PXD004888-1

PXD004888 is an original dataset announced via ProteomeXchange.

Title	Quantitative Proteomic Analysis of Extracellular Matrix Extracted from Mono- and Dual-Species Biofilms of Fusobacterium nucleatum and Porphyromonas gingivalis
Description	Background The Gram-negative bacteria Fusobacterium nucleatum and Porphyromonas gingivalis are associated with periodontitis and members of a complex microbial biofilm. The self-produced extracellular polymeric matrix (EPM) of biofilms generally consists of lipids, exopolysaccharides, nucleic acids and proteins. The proteinaceous components of the biofilm matrix play many roles in biofilm development and function. In this study the protein composition of the matrices in mono- and dual-species biofilms of F. nucleatum and P. gingivalis were analyzed. Methods The bacteria were grown in a static biofilm model. Extraction of EPM was performed by careful mechanical shearing and filtration. Initial tryptic digestion of EPMs was followed by liquid chromatography-tandem mass spectrometry to analyze the resulting peptide mixtures. Quantitative proteomic software MaxQuant was then employed for protein identifications and label-free quantitative (LFQ) analysis. Functional analyses of identified proteins were applied in classification and prediction of their possible roles in EPM. Results We identified 542 proteins in the matrix of F. nucleatum, 93 proteins in the matrix of P. gingivalis and 280 proteins in the dual-species biofilm matrix. Similarly, relative quantification based on LFQ intensity scores identified generally higher protein amounts in F. nucleatum and dual species EMPs, when compared to P. gingivalis EPM. Acetyl-CoA acetyltransferase, alkyl hydroperoxide reductase C22 protein, neutrophil-activating protein A, tryptophanase and glutamate dehydrogenase were the top five proteins in the matrix of F. nucleatum biofilm. The oxidoreductase NAD-specific glutamate dehydrogenase and the proteolytic and adhesive protein Lys-gingipain were most abundant in P. gingivalis EPM. In the dual species EPM, F. nucleatum contributed to four out of the five with glutamate dehydrogenase on top. NAD-specific dehydrogenase from P. gingivalis was among the top five. Functional analyses with respect to virulence for example, revealed the stress-induced protein yicC in F. nucleatum EPM, while hemagglutinin HagA and fimbriae minor component FimD were among the top 5 in P. gingivalis EPM. Conclusions We showed that the biofilm matrix of two important periodontal pathogens is abundant in proteins and nearly 70% of all EPM proteins originate from F. nucleatum when grown together with P. gingivalis. Outer membrane proteins, virulence related and oxidative stress proteins were among the most abundant proteins identified.
HostingRepository	PRIDE
AnnounceDate	2017-03-16
AnnouncementXML	Submission_2017-03-16_02:17:07.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marwan Mansoor Ali Mohammed
SpeciesList	scientific name: Fusobacterium nucleatum subsp. nucleatum ATCC 25586; NCBI TaxID: 190304; scientific name: Porphyromonas gingivalis ATCC 33277; NCBI TaxID: 431947;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2016-08-23 03:37:22	ID requested
⏵ 1	2017-03-16 02:17:08	announced
2	2024-10-22 04:32:17	announced	2024-10-22: Updated project metadata.

Mohammed MMA, Pettersen VK, Nerland AH, Wiker HG, Bakken V, Quantitative proteomic analysis of extracellular matrix extracted from mono- and dual-species biofilms of Fusobacterium nucleatum and Porphyromonas gingivalis. Anaerobe, 44():133-142(2017) [pubmed]

curator keyword: Biological

submitter keyword: Bacterial biofilms, extracellular polymeric matrix, Fusobacterium nucleatum, Porphyromonas gingivalis, label-free quantitative tandem mass spectrometry, proteomics.

Vidar Bakken
contact affiliation	The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
contact email	Vidar.Bakken@uib.no
lab head
Marwan Mansoor Ali Mohammed
contact affiliation	The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
contact email	drmarwan98@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004888
     1. Label: PRIDE project
     2. Name: Quantitative Proteomic Analysis of Extracellular Matrix Extracted from Mono- and Dual-Species Biofilms of Fusobacterium nucleatum and Porphyromonas gingivalis