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

Stefan Schulze,María Inés Giménez,Mechthild Pohlschroder,Christian Fufezan,Michael Hippler,Roberto A Paggi,Zivojin Jevtic,Anita Marchfelder,Rosana De Castro,Georgio Legerme,Micaela Cerletti,Zachary Adams,Sébastien Ferreira-Cerca,Christof Lenz,Henning Urlaub,Julie Maupin-Furlow,Friedhelm Pfeiffer,Robert Knüppel,Ansgar Poetsch

doi:10.1038/s41467-020-16784-7

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.

Highlights

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
H. volcanii is a halophilic archaeon and, facilitated by a wide range of genetic and molecular biology tools[28], it is the model of choice to study a variety of cellular processes, leading to the most extensive proteomic studies completed amongst archaea far (Supplementary Table 1)
We chose to perform our initial reanalysis on 12 diverse H. volcanii MS datasets comprising more than 23 million spectra (Fig. 1)

Summary

Introduction

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. 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 Nterminal protein maturation, N-glycosylation, and metabolism. While large-scale datasets for various prokaryotes exist, they are limited in their proteome coverage, analysis of various biological conditions, large-scale integration of multiple datasets and/or straightforward extensibility. The ArcPP includes an increase in scale (by roughly an order of magnitude) of the combined datasets, extensive bioinformatic analysis of the detected proteins, the achieved depth of proteome sequence coverage as well as the comparison of datasets in regard to technical and biological aspects. Insights into archaeal cell biology are gained through this combined reanalysis of proteomic datasets, supported by interdisciplinary expertise

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Results