Mobile DNA

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Mobile DNA

• Chapter 15.
• ??? ????
• http//genomed.dlearn.kmu.edu.tw

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Sub-cellular Genetic Elements as Gene Creatures

• Gene elements Any molecule or segment of DNA or
  RNA that carries genetic information and acts as
  a heritable unit.
• Gene creature lack their own cells but carry
  genetic information.

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Most moble DNA consists of Transposable Elements.

• Transposable elements
• Includes DNA-based transposons and
  retro-transposons.
• transposon Tn (usually define the DNA-based
  Tn)
• jumping genes (popular name)
• ? jump transposition

Transposons are scattered throughout the DNA of
all forms of life.
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replicate
Without ori in inserted DNA ? die
Tn are always inserted into other DNA molecule.
Fig15-1. Transposable elements are never free.
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• Replicon
• A molecule of DNA or RNA that is
  self-replicating.
• it has its own origin of replication.
• example chromosomes, plasmids, virus genome
  replicon

Note Transposons are not replicon
Transposons lacks of replicaion origin of their
own.
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• DNA-based Tn
• 1.New copy generated
• (complex or replicative transposition)
• 2. Original copy move, leaving a gap in old
  place.
• (conservative or cut-and-paste transposition)

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Transposable elements are classified based on
their mechanism of movement.
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Essential Components of a Transposon
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1
2
Recognize the target sequence (at host)
Tn will often accept a target site with a
sequence that is near match to the preferred
target sequences.
Due to short length and low specificity, multiple
copies of the target sequence will be found
almost random.
Fig15-2.
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• Many larger Tn carry a variety of genes unrelated
  to transposition itself.
• e.g., antibiotic resistence genes,
• virulence genes,
• metabolic genes

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Insertion sequences -the simplest transposons
(20/23match)
Composite Tn
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Turn off transposition
IS jump to new location
Frequency of frameshift determine the damage
degree of host.
IS contain no genes that provide a convenient
phenotype. ? but cause insertion inactivation of
target genes.
Fig15-3 Structure of an insertion sequence.
(bacteria, virus, plasmid)
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Movement by conservative transposition
Which it is called conservative? ? because the
DNA of the transposon is not altered during move.
It is highly possible that this damaged DNA
molecule will not repaired and is doomed. If
repaired, the Tn in new location may still hurt
the host. High freq of transposition ? severely
damage the host chromosome. ? transposition need
tightly regulated.
2 ssb ? (start) 1 dsb ? (end)
Cut-and-paste
Fig15-4. Outline of Conservative transposition.
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ss overhang
Fig15-5. Movement by Conservative Transposition.
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Complex transposons move by replicative
transposition.
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The original Tn is not damaged.
Fig15-6. Outline of Replicative Transposition.
complex Transposition
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IRS
Although the complex Tn is replicated while
moving, they are not replicons, as they have no
origin of replication.
Fig15-7. Components of a complex transposon.
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split
Cointegrate Temporary structure formed by
linking the strands of two molecules of DNA
during transposition, recombination, similar
processes.
Fig15-8. Replicative transposition forms a
cointegrate.
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• Replicative and Conservative transposition are
  related.
• ? similar at mechanistic level.

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ssb
dsb
Common steps
3 end join 5 target open DNA. 3 end as primers
for fill in
Fig15-9. Replicative and conserative
transposition are related.
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• Composite transposons

Composite Tn 2 IS surrounding a central
block of genes
Move independent
composite transposon
Fig15-10. Principle of the composite transposon.
Several posibilies.
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Accumulate on non-essential regions.
This is important if Tn carries internal genes
that enhance the survival of the host cell.
In practice, all stages from newly formed to
fully fused composite Tn are found in bacteria.
? laboratory genetic manipulation is easy.
Fig15-11. Evolution of a composite transposon.
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• Transposition may rearrange host DNA

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Fig15-12. Insertion created by using inside ends
to transpose.
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Fig15-13. Deletions and Inversions made by
abortive transposition.
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• Transposable elements in eukaryotes
• Barbara McClintock (1902-1992)
• Cold Spring Harbor Laboratory, NY
• Nobel Prize in Physiology and Medicine 1983
• for her discovery of mobil genetic elements
• Studied transposable elements in corn (Zea mays)
  1940s-1950s
• (formerly identified as mutator genes by Marcus
  Rhoades 1930s)
• Nonautonomous DNA tn (Ds) require the activator
  (Ac) to be in the same cells.

