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Transposible
elements
Viruses and viroids
Transposons, TE
= mobile genetic elements
-
sequences of DNA that can move around to different
positions within the genome of a single cell (transposition),
-
cause mutations and chromosomal rearrangements
-
identified in Prokaryotes and all Eukaryotes:
(with exception of parasitic Plasmodium falciparum)
animals 3-45%, fungi 2-20%, plants 10-80%
in plants:
- thousands of families, form majority of repetitive DNA
Basic classification of TE
•
DNA transposons - „CUT and PASTE“
(rarely „COPY and PASTE“)
typically: transposase cleaves out, inserts to new site
•
Retrotransposons - „COPY and PASTE“
typically:
- reverse transcriptase - DNA copies from TE transcripts
- integrase - insertion
Basic classification of TE
- self-sufficiency
• Autonomous elements
– encode genes necessary for transposition/
replication
• Non-autonomous
– derivatives of autonomous elements
– lost of genes for transposition/replication
– keep sequences necessary for transposition
(can be mobilized by related autonomous elements!)
Discovery of transposons
Barbara McClintock (1902-1992)
Nobel prize in Physiology and Medicine 1983
Mobile genetic elements in maize 1940-1950
Discovery of TE
- study
of chromosomal breakage
- increased frequency in certain site
(= marker „dissociation“ Ds)
- location of Ds was unstable after
crossing with some lines
(= line carrying „activator“ Ac)
Discovery of TE
- in one location – Ds insertion
was connected with loss of purple
pigment of endosperm
- after crossing with activator line
pigment synthesis was recovered
in some cells
Barbara McClintock (1902-1992)
1951: formulated basic context of epigenetics:
"[T]he progeny of two (such) sister cells are not alike with respect to the types
of gene alteration that will occur. Differential mitoses also produce the
alterations that allow particular genes to be reactive. Other genes, although
present, may remain inactive. This inactivity or suppression is considered
to occur because the genes are ‘covered' by other nongenic
chromatin materials. Gene activity may be possible only when a
physical change in this covering material allows the reactive
components of the gene to be ‘exposed' and thus capable of
functioning."
Classification of TE
1. Class:
- replication with/without RNA intermediate
• DNA transposons
• Retrotransposons
2. Subclass: - mechanism of replication (DNA transposones)
3. Order:
- basic structural features
4. Superfamily: - similarity of sequences
Nature Rev. Genet., 2007
Basic TE subclasses
/replication
protein + helicase
Lisch 2013, Nature Rev. Genet.
Class II: DNA transposons
DNA transposons - subclass I
transposition: break, religation
- terminal inverted repeats recognized by transposase
(fungal TE Crypton encodes recombinase instead of transposase)
- duplication of short seq. (2-8 bp) = footprint after transposition
- clustering in genom, hundreds of copies
Multiplication of DNA transposons
Activation during replication - how?
Hemimethylated state?
