PXD027261

PXD027261 is an original dataset announced via ProteomeXchange.

Title	Strength of a “single-tube” protocol for protein isolation from multiple cell fractions shown for the plant pathogen Xanthomonas campestris pv. campestris B100 with a focus on proteins involved in the biosynthesis of the exopolysaccharide xanthan
Description	Xanthomonas campestris pv. campestris (Xcc) B100 is a phytopathogenic bacterium, which uses xanthan, a secreted heterogeneous exopolysaccharide in both stages of infection of Brassicaceae. Until now, proteome analysis of Xcc lacking a detailed view on the proteins involved in xanthan biosynthesis. Proteins involved in the biosynthesis of this polysaccharide are located near, in or at the cell membrane. This study aims to establish a robust and rapid protocol for a comprehensive proteome analysis of Xcc strains, without the need to isolate different cell fractions. Therefore, a method for the analysis of the whole cell proteome was compared to the isolation of specific fractions regarding the total number of identified proteins, the overlap as well as the differences between the approaches. The whole cell proteome analysis using the “single-tube” preparation protocol resulted in more than 2,000 identified proteins with a coverage of 95.11% of the cell fraction specific identifications. To prove the usability of the protocol to study natural product formation at the envelope with proteins distributed over various cell fractions, Gum proteins of Xcc B100 were identified and quantified by a label free quantification (LFQ) approach. Thus, expression profiles of 9 out of 12 Gum proteins comparing stationary phase and growth phase were measured and showed differential expression levels within the operon structure. Five out of ten identified Gum proteins show a differential regulation indicating regulatory mechanisms beyond transcription level.
HostingRepository	PRIDE
AnnounceDate	2022-02-16
AnnouncementXML	Submission_2022-02-16_12:40:21.204.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julia Voss
SpeciesList	scientific name: Xanthomonas campestris pv. campestris str. B100; NCBI TaxID: 509169;
ModificationList	monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-12 22:18:46	ID requested
⏵ 1	2022-02-16 12:40:23	announced

Hahn J, Koch D, Niehaus K, Ortseifen V, Analysis of Gum proteins involved in xanthan biosynthesis throughout multiple cell fractions in a "single-tube". J Proteomics, 257():104513(2022) [pubmed]

submitter keyword: “single-tube” protocol

LFQ analysis

multiple cell fraction analysis

Xanthomonas campestris - xanthan biosynthesis

QExactive Plus

Dr. Vera Ortseifen
contact affiliation	Cebitec, Bielefeld University
contact email	vera@cebitec.uni-bielefeld.de
lab head
Julia Voss
contact affiliation	Bielefeld University, Center for Biotechnology
contact email	juvoss@cebitec.uni-bielefeld.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027261
     1. Label: PRIDE project
     2. Name: Strength of a “single-tube” protocol for protein isolation from multiple cell fractions shown for the plant pathogen Xanthomonas campestris pv. campestris B100 with a focus on proteins involved in the biosynthesis of the exopolysaccharide xanthan