‘‘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
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