Systematic analysis of protein turnover in primary cells

Toby Mathieson, Holger Franken, Jan Kosinski, Nils Kurzawa, Nico Zinn, Gavain Sweetman, Daniel Poeckel, Vikram S. Ratnu, Maike Schramm, Isabelle Becher, Michael Steidel, Kyung-Min Noh, Giovanna Bergamini, Martin Beck (), Marcus Bantscheff () and Mikhail M. Savitski ()
Additional contact information
Toby Mathieson: GlaxoSmithKline
Holger Franken: GlaxoSmithKline
Jan Kosinski: European Molecular Biology Laboratory
Nils Kurzawa: European Molecular Biology Laboratory
Nico Zinn: GlaxoSmithKline
Gavain Sweetman: GlaxoSmithKline
Daniel Poeckel: GlaxoSmithKline
Vikram S. Ratnu: European Molecular Biology Laboratory
Maike Schramm: European Molecular Biology Laboratory
Isabelle Becher: European Molecular Biology Laboratory
Michael Steidel: GlaxoSmithKline
Kyung-Min Noh: European Molecular Biology Laboratory
Giovanna Bergamini: GlaxoSmithKline
Martin Beck: European Molecular Biology Laboratory
Marcus Bantscheff: GlaxoSmithKline
Mikhail M. Savitski: European Molecular Biology Laboratory

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract A better understanding of proteostasis in health and disease requires robust methods to determine protein half-lives. Here we improve the precision and accuracy of peptide ion intensity-based quantification, enabling more accurate protein turnover determination in non-dividing cells by dynamic SILAC-based proteomics. This approach allows exact determination of protein half-lives ranging from 10 to >1000 h. We identified 4000–6000 proteins in several non-dividing cell types, corresponding to 9699 unique protein identifications over the entire data set. We observed similar protein half-lives in B-cells, natural killer cells and monocytes, whereas hepatocytes and mouse embryonic neurons show substantial differences. Our data set extends and statistically validates the previous observation that subunits of protein complexes tend to have coherent turnover. Moreover, analysis of different proteasome and nuclear pore complex assemblies suggests that their turnover rate is architecture dependent. These results illustrate that our approach allows investigating protein turnover and its implications in various cell types.

Date: 2018
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03106-1

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DOI: 10.1038/s41467-018-03106-1

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