Journal Article

FZJ-2020-00804

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png ExteNDing Proteome Coverage with Legumain as a Highly Specific Digestion Protease

Soh, W. T. ; Demir, F.FZJ* ; Dall, E. ; Perrar, A.FZJ* ; Dahms, S. O. ; Kuppusamy, M.FZJ* ; Brandstetter, H. ; Huesgen, P. F. (Corresponding author)FZJ*

2020
American Chemical Society Columbus, Ohio

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Please use a persistent id in citations: http://hdl.handle.net/2128/24396  doi:10.1021/acs.analchem.9b03604

Abstract: Bottom-up mass spectrometry-based proteomics utilizes proteolytic enzymes with well characterized specificities to generate peptides amenable for identification by high-throughput tandem mass spectrometry. Trypsin, which cuts specifically after the basic residues lysine and arginine, is the predominant enzyme used for proteome digestion, although proteases with alternative specificities are required to detect sequences that are not accessible after tryptic digest. Here, we show that the human cysteine protease legumain exhibits a strict substrate specificity for cleavage after asparagine and aspartic acid residues during in-solution digestions of proteomes extracted from Escherichia coli, mouse embryonic fibroblast cell cultures, and Arabidopsis thaliana leaves. Generating peptides highly complementary in sequence, yet similar in their biophysical properties, legumain (as compared to trypsin or GluC) enabled complementary proteome and protein sequence coverage. Importantly, legumain further enabled the identification and enrichment of protein N-termini not accessible in GluC- or trypsin-digested samples. Legumain cannot cleave after glycosylated Asn residues, which enabled the robust identification and orthogonal validation of N-glycosylation sites based on alternating sequential sample treatments with legumain and PNGaseF and vice versa. Taken together, we demonstrate that legumain is a practical, efficient protease for extending the proteome and sequence coverage achieved with trypsin, with unique possibilities for the characterization of post-translational modification sites.

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Contributing Institute(s):

1. Analytik (ZEA-3)

Research Program(s):

1. 582 - Plant Science (POF3-582) (POF3-582)
2. 553 - Physical Basis of Diseases (POF3-553) (POF3-553)
3. ProPlantStress - Proteolytic processing in plant stress signal transduction and responses to abiotic stress and pathogen attack (639905) (639905)

Appears in the scientific report 2020

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Database coverage:
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