PXD005929

PXD005929 is an original dataset announced via ProteomeXchange.

Title	Outer Membrane Proteome of Veillonella parvula: a Diderm Firmicute of the Human Microbiome
Description	Veillonella parvula is a biofilm-forming commensal found in the lungs, vagina, mouth, and gastro-intestinal tract of humans, yet it may also develop into an opportunistic pathogen. Furthermore the presence of Veillonella has been associated with the development of a healthy immune system in infants. Veillonella belongs to the Negativicutes, a diverse clade of bacteria that represent an evolutionary enigma: they are phylogenetically placed within Gram-positive (monoderm) Firmicutes yet maintain an outer membrane (OM) with lipopolysaccharide similar to classic Gram-negative (diderm) bacteria. The OMs of Negativicutes have unique characteristics, such as the replacement of Braun’s lipoprotein by OmpM for anchoring the outer membrane to the peptidoglycan. Through phylogenomic analysis, we have recently provided the first bioinformatic annotation of the Negativicute diderm cell envelope. We showed that it is a unique type of envelope that was present in the ancestor of present-day Firmicutes and lost multiple times independently in this phylum, giving rise to the monoderm architecture. However, little experimental data is presently available for any Negativicute cell envelope. Here, we have performed the first experimental proteomic characterization of the cell envelope of these atypical diderm Firmicutes, producing an OM proteome of Veillonella parvula. We initially conducted a thorough bioinformatics analysis of all 1844 predicted proteins from Veillonella parvula DSM 2008’s genome using seven different localization prediction programs. These results were then complemented by protein extraction with surface exposed protein tags and subcellular fractionation, which were then sequenced by liquid chromatography tandem mass spectrometry. The merging of proteomics and bioinformatics results allowed identification of 76 OM proteins. Their annotation markedly extends previous inferences on the nature of the cell envelope of Negativicutes, and provides important information on the role of OM systems in the lifestyle of Veillonella.
HostingRepository	PRIDE
AnnounceDate	2017-07-19
AnnouncementXML	Submission_2017-07-19_00:14:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Magalie Duchateau
SpeciesList	scientific name: Veillonella parvula DSM 2008; NCBI TaxID: 479436;
ModificationList	L-methionine (R)-sulfoxide; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-15 07:38:39	ID requested
⏵ 1	2017-07-19 00:14:16	announced

Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo S, A Diderm Firmicute of the Human Microbiome. Front Microbiol, 8():1215(2017) [pubmed]

curator keyword: Biological

submitter keyword: Veillonella parvula, Outer Membrane Proteome

Simonetta Gribaldo
contact affiliation	Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
contact email	simonetta.gribaldo@pasteur.fr
lab head
Magalie Duchateau
contact affiliation	Institut Pasteur
contact email	magalie.duchateau@pasteur.fr
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/2017/07/PXD005929

PRIDE project URI

• PRIDE
  1. PXD005929
     1. Label: PRIDE project
     2. Name: Outer Membrane Proteome of Veillonella parvula: a Diderm Firmicute of the Human Microbiome