Mobile DNA

1. Mobile DNA Chapter 15. 張學偉 助理教授 http://genomed.dlearn.kmu.edu.tw

2. 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.

3. 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.

4. replicate Without ori in inserted DNA  die Tn are always inserted into other DNA molecule. Fig15-1. Transposable elements are never free.

6. 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.

7. 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)

8. Transposable elements are classified based on their mechanism of movement.

9. 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.

11. Many larger Tn carry a variety of genes unrelated to transposition itself. e.g., antibiotic resistence genes, virulence genes, metabolic genes

12. Insertion sequences -the simplest transposons (20/23match) Composite Tn

13. 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)

14. 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.

15. ss overhang Fig15-5. Movement by Conservative Transposition.

16. Complex transposons move by replicative transposition.

17. The original Tn is not damaged. Fig15-6. Outline of Replicative Transposition. = complex Transposition

18. 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.

19. 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.

20. Replicative and Conservative transposition are related. •  similar at mechanistic level.

21. 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.

23. 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.

24. 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.

25. Transposition may rearrange host DNA

26. Fig15-12. Insertion created by using inside ends to transpose.

27. Fig15-13. Deletions and Inversions made by abortive transposition.

28. 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.

29. 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

30. patch Fig15-15. Movement of Ds element gives mottled corn.

31. 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.

32. Retro-Elements Make an RNA copy Long terminal repeats of retrovirus Found most often in eukaryotes Fig15-16. Structure of Ty-1 retrotransposon. = retroposon

33. Fig15-17. Movement of Ty-1 retrotransposon (Tn of yeast 1).

34. 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。

35. Repetitive DNA of Mammals 25% 45% 8% 21% 13% 3% LINE1 = 5 %

36. 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 (Shortinterspersed nuclear element) retrovirus-like elements (e.g,LTR; long terminal repeat)

37. 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.

38. 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.

39. 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]

40. Very rarely LINE-1 make a new copy of itself and may insert in somewhere in DNA. •  genetic diseases.

41. Retro-Insertion of Host-Derived DNA

42. complementary Fig15-19. Creation of a processed pseudogene. = retro-psuedogene

43. Processed pseudogenes arise from integration of reverse transcribed mRNA

44. 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.

45. SINEs are special class of processed pseudogenes that were original derived from host DNA sequences.

46. Non-coding RNA Derived from 7sl DR DR Direct repeat Fig15-20. Origin of the Alu element from 7SL RNA.

47. Repeats such as Alu sequences are collectively called SINE.

48. Retrons encode bacterial reverse transcriptase

49. Template & primer Fig15-21. Structure of a retron and its gene products. (bacterial)

50. Often insert to virus  In turn insert to bacterial chromosome Fig15-22. Retron RNA and RNA/DNA hybrid.