2. High Frequency of Recombination (Hfr)...bacteria exhibiting a high frequency of recombination, …the F factor is integrated into the chromosomal genome.

3. F factor and Chromosomal DNA are Transferred

4. Recombination Requires Crossing over Double Crossover

5. Incomplete Transfer of DNA Interrupted Mating: a break in the pilus during conjugation stops the transfer of DNA, Transfer occurs at a constant rate, –provides a means to map bacterial genes.

6. How Do You Interrupt Bacterial Mating spread on agar mate for specified time frappe

7. Hfr and Mapping HfrH str s (sensitive to streptomycin) thr + (able to synthesize the amino acid threonine) azi r (resistant to sodium azide) ton r (resistant to bacteriophage T1) lac + (able to grow with lactose as sole source of carbon) gal + (able to grow with galactose as sole source of carbon) F - str r (resistant to streptomycin thr - (threonine auxotroph) azi s (sensitive to sodium azide) ton s (sensitive to phage T1) lac - (unable to grow on lactose) gal - (unable to grow on galactose)

8. Hfr and Mapping HfrH str s (sensitive to streptomycin) thr + (able to synthesize the amino acid threonine) F - str r (resistant to streptomycin) thr - (threonine auxotroph) Streptomycin kills the HfrH cells in the mating mix. No threonine kills the F - cells in the mating mix.

9. Hfr and Mapping HfrH azi r (resistant to sodium azide) ton r (resistant to bacteriophage T1) lac + (able to grow with lactose as sole source of carbon) gal + (able to grow with galactose as sole source of carbon) F - azi s (sensitive to sodium azide) ton s (sensitive to phage T1) lac - (unable to grow on lactose) gal - (unable to grow on galactose)

10. Interrupting Bacterial Mating spread on selective media mate 9 minblend

11. Replica Plating After 9 minutes, only azide resistant cells grow.

12. 10 Minutes Azide, and bacteriophage resistant cells grow.

13. 15 Minutes Azide, and bacteriophage resistant cells, and lactose utilizing cells.

14. 18 Minutes All recombinants grow.

15. % cells with markers

16. Bacterial Map Distances units = minutes

17. HfrH

18. F factor inserts in different regions of the bacterial chromosome, Also inserts in different orientations.

19. Replication Origin Hfr Order of transfer strain H thr azi ton lac pur gal his gly thi 1 thr thi gly his gal pur lac ton azi 2 lac pur gal his gly thi thr azi ton 3 gal pur lac ton azi thr thi gly his

20. F factor Hfr F-F- A a Indicates direction of transfer. A A a Hfr DNA that is not incorporated in the F - strand, and DNA that has crossed out of the F - strand is digested.

21. F factor Hfr F-F- A Leading Gene: the first gene transferred is determined empirically. A Hfr A F-F- A A transfers first. A transfers last.

22. Hfr Order of transfer strain H thr azi ton lac pur gal his gly thi 1 thr thi gly his gal pur lac ton azi 2 lac pur gal his gly thi thr azi ton 3 gal pur lac ton azi thr thi gly his

24. Microbes… …in the news.

25. Hfr and Mapping HfrH str s (sensitive to streptomycin) thr + (able to synthesize the amino acid threonine) azi r (resistant to sodium azide) ton r (resistant to bacteriophage T1) lac + (able to grow with lactose as sole source of carbon) gal + (able to grow with galactose as sole source of carbon) F - str r (resistant to streptomycin thr - (threonine auxotroph) azi s (sensitive to sodium azide) ton s (sensitive to phage T1) lac - (unable to grow on lactose) gal - (unable to grow on galactose)

26. Hfr and Mapping HfrH str s (sensitive to streptomycin) thr + (able to synthesize the amino acid threonine) F - str r (resistant to streptomycin) thr - (threonine auxotroph) Streptomycin kills the HfrH cells in the mating mix. No threonine kills the F - cells in the mating mix, * also, azide, T1 phage, and a lack of carbon source.

27. Hfr and Mapping HfrH azi r (resistant to sodium azide) ton r (resistant to bacteriophage T1) lac + (able to grow with lactose as sole source of carbon) gal + (able to grow with galactose as sole source of carbon) F - azi s (sensitive to sodium azide) ton s (sensitive to phage T1) lac - (unable to grow on lactose) gal - (unable to grow on galactose)

28. Bacterial Map Distances units = minutes

29. E. coli Map 0 minutes is at the threonine, 100 minutes is required to transfer complete genome,

30. Typical Problem

32. combine

35. +

36. Join Maps Refer to partial maps for map distances. 11.5 minutes 26 minutes

37. Practice Insights and Solutions, #2, Problem 7.17, 7.18, 7.19.

38. Treponema pallidum

39. Transformation heritable exchange brought about by the incorporation of exogenous DNA, –usually DNA from same, or similar species.

40. Donor and Recipient Not all cells are competent to receive DNA.

41. Competence …a transient state or condition in which a cell can bind and internalize exogenous DNA molecules, …often a result of severe conditions, –heat/cold, –starvation, etc.

42. Competent Cell Genes are expressed that produce proteins that, in turn, span the cell membrane.

43. Exogenous DNA Binds Receptor …and is transported across the cell membrane.

44. Complementary Strand Degraded...one strand of the exogenous DNA is degraded also.

45. Exogenous DNA Incorporated Heteroduplex

46. Cell Divides

47. Transformation and Mapping transformed DNA is generally 10,000 - 20,000 base pairs in length, –carries more than one gene, When two or more genes are received from the same transformation event, they are said to be co-transformed.

