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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.
Most moble DNA consists of Transposable Elements.
• Transposable elements
1.Includes: DNA-based transposons and retro-transposons.
2.= transposon [Tn] (usually define the DNA-based Tn)
3.= jumping genes (popular name)
44 jump = transposition
Transposons are scattered throughout the DNA of all forms of life.
Fig15-1. Transposable elements are never free.
Tn are always inserted into other DNA molecule.
replicate
Without ori in inserted DNA die
• 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.
Fig15-2.
Essential Components of a Transposon
1 12
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.
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
Fig15-3 Structure of an insertion sequence. (bacteria, virus, plasmid)
IS jump to new location
Turn off transposition
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.
Fig15-4. Outline of Conservative transposition.
Movement by conservative transposition
= Cut-and-paste
2 ssb ? (start)1 dsb ? (end)
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.
Fig15-5. Movement by Conservative Transposition.
ss overhang
Complex transposons move by replicative transposition.
Fig15-6. Outline of Replicative Transposition. = complex Transposition
The original Tn is not damaged.
Fig15-7. Components of a complex transposon.
IRS
Although the complex Tn is replicated while moving, they are not replicons, as they have no origin of replication.
Fig15-8. Replicative transposition forms a cointegrate.
Cointegrate = Temporary structure formed by linking the strands of two molecules of DNA during transposition, recombination, similar processes.
split
• Replicative and Conservative transposition are related.
similar at mechanistic level.
Fig15-9. Replicative and conserative transposition are related.
Common steps
dsb
ssb
3’ end join 5’ target open DNA.3’ end as primers for fill in
Fig15-10. Principle of the composite transposon. Several posibilies.
Composite Tn = 2 IS surrounding a central block of genes
•Composite transposons
Move independent
composite transposon
Fig15-11. Evolution of a composite transposon.
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.
• 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.
Fig15-14. Ac/Ds family of transposons in Maize. Simple & conservative Tn
•Transposons in higher life forms
Fully functional 4500bp
Vary in size and defective (derived from Ac)
NonautonomousAc/Ds don’t need to be on the same chromosome.Ac is autonomous.Ds is non-autonomous.
Fig15-15. Movement of Ds element gives mottled corn.
patch
• 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.
Fig15-16. Structure of Ty-1 retrotransposon.
•Retro-Elements Make an RNA copy
= retroposon
Found most often in eukaryotes
Long terminal repeats of retrovirus
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。
21% 13%8% 3%
45%25%
Repetitive DNA of Mammals
LINE1 = 5 %
Mobile genetic elements of human (dispersed repeat) included: transposition & retrotransposition:
retrotransposition: moving in the form of RNA by element coding for reverse transcriptase. including:
transposition: moving in the form of DNA by element coding for transposases.
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 missingsome of the genes required for transposition; however, these elements canstill move because other copies of the element in the genome encodethe necessary gene products.
Fig15-18. Structure of LINE-1 (L1) element.
transposase
Most human LINE-1 sequences are defective due to deletion. Lack of LTR
Derived from Poly-A tail
Genetic organization of a typical LINS & SINE [Fig11-34]
LINE promote their own transposition and even transpose cellular RNA
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.
• 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
Fig15-19. Creation of a processed pseudogene.
complementary
= 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.
Fig15-20. Origin of the Alu element from 7SL RNA.
Derived from 7sl
Non-coding RNA
DR DR
Direct repeat
Repeats such as Alu sequences are collectively called SINE.
• Retrons encode bacterial reverse transcriptase
Fig15-21. Structure of a retron and its gene products. (bacterial)
Template & primer
Fig15-22. Retron RNA and RNA/DNA hybrid.
Often insert to virus In turn insert to bacterial chromosome
• 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.
Fig15-24.Conjugative transposon.
•Conjugative Transposons
• Integrons collect genes for transposons
Fig15-25. Integrons collect antibiotic resistance genes.
Integration site + intergrase
• 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.
Three types of CSSR recombination [Fig11-3]
Recognition site
Direct repeat for crossover region
Inverted repeat
Because the crossover region is asymmetric, a given recombination always has a defined polarity IR (inverted repeat) or DR (direct repeat)
Genetic organization of three classes of Tn [Fig11-19]
No IR (inverted repeat)
Other gene
Long terminal repeat
(non-viral retrotransposons)
(untranslated regions)
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