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Proteome-wide detection of S-nitrosylation targets and motifs using bioorthogonal cleavable-linker-based enrichment and switch technique

Author

Listed:
  • Ruzanna Mnatsakanyan

    (Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.)

  • Stavroula Markoutsa

    (Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.)

  • Kim Walbrunn

    (Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.)

  • Andreas Roos

    (Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.
    University Hospital Essen, University of Duisburg-Essen)

  • Steven H. L. Verhelst

    (Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.
    KU Leuven - University of Leuven)

  • René P. Zahedi

    (Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.
    McGill University
    McGill University)

Abstract

Cysteine modifications emerge as important players in cellular signaling and homeostasis. Here, we present a chemical proteomics strategy for quantitative analysis of reversibly modified Cysteines using bioorthogonal cleavable-linker and switch technique (Cys-BOOST). Compared to iodoTMT for total Cysteine analysis, Cys-BOOST shows a threefold higher sensitivity and considerably higher specificity and precision. Analyzing S-nitrosylation (SNO) in S-nitrosoglutathione (GSNO)-treated and non-treated HeLa extracts Cys-BOOST identifies 8,304 SNO sites on 3,632 proteins covering a wide dynamic range of the proteome. Consensus motifs of SNO sites with differential GSNO reactivity confirm the relevance of both acid-base catalysis and local hydrophobicity for NO targeting to particular Cysteines. Applying Cys-BOOST to SH-SY5Y cells, we identify 2,151 SNO sites under basal conditions and reveal significantly changed SNO levels as response to early nitrosative stress, involving neuro(axono)genesis, glutamatergic synaptic transmission, protein folding/translation, and DNA replication. Our work suggests SNO as a global regulator of protein function akin to phosphorylation and ubiquitination.

Suggested Citation

  • Ruzanna Mnatsakanyan & Stavroula Markoutsa & Kim Walbrunn & Andreas Roos & Steven H. L. Verhelst & René P. Zahedi, 2019. "Proteome-wide detection of S-nitrosylation targets and motifs using bioorthogonal cleavable-linker-based enrichment and switch technique," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10182-4
    DOI: 10.1038/s41467-019-10182-4
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    Cited by:

    1. Renan B. Ferreira & Ling Fu & Youngeun Jung & Jing Yang & Kate S. Carroll, 2022. "Reaction-based fluorogenic probes for detecting protein cysteine oxidation in living cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Guochen Qin & Menghuan Qu & Bei Jia & Wei Wang & Zhuojun Luo & Chun-Peng Song & W. Andy Tao & Pengcheng Wang, 2023. "FAT-switch-based quantitative S-nitrosoproteomics reveals a key role of GSNOR1 in regulating ER functions," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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