PXD043566

PXD043566 is an original dataset announced via ProteomeXchange.

Title	Proteomics analysis reveals a role for E. coli polyphosphate kinase in regulation of membrane structure and polymyxin resistance via the BasS-BasR two component system
Description	Polyphosphates (polyP) are chains of inorganic phosphates that can reach 1000s of residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (∆ppk mutants) during nutrient starvation and to identify novel pathways regulated by PPK. In response to nutrient starvation, we found 92 proteins significantly differentially expressed between wild-type and ∆ppkmutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport while Δppkmutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK cells remain inappropriately primed for growth. From our data set, we were particularly interested in Arn and EptA proteins, which were downregulated in ∆ppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins, and provide evidence that this mis-regulation in ∆ppk cells stems from a failure to induce the BasS/BasR two component system during starvation. We also show that ∆ppk mutants unable to upregulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in diverse pathways impacted by PPK.
HostingRepository	PRIDE
AnnounceDate	2024-02-14
AnnouncementXML	Submission_2024-02-14_11:29:01.871.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Iryna Abramchuk
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-05 13:05:13	ID requested
⏵ 1	2024-02-14 11:29:02	announced

Dataset with its publication pending

submitter keyword: LC-MSMS, cell culture, bacteria, label-free quantification,E. coli

Michael Downey
contact affiliation	Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
contact email	mdowne2@uottawa.ca
lab head
Iryna Abramchuk
contact affiliation	University of Ottawa
contact email	iabra008@uottawa.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD043566
     1. Label: PRIDE project
     2. Name: Proteomics analysis reveals a role for E. coli polyphosphate kinase in regulation of membrane structure and polymyxin resistance via the BasS-BasR two component system