PXD059123

PXD059123 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic annotation of T6SS components identified in Bacteroides fragilis secretome
Description	Bacteroides fragilis (Bf)'s T6SS locus has been characterized and shown to have functional activity in competition experiments. It has been demonstrated that symbiont nontoxigenic Bf strains have a more effective “weapon” effect on pathogenic Bf, which is realized through the activity of effector-immune (E-I) protein pairs. Intensive study of the T6SS structure has led to an understanding of certain issues related to its functional activity, but the exact regulatory mechanisms of E-I protein pair activity remain unclear. Proteomic annotation of T6SS components and detailed descriptions of all immune-effector pairs are currently available. In this research, we performed detailed proteogenomic analysis and subsequent proteomic annotation of the T6SS components of the toxigenic Bf BOB25. Fractionated cells, cultivated media and vesicles were prepared for proteome analysis by HPLC-MS/MS. Proteogenomic annotation and comparative genomic study of the T6SS loci of the toxigenic Bf BOB25 were carried out by comparison with the reference genomes of the following Bf strains: JIM10, NCTC 9343 and 638R. According to the data obtained, T6SS components were represented in all types of the analysed samples. The following components of the T6SS were identified in culture media and cells: ClpV (TssH), TssK, TssC, TssB, Hcp (TssD), and TetR. The predicted effector protein AKA51715.1 (VU15_08315) was also detected in media. The greatest amount of T6SS proteins, including the Hcp protein, was detected in the vesicle samples, which was also observed by TEM. Potential effectors, including AKA51715.1 (VU15_08315), AKA51716.1 (VU15_08320), AKA51728.1 (VU15_08385) and the immune protein AKA51727.1 (VU15_08380), were detected in vesicles. The presence of the immune and effector proteins in the Bf secretome indicates the high activity of the T6SS without bacterial competition. It is possible that the T6SS is also used by bacteria to regulate population size by altering the activity of different repertoires of E-I pairs.
HostingRepository	PRIDE
AnnounceDate	2025-01-31
AnnouncementXML	Submission_2025-01-31_04:29:18.280.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ivan Butenko
SpeciesList	scientific name: Bacteroides fragilis; NCBI TaxID: 817;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-22 02:18:51	ID requested
⏵ 1	2025-01-31 04:29:18	announced

10.3389/FMICB.2025.1495971;

submitter keyword: SDS‒PAGE, TripleTOF 5600,Bacteroides fragilis, vesicles

Dr. Natalya Zakharzhevskaya
contact affiliation	Scientific Research Institute of Physical-Chemical Medicine (SRI PCM FMBA of Russia), Russia, Moscow Laboratory of molecular pathophysiology
contact email	natazaha@gmail.com
lab head
Ivan Butenko
contact affiliation	Scientific Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
contact email	ivan.butenko@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD059123
     1. Label: PRIDE project
     2. Name: Proteogenomic annotation of T6SS components identified in Bacteroides fragilis secretome