Discovery and characterization of antiphage systems in the lactococcal plasmidome

Simple item page
dc.check.date2026-05-31
dc.contributor.advisorvan Sinderen, Douwe
dc.contributor.advisorMahony, Jennifer
dc.contributor.authorGrafakou, Andriana
dc.contributor.funderScience Foundation Ireland
dc.date.accessioned2025-02-06T14:16:08Z
dc.date.available2025-02-06T14:16:08Z
dc.date.issued2024en
dc.date.submitted2024
dc.description.abstractLactococcus lactis and Lactococcus cremoris are important bacterial species that are widely used in the production of fermented dairy products such as buttermilk and cheese. However, the non-sterile dairy environment exposes them to (bacterio)phage infections, which can cause substantial economic losses. To counteract phage threats, bacteria have evolved various defence mechanisms, including abortive infection (Abi) systems. Abi systems are activated upon phage infection, and they typically interfere with essential cellular functions, thereby significantly limiting phage propagation. In Chapter 1, we review the existing literature of 34 lactococcal Abi-like systems. Using the latest structural and functional prediction tools, we categorize certain Abi-like systems through structural superimposition and hypothesize their potential mechanisms based on predicted domain information. We also examine previously established mechanisms of action of certain Abi-like systems. In Chapter 2, we use Lactococcus as a model to identify novel plasmid-encoded antiphage systems, leveraging the fact that many of the first Abi systems were discovered in these bacteria. A systematic evaluation of candidate defence systems led to the discovery of seven new plasmid-encoded antiphage systems (Rhea, Aristaios, Kamadhenu, Fliodhais, Audmula, Rugutis, Hesat), which seem to be widely distributed across bacteria, as well as five systems (PARIS, type I and II CBASS, Lamassu, Septu), homologues of which had previously been identified as antiphage systems in other bacteria. These systems confer resistance against the most prevalent lactococcal phages, and all but one were shown to exhibit characteristics of abortive infection systems. Insights into their mechanisms of action were gained through structural and domain predictions. In Chapter 3, functional insights into three novel plasmid-encoded lactococcal Abi-like antiphage systems are presented. Their effectiveness in milk-based media was established, supporting their application potential to enhance the reliability of dairy fermentations. Our findings indicate that two of these systems do not directly impede phage genome replication, transcription, or translation, while one was found to interfere specifically with phage transcription. Additionally, the plasmid carrying one of these systems was successfully transferred via conjugation to various lactococcal strains, each of which showed a significant increase in phage resistance. In Chapter 4, mechanistic insights into the identified antiphage systems were established by isolating phage escape mutants that had overcome these systems. Genome analysis of these phage escape mutants revealed mutations in various genes, some of which encode proteins that appear to activate specific antiphage systems (terminase large subunit, major capsid protein, hypothetical proteins and major tail proteins), while others might act as targets (ssDNA annealing proteins). The cross-resistance of some phage escape mutants to different antiphage systems, as well as the activation of some systems by phage proteins with similar functions, indicates mechanistic commonalities among various antiphage systems. Additionally, we propose a novel mode of action for one antiphage system. Our findings demonstrate that the co-evolution of Lactococcus species with their phages, spurred by their widespread use in dairy fermentation, has driven the acquisition of a diverse range of phage defence mechanisms, with plasmids serving as a rich source of such antiphage systems. Expanding our understanding of the lactococcal phage resistome not only offers practical solutions to the persistent phage challenges in industrial food fermentations but also holds potential for broader applications in biotechnology and biomedicine, while providing deeper insights into the dynamics of phage-host interactions.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdf
dc.identifier.citationGrafakou, A. 2024. Discovery and characterization of antiphage systems in the lactococcal plasmidome. PhD Thesis, University College Cork.
dc.identifier.endpage253
dc.identifier.urihttps://hdl.handle.net/10468/16995
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.projectScience Foundation Ireland (12/RC/2273‐P2)
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Spokes Programme::Rolling Call/17/SP/4678/IE/BacTrans – Natural DNA Transfer Systems for Bacterial Starter Cultures/
dc.rights© 2024, Andriana Grafakou.
dc.rights.urihttps://creativecommons.org/licenses/by-nc-sa/4.0/
dc.subjectBacterial immunity
dc.subjectAntiphage systems
dc.subjectLactococcus
dc.subjectLactococci
dc.subjectPhage resistance
dc.subjectPhage defence
dc.subjectAbortive infection
dc.subjectPlasmidome
dc.subjectPlasmids
dc.titleDiscovery and characterization of antiphage systems in the lactococcal plasmidomeen
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
Files
Original bundle
Now showing 1 - 2 of 2
Thumbnail Image
Name:
GrafakouA_PhD2024.pdf
Size:
4.96 MB
Format:
Adobe Portable Document Format
Description:
Full Text E-thesis
Thumbnail Image
Name:
GrafakouA_PhD2024_Submission for Examination Form.pdf
Size:
430 KB
Format:
Adobe Portable Document Format
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
5.2 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Research Theses
APC Microbiome Ireland - Doctoral Theses
College of Science, Engineering and Food Science - Doctoral Theses
Microbiology - Doctoral Theses