Transposition and transposable elements

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Transposition and transposable elements
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Transposable elements

• mobile genetic elements
• comprise 45 of human chromosomal DNA middle
  repetitive DNA
• contribute to spontaneous mutation, genetic
  rearrangements, horizontal transfer of genetic
  material
• aid speciation and genomic change (in bacteria
  transposons are often associated with antibiotic
  resistance genes)
• cells must depress transposition to insure
  genetic stability

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Types of transposable elements

• DNA vs. RNA
• viral vs. nonviral
• replicative mechanism vs. excision mechanism

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transposon
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insertion mutation
transposon
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Discovery of transposons

• Barbara McClintock 1950s Ac Ds system in maize
  influencing kernel colorunstable
  elementschanging map positionpromote
  chromosomal breaks
• Rediscovery of bacterial insertion
  sequencessource of polar mutationsdiscrete
  change in physical length of DNAinverted repeat
  ends form lollipops in EM after
  denaturation/reannealing

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Composite bacterial transposons

• repeated ends, usually inverted, sometimes direct
• repeated ends themselves are IS elements and can
  independently transpose
• ends mobilize all intervening DNA
• often antibiotic resistance genes (examples Tn3
  (ampicillin), Tn5 (kanamycin), Tn10
  (tetracycline)
• often reside on plasmids

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Basic minimal insertion sequence structure
tnp ORF
ends genetically required, in cis tnp
(transposase) genetically required, trans-acting
Element 1 Element 2 Transposition?
wt wt 1 and 2
ends- ends- neither
trp- tnp- neither
ends- wt only 2
tnp- wt 1 and 2
tnp- ends- only 1
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Structure of Tn3
4957 bp
3 trans-acting genes
2 cis-acting sites
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tnpR and res mutations cause accumulation of
co-integrate structure
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2 types of DNA tranposons

• excisive mechanismexamples Tn5, Tn10, P
  elements
• replicative mechanismexamples Tn3,
  bacteriophage Mu

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Replicative transposons

• orignal cut of transposon is only nick and only
  one strand is initially ligated
• element replicates through itself
• produces as intermediate a co-integrate
  structure
• co-integrate is resolved by resolvase (as TnpR of
  Tn3) and at specific site (as res of Tn3)

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Excisive transposons

• cut-and-paste mechanism
• cut themselves out of original site, producing
  double strand break
• cut target site and ligate to element ends,
  thereby inserting at new site
• original site break repaired usually with sister
  chromosome, restoring transposon at original
  site sometimes end healed without transposon,
  can also be associated with deletion at excision
  site

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Source of target site duplication TSD
GAC
CTG
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degenerate transposons

• many naturally occurring transposable elements
  have suffered mutation and are no longer active
• some of these may have cis-acting end mutations
  and cannot be mobilized
• others may have intact ends but no transposase
  these can be mobilized by a element that is tnp
  (autonomous element)
• Ac Ds system is an example of latter Ac
  (activator) can mobilize Ds (dissociator)
• MITEs (minature inverted repeat transposable
  elements) are nonautonomous DNA elements
• SINEs are retrotransposon version (LINEs)

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Comparison of transposition reactions
Direct transesterification reactions DDE motif
transposase (integrase)
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Comparison of tranposase structural organization
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Mechanism of transposases and retroviral
integrases
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Classification of retroelements

• Have obligate RNA intermediate, use reverse
  transcriptase (RT, RNA-dependent DNA polymerase)
• LTR-retroelements long terminal
  repeatsTy1/copia, Ty3/gypsy, retroviruses
• Non-LTR-retroelements retroposonsLINES

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Characteristics of LTR retroelements

• Long terminal repeats required for replication
  cycle
• Genes gag, pol, (viruses also have env)
• Pol is polyprotein which gives rise to RT
  (reverse transcriptase), IN (integrase) RH (RNase
  H), PR (protease)
• Forms VLPs virus-like particles
• Integrase is functionally and structurally
  similar to transposase of DNA transposons, DDE
  motif
• Integration gives characteristic TSD

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LTR element replication
tRNA primer
Multiple template jumps
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Characteristics of non-LTR retroelements

• 2 ORFs, orf1, orf2
• Variable TSD
• ORF2 gives rise to EN, endonuclease, (similar to
  APE) and RT
• Uses target primed reverse transcription TPRT
• Can transduce 3 downstream non-element segments

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Target-primed reverse transcription
Explains Insertions are often 5
truncated Transduction of 3 markers
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Human L1 (LINE-1) retroelement

• 15 of human DNA
• 520,000 copies, only 3-5,000 are full-length
• Associated with human disease loci
• Transpose specifically in germ line

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