Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability

Area of Science:

• Microbiology
• Molecular Biology
• Genetics

Background:

• Bacteriophages (phages) are viruses that infect bacteria and possess small genomes.
• Recombination is crucial for phage replication and diversification, with bacteria like E. coli utilizing Chi motifs for DNA repair.
• Bacteriophage Lambda inhibits host RecBCD and encodes its own recombination machinery to avoid degradation.

Purpose of the Study:

• To investigate the strategies employed by lambdoid phages regarding host recombination machinery.
• To understand the relationship between phage genome structure, recombination strategies, and evolvability.
• To determine how phages discriminate between self and non-self DNA.

Main Methods:

• Comparative genomic analysis of 275 lambdoid phage genomes.
• Identification and quantification of Chi motifs within phage genomes.
• Correlation analysis between phage recombinase presence/absence and Chi motif distribution.
• Assessment of genome mosaicism and gene repertoire diversity.

Main Results:

• Half of the analyzed lambdoid phages encode their own recombinases; the rest rely on host machinery.
• Phages lacking recombinases frequently contain high numbers of Chi motifs, especially near replication and packaging sites.
• Phages encoding recombinases and inhibiting host machinery typically lack Chi motifs.
• Phages with autonomous recombination machinery exhibit more mosaic genomes and larger pan-genomes.

Conclusions:

• Lambdoid phages exhibit distinct strategies for managing host recombination, influencing their genome structure.
• The presence or absence of Chi motifs correlates with the phage's reliance on host or autonomous recombination.
• Autonomous recombination machinery enhances phage evolvability through increased genome mosaicism and gene diversity.