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Precise Phage Mutagenesis with NgTET-Assisted CRISPR-Cas Systems
Published on: October 14, 2025
624
Lactococcal mobile genetic elements harbour a diverse phage defensome rich in restriction-modification systems
Brian McDonnell1,2, Philip Kelleher1,2, Alexey Fomenkov3
1School of Microbiology, University College Cork, Cork, T12 Y337, Ireland.
Nucleic Acids Research
|September 9, 2025
Summary
This study maps the genomes and phage defense systems of 43 lactococcal strains, revealing plasmids as key reservoirs for mobile defense genes. These findings highlight the importance of mobile genetic elements in bacterial immunity.
Area of Science:
- Microbiology
- Genomics
- Bacteriophage Research
Background:
- Lactococcal strains are crucial in dairy fermentation.
- Understanding their defense mechanisms against phages is vital for industrial applications.
- Previous studies have not comprehensively cataloged their mobile phage defense systems.
Purpose of the Study:
- To reconstruct genomes and characterize the plasmidome and methylome of 43 lactococcal strains.
- To identify and catalog phage defense systems and mobile elements within these strains.
- To investigate the mobility and function of phage defense systems, particularly restriction-modification systems.
Main Methods:
- Combined long- and short-read sequencing for genome reconstruction.
- Identification and cataloging of antiphage genes and phage defense systems.
- Cross-correlation analysis with mobile elements and characterization of restriction-modification systems.
Main Results:
- Reconstructed 43 lactococcal genomes, detailing 269 plasmids and identifying 953 antiphage genes (538 defense systems).
- Found that nearly 60% of these defense systems are mobile, with restriction-modification systems being a major component.
- Matched 46 unique methylated motifs to their corresponding methylating enzymes and demonstrated antiphage activity.
Conclusions:
- The dairy lactococcal plasmidome is a significant reservoir of mobile phage defense systems, including orphan HsdS-encoding genes.
- Mobile genetic elements play a crucial role in the evolution and dissemination of bacterial immunity in lactococci.
- This comprehensive survey provides insights into bacterial adaptation and phage-host interactions in lactic acid bacteria.
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