pseudoattP

pseudoattP refers to genomic sequences that resemble the attachment site attP used by certain site-specific recombinases but are not bona fide attP sites. In the context of phage-derived integrases such as phiC31, attP is the DNA sequence on the invading element that recombines with an attB site in the host genome to form integrated sequences flanked by attL and attR. pseudoattP sites are host genomic loci that show partial similarity to attP and can be recognized by the integrase, sometimes supporting recombination at reduced efficiency. Their existence helps explain observed off-target integrations during genome engineering with site-specific recombinases.

Characteristics include core motifs similar to attP but lacking complete recognition features; distribution is widespread but variable among species; recognition is influenced by the particular integrase and host factors. Mechanistically, recombination at a pseudoattP requires alignment with attB and catalytic activity of the integrase; efficiency is generally much lower than at true attP.

Significance: For gene therapy and synthetic biology, pseudoattP sites represent an off-target risk; they complicate assessment of integration specificity. Methods to identify them include genome-wide mapping of integration events after integrase exposure, sequencing, and motif analysis.

Mitigation and design: to reduce off-target events, researchers may choose integrases with higher specificity, engineer integrases with narrowed recognition, pre-screen target genomes for pseudoattP-like motifs, or use delivery strategies that limit exposure. See also attP, attB, site-specific recombination.