PXD057710-1

PXD057710 is an original dataset announced via ProteomeXchange.

Title	Fine-tuning regulation of (p)ppGpp-driven outer membrane vesicle formation in Acinetobacter baumannii
Description	While the roles of (p)ppGpp on cytosolic proteins are well established, its effects on membrane remodeling remain elusive. The translocation of signal recognition particle (SRP)-dependent proteins can be regulated by binding (p)ppGpp to two key GTPase components: FtsY, which interacts with SecYEG, and Ffh, a homolog of SRP54. A (p)ppGpp-specific Broccoli RNA aptamer and the chemometer PyDPA were used to measure the (p)ppGpp levels in the ΔrelA and ΔrelA/ΔspoT strains of Acinetobacter baumannii, confirming a stepwise reduction in (p)ppGpp levels: wild type > ΔrelA > ΔrelA/ΔspoT. The overproduction of outer membrane vesicles (OMVs) in the ΔrelA strain with intermediate (p)ppGpp levels contrasts with reduced production in the ΔrelA/ΔspoT strain, highlighting an unexpected non-linear relationship between OMV production and (p)ppGpp levels. Scanning- and transmission- electron microscope (SEM and TEM) analyses revealed intriguing (p)ppGpp-dependent effects on cell envelope integrity, as the relA mutant showed outer membrane disruption leading to OMV formation, while the relA/spoT mutant maintained an intact outer membrane, suggesting a correlation between (p)ppGpp levels and membrane stability. Western blotting and proteomics analyses revealed significant OmpA accumulation in the inner membrane of the ΔrelA/ΔspoT strain and SRP-dependent inner membrane proteins such as NuoB, NuoL, and TolA in the ΔrelA strain, indicating that (p)ppGpp levels are crucial for regulating membrane protein incorporation in A. baumannii. The regulation of (p)ppGpp levels using the CRISPRi system revealed that outer membrane disruption and OMV formation were most significant at intermediate (p)ppGpp concentrations, highlighting the importance of fine-tuning (p)ppGpp for the regulation of bacterial phenotypes.
HostingRepository	PRIDE
AnnounceDate	2025-03-15
AnnouncementXML	Submission_2025-03-15_10:46:28.705.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	sunyong Han
SpeciesList	scientific name: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377); NCBI TaxID: 400667;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-10 13:44:01	ID requested
⏵ 1	2025-03-15 10:46:29	announced

Dataset with its publication pending

submitter keyword: Membrane remodeling, Membrane disruption,Acinetobacter baumannii, Outer membrane vesicle, Stringent response, (p)ppGpp

Woojun Park
contact affiliation	Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
contact email	wpark@korea.ac.kr
lab head
sunyong Han
contact affiliation	Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
contact email	gksrbdyd97@korea.ac.kr
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/2025/03/PXD057710

PRIDE project URI

• PRIDE
  1. PXD057710
     1. Label: PRIDE project
     2. Name: Fine-tuning regulation of (p)ppGpp-driven outer membrane vesicle formation in Acinetobacter baumannii