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

ADAMS, ZACHARY; FERREIRA-CERCA, SÉBASTIEN; HIPPLER, MICHAEL; LEGERME, GEORGIO; MAUPIN-FURLOW, JULIE; POETSCH, ANSGAR; SCHULZE, STEFAN; DE CASTRO, ROSANA; GIMÉNEZ, MARÍA INÉS; KNÜPPEL, ROBERT; MARCHFELDER, ANITA; PFEIFFER, FRIEDHELM; POHLSCHRODER, MECHTHILD; SCHULZE, STEFAN; DE CASTRO, ROSANA; GIMÉNEZ, MARÍA INÉS; KNÜPPEL, ROBERT; MARCHFELDER, ANITA; PFEIFFER, FRIEDHELM; POHLSCHRODER, MECHTHILD; CERLETTI, MICAELA; FUFEZAN, CHRISTIAN; JEVTIC, ZIVOJIN; LENZ, CHRISTOF; PAGGI, ROBERTO A.; URLAUB, HENNING; CERLETTI, MICAELA; FUFEZAN, CHRISTIAN; JEVTIC, ZIVOJIN; LENZ, CHRISTOF; PAGGI, ROBERTO A.; URLAUB, HENNING; ADAMS, ZACHARY; FERREIRA-CERCA, SÉBASTIEN; HIPPLER, MICHAEL; LEGERME, GEORGIO; MAUPIN-FURLOW, JULIE; POETSCH, ANSGAR

NATURE COMMUNICATIONS

SPRINGER NATURE

Lugar: London; Año: 2020 vol. 11

2041-1723

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 archaealproteomes. 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 Nterminalprotein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.