Mobile & Transposa ble Elements

1. Jumping Genes Mobile & Transposable Elements

2. Ethnobotany

3. mosaic kernels

4. 1938: Marcus Rhoades reported odd phenotypic ratios in corn. Self pollination of a pigmented corn kernel yielded: 12 : 3 : 1 pigmented : dotted : colorless

5. A hypothesis: Two mutations at unlinked loci: 1. pigment gene A1 mutated to colorless mutant a1, and 2. a dominant allele for dotting (Dt) appeared. The presence of the Dt allele caused spots of pigment to appear.

6. Barbara McClintock 1902-1992

7. Barbara McClintock 1902-1992

11. Transposition = the movement of genetic information from one chromosomal location, the donor site, to another, the target site.

12. DNA sequences that can change their genomic location intragenomically either autonomously or non-autonomouslyare called transposable elements.

13. “copy-and-paste” “cut-and-paste”

14. Retrotransposons can be divided into five orders on the basis of their mechanistic features, sequence organization, and reverse transcriptase phylogeny: LTR retrotransposons, DIRS-like elements, Penelope-like elements, LINEs, and SINEs.

16. When a transposable element is inserted into a host genome, a small segment of the host DNA (usually 4-12 bp) is duplicated at the insertion site.

19. Transposition = the movement of genetic information from one chromosomal location, the donor site, to another, the target site.

20. DNA sequences that can change their genomic location intragenomically either autonomously or non-autonomouslyare called transposable elements.

21. Classifications of Transposable Elements

22. Transposition may be replicative or conservative. Replicative transposition will result in two copies of the element, one at the donor site and one at the target site. Following conservative transposition the transposable element will only be found at the target site, with no change in copy number.

23. Conservative transposition = “cut-and-paste” transposition

24. Duplicative transposition = “copy-and-paste” transposition

25. DNA-mediated and RNA-mediated transposable elements: • Class I transposable elements (retrotransposons). • Class II transposable elements (DNA transposons).

27. Autonomous and nonautonomous transposable elements Autonomous transposable elements encode all the components of the transposition machinery. Nonautonomous transposable elements appropriate the transposition machinery of autonomous transposable elements.

28. Active and fossil transposable elements A transposable element is defined as active if it contains all the necessary sequence elements for either autonomous or nonautonomous transposition. Active elements may be rendered defective by different types of mutation, in which case they are referred to as fossil transposable elements.

29. Active and fossil transposable elements A transposable-element family may contain different combinations of active autonomous, active nonautonomous, fossil autonomous, and fossil nonautonomous transposable elements. For example, the human genome contains approximately 50,000 fossil autonomous and 200,000 fossil nonautonomous DNA transposons. Intriguingly, the human genome seems to contain NO active DNA transposons.

30. According to the numbers and kinds of genes they contain, DNA-mediated transposable elements are divided into insertion sequences and transposons.

32. Foundin Escherichia coli and Shigella dysinteria. Length = 770 nucleotides, including two inverted terminal repeats, 23 bp each. Contains two out-of-phase reading frames, insA and insB, from which a single protein is produced by translational frameshifting at a run of adenines. The N-terminal is an inhibitor of transposition; the C-terminal is a transposase, an enzyme that catalyzes the insertion of transposable elements into insertion sites.

33. Carriers and non-carriers of the insertion sequence can be separated by centrifugation because the carriers are heavier.

34. INSERTION SEQUENCES (IS) Insertion sequences were first discovered in the gal operon of E. coli. Galactose (gal) operon galK galT galM galE galE = UDP-galactose 4-epimerase galT = galactose-l-phosphate uridylyltransferase galK = galactokinase galM = mutarotase

35. Galactose (gal) operon galK galT galM galE IS Insertion of an IS affects only the transcription of the genes downstream from the insertion. For example, if the IS occurs in the galT gene, the galT, galK and galM genes will be disrupted, but galE will not be. This phenomenon is known as a POLAR mutation.

40. Stupidity

41. Composite Hypercomposite transposons contain two or more transposons.

42. (symmetrical-inverted) Tn3 from E. coli confers streptomycin resistance. tnpR and bla are transcribed on one strand; tnpA on the other. Tn3 is flanked by 38-bp-long inverted repeats. (asymmetrical) Tn554 from Staphylococcus aureus lacks terminal repeats and contains 8 protein-coding genes. Three of the genes are transcribed as a unit and encode transposases (tnpA, tnpB, and tnpO). The spc and ermA genes confer spectinomycin and erythromycin resistance, respectively.

43. Composite transposon Tn9 from Escherichia coli contains two copies of IS1 flanking the cat gene, which encodes a chloramphenicol-resistance protein.

44. Some mobile elements can transpose themselves in all cells; others are cell-specific. Tc1 elements in the nematode Caenorhabditis elegans and P elements in Drosophilamelanogaster are usually mobile only in germ cells.

45. Transposition of many elements is regulated by developmental stage. From an evolutionary point of view, the developmental timing of transposition is particularly important, because it affects the propagation of the transposable element to future generations.

46. LINE-1 transposable elements in mammals are particularly active during leptotene and zygotene, when DNA-strand breakages occur. This offers an opportunity for transposable elements to insert themselves into new sites.

47. Genomic locations of target sites for transposition: Exclusive genomic preference: In the vast majority of cases IS4 incorporates itself in the galactosidase operon of Escherichia coli, and thus each bacterium contains mostly one copy of IS4. Complete randomness: Bacteriophage Mu transposes itself at random within the genome. Intermediate genomic preference: 40% of all Tn10 transposons in E. coli are found in the lacZ gene, which constitutes a minute fraction of the host genome.

48. Genomic locations of target sites for transposition: Affinity for a particular nucleotide composition:IS1 favors AT-rich sites. Affinity for a particular sequence:IS630 has a special affinity for 5'—CTAG—3' sequences. Chromosomal preference:TRIM elements in Drosophila miranda exhibit a preference for the Y chromosome.

49. Hotspots for P element insertion in the X chromosome of Drosophila melanogaster

50. Genomic locations of target sites for transposition: The DIRS-1 transposable element in the slime mold Dictyostelium discoideum