1. Recombination Homologous recombination Site-specific recombination Transposition Different sets of proteins are responsible for the different types of DNA exchange.

2. Catalyzed by recombinases, serine or tyrosine recombinases.

3. Insertion of the phage lambda genome into the E. coli genome. Catalyzed by sequence-specific recombinase (integrase) a special type I topoisomerase. 4600 kb 48 kb

4. Site-specific recombination either integrates, deletes, or reverses a DNA sequence Insertion Deletion (reversal of insertion) Inversion

5. Figure 15.4 Genomes 3 (© Garland Science 2007) Mechanism of type I DNA topoisomerases

6. Mechanisms of serine and tyrosine recombinases

7. Chemistry of site-specific recombination 5’ phosphate remains covalently linked to the recombinase, as in reactions of other topoisomerases. Reaction creates a single-strand break (nick). Reaction is reversible.

8. Serine recombinases bound to DNA Recombinases (dimers) dsDNA

9. Cre recombinases (tyrosine recombinases) bound to a Holliday junction Recombinases (dimers) dsDNA

10. Cre recombinases (tyrosine recombinases)

11. Figure 17.14 Genomes 3 (© Garland Science 2007) Removal of the kanamycin resistance gene by induced expression of the Cre recombinase

13. Example for insertion of DNA by site-specific recombination: Insertion of phage lambda genome into the E. coli genome

14. Lytic and lysogenic life cycles of phage lambda

15. Example for insertion of DNA by site-specific recombination: Insertion of phage lambda genome into the E. coli genome Integration requires a recombinase (called lambda integrase) and the integration host factor (IHF) encoded by a gene in the E. coli genome.

16. The integration host factor (IHF) bends the DNA to bring the cleavage sites together IHF

17. The recombination site in phage lambda IHF integrase

18. Insertion of the phage lambda genome into the E. coli genome. Catalyzed by sequence-specific recombinase (integrase) a special type I topoisomerase. attL attR

19. Binding of an “excisionase” to X sites in attR and attL brings the sites together for excision of the phage genome IHF integrase Excisionase (encoded in the phage genome)

20. Example for inversion of DNA by site-specific recombination: DNA inversion by the Hin recombinase of Salmonella Encodes H2 flagellin Encodes a repressor of H1 flagellin expression

21. Negative DNA supercoiling is required for Hin recombinase -catalyzed inversion Fis (DNA-bending protein) together with HU enhances inversion ≈ 1000-fold ≈ 60 bp

22. Resolving multimeric circular DNA structures by site- specific recombination

23. Action of Xer recombinases

24. Recombination Homologous recombination Site-specific recombination Transposition Different sets of proteins are responsible for the different types of DNA exchange.

25. Transposition

26. Transposons are present in all forms of life

27. Table 9.3 Genomes 3 (© Garland Science 2007) 45.8% Transposons in the human genome

28. DNA and RNA transposons