Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry

Gustavo Monteiro Silva, Wei Wei, Sandhya Manohar, Christine Vogel

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Protein ubiquitination is a widespread modification serving many roles in neuronal development and function. Moreover, the accumulation of ubiquitinated proteins is a prominent feature of neurodegeneration and oxidative stress related diseases. The emerging diversity of ubiquitin signals beyond protein degradation—based on distinct types of polyubiquitin chains—necessitates tools that specifically and quantitatively investigate its different functions. Polyubiquitin chains linked by lysine 63 (K63) relate to neurodegenerative diseases, but most of their targets and functions have not yet been elucidated. K63- linked ubiquitin has been implicated in DNA repair signaling, endocytosis, and inclusion body clearance. In addition, we recently identified an important role of K63 ubiquitin in regulating translation in response to oxidative stress in yeast. The change in K63 ubiquitination in response to hydrogen peroxide is conserved in mouse hippocampal HT22 cells, highlighting the importance of this modification in higher eukaryotes. In this chapter, we discuss cutting-edge methodologies available to investigate protein ubiquitination in a proteome-wide and quantitative manner, and we present a method to simultaneously isolate and identify the specific targets of K63 ubiquitin. This method relies on the use of a selective K63 ubiquitin isolation tool with subsequent analysis of protein content by high-resolution mass spectrometry. The proposed workflow can be combined with additional methods for ubiquitin analysis and applied to several research models. This approach can also provide the scientific basis for the development of new tools to isolate and identify targets of other ubiquitin linkages.

Original languageEnglish (US)
Title of host publicationNeuromethods
PublisherHumana Press Inc.
Pages111-125
Number of pages15
Volume114
DOIs
StatePublished - Nov 18 2015

Publication series

NameNeuromethods
Volume114
ISSN (Print)08932336
ISSN (Electronic)19406045

Fingerprint

Ubiquitinated Proteins
Ubiquitin
Mass spectrometry
Mass Spectrometry
Ubiquitination
Polyubiquitin
Oxidative stress
Proteins
Oxidative Stress
Neurodegenerative diseases
Workflow
Inclusion Bodies
Proteome
Endocytosis
Eukaryota
DNA Repair
Neurodegenerative Diseases
Yeast
Hydrogen Peroxide
Lysine

Keywords

  • K63 ubiquitin
  • Mass spectrometry
  • Neurons
  • Oxidative stress

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)
  • Neuroscience(all)
  • Psychiatry and Mental health

Cite this

Silva, G. M., Wei, W., Manohar, S., & Vogel, C. (2015). Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry. In Neuromethods (Vol. 114, pp. 111-125). (Neuromethods; Vol. 114). Humana Press Inc.. https://doi.org/10.1007/7657_2015_95

Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry. / Silva, Gustavo Monteiro; Wei, Wei; Manohar, Sandhya; Vogel, Christine.

Neuromethods. Vol. 114 Humana Press Inc., 2015. p. 111-125 (Neuromethods; Vol. 114).

Research output: Chapter in Book/Report/Conference proceedingChapter

Silva, GM, Wei, W, Manohar, S & Vogel, C 2015, Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry. in Neuromethods. vol. 114, Neuromethods, vol. 114, Humana Press Inc., pp. 111-125. https://doi.org/10.1007/7657_2015_95
Silva GM, Wei W, Manohar S, Vogel C. Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry. In Neuromethods. Vol. 114. Humana Press Inc. 2015. p. 111-125. (Neuromethods). https://doi.org/10.1007/7657_2015_95
Silva, Gustavo Monteiro ; Wei, Wei ; Manohar, Sandhya ; Vogel, Christine. / Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry. Neuromethods. Vol. 114 Humana Press Inc., 2015. pp. 111-125 (Neuromethods).
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