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• Transposons in higher life forms

Fully functional 4500bp
Vary in size and defective (derived from Ac)
Nonautonomous Ac/Ds dont need to be on the same
chromosome. Ac is autonomous. Ds is
non-autonomous.
Fig15-14. Ac/Ds family of transposons in Maize.
Simple conservative Tn
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patch
Fig15-15. Movement of Ds element gives mottled
corn.
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• The most widely distributed Tn in higher
  organisms are those of the Tc1/mariner family.
• The first member of Tc1 from nematode
• and Mariner from fly.
• ?Found in fungi, plants, animals, protozons.

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• Retro-Elements Make an RNA copy

Long terminal repeats of retrovirus
Found most often in eukaryotes
Fig15-16. Structure of Ty-1 retrotransposon.
retroposon
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Fig15-17. Movement of Ty-1 retrotransposon (Tn of
yeast 1).
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Repetitive DNA of Mammals
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13
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3
LINE1 5
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Mobile genetic elements of human (dispersed
repeat) included transposition
retrotransposition
transposition moving in the form of DNA
by element coding for transposases.
retrotransposition moving in the form
of RNA by element coding for reverse
transcriptase. including

LINEs (Long interspersed nuclear element) SINEs
(Short interspersed nuclear element)
retrovirus-like elements (e.g,LTR long terminal
repeat)
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Non-autonomous This refers to the fact that many
of the transposable elements are missing some of
the genes required for transposition however,
these elements can still move because other
copies of the element in the genome encode the
necessary gene products.
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Derived from Poly-A tail
transposase
Most human LINE-1 sequences are defective due to
deletion. ? Lack of LTR
Fig15-18. Structure of LINE-1 (L1) element.
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The sequences of LINE and SINE look like simple
genes. Poly-A help generate the primer terminus
for RT ? Any mRNA should be an attractive
substrate for transposition via
target-primed reverse transcription mechanism.
LINE promote their own transposition and even
transpose cellular RNA
Genetic organization of a typical LINS SINE
Fig11-34
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• Very rarely LINE-1 make a new copy of itself and
  may insert in somewhere in DNA.
• ? genetic diseases.

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• Retro-Insertion of Host-Derived DNA

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complementary
Fig15-19. Creation of a processed pseudogene.
retro-psuedogene
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Processed pseudogenes arise from integration of
reverse transcribed mRNA
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Evidence 1. many of the poly-A retrotransposons
(LINE SINE) that have been detected by
large-scale genomic sequencing are truncated
elelments. ? most of these are missing region
from 5end. ? lost the ability to transpose. 2.
Processed pseudogenes ? not expressed by cell due
to lack of promoter, intron or truncate near
5end. (many cellular gene had been truncated at
5end) ? these pseudogenes are often flanked by
short repeat ? this is structure of LINE-promoted
transpoistion of cellular mRNA.
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SINEs are special class of processed pseudogenes
that were original derived from host DNA
sequences.
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Non-coding RNA
Derived from 7sl
DR
DR
Direct repeat
Fig15-20. Origin of the Alu element from 7SL RNA.
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Repeats such as Alu sequences are collectively
called SINE.
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• Retrons encode bacterial reverse transcriptase

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Template primer
Fig15-21. Structure of a retron and its gene
products. (bacterial)
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Often insert to virus ? In turn insert to
bacterial chromosome
Fig15-22. Retron RNA and RNA/DNA hybrid.
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• The Multitude of Transposable Elements.

Conjugative transposons Both transpose and
promote conjugation like fertility plasmids.
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• Bacteriophage Mu is a Transposon
• transduction

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Fig15-23. Bacteriophage Mu is a transposon.
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• Conjugative Transposons

Fig15-24.Conjugative transposon.
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• Integrons collect genes for transposons

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Integration site intergrase
Fig15-25. Integrons collect antibiotic resistance
genes.
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• selfish DNA ? perform no useful function but
  merely inhabit the chromosome
• Junk DNA defective selfish DNA cannot move ,
  e.g., most of them become defective and lose
  ability to form virus particle.

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Fig15-26. Junk DNA is defective selfish DNA.
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• Homing Introns

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Fig15-27.Homing intron inserts in a unique
location.
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Fig15-28.Homing Retro-intron inserts via RNA
Intermediate.
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Homologous Recombination (Ch14) ? occur between
any two highly similar regions of DNA, regardless
of the sequence
Site-Specific Recombination (Ch14) and
Transposition of DNA (Ch 15) ? SSR occur between
two defined sequences elements. ? Tn occur
between one specific seq and non-specific DNA
sites.
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Direct repeat for crossover region
Recognition site
Inverted repeat
Three types of CSSR recombination Fig11-3
Because the crossover region is asymmetric, a
given recombination always has a defined
polarity ? IR (inverted repeat) or DR (direct
repeat)
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Other gene
Long terminal repeat
No IR (inverted repeat)
(non-viral retrotransposons)
(untranslated regions)
Genetic organization of three classes of Tn
Fig11-19