Bacteriophage lambda site-specific recombination proceeds with a defined order of strand exchanges.

Area of Science:

• Molecular Biology
• Genetics
• Microbiology

Background:

• Bacteriophage lambda integration into bacterial genomes occurs through two strand exchanges forming a Holliday structure.
• Understanding the mechanism and directionality of these exchanges is crucial for comprehending viral integration and excision processes.

Purpose of the Study:

• To investigate the strand bias in bacteriophage lambda integration and excision.
• To determine the factors influencing the order of strand exchanges during recombination.
• To elucidate the role of DNA homology and attP/attB site structure in recombination directionality.

Main Methods:

• Utilized phosphorothioate substitutions at recombination sites to assess strand-specific exchange.
• Analyzed accumulated Holliday structures to identify strand initiation bias.
• Engineered alterations in the attP site's relative orientation and evaluated their impact on strand-exchange bias.

Main Results:

• Phosphorothioate substitutions revealed a significant strand bias in Holliday structure formation.
• Holliday structures exclusively formed via recombination of a specific pair of strands, indicating a strong initiation bias.
• Altering attP site orientation showed that distant elements, not the core sequence, dictate strand-exchange bias.

Conclusions:

• Bacteriophage lambda integration exhibits a strong, non-random strand-exchange bias.
• Excision is not a simple reversal of integration at the strand-exchange level.
• The bias is dictated by asymmetric interactions involving distant attP elements and attB, likely mediated by a nucleosome-like structure.