The proteome landscape of the kingdoms of life

Johannes B. Müller, Philipp E. Geyer, Ana R. Colaço, Peter V. Treit, Maximilian T. Strauss, Mario Oroshi, Sophia Doll, Sebastian Virreira Winter, Jakob M. Bader, Niklas Köhler, Fabian Theis, Alberto Santos and Matthias Mann ()
Additional contact information
Johannes B. Müller: Max Planck Institute of Biochemistry
Philipp E. Geyer: Max Planck Institute of Biochemistry
Ana R. Colaço: University of Copenhagen
Peter V. Treit: Max Planck Institute of Biochemistry
Maximilian T. Strauss: Max Planck Institute of Biochemistry
Mario Oroshi: Max Planck Institute of Biochemistry
Sophia Doll: Max Planck Institute of Biochemistry
Sebastian Virreira Winter: Max Planck Institute of Biochemistry
Jakob M. Bader: Max Planck Institute of Biochemistry
Niklas Köhler: Helmholtz Zentrum München–German Research Center for Environmental Health, Institute of Computational Biology
Fabian Theis: Helmholtz Zentrum München–German Research Center for Environmental Health, Institute of Computational Biology
Alberto Santos: University of Copenhagen
Matthias Mann: Max Planck Institute of Biochemistry

Nature, 2020, vol. 582, issue 7813, 592-596

Abstract: Abstract Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported1, advances in mass-spectrometry-based proteomics2 have enabled increasingly comprehensive identification and quantification of the human proteome3–6. However, there have been few comparisons across species7,8, in stark contrast with genomics initiatives9. Here we use an advanced proteomics workflow—in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system—for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides from Bacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org.

Date: 2020
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DOI: 10.1038/s41586-020-2402-x

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