (Tyrosine recombinases (integrase integrase family)family)

Serine recombinases (resolvase-DNA Serine recombinases (resolvase-DNA invertase recombinases)invertase recombinases)

Site-specific recombination by David J Sherratt [www.els.net]

Recombination core sites of S and Y recombinases

Site-specific recombinationSite-specific recombination

FIG 1: Site-specific recombination by David J Sherratt [www.els.net]

Serine recombinasetyrosine recombinaseSite-specific recombinationSite-specific recombination

FIG 3: Site-specific recombination by David J Sherratt [www.els.net]

TranspositionTransposition

Discrete sequences (transposable elements Discrete sequences (transposable elements

or TEs) in the genome that have the ability or TEs) in the genome that have the ability

to translocate or copy itself across to other to translocate or copy itself across to other

parts of the genome parts of the genome without any without any

requirement for sequence homologyrequirement for sequence homology

Transposable elements move from Transposable elements move from place to place in the genomeplace to place in the genome

1930s Marcus Rhoades and 1950s Barbara 1930s Marcus Rhoades and 1950s Barbara McClintock – transposable elements in cornMcClintock – transposable elements in corn

1983 McClintock received Nobel Prize1983 McClintock received Nobel Prize

Found in all organismsFound in all organisms Most 50 – 10,000 bpMost 50 – 10,000 bp May be present hundreds of times in a genomeMay be present hundreds of times in a genome

TEs can generate mutations in adjacent genesTEs can generate mutations in adjacent genes

TE in MaizeTE in Maize

Fig 15.19 Genes VII by Fig 15.19 Genes VII by B. LewinB. Lewin

Transposition can occur via Transposition can occur via

RNA intermediateRNA intermediate

Class I TEsClass I TEs - - transpose via a RNA transpose via a RNA intermediateintermediate RetroposonsRetroposons retrotransposonsretrotransposons

DNA intermediateDNA intermediate - - transpose via a DNA transpose via a DNA intermediateintermediate Class II TEsClass II TEs - - catalysed by the enzyme catalysed by the enzyme

transposasetransposase

DNA intermediateDNA intermediateClass II TEsClass II TEs

IS elements and transposons IS elements and transposons

bounded by bounded by terminal inverted repeats terminal inverted repeats (TIR)(TIR)

Prokaryotic IS elements (e.g. IS10, Ac/Ds, Prokaryotic IS elements (e.g. IS10, Ac/Ds, mariner) encode only transposase mariner) encode only transposase sequences sequences

eukaryotic transposons encode additional eukaryotic transposons encode additional genes such as antibiotic resistance genes such as antibiotic resistance genesgenes

DNA intermediateDNA intermediate

Transposons encode transposase enzymes that Transposons encode transposase enzymes that catalyze events of transpositioncatalyze events of transposition

Fig. 13.24 a

RNA intermediateRNA intermediateClass I TEsClass I TEs – –

transpose via a RNA transpose via a RNA intermediate intermediate

RetroposonsRetroposons are are structurally similar structurally similar to mRNAto mRNA

retrotransposonsretrotransposons are structurally are structurally similar to similar to retroviruses and retroviruses and are bound by long are bound by long terminal repeats terminal repeats (LTR)(LTR)

Class I TEs encode a reverse transciptase-like Class I TEs encode a reverse transciptase-like enzymeenzyme

RetroposonRetroposon

Poly-A tail at 3’ end Poly-A tail at 3’ end of RNA-like DNA of RNA-like DNA strandstrand

retrotransposonretrotransposon Long terminal Long terminal repeat (LTRs) repeat (LTRs) oriented in same oriented in same direction on direction on either end of either end of element element

Fig. 13.23 a

Fig. 13.23 b

Transposons are now classified Transposons are now classified into 5 familiesinto 5 families

On the basis of their transposase proteinsOn the basis of their transposase proteins

1)      DDE-transposases1)      DDE-transposases2)      RT/En transposases2)      RT/En transposases

(reverse transcriptase/endonuclease) (reverse transcriptase/endonuclease) 3)  Tyrosine (Y) transposases 3)  Tyrosine (Y) transposases 4)      Serine (S) transposases4)      Serine (S) transposases5) 5) Rolling circle (RC) or Y2 transposasesRolling circle (RC) or Y2 transposases

Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77))

DDE-transposasesDDE-transposases

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

RT/En transposases (reverse transcriptase/endonucleaseRT/En transposases (reverse transcriptase/endonuclease

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

Tyrosine (Y) transposasesTyrosine (Y) transposases

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

Serine (S) transposasesSerine (S) transposases

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

Rolling circle (RC) or Y2 transposasesRolling circle (RC) or Y2 transposases

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

Common mechanism of Common mechanism of transpositiontransposition

Transposase requiredTransposase required Regulation of transposase expression Regulation of transposase expression

controls transpositioncontrols transposition

Catalytic domain of transposase involved in Catalytic domain of transposase involved in transphosphorylation step that initiates transphosphorylation step that initiates DNA cleavage & strand transfer. DNA cleavage & strand transfer.

Common mechanism of Common mechanism of transpositiontransposition

2 sequential steps2 sequential steps

    Site specific cleavage of DNA at the end of TESite specific cleavage of DNA at the end of TE

Complex of transposase-element ends brought Complex of transposase-element ends brought to DNA target where strand transfer is to DNA target where strand transfer is carried out by covalent joining of 3’end of carried out by covalent joining of 3’end of TE to target DNA TE to target DNA

Common mechanism of transpositionCommon mechanism of transposition Fig 15.14

Fig 15.10