Skip to main content

Dynamic SILAC to Determine Protein Turnover in Neurons and Glia

  • Protocol
  • First Online:
SILAC

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2603))

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Schoenheimer R, Rittenberg D (1938) The application of isotopes to the study of intermediary metabolism. Science 87:221–226

    Article  CAS  PubMed  Google Scholar 

  2. Ciechanover A (2005) Proteolysis: from the lysosome to ubiquitin and the proteasome. Nat Rev Mol Cell Biol 6:79–87

    Article  CAS  PubMed  Google Scholar 

  3. Collins GA, Goldberg AL (2017) The logic of the 26S proteasome. Cell 169:792–806

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Dikic I (2017) Proteasomal and autophagic degradation systems. Annu Rev Biochem 86:193–224

    Article  CAS  PubMed  Google Scholar 

  5. Hershey JWB, Sonenberg N, Mathews MB (2012) Principles of translational control: an overview. Cold Spring Harb Perspect Biol 4:a011528

    Article  PubMed  PubMed Central  Google Scholar 

  6. Tai HC, Schuman EM (2008) Ubiquitin, the proteasome and protein degradation in neuronal function and dysfunction. Nat Rev Neurosci 9:826–838

    Article  CAS  PubMed  Google Scholar 

  7. Hipp MS, Kasturi P, Hartl FU (2019) The proteostasis network and its decline in ageing. Nat Rev Mol Cell Biol 20:421–435

    Article  CAS  PubMed  Google Scholar 

  8. Vilchez D, Saez I, Dillin A (2014) The role of protein clearance mechanisms in organismal ageing and age-related diseases. Nat Commun 5:5659

    Article  CAS  PubMed  Google Scholar 

  9. Ross AB, Langer JD, Jovanovic M (2020) Proteome turnover in the spotlight: approaches, applications, and perspectives. Mol Cell Proteomics 20:100016

    Article  PubMed  PubMed Central  Google Scholar 

  10. 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

    Article  CAS  PubMed  Google Scholar 

  11. 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

    Article  Google Scholar 

  12. 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

    Article  CAS  PubMed  Google Scholar 

  13. Wiśniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6:359–362

    Article  PubMed  Google Scholar 

  14. 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

    Article  CAS  PubMed  Google Scholar 

  15. 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

    Article  CAS  PubMed  Google Scholar 

  16. Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11:2301–2319

    Article  CAS  PubMed  Google Scholar 

  17. 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

    Article  PubMed  PubMed Central  Google Scholar 

  18. 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

    Article  PubMed  PubMed Central  Google Scholar 

  19. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Erin M. Schuman or Julian D. Langer .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

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

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2863-8_1

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2862-1

  • Online ISBN: 978-1-0716-2863-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics