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

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

NATURE COMMUNICATIONS

Nature Publishing group

Año: 2020 vol. 11

2041-1723

While many aspects of archaeal cell biology remain relatively unexplored, systems biologyapproaches like mass spectrometry (MS) based proteomics offer an opportunity for rapidadvances. Unfortunately, the enormous amount of MS data generated often remainsincompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specificbiological expertise for data interpretation. Here we present the initiation of the ArchaealProteome Project (ArcPP), a community-based effort to comprehensively analyze archaealproteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasetsfrom various strains and culture conditions. Optimized peptide spectrum matching, with strictcontrol of false discovery rates, facilitates identifying > 72% of the reference proteome, with amedian protein sequence coverage of 51%. These analyses, together with expert knowledgein diverse aspects of cell biology, provide meaningful insights into processes such as Nterminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as aninvaluable blueprint for comprehensive prokaryotic proteomics.