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

Stefan Schulze, Zachary Adams, Micaela Cerletti, Rosana Castro, Sébastien Ferreira-Cerca, Christian Fufezan, María Inés Giménez, Michael Hippler, Zivojin Jevtic, Robert Knüppel, Georgio Legerme, Christof Lenz, Anita Marchfelder, Julie Maupin-Furlow, Roberto A. Paggi, Friedhelm Pfeiffer, Ansgar Poetsch, Henning Urlaub and Mechthild Pohlschroder ()
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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
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
Anita Marchfelder: Biology II, Ulm University
Julie Maupin-Furlow: University of Florida
Roberto A. Paggi: National University of Mar del Plata
Friedhelm Pfeiffer: Max Planck Institute of Biochemistry
Ansgar Poetsch: Ruhr University Bochum
Henning Urlaub: Max Planck Institute for Biophysical Chemistry
Mechthild Pohlschroder: University of Pennsylvania

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-16784-7

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