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The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Author

Listed:
  • Stefan Schulze

    (University of Pennsylvania)

  • Zachary Adams

    (University of Florida)

  • Micaela Cerletti

    (National University of Mar del Plata)

  • Rosana Castro

    (National University of Mar del Plata)

  • Sébastien Ferreira-Cerca

    (University of Regensburg)

  • Christian Fufezan

    (Heidelberg University)

  • María Inés Giménez

    (National University of Mar del Plata)

  • Michael Hippler

    (University of Münster
    Okayama University)

  • Zivojin Jevtic

    (Max Planck Institute for Biophysical Chemistry)

  • Robert Knüppel

    (University of Regensburg)

  • Georgio Legerme

    (University of Pennsylvania)

  • Christof Lenz

    (Max Planck Institute for Biophysical Chemistry
    University Medical Center Göttingen)

  • Anita Marchfelder

    (Biology II, Ulm University)

  • Julie Maupin-Furlow

    (University of Florida
    University of Florida)

  • Roberto A. Paggi

    (National University of Mar del Plata)

  • Friedhelm Pfeiffer

    (Max Planck Institute of Biochemistry)

  • Ansgar Poetsch

    (Ruhr University Bochum
    Center for Marine and Molecular Biotechnology
    Ocean University of China)

  • Henning Urlaub

    (Max Planck Institute for Biophysical Chemistry
    University Medical Center Göttingen)

  • Mechthild Pohlschroder

    (University of Pennsylvania)

Abstract

While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.

Suggested Citation

  • Stefan Schulze & Zachary Adams & Micaela Cerletti & Rosana Castro & Sébastien Ferreira-Cerca & Christian Fufezan & María Inés Giménez & Michael Hippler & Zivojin Jevtic & Robert Knüppel & Georgio Lege, 2020. "The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16784-7
    DOI: 10.1038/s41467-020-16784-7
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    Cited by:

    1. Heather Schiller & Yirui Hong & Joshua Kouassi & Theopi Rados & Jasmin Kwak & Anthony DiLucido & Daniel Safer & Anita Marchfelder & Friedhelm Pfeiffer & Alexandre Bisson & Stefan Schulze & Mechthild P, 2024. "Identification of structural and regulatory cell-shape determinants in Haloferax volcanii," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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