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Mobile DNA
Chapter 15.
張學偉 助理教授
http://genomed.dlearn.kmu.edu.tw
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.
Most moble DNA consists of Transposable Elements.
• Transposable elements
1.Includes: DNA-based transposons and
retro-transposons.
2.= transposon [Tn] (usually define the DNAbased Tn)
3.= jumping genes (popular name)
4. jump = transposition
Transposons are scattered throughout the DNA of all forms of life.
replicate
Without ori in inserted DNA  die
Tn are always inserted into other DNA molecule.
Fig15-1. Transposable elements are never free.
• 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.
• 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)
Transposable elements are classified based on their
mechanism of movement.
Essential Components of a Transposon
1
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.
Many larger Tn carry a variety of genes
unrelated to transposition itself.
e.g., antibiotic resistence genes,
virulence genes,
metabolic genes
Insertion sequences
-the simplest transposons
(20/23match)
Composite Tn
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)
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.
2 ssb ? (start)
1 dsb ? (end)
High freq of transposition  severely
damage the host chromosome.
 transposition need tightly regulated.
Fig15-4. Outline of Conservative transposition. = Cut-and-paste
ss overhang
Fig15-5. Movement by Conservative Transposition.
Complex transposons move by replicative
transposition.
The original Tn is not damaged.
Fig15-6. Outline of Replicative Transposition. = complex Transposition
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.
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.
• Replicative and Conservative transposition
are related.
•  similar at mechanistic level.
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.
•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.
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.
• Transposition may rearrange host DNA
Fig15-12. Insertion created by using inside ends to transpose.
Fig15-13. Deletions and Inversions made by abortive transposition.
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.
•Transposons in higher life forms
Fully functional 4500bp
Vary in size and defective (derived from Ac)
Nonautonomous
Ac/Ds don’t 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
patch
Fig15-15. Movement of Ds element gives mottled corn.
• 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.
•Retro-Elements Make an RNA copy
Long terminal repeats of
retrovirus
Found most often in eukaryotes
Fig15-16. Structure of Ty-1 retrotransposon. = retroposon
Fig15-17. Movement of Ty-1 retrotransposon (Tn of yeast 1).
Yayoi culture 彌生文化
西元前250?～西元250?
年
繼繩紋文化的日本史前
文化。原起自九州，後
向東北關東平原擴展。
彌生時代人開始製作青
銅器和鐵器，從事紡織。
並利用由中國傳來的水
稻種植方法。彌生陶器
是未經上釉的。早期彌
生陶器的特徵是表面有
鏤刻裝飾；中期表面刻
有波紋裝飾。類似中國
漢代青銅製品有銅鏡和
銅錢。
Repetitive DNA of Mammals
25%
8%
45%
21% 13%
LINE1 = 5 %
3%
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)
Figure 9.25
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.
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.
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]
• Very rarely LINE-1 make a new copy of
itself and may insert in somewhere in DNA.
•  genetic diseases.
• Retro-Insertion of Host-Derived DNA
complementary
Fig15-19. Creation of a processed pseudogene. = retro-psuedogene
Processed pseudogenes arise from integration of reverse transcribed mRNA
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 5’end.
 lost the ability to transpose.
2. Processed pseudogenes
 not expressed by cell due to lack of promoter, intron
or truncate near 5’end. (many cellular gene had been
truncated at 5’end)
 these pseudogenes are often flanked by short repeat
 this is structure of LINE-promoted transpoistion of
cellular mRNA.
SINEs are special class of processed pseudogenes that
were original derived from host DNA sequences.
Non-coding RNA
Derived from 7sl
DR
Direct repeat
Fig15-20. Origin of the Alu element from 7SL RNA.
DR
Repeats such as Alu sequences are collectively called SINE.
• Retrons encode bacterial reverse
transcriptase
Template & primer
Fig15-21. Structure of a retron and its gene products. (bacterial)
Often insert to virus
 In turn insert to
bacterial chromosome
Fig15-22. Retron RNA and RNA/DNA hybrid.
• The Multitude of Transposable Elements.
Conjugative transposons:
Both transpose and promote conjugation like fertility plasmids.
• Bacteriophage Mu is a Transposon
[transduction]
Fig15-23. Bacteriophage Mu is a transposon.
•Conjugative Transposons
Fig15-24.Conjugative transposon.
• Integrons collect genes for transposons
Integration site + intergrase
Fig15-25. Integrons collect antibiotic resistance genes.
• 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.
Fig15-26. Junk DNA is defective selfish DNA.
• Homing Introns
Fig15-27.Homing intron inserts in a unique location.
Fig15-28.Homing Retro-intron inserts via RNA Intermediate.
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.
Recognition site
Direct repeat
for crossover region
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)
Other gene
Long terminal repeat
(non-viral retrotransposons)
No IR (inverted repeat)
(untranslated regions)
Genetic organization of three classes of Tn [Fig11-19]