MassIVE MSV000083881

Partial Public PXD014091

A proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationships

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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. [doi:10.25345/C56D3N] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Listeria ; proteotype ; proteogenomics ; smORFs ; DIA ; PRM ; EGD-e ; ScottA ; MassIVE.quant reviewed - Platinum

Contact

Principal Investigators:
(in alphabetical order) 		Bernd Wollscheid, ETHZ, Switzerland
Submitting User: Sandra

Publications

Varadarajan AR, Goetze S, Pavlou MP, Grosboillot V, Shen Y, Loessner MJ, Ahrens CH, Wollscheid B.
A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype-Proteotype-Phenotype Relationships.
J. Proteome Res. 2020 Apr 3;19(4):1647-1662. Epub 2020 Mar 6.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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