‘‘mobile’ DNA: transposable elementsmobile’ DNA: transposable elements

Transposable elementsTransposable elements

Discrete sequences in the genome that have Discrete sequences in the genome that have

the ability to translocate or copy itself the ability to translocate or copy itself

across to other parts of the genome across to other parts of the genome without without

any requirement for sequence homology any requirement for sequence homology byby

using a self-encoded recombinase called using a self-encoded recombinase called

transposase transposase

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

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

1983 McClintock received Nobel 1983 McClintock received Nobel PrizePrize

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

a genomea genome

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

TEs in MaizeTEs in Maize

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

Classes of transposable elementsClasses of transposable elements

Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632

Common mechanism of transpositionCommon mechanism of transposition Transposons encode transposases that Transposons encode transposases that

catalyse transposition eventscatalyse transposition events Regulation of transposase expression Regulation of transposase expression

essentialessential

Fig13.24a: Hartwell

Common mechanism of transpositionCommon mechanism of transposition

Common mechanism of transpositionCommon mechanism of transposition

2 sequential steps2 sequential steps

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

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

transpososome

Common mechanism of transpositionCommon mechanism of transposition transposase (blue) binds and assembles a paired end complex transposase (blue) binds and assembles a paired end complex

(PEC) by dimerization, a process that might involve divalent (PEC) by dimerization, a process that might involve divalent metal ions (Memetal ions (Me2+2+). ).

PEC is then active for the cleavage reactions that remove PEC is then active for the cleavage reactions that remove flanking donor DNA (thin black lines) and transfer of the flanking donor DNA (thin black lines) and transfer of the transposon ends into target DNA (black dotted line).transposon ends into target DNA (black dotted line).

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

Catalytic domain of transposase involved in a transphosphorylation Catalytic domain of transposase involved in a transphosphorylation reaction that initiates DNA cleavage & strand transferreaction that initiates DNA cleavage & strand transfer

Fig 15.14

Fig 15.10GenesVII Lewin

How transposons moveHow transposons move

RNA intermediatesRNA intermediates Class I TEsClass I TEs – –

Use a ‘copy & paste’ Use a ‘copy & paste’ mechanismmechanism

DNA intermediatesDNA intermediates Class II TEsClass II TEs Use a ‘cut and paste’ mechanism Use a ‘cut and paste’ mechanism Generally short sequencesGenerally short sequences

Transposition can occur viaTransposition can occur via

See interspersed repeats from the repetitive elements lecture

DNA intermediateDNA intermediateClass II TEsClass II TEs

IS elements and transposonsIS elements and transposons

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

DNA intermediateDNA intermediateClass II TEsClass II TEs

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

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

Some types of rearrangements mediated by DNA Some types of rearrangements mediated by DNA transposonstransposons

Gene (2005)345 pp91-100

Class I TEs encode a reverse transcriptase-Class I TEs encode a reverse transcriptase-like enzymelike enzyme

RetroposonRetroposonRetroposonsRetroposons are are

structurally similar structurally similar to mRNAto mRNA

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

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

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

Fig. 13.23 a

retrotransposon

Class 1 TEsClass 1 TEs

LTR retrotransposonsLTR retrotransposons

RetroposonsRetroposons

Transposons move in different Transposons move in different waysways

Classified into 5 families on the basis of their Classified into 5 families on the basis of their transposition pathwaystransposition pathways

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-transposasesContains invariant DDE motif Contains invariant DDE motif

responsible for excision and responsible for excision and integrationintegration

DDE motif facilitates catalysis DDE motif facilitates catalysis by divalent metal ionsby divalent metal ions

2 step catalysis occurs on 2 step catalysis occurs on transpososometranspososome

Characterised by target Characterised by target duplication, the length of duplication, the length of which is specific for each which is specific for each transposontransposon

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/endonuclease)RT/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

Related to Y recombinasesRelated to Y recombinases

Transposon is excised out Transposon is excised out to generate a circular to generate a circular intermediateintermediate

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))

Some transposons can encode Some transposons can encode integronsintegrons

Integrons are assembly platforms — DNA Integrons are assembly platforms — DNA elements that acquire open reading frames elements that acquire open reading frames embedded in exogenous gene cassettes and convert embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct them to functional genes by ensuring their correct expression. expression.

e.g. bacterial Tn7 also encodes an integron — a e.g. bacterial Tn7 also encodes an integron — a DNA segment containing several cassettes of DNA segment containing several cassettes of antibiotic-resistance genes. These cassettes can antibiotic-resistance genes. These cassettes can undergo rearrangements in hosts that express a undergo rearrangements in hosts that express a related recombinase, leading to alternative related recombinase, leading to alternative combinations of antibiotic-resistance genes.combinations of antibiotic-resistance genes.

Mazel Nature Reviews Microbiology 4, 608–620 (August 2006)

IntegronsIntegrons

Mobile IntegronsMobile Integrons

SuperintegronsSuperintegrons

ReferencesReferences

1)1) Chapter 9 pp 265-268 Chapter 9 pp 265-268 HMG 3 by HMG 3 by Strachan and Strachan and

ReadRead

2)2) Chapter 10: pp 339-348Chapter 10: pp 339-348Genetics from genes to Genetics from genes to genomes by genomes by Hartwell et alHartwell et al (2/e) (2/e)

3)3) Nature (2001) Nature (2001) 409: pp 409: pp 879-891879-891