48. Linkage in Bacteria genes that are closer together, have a higher probability of being co-transformed, –higher probability of being on same donor DNA, –lower chance of crossover event between genes, probability of transformation by two separate events is low, linkage in bacteria refers to proximity.

50. Transposable Elements …a segment of DNA that can move to, or move a copy of itself to another locus on the same or a different chromosome (hopping DNA), …may be a single insertion sequence, or a more complex structure (transposon) consisting of two insertion sequences and one or more intervening genes.

51. Transposable Elements mobile DNA Transposon: carries one or more genes.

52. Why Transposons? …the DNA sequence between the transposable elements may confer an adaptive advantage, –or at differing dosages, …upon mobilization, the transposon may ‘hop’ into a part of the genome that is being expressed at a higher or lower rate, …other?

53. Recombinases Enzymes that catalyze recombination via “crossing-over” event, –just as sister chromatids can recombine during Prophase I, any DNA can “cross-over” and recombine under the right circumstances.

54. Cre/lox Recombination The enzyme Cre recombinase associates specifically with the loxp locus, - the gene that codes for Cre is elsewhere in the genome, and is under transcriptional control.

55. Integrons Site specific recombinase, plus adjacent recognition region

56. Integron Excision

57. Hop In, Hop Out …the transposable elements, transposons and integrons, etc. may confer a temporary advantage, …once the selective pressure is over, the transposable element can re-mobilize and exit a disrupted gene, and in many cases return the gene to its original state, –may transpose to a conjugative plasmids, or near Hfr integration sites for wide spread dispersal, …integron cassettes can also excise, and picked up by other genetic elements.

58. And, Self-Mutate? …transposable elements are often mobilized during environmental stress, –cassettes are shuttled from cell to cell, etc. …for example: out of billions of cells, one cell may have a transposable element that inactivates a specific gene, –upon inactivation, the cell may have an adaptive advantage.

59. Transposition normal gene, normal RNA, normal protein, transposon inserted in gene, abnormal RNA, abnormal protein, loss of function.

60. T4 Bacteriophage …infects E. coli,

61. Transduction …virally mediated gene transfer from one bacterium to another, …bacteria viruses are termed bacteriophages.

62. Two Bacteriophage Strategies Lytic, –a type of viral life cycle resulting in the release of new phages by death and lysis of the host cell, Lysogenic, –a type of viral life cycle in which the visus becomes incorporated into the host cell’s chromosome.

63. Lytic Cycle specific transmembrane phage/bacteria binding sites, virus DNA inserted into host cell, 1. host cell physiology is shut down, 2. host cell physiology is used for phage work, 3. phage DNA replicated, capsule parts made, 4. phage reassemble with repackaged DNA, 5. host cell is degraded and lyses.

64. Generalized Transduction …enzymatic process which can result in the transfer of any bacterial gene between related strains of bacteria.

65. Phage Infects Host Specific Binding Sites, Phage DNA inserted, Upon infection, host cell physiology is shut down, we’ll follow gene C +.

66. Phage Hijacks the Host Cell’s Transcription/Translation Machinery Host cell degraded, the host chromosome is cut, Phage replicates own DNA, makes protein head etc., gene C + is present on a DNA fragment.

67. Cell Lyses, Phage Move On C + is packaged instead of phage DNA in one of thousands of new phages, phage particle with C + moves to another host cell.

68. End of the Route Host Chromosome, Phage DNA, inserted in Genome, via double crossover. packaged host DNA, inserted in cell,

69. Virulent Phages …reproduce via the lytic cycle only.

70. Two Bacteriophage Strategies Lytic, –a type of viral life cycle resulting in the release of new phages by death and lysis of the host cell, Lysogenic, –a type of viral life cycle in which the visus becomes incorporated into the host cell’s chromosome.

71. Lytic vs Lysogenic viral DNA is incorporated into the host genome.

72. Lysogeny …the integration of viral DNA into the bacterial genome, –a virus that can integrate into the genome is termed temperate, –an integrated phage is termed a prophage.

73. Prophage …non-virulent units that are inserted in the host chromosome, and multiply via binary fission along with the host DNA, …prophage can re-enter the lytic cycle to complete the virus life cycle.

74. Phage Induction …prophage express a repressor protein that inhibits further infection, –also inhibits prophage DNA excision genes, and genes used during the lytic cycle, …environmental cues (especially events that damage DNA) block the expression of the repressor protein, –prophage excises and enters a lytic cycle.

75. Specialized Transduction …upon excision of the prophage, adjacent host DNA is taken along, …the completion of the lytic cycle and subsequent infection of another host moves the flanking DNA to another bacterium.

76. Normal Excision

77. Abnormal Excision flanking DNA is removed.

78. Transfer to Other Cells

79. Bacteria are Geniuses Cloning: identical copies, Gene therapy: insertion of a healthy, or functional gene into a organism lacking a good gene, Harness Mutation: to deal with stress and speed evolution, Defense: develop genes to ward off poisons, predators, etc., then share the goods, Genetic engineering: inserting DNA into another organism to do your bidding (Friday),

80. Coming Up Virus then Plant Biotechnology Virus Paper for Friday… –Short paper intro Weds. and questions. Plant GMO’s –…bacteria also have plasmids (T Plasmids) that they transfer to other organisms, –…upon infection, the T plasmid enters the host cell, becomes incorporated in the host genome, and the T plasmid genes become expressed, –…Agrobacterium tumefaceins transfers genes that force plants to make strange sugars, that only the Agrobacterium can digest.