Recombination

• Homologous recombination

• Site-specific recombination

• Transposition

Different sets of proteins are responsible for thedifferent 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.

4600 kb

48 kb

Site-specific recombination either integrates, deletes, or reversesa 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

dsDNA

Cre recombinases (tyrosinerecombinases) bound to aHolliday junction

Recombinases(dimers)

dsDNA

dsDNA

Cre recombinases (tyrosinerecombinases)

Figure 17.14 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 lifecycles 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 theintegration host factor (IHF) encodedby 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

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

integrase

Excisionase(encoded in the phage genome)

Example for inversion of DNA by site-specific recombination:DNA inversion by the Hin recombinase of Salmonella

EncodesH2 flagellin

Encodes a repressorof H1 flagellin expression

Negative DNA supercoiling is required for Hin recombinase-catalyzed inversion

Fis (DNA-bending protein) together with HUenhances 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 thedifferent 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