PXD011263

PXD011263 is an original dataset announced via ProteomeXchange.

Title	Investigating Lactococcus lactis MG1363 response to phage p2 infection at the proteome level
Description	Phages are viruses that specifically infect and kill bacteria. Bacterial fermentation and biotechnology industries see them as enemies, however, they are also investigated for the treatment or prevention of infections caused by multidrug resistant bacteria. Whether foes or allies, their importance is undeniable. Despite decades of research some aspects of phage biology are still poorly understood. In this study, we used label-free quantitative proteomics to reveal the proteotypes of Lactococcus lactis MG1363 during infection by the virulent phage p2, a model for studying the biology of phages infecting Gram-positive bacteria. Our approach resulted in the high-confidence detection and quantification of 59% of the theoretical bacterial proteome, including 226 bacterial proteins detected only during phage infection and 6 proteins unique to uninfected bacteria. We also identified many bacterial proteins of differing abundance during the infection. Using this high-throughput proteomic datasets, we selected specific bacterial genes for inactivation using CRISPR-Cas9 to investigate their involvement in phage replication. One knockout mutant lacking gene llmg_0219 showed resistance to phage p2 due to a deficiency in phage adsorption. Furthermore, we detected and quantified 78% of the theoretical phage proteome and identified many proteins of phage p2 that had not been previously detected. Among others, we uncovered a conserved small phage protein (ORFN1) coded by an unannotated gene. We also applied a targeted approach to achieve greater sensitivity and identify undetected phage proteins that were expected to be present. This allowed us to follow the fate of ORF46, a small phage protein of low abundance. In summary, this work offers a unique view of the virulent phages’ takeover of bacterial cells and provides novel information on phage-host interactions.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:49:15.467.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Otto
SpeciesList	scientific name: Lactococcus lactis subsp. cremoris MG1363; NCBI TaxID: 416870; scientific name: Lactococcus phage; NCBI TaxID: 12374;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Velos; TSQ Vantage

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-03 08:02:58	ID requested
1	2019-01-29 06:00:00	announced
⏵ 2	2024-10-22 04:49:20	announced	2024-10-22: Updated project metadata.

10.1074/mcp.ra118.001135;

Lemay ML, Otto A, Maa, ß S, Plate K, Becher D, Moineau S, MG1363 Response to Phage p2 Infection at the Proteome Level. Mol Cell Proteomics, 18(4):704-714(2019) [pubmed]

submitter keyword: genome editing, Lactococcus lactis, label-free quantification, mass spectrometry-based proteomics,Phage infection

Prof. Dr. Becher
contact affiliation	Institut für Mikrobiologie Dept. Mikrobielle Proteomik Universität Greifswald Felix-Hausdorff-Str. 8 17489 Greifswald
contact email	dbeche@uni-greifswald.de
lab head
Andreas Otto
contact affiliation	Institute for Microbiology
contact email	andreas.otto@uni-greifswald.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/01/PXD011263

PRIDE project URI

• PRIDE
  1. PXD011263
     1. Label: PRIDE project
     2. Name: Investigating Lactococcus lactis MG1363 response to phage p2 infection at the proteome level