Phosphoproteomic and bioinformatic methods for analyzing signaling in vertebrate axon growth and regeneration

•Phosphoproteomics enables comprehensive identification of phosphorylation sites.•Bioinformatics enables identification of activated kinases of the phosphoproteome.•Using phosphoproteomics, we identified phosphorylated sites related to axon growth.•Mammalian phosphorylation systems differ markedly f...

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Bibliographic Details
Published in:Journal of neuroscience methods 2020-06, Vol.339, p.108723-108723, Article 108723
Main Authors: Igarashi, Michihiro, Kawasaki, Asami, Ishikawa, Yuya, Honda, Atsuko, Okada, Masayasu, Okuda, Shujiro
Format: Article
Language:English
Subjects:
GAP-43
growth cone
MAP1B
phosphoproteomics
protein phosphorylation
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Summary:•Phosphoproteomics enables comprehensive identification of phosphorylation sites.•Bioinformatics enables identification of activated kinases of the phosphoproteome.•Using phosphoproteomics, we identified phosphorylated sites related to axon growth.•Mammalian phosphorylation systems differ markedly from nematode and fly systems. Phosphorylation is the most important post-translational modification of proteins in many cells, including neurons. Phosphoproteomics is a relatively new technique for comprehensively identifying phosphorylation sites in the whole proteome of a given system. We applied this method to developmental neurobiology research to understand the signaling pathways that regulate the mammalian growth cone, which is formed at the tips of developing neurites to ensure accurate neuronal network formation. Using this powerful technique, we identified at least four phosphorylation sites tightly associated with axon growth. Because phosphoproteomic results include relatively large numbers of phosphopeptides, the data are typically analyzed using bioinformatics. We utilized three bioinformatics tools to identify the responsible protein kinases, the putative functions of the phosphorylated protein groups, and the evolutional aspects of the phosphorylated proteins. Collectively, these data indicate phosphoproteomics is a cutting-edge tool for neuroscience research.
ISSN:0165-0270
1872-678X
DOI:10.1016/j.jneumeth.2020.108723