PXD056297

PXD056297 is an original dataset announced via ProteomeXchange.

Title	The copper-induced viable-but-non-culturable state in Cupriavidus metallidurans CH34 is characterized by distinct proteomic response patterns- Part II
Description	Copper-based materials are actively explored for their potential as antimicrobial agents. However, recent studies show that sublethal concentrations of Cu ions can induce the viable-but-non-culturable (VBNC) cell state in certain bacteria, hampering with contamination control and monitoring. Despite the growing number of omics studies investigating the VBNC state, the underlying molecular mechanisms remain largely enigmatic. Here, we determine variations in protein expression of Cupriavidus metallidurans CH34 in different phases of the Cu-induced VBNC state via quantitative LC-MS/MS analysis at multiple sample time points. With this approach, we aimed to reveal cellular adaptations triggering VBNC formation and the characteristic spontaneous recovery of culturability (resuscitation). Entry into the VBNC state correlated with a widespread response to oxidative stress as well as restricted pyruvate metabolism. The expression of specific metal resistance determinants changed with Cu exposure time and culminated in strong upregulation of proteins linked to periplasmic Cu ion detoxification during the resuscitation phase. We suggest that this delayed induction of Cu resistance proteins is caused by the gradual reconstitution of cellular energy reserves through degradation of polyhydroxybutyrate granules. Furthermore, Cu-treated cells showed upregulation of several chemotaxis proteins, and increased cell motility was observed phenotypically. Our results reveal highly dynamic proteomic response patterns and contribute fundamental insights into the VBNC state, while also emphasizing the advantages of time-resolved proteomic analysis.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_03:39:19.023.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD056297
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Surya Gupta
SpeciesList	scientific name: Cupriavidus metallidurans CH34; NCBI TaxID: 266264;
ModificationList	No PTMs are included in the dataset
Instrument	autoflex

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-26 13:59:50	ID requested
⏵ 1	2025-05-07 03:39:19	announced

10.6019/PXD056297;

Patocka T, Gupta S, Mastroleo F, Leys N, Matroule JY, Van Houdt R, Time-resolved proteomic profiling of Cupriavidus metallidurans CH34 in the copper-induced viable-but-nonculturable state. Metallomics, 17(3):(2025) [pubmed]

10.1093/mtomcs/mfaf007;

submitter keyword: resuscitation, metabolism,metal resistance, dormancy, copper, LC-MS/MS

Natalie Leys
contact affiliation	head of Microbiology Unit, SCK CEN
contact email	natalie.leys@sckcen.be
lab head
Surya Gupta
contact affiliation	SCKCEN
contact email	surya.gupta@sckcen.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD056297
     1. Label: PRIDE project
     2. Name: The copper-induced viable-but-non-culturable state in Cupriavidus metallidurans CH34 is characterized by distinct proteomic response patterns- Part II