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Proteome-wide identification of predominant subcellular protein localizations in a bacterial model organism

Stekhoven, Daniel J. and Omasits, Ulrich and Quebatte, Maxime and Dehio, Christoph and Ahrens, Christian H.. (2014) Proteome-wide identification of predominant subcellular protein localizations in a bacterial model organism. Journal of Proteomics , 99. pp. 123-137.

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Official URL: https://edoc.unibas.ch/66842/

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Abstract

Proteomics data provide unique insights into biological systems, including the predominant subcellular localization (SCL) of proteins, which can reveal important clues about their functions. Here we analyzed data of a complete prokaryotic proteome expressed under two conditions mimicking interaction of the emerging pathogen Bartonella henselae with its mammalian host. Normalized spectral count data from cytoplasmic, total membrane, inner and outer membrane fractions allowed us to identify the predominant SCL for 82% of the identified proteins. The spectral count proportion of total membrane versus cytoplasmic fractions indicated the propensity of cytoplasmic proteins to co-fractionate with the inner membrane, and enabled us to distinguish cytoplasmic, peripheral inner membrane and bona fide inner membrane proteins. Principal component analysis and k-nearest neighbor classification training on selected marker proteins or predominantly localized proteins, allowed us to determine an extensive catalog of at least 74 expressed outer membrane proteins, and to extend the SCL assignment to 94% of the identified proteins, including 18% where in silico methods gave no prediction. Suitable experimental proteomics data combined with straightforward computational approaches can thus identify the predominant SCL on a proteome-wide scale. Finally, we present a conceptual approach to identify proteins potentially changing their SCL in a condition-dependent fashion.
Faculties and Departments:05 Faculty of Science
05 Faculty of Science > Departement Biozentrum > Infection Biology > Molecular Microbiology (Dehio)
UniBasel Contributors:Dehio, Christoph and Qu├ębatte, Maxime
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Elsevier
ISSN:1874-3919
e-ISSN:1876-7737
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:11 Sep 2020 11:31
Deposited On:11 Sep 2020 11:31

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