Proteomic analysis of Escherichia coli protein fractions resistant to solubilization by ionic detergents
- Authors: Antonets K.S.1,2, Volkov K.V.1, Maltseva A.L.1, Arshakian L.M.1, Galkin A.P.1,2, Nizhnikov A.A.1,2
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Affiliations:
- Department of Genetics and Biotechnology
- Vavilov Institute of General Genetics, St. Petersburg Branch
- Issue: Vol 81, No 1 (2016)
- Pages: 34-46
- Section: Article
- URL: https://journals.rcsi.science/0006-2979/article/view/150759
- DOI: https://doi.org/10.1134/S0006297916010041
- ID: 150759
Cite item
Abstract
Amyloids are protein fibrils adopting structure of cross-beta spine exhibiting either pathogenic or functionally significant properties. In prokaryotes, there are several groups of functional amyloids; however, all of them were identified by specialized approaches that do not reveal all cellular amyloids. Here, using our previously developed PSIA (Proteomic Screening and Identification of Amyloids) approach, we have conducted a proteomic screening for candidates for novel amyloid-forming proteins in Escherichia coli as one of the most important model organisms and biotechnological objects. As a result, we identified 61 proteins in fractions resistant to treatment with ionic detergents. We found that a fraction of proteins bearing potentially amyloidogenic regions predicted by bioinformatics algorithms was 3-5-fold more abundant among the identified proteins compared to those observed in the entire E. coli proteome. Almost all identified proteins contained potentially amyloidogenic regions, and four of them (BcsC, MukB, YfbK, and YghJ) have asparagineand glutamine-rich regions underlying a crucial feature of many known amyloids. In this study, we demonstrate for the first time that at the proteome level there is a correlation between experimentally demonstrated detergent-resistance of proteins and potentially amyloidogenic regions predicted by bioinformatics approaches. The data obtained enable further comprehensive characterization of entirety of amyloids (or amyloidome) in bacterial cells.
About the authors
K. S. Antonets
Department of Genetics and Biotechnology; Vavilov Institute of General Genetics, St. Petersburg Branch
Email: ant.nizhnikov@gmail.com
Russian Federation, St. Petersburg, 199034; St. Petersburg, 199034
K. V. Volkov
Department of Genetics and Biotechnology
Email: ant.nizhnikov@gmail.com
Russian Federation, St. Petersburg, 199034
A. L. Maltseva
Department of Genetics and Biotechnology
Email: ant.nizhnikov@gmail.com
Russian Federation, St. Petersburg, 199034
L. M. Arshakian
Department of Genetics and Biotechnology
Email: ant.nizhnikov@gmail.com
Russian Federation, St. Petersburg, 199034
A. P. Galkin
Department of Genetics and Biotechnology; Vavilov Institute of General Genetics, St. Petersburg Branch
Email: ant.nizhnikov@gmail.com
Russian Federation, St. Petersburg, 199034; St. Petersburg, 199034
A. A. Nizhnikov
Department of Genetics and Biotechnology; Vavilov Institute of General Genetics, St. Petersburg Branch
Author for correspondence.
Email: ant.nizhnikov@gmail.com
Russian Federation, St. Petersburg, 199034; St. Petersburg, 199034