PXD047143-1

PXD047143 is an original dataset announced via ProteomeXchange.

Title	Characterization of the O-Glycoproteome of Prevotella intermedia
Description	Prevotella intermedia is a Gram-negative bacterium belonging to the Bacteroidetes phylum and is notably linked to periodontitis. Several other species within this phylum have been reported to possess the general O-glycosylation system, and the O-glycoproteome has been well characterized in Tannerella forsythia, Porphyromonas gingivalis, and Flavobacterium johnsoniae. In this study, we used electron cryotomography (cryoET) to view the ultrastructure of P. intermedia for the first time, revealing an electron dense surface layer surrounding both cells and outer membrane vesicles (OMVs). Interestingly, the OMVs were frequently large (>200 nm) and were of two types, with the lumens being either electron dense or translucent. LC-MS/MS analyses of OMVs and various cell fractions of P. intermedia resulted in the identification of 1655 proteins including 62 predicted T9SS cargo proteins. Consistent with the presence of large OMVs with electron dense lumens, periplasmic proteins contributed to nearly half the protein content of OMVs. For the glycoproteome, 445 unique O-glycosylation sites within 226 glycoproteins were identified. The O-glycosylation motif exhibited a much broader range than reported in other species, with O-glycosylation found at D(S/T)(A/I/L/M/T/V/S/C/G/F/N/E/Q/D/P). A single major O-glycan was identified of delta mass 1531.48 Da and its sequence was determined by MS2 and MS3 analyses using a combination of CID and HCD fragmentation modes. Following partial deglycosylation with trifluoromethanesulfonic acid, the O-glycan sequence was confirmed to be dHex-dHex-HexNAc(HPO3-C6H12O5)-dHex-Hex-HexA-Hex(dHex). Bioinformatic analyses of O-glycoprotein localization predicted 73 periplasmic proteins, 53 inner membrane proteins, 52 lipoproteins, 26 outer membrane proteins, and 14 proteins secreted by the T9SS.
HostingRepository	PRIDE
AnnounceDate	2024-02-14
AnnouncementXML	Submission_2024-02-14_13:53:22.752.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD047143
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Paul Veith
SpeciesList	scientific name: Prevotella intermedia ATCC 25611 = DSM 20706; NCBI TaxID: 1122984;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-21 18:33:04	ID requested
⏵ 1	2024-02-14 13:53:23	announced

10.6019/PXD047143;

submitter keyword: outer membrane vesicles,O-glycosylation, Bacteroidetes, type IX secretion system

Eric Reynolds
contact affiliation	Melbourne Dental School, University of Melbourne Parkville, Victoria, Australia
contact email	e.reynolds@unimelb.edu.au
lab head
Paul Veith
contact affiliation	Melbourne Dental School
contact email	pdv@unimelb.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD047143
     1. Label: PRIDE project
     2. Name: Characterization of the O-Glycoproteome of Prevotella intermedia