Prophages and bacterial genomics: what have we learned so far?

Area of Science:

• Genomics
• Microbiology
• Virology

Background:

• Bacterial genome sequencing is rapidly advancing.
• Integrated virus genomes, known as prophages, are frequently found within bacterial genomes.
• Prophages can represent a significant portion (10-20%) of a bacterium's genome and contribute to intraspecies variation.

Purpose of the Study:

• To emphasize the necessity of accurately recognizing and understanding prophages within bacterial genomes.
• To explore the evolutionary insights gained from analyzing prophage sequences.
• To highlight the functional relevance of prophages, including defective ones, in bacterial biology.

Main Methods:

• Analysis of published bacterial genome sequences.
• Identification and characterization of integrated virus genomes (prophages).
• Comparative genomics of specific prophages (e.g., Rac in Escherichia coli, Pnm in Neisseria meningitidis).

Main Results:

• 51 out of 82 sequenced bacterial genomes contain prophages, with 230 putative prophages identified.
• Many prophages are defective and undergoing mutational decay.
• Evidence suggests some prophages can persist for millions of years and undergo recombination.
• Functional genes are present in many defective prophages, indicating a reservoir of temperate bacteriophage genes.

Conclusions:

• Accurate identification and comprehension of prophages are essential for a complete understanding of bacterial genomes.
• Prophages play a significant role in bacterial evolution and host adaptation.
• Defective prophages harbor functional genes, contributing to the broader bacteriophage gene pool.