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J Proteomics. 2018 Jun 15;181:16-23. doi: 10.1016/j.jprot.2018.03.026. Epub 2018 Mar 30.

Differential biotin labelling of the cell envelope proteins in lipopolysaccharidic diderm bacteria: Exploring the proteosurfaceome of Escherichia coli using sulfo-NHS-SS-biotin and sulfo-NHS-PEG4-bismannose-SS-biotin.

Author information

1
Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France; GSK, Via Fiorentina 1, 53100 Siena, Italy.
2
Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France.
3
INRA, Plate-Forme d'Exploration du Métabolisme, F-63122 Saint-Genès Champanelle, France.
4
Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France; INRA, Plate-Forme d'Exploration du Métabolisme, F-63122 Saint-Genès Champanelle, France.
5
Centre de Recherche en Nutrition Humaine Auvergne, UMR UCA INSERM U1071, USC-INRA 2018, Clermont Université - Université d'Auvergne, Faculté de Pharmacie, CHU Clermont-Ferrand, Service Bactériologie Mycologie Parasitologie, Clermont-Ferrand, France.
6
GSK, Via Fiorentina 1, 53100 Siena, Italy.
7
Université Clermont Auvergne, INRA, UMR454 MEDiS, F-63000 Clermont-Ferrand, France. Electronic address: mickael.desvaux@inra.fr.

Abstract

Surface proteins are the major factor for the interaction between bacteria and its environment, playing an important role in infection, colonisation, virulence and adaptation. However, the study of surface proteins has proven difficult mainly due to their hydrophobicity and/or relatively low abundance compared with cytoplasmic proteins. To overcome these issues new proteomic strategies have been developed, such as cell-surface protein labelling using biotinylation reagents. Sulfo-NHS-SS-biotin is the most commonly used reagent to investigate the proteins expressed at the cell surface of various organisms but its use in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria) remains limited to a handful of species. While generally pass over in silence, some periplasmic proteins, but also some inner membrane lipoproteins, integral membrane proteins and cytoplasmic proteins (cytoproteins) are systematically identified following this approach. To limit cell lysis and diffusion of the sulfo-NHS-SS-biotin through the outer membrane, biotin labelling was tested over short incubation times and proved to be as efficient for 1 min at room temperature. To further limit labelling of protein located below the outer membrane, the use of high-molecular weight sulfo-NHS-PEG4-bismannose-SS-biotin appeared to recover differentially cell-envelope proteins compared to low-molecular weight sulfo-NHS-SS-biotin. Actually, the sulfo-NHS-SS-biotin recovers at a higher extent the proteins completely or partly exposed in the periplasm than sulfo-NHS-PEG4-bismannose-SS-biotin, namely periplasmic and integral membrane proteins as well as inner membrane and outer membrane lipoproteins. These results highlight that protein labelling using biotinylation reagents of different sizes provides a sophisticated and accurate way to differentially explore the cell envelope proteome of lipopolysaccharidic diderm bacteria.

SIGNIFICANCE:

While generally pass over in silence, some periplasmic proteins, inner membrane lipoproteins (IMLs), integral membrane proteins (IMPs) and cytoplasmic proteins (cytoproteins) are systematically identified following cell-surface biotin labelling in lipopolysaccharidic diderm bacteria (archetypal Gram-negative bacteria). The use of biotinylation molecules of different sizes, namely sulfo-NHS-SS-biotin and sulfo-NHS-PEG4-bismannose-SS-biotin, was demonstrated to provide a sophisticated and accurate way to differentially explore the cell envelope proteome of lipopolysaccharidic diderm bacteria.

KEYWORDS:

Outer membrane lipoproteins; Outer membrane proteins; Protein biotinylation; Secretome; Subproteome; Surfaceome

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