Mechanisms of Site-Specific Recombination

Abstract

Integration, excision, and inversion of defined DNA segments commonly occur through site-specific recombination, a process of DNA breakage and reunion that requires no DNA synthesis or high-energy cofactor. Virtually all identified site-specific recombinases fall into one of just two families, the tyrosine recombinases and the serine recombinases, named after the amino acid residue that forms a covalent protein-DNA linkage in the reaction intermediate. Their recombination mechanisms are distinctly different. Tyrosine recombinases break and rejoin single strands in pairs to form a Holliday junction intermediate. By contrast, serine recombinases cut all strands in advance of strand exchange and religation. Many natural systems of site-specific recombination impose sophisticated regulatory mechanisms on the basic recombinational process to favor one particular outcome of recombination over another (for example, excision over inversion or deletion). Details of the site-specific recombination processes have been revealed by recent structural and biochemical studies of members of both families.

Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

“…The tyrosine recombinase/integrase family is one of two families of all site-specific recombinases. It utilizes a catalytic tyrosine to break and rejoin single strands in pairs to form a Holliday junction intermediate [15]. DRs are generally required to identify recombination partners.…”

Risks from GMOs due to Horizontal Gene Transfer

“…Many integrative plasmids and bacterial viruses recognise a specific sequence (attachment site), usually less than 30 base pairs in the recipient genome, where integration is targeted (Grindley et al, 2006). Nearly all site-specific recombinases belong to either the tyrosine or serine families of recombinases, which use the break and join mechanism of recombination.…”

Predicting Knot or Catenane Type of Site-Specific Recombination Products

“…17 The serine and tyrosine recombinases also differ in their mechanism of cutting and rejoining DNA at the crossover sites. Both families are large: a phylogenetic analysis has been performed on 72 serine recombinases 44 and a recent iterative PSI-BLAST search documents approximately 1000 related sequences of putative tyrosine recombinases.…”

“…44 These recombinases may trap a fixed number of supercoils before initiating recombination. 17 For example, Tn3 resolvase requires three negative supercoils to be trapped by the binding of (non-active) resolvase molecules. These trapped supercoils (outside of the recombinase complex) together with the recombinase complex itself are known as the synaptic complex .…”

“…The DNA-protein complex then proceeds through an intermediary structure (a Holliday junction) before repeating the process with the other two DNA backbones. 17,49 Most tyrosine recombinases, including Flp, λ Int and Cre, tolerate varying number of supercoils outside of the recombinase complex. However, there are exceptions, most notably XerCD, which trap a fixed number of supercoils using accessory proteins before initiating cleavage.…”