PXD023608-1

PXD023608 is an original dataset announced via ProteomeXchange.

Title	Time-resolved proteome analysis of Listeria monocytogenes during infection reveals the role of the AAA+ chaperone ClpC for host cell adaptation
Description	The cellular proteome is the set of expressed proteins at a given time and defines an organism's phenotype under specific conditions. The proteome is shaped and remodeled by both protein synthesis and degradation. In this study, we combined metabolic and chemical isobaric peptide labeling to simultaneously determine protein decay and de novo synthesis of intracellular Listeria monocytogenes, while focusing on the role of the AAA+ chaperone protein ClpC. ClpC associates with the peptidase ClpP to form an ATP-dependent protease complex and has been shown to play a role in virulence development in the human pathogen L. monocytogenes. However, the mechanism by which ClpC is involved in the survival and proliferation of intracellular L.monocytogenes remains elusive. We observed extensive proteome remodeling in L. monocytogenes upon interaction with the host, supporting the hypothesis that ClpC-dependent protein degradation is required to initiate bacterial adaptation mechanisms. We identified more than 100 putative ClpC target proteins through their stabilization in a clpC deletion strain. Beyond the identification of direct targets, we also observed indirect effects of the clpC deletion on the protein abundance in diverse cellular and metabolic pathways, such as iron acquisition and flagellar assembly. Overall, our data highlights the crucial role of ClpC for L. monocytogenes adaptation to the host environment through proteome remodeling. Importance Survival and proliferation of pathogenic bacteria inside the host depend on their ability to adapt to the changing environment. It is therefore important to profile the underlying changes on the bacterial proteome level during the infection process to understand pathogenesis and host-dependent adaptation processes. The interplay between protein synthesis and decay governs cellular protein abundance. SILAC pulse labeling enables direct readout of these events during infection. Combining this approach with tandem-mass-tag (TMT) labeling enabled multiplexed and time-resolved bacterial proteome quantification during infection. We applied this integrated approach to investigate protein turnover during the temporal progression of bacterial adaptation to the host on a system-wide scale. Our experimental approach can easily be transferred to probe the proteome remodeling in other bacteria under a variety of perturbations.
HostingRepository	PRIDE
AnnounceDate	2021-07-16
AnnouncementXML	Submission_2021-07-15_23:06:49.447.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Frese
SpeciesList	scientific name: Listeria monocytogenes; NCBI TaxID: 1639;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-15 03:00:38	ID requested
⏵ 1	2021-07-15 23:06:49	announced

Dataset with its publication pending

submitter keyword: Mass-spectrometry, proteomics, tandem-mass-tag, pulsed SILAC, Listeria monocytogenes, proteolysis, ClpC, AAA+, infection, adaptation, host-pathogen interactions

Christian Frese
contact affiliation	Max Planck Unit for the Science of Pathogens, Berlin, Germany
contact email	frese@mpusp.mpg.de
lab head
Christian Frese
contact affiliation	Max Planck Unit for the Science of Pathogens
contact email	frese@mpusp.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023608
     1. Label: PRIDE project
     2. Name: Time-resolved proteome analysis of Listeria monocytogenes during infection reveals the role of the AAA+ chaperone ClpC for host cell adaptation