Recombination Homologous recombination Site-specific recombination Transposition Different sets of proteins are responsible for the different types of DNA exchange.
Catalyzed by recombinases, serine or tyrosine recombinases.
Insertion of the phage lambda genome into the E. coli genome. Catalyzed by sequence-specific recombinase (integrase) a special type I topoisomerase kb 48 kb
Site-specific recombination either integrates, deletes, or reverses a DNA sequence Insertion Deletion (reversal of insertion) Inversion
Figure 15.4 Genomes 3 (© Garland Science 2007) Mechanism of type I DNA topoisomerases
Mechanisms of serine and tyrosine recombinases
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.
Serine recombinases bound to DNA Recombinases (dimers) dsDNA
Cre recombinases (tyrosine recombinases) bound to a Holliday junction Recombinases (dimers) dsDNA
Cre recombinases (tyrosine recombinases)
Figure Genomes 3 (© Garland Science 2007) Removal of the kanamycin resistance gene by induced expression of the Cre recombinase
Example for insertion of DNA by site-specific recombination: Insertion of phage lambda genome into the E. coli genome
Lytic and lysogenic life cycles of phage lambda
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.
The integration host factor (IHF) bends the DNA to bring the cleavage sites together IHF
The recombination site in phage lambda IHF integrase
Insertion of the phage lambda genome into the E. coli genome. Catalyzed by sequence-specific recombinase (integrase) a special type I topoisomerase. attL attR
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)
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
Negative DNA supercoiling is required for Hin recombinase -catalyzed inversion Fis (DNA-bending protein) together with HU enhances inversion ≈ 1000-fold ≈ 60 bp
Resolving multimeric circular DNA structures by site- specific recombination
Action of Xer recombinases
Recombination Homologous recombination Site-specific recombination Transposition Different sets of proteins are responsible for the different types of DNA exchange.
Transposition
Transposons are present in all forms of life
Table 9.3 Genomes 3 (© Garland Science 2007) 45.8% Transposons in the human genome
DNA and RNA transposons