Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions

• DOI: 10.1038/s41467-018-06519-0
• Publication Date: 2018-10-08T09:16:40Z
• Authors: Eugenio F. Fornas...; Sunit Mandad; Hanna Wildhagen; Mihai Alevra; Burkhard Rammner; Sarva Keihani; Felipe Opazo; Inga Urban; Till Ischebeck; M. Sadman Sakib; Maryam K. Fard; Koray Kirli; Tonatiuh Pena Cen...; Ramon O. Vidal; Raza-Ur Rahman; Eva Benito; André Fischer; Sven Dennerlein; Peter Rehling; Ivo Feussner; Stefan Bonn; Mikael Simons; Henning Urlaub; Silvio O. Rizzoli
• Keywords: Male; 0301 basic medicine; Science; genetics [beta-Galactosidase]; Q; Brain; Computational Biology; metabolism [Hippocampus]; 612; Models, Theoretical; 573; beta-Galactosidase; Hippocampus; Article; Mass Spectrometry; metabolism [beta-Galactosidase]; Mice; 03 medical and health sciences; metabolism [Brain]; Animals; ddc:500

AbstractThe turnover of brain proteins is critical for organism survival, and its perturbations are linked to pathology. Nevertheless, protein lifetimes have been difficult to obtain in vivo. They are readily measured in vitro by feeding cells with isotopically labeled amino acids, followed by mass spectrometry analyses. In vivo proteins are generated from at least two sources: labeled amino acids from the diet, and non-labeled amino acids from the degradation of pre-existing proteins. This renders measurements difficult. Here we solved this problem rigorously with a workflow that combines mouse in vivo isotopic labeling, mass spectrometry, and mathematical modeling. We also established several independent approaches to test and validate the results. This enabled us to measure the accurate lifetimes of ~3500 brain proteins. The high precision of our data provided a large set of biologically significant observations, including pathway-, organelle-, organ-, or cell-specific effects, along with a comprehensive catalog of extremely long-lived proteins (ELLPs).