Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses

• Published in: Neuron (Cambridge, Mass.) Vol. 92; no. 2; pp. 358 - 371
• Main Authors: Schanzenbächer, Christoph T., Sambandan, Sivakumar, Langer, Julian D., Schuman, Erin M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19.10.2016; Elsevier Limited; Cell Press
• Subjects: Amino acids; Animals; Animals, Newborn; Anisomycin - pharmacology; Axon Guidance - drug effects; Bicuculline - pharmacology; BONCAT; Brain-derived neurotrophic factor; Cells, Cultured; Chromatography, Liquid; Data processing; Experiments; GABA-A Receptor Antagonists - pharmacology; Gene expression; Hippocampus - cytology; Hippocampus - drug effects; Hippocampus - metabolism; Homeostasis; homeostatic scaling; Kinases; Metabolism; Neuronal Outgrowth - drug effects; Neuronal Plasticity; Neurons; Neurons - drug effects; Neurons - metabolism; NeuroResource; Patch-Clamp Techniques; Protein synthesis; Protein Synthesis Inhibitors - pharmacology; Proteins; Proteome - drug effects; Proteome - metabolism; proteomics; Pseudopodia - drug effects; Pseudopodia - metabolism; Rats; Rats, Sprague-Dawley; Receptors, Glutamate - drug effects; Receptors, Glutamate - metabolism; Rodents; Synapses - drug effects; Synapses - metabolism; synaptic plasticity; Tandem Mass Spectrometry; transcriptomics; transcriptomics; BONCAT; protein synthesis; homeostatic scaling; synaptic plasticity; proteomics
• ISSN: 0896-6273; 1097-4199
• DOI: 10.1016/j.neuron.2016.09.058

Homeostatic scaling adjusts the strength of synaptic connections up or down in response to large changes in input. To identify the landscape of proteomic changes that contribute to opposing forms of homeostatic plasticity, we examined the plasticity-induced changes in the newly synthesized proteome. Cultured rat hippocampal neurons underwent homeostatic up-scaling or down-scaling. We used BONCAT (bio-orthogonal non-canonical amino acid tagging) to metabolically label, capture, and identify newly synthesized proteins, detecting and analyzing 5,940 newly synthesized proteins using mass spectrometry and label-free quantitation. Neither up- nor down-scaling produced changes in the number of different proteins translated. Rather, up- and down-scaling elicited opposing translational regulation of several molecular pathways, producing targeted adjustments in the proteome. We discovered ∼300 differentially regulated proteins involved in neurite outgrowth, axon guidance, filopodia assembly, excitatory synapses, and glutamate receptor complexes. We also identified differentially regulated proteins that are associated with multiple diseases, including schizophrenia, epilepsy, and Parkinson’s disease. •Newly synthesized proteins were metabolically labeled during homeostatic scaling•Approximately 6,000 newly synthesized proteins were detected using mass spectrometry•Over 300 proteins were differentially regulated by synaptic up- and down-scaling•Important synaptic proteins and disease-related proteins were regulated Schanzenbächer et al. discover the newly synthesized proteome in response to the global activity manipulations that bring about homeostatic synaptic scaling. The synthesis of over 300 proteins was significantly differentially regulated by the induction of scaling, including neurotransmitter receptors, scaffolding, and signaling molecules.