Abstract
Cellular protein turnover—the net result of protein synthesis and degradation—is crucial to maintain protein homeostasis and cellular function under steady-state conditions and to enable cells to remodel their proteomes upon a perturbation. In brain cells, proteins are continuously turned over at different rates depending on various factors including cell type, subcellular localization, cellular environment, and neuronal activity. Here we describe a workflow for the analysis of protein synthesis, degradation, and turnover in primary cultured rat neurons and glia using dynamic/pulsed SILAC and mass spectrometry.
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References
Schoenheimer R, Rittenberg D (1938) The application of isotopes to the study of intermediary metabolism. Science 87:221–226
Ciechanover A (2005) Proteolysis: from the lysosome to ubiquitin and the proteasome. Nat Rev Mol Cell Biol 6:79–87
Collins GA, Goldberg AL (2017) The logic of the 26S proteasome. Cell 169:792–806
Dikic I (2017) Proteasomal and autophagic degradation systems. Annu Rev Biochem 86:193–224
Hershey JWB, Sonenberg N, Mathews MB (2012) Principles of translational control: an overview. Cold Spring Harb Perspect Biol 4:a011528
Tai HC, Schuman EM (2008) Ubiquitin, the proteasome and protein degradation in neuronal function and dysfunction. Nat Rev Neurosci 9:826–838
Hipp MS, Kasturi P, Hartl FU (2019) The proteostasis network and its decline in ageing. Nat Rev Mol Cell Biol 20:421–435
Vilchez D, Saez I, Dillin A (2014) The role of protein clearance mechanisms in organismal ageing and age-related diseases. Nat Commun 5:5659
Ross AB, Langer JD, Jovanovic M (2020) Proteome turnover in the spotlight: approaches, applications, and perspectives. Mol Cell Proteomics 20:100016
Cambridge SB, Gnad F, Nguyen C, Bermejo JL, Kruger M, Mann M (2011) Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. J Proteome Res 10:5275–5284
Schwnhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2011) Global quantification of mammalian gene expression control. Nature 473:337–342
Selbach M, Schwanhausser B, Thierfleder N, Fang Z, Khanin R, Rajewsky N (2008) Widespread changed in protein synthesis induced by microRNAs. Nature 455:58–63
Wiśniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6:359–362
Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2:1896–1906
Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372
Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11:2301–2319
Dörrbaum AR, Kochen L, Langer JD, Schuman EM, Chao MV (2018) Local and global influences on protein turnover in neurons and glia. elife 7:e34202
Dörrbaum AR, Alvarez-Castelao B, Nassim-Assir B, Langer JD, Schuman EM, Chao MV, Dulac C (2020) Proteome dynamics during homeostatic scaling in cultured neurons. elife 9:e52939
Fusco CM, Desch K, Dörrbaum AR, Wang M, Staab A, Chan ICW et al (2021) Neuronal ribosomes exhibit dynamic context-dependent exchange of ribosomal proteins. Nat Commun 12:6127
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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
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Dörrbaum, A.R., Schuman, E.M., Langer, J.D. (2023). Dynamic SILAC to Determine Protein Turnover in Neurons and Glia. In: Luque-Garcia, J.L. (eds) SILAC. Methods in Molecular Biology, vol 2603. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2863-8_1
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DOI: https://doi.org/10.1007/978-1-0716-2863-8_1
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