PXD014091

PXD014091 is an original dataset announced via ProteomeXchange.

Title	A proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationships
Description	Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, the third most common foodborne disease. Many different Listeria strains and seroptypes exist, however a proteogenomic resource which would provide a basis for bridging the gap in the molecular understanding between the Listeria genotype and phenotypes via proteotypes is still missing. Here we devised a next-generation proteogenomics strategy which enables the community now to rapidly proteotype Listeria strains and relate the information back to the genotype. Based on sequencing and de novo assembly of the two most commonly used Listeria strain model systems, EGD-e and ScottA, we established a comprehensive Listeria proteogenomic database. A genome comparison established core and strain-specific genes with potential relevance for virulence differences. Next we established a DIA/SWATH-based proteotyping strategy, including a new and robust sample preparation workflow, enabling the reproducible, sensitive and relative quantitative measurement of Listeria proteotypes. This re-usable DIA/SWATH library and new public resource covers 70% of the potentially expressed ORFs of Listeria and represents the most extensive spectral library for Listeria proteotype analysis to date. We used these two new resources to investigate the Listeria proteotype in three states mimicking the upper gastrointestinal passage. Exposure of Listeria to bile salts at 37 °C, mimicking conditions encountered in the duodenum, showed significant proteotype perturbations including an increase of FlaA, the structural protein of flagella. Given that Listeria is known to lose its flagella above 30 °C, this was an unexpected finding. The formation of flagella, which might have implications within the infectivity cycle, was validated by parallel reaction monitoring, light and scanning electron microscopy. QPCR data of flaA transcripts showed no significant differences suggesting a regulation at the post-transcriptional level. Together, we provide a comprehensive proteogenomic resource and toolbox for the Listeria community enabling the analysis of Listeria genotype-proteotype-phenotype relationships.
HostingRepository	MassIVE
AnnounceDate	2020-06-16
AnnouncementXML	Submission_2020-06-16_09:57:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Goetze
SpeciesList	scientific name: Listeria monocytogenes EGD-e; NCBI TaxID: 169963; scientific name: Listeria monocytogenes str. Scott A; NCBI TaxID: 1027396;
ModificationList	Carbamidomethyl; Oxidation; Acetyl
Instrument	Orbitrap Fusion; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-01 14:35:06	ID requested
1	2020-02-06 07:34:19	announced
⏵ 2	2020-06-16 09:57:50	announced	2020-06-16: Adding publication [PMID32091902] to dataset [MSV000083881]

Varadarajan AR, Goetze S, Pavlou MP, Grosboillot V, Shen Y, Loessner MJ, Ahrens CH, Wollscheid B, Genotype-Proteotype-Phenotype Relationships. J Proteome Res, 19(4):1647-1662(2020) [pubmed]

submitter keyword: Listeria, proteotype, proteogenomics, smORFs, DIA, PRM, EGD-e, ScottA

Bernd Wollscheid
contact affiliation	ETHZ
contact email	bernd.wollscheid@hest.ethz.ch
lab head
Sandra Goetze
contact affiliation	ETHZ
contact email	sgoetze@ethz.ch
dataset submitter

MassIVE dataset URI

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://massive.ucsd.edu/MSV000083881/