+ break repair by homologous recombination
(TE can be restored)
Examples of DNA transposons – subclass I:
- Ac, Spm, Mu (maize), Tam (Antirrhinum), TphI (petunia),
TagI (Arabidopsis)
- non-autonomous: Ac/Ds, Spm/dSpm
- Stowaway, Tourist >10 000 copies
DNA transposons – subclass 2
Helitrons – single strand breake and strand displacement
- Rep/helikase-like, replication protein A-like
- maize: 4 - 10 000 gene fragments mobilized by helitrons
Class I: Retrotransposons
Retrotransposons
- replication through RNA intermediate (multiple offspring)
- related to retroviruses
- millions of copies
- huge portions of genome (up to 40-80 % of genome size)
- element size 1-13 kbp
Order LTR – most important in plants
- LTR (long terminal repeat) - promotor, terminator, direct repeat
- dubling of short target sequence
- gag (nucleocapsid),
- pol (protease, reverse transcriptase-RNase H, integrase)
Retrotransposons LTR - replication
- LTR (U3, R, U5)
- PBS
tRNA primer
-skips between
templates
(direct repeat)
Examples of LTR retrotransposons
BARE-1, barley, 12,1 kbp, >50 000 copies, transcript in leaves and callus
PREM-2, maize, 9,5 kbp, >10 000 copies, transcript in microspores
Tnt1, tobacco, 5,3 kbp, >100, activated after wounding, patogen attack,
Ty3 – gypsy group – ancestors of Caulimoviruses, hypothetical ancestors
of animal retroviruses (env-like sequence)
Athila, A.t., 10,5 kbp, >10000, paracentromeric regions
Retrotransposons without LTR
LINE (long interspersed nuclear elements)
SINE (short interspersed nuclear elements)
LINE
APE – endonuklease, RH – RNase H
LINE
- phylogenetically most original, ancestors of LTR
- 5´region – promoter; 3´ region - terminator
Cin4, maize, 1-6,8kbp, 50-100, various truncated forms
SINE
- non-autonomous – use RT of other elements
- derived from products of RNA polymerase III (tRNA, 7SLRNA, (rRNA))
- < 500 nt
Regulation of transposon activity
- both endogenous and by plant cell
- mostly inactive – methylated (prevents activity and also
illegitime recombination (crossing over)
- often developmentally regulated activation
- rarely activation by environmental conditions:
Tam1 (1000x at 15°C)
Reme1– activation by UV light
Maintenance methylation of TE
Zemach et al. 2013
Role of TE in evolution
causing mutations = increasing variability
- modulation of expression (activation, repression, developmentally- or
stress- induced) – important during domestication (WHY?)
- new gene evolution
- genome evolution
- in plants no direct profit – no genes directly increasing fitness (like
resistances in bacteria)
- increase in fitness by random mutation – low probability, but possible
(really occuring)
Transposon-mediated mutagenesis
- site of insertion
- character of transposon regulatory sequences
Promotor
5´UTR exon
intron
exon
3´UTR
terminator
- modulation of transcription (spatial, temporal) – promoter,
enhancers
- transcript stability and splicing
- changes in protein sequence (footprints, frame-shift) –
possible role in evolution of new genes
TE affected expression of TF VvmybA1
- regulation of antokyan synthesis genes
(Kobayashi et al. 2004, Science)
TE affected gene expression - examples
Maize: – inactivation of CCT (photoperiod response) by CACTA-like element
(DNA TE) insertion to promoter
– allowed cultivation in temporal climate (long-day flowering)
block of branching (TE enhancer  OE of inhibitor) (Yang et al. 2013, PNAS)
Red orange:
Ruby – myb TF
(regulation of antokyan genes)
activated by TE insertion
- cold induced expression
in fruits
(Butelli et al. 2012, Plant Cell)
Transposon mutagenesis
- mainly in Arabidopsis
- insertional mutagenesis (alternative to T-DNA mutagenesis – see later)
– easy detection of the site of insertion (x chemical mutagenesis)
- DNA transposons from maize – low frequency of transposition
- two-component systém (transposase/Ds)
Gene for transposase
R Ds
Line with non-autonomous
element in resistance gene
R
(inducible expression)
Ds
Selection of resistant plants = with transposed transposon
Selection in next for plants without transposase gene
- frequent mutagenesis of near genes – clustering (20 % in 1Mb around)
- reintroduction of transposase – possibility to reverse the mutation
Role in gene evolution
- insertional mutagenesis (premature termination), footprints
- participation in gene duplications
- directly or via recombination (TE = homologous repeats)
- formation of intron-less gene copies (reverse transcription)
- genes of TE origin „domesticated“ by many eucaryotic organisms
for new functions (telomerase, syncitin, ….)
- new gene formation by fusions of mobilized gene fragments (helitrons)
Role in genome evolution
• Chromosomal rearrangements
- changes of linkage groups
- speciation (incompatibility)
• Increase in genome size („genomic obesity“)
multiplication of TE x homologous recombination
can prevent or even decrease genome size (2n cottons – 2 -3x
genome size differences by active recombination; Hawkins 2009 PNAS)