Analysis of Proteins That Rapidly Change Upon Mechanistic/Mammalian Target of Rapamycin Complex 1 (mTORC1) Repression Identifies Parkinson Protein 7 (PARK7) as a Novel Protein Aberrantly Expressed in Tuberous Sclerosis Complex (TSC)

Abstract

Many biological processes involve the mechanistic/mammalian target of rapamycin complex 1 (mTORC1). Thus, the challenge of deciphering mTORC1-mediated functions during normal and pathological states in the central nervous system is challenging. Because mTORC1 is at the core of translation, we have investigated mTORC1 function in global and regional protein expression. Activation of mTORC1 has been generally regarded to promote translation. Few but recent works have shown that suppression of mTORC1 can also promote local protein synthesis. Moreover, excessive mTORC1 activation during diseased states represses basal and activity-induced protein synthesis. To determine the role of mTORC1 activation in protein expression, we have used an unbiased, large-scale proteomic approach. We provide evidence that a brief repression of mTORC1 activity in vivo by rapamycin has little effect globally, yet leads to a significant remodeling of synaptic proteins, in particular those proteins that reside in the postsynaptic density. We have also found that curtailing the activity of mTORC1 bidirectionally alters the expression of proteins associated with epilepsy, Alzheimer's disease, and autism spectrum disorder-neurological disorders that exhibit elevated mTORC1 activity. Through a protein-protein interaction network analysis, we have identified common proteins shared among these mTORC1-related diseases. One such protein is Parkinson protein 7, which has been implicated in Parkinson's disease, yet not associated with epilepsy, Alzheimers disease, or autism spectrum disorder. To verify our finding, we provide evidence that the protein expression of Parkinson protein 7, including new protein synthesis, is sensitive to mTORC1 inhibition. Using a mouse model of tuberous sclerosis complex, a disease that displays both epilepsy and autism spectrum disorder phenotypes and has overactive mTORC1 signaling, we show that Parkinson protein 7 protein is elevated in the dendrites and colocalizes with the postsynaptic marker postsynaptic density-95. Our work offers a comprehensive view of mTORC1 and its role in regulating regional protein expression in normal and diseased states. The mechanistic/mammalian target of rapamycin complex 1 (mTORC1) 1 is a serine/threonine protein kinase that is highly Author contributions: FN and KRG designed research. FN and SN conducted experiments and analyzed data. SN performed bioinformatics analyses. ES and YM conducted mass spectrometry analyses. GS facilitated mass spectrometry experiments and provided technical advice. GAD and BVZ provided the virus and performed stereotaxic injections. FN, SN, and KRG wrote the manuscript. 1 The abbreviations used are: mTORC1, mechanistic/mammalian target of rapamycin complex 1; AD, Alzheimer's disease; AHA, azidohomoalanine; APP, amyloid precursor protein; ASD, autism spectrum disorder; BONCAT, bioorthogonal noncanonical amino acid

mTORC1 Is a Local, Postsynaptic Voltage Sensor Regulated by Positive and Negative Feedback Pathways

“…Our recent finding that acute inhibition of mTORC1 activity disrupts the expression of proteins that are involved in ion homeostasis and membrane potential at the synapse supports the close relationship of mTORC1 signaling in maintaining a normal electrochemical gradient of the postsynaptic membrane (Niere et al, 2016). Using the unbiased approach of tandem mass spectrometry (MS/MS) to identify changes in protein composition at the postsynaptic site, we found proteins whose functions affect the membrane potential (Table 1).…”

Pushing the threshold: How NMDAR antagonists induce homeostasis through protein synthesis to remedy depression

“…Interestingly, sleep deprivation also mediates a rapid antidepressant effect (McClung, 2007). In fruit flies, a screen designed to find mutants with a short sleeping phenotype identified the shaker locus (Kv1) (Cirelli et al, 2005), a channel whose expression is repressed by mTORC1 activity (Niere et al, 2016; Raab-Graham et al, 2006; Sosanya et al, 2015a; Sosanya et al, 2015b; Sosanya et al, 2013). It will be interesting if like HCN, reduced levels of Kv1.1 feedback to increase mTORC1/BDNF signaling resulting in antidepressant behaviors.…”

“…Clues may come from recent work that examines dendritic protein synthesis in the presence of the mTORC1 inhibitor rapamycin in vivo (Niere et al, 2015). While the role of mTORC1 activity to promote translation of mRNAs is grounded in its established function of phosphorylating eIF4BP and ribosomal S6 kinase (Hay and Sonenberg, 2004), a few studies suggest a separate and likely just as important role for mTORC1 activity in repressing mRNA translation of specific transcripts (Niere et al, 2015; Raab-Graham et al, 2006; Sosanya et al, 2013). Interestingly, Niere et al, using the unbiased approach of mass spectrometry, demonstrates that the number of proteins that increase at the synapse with mTORC1 inhibition is approximately equal in number to those whose expression is reduced (Niere et al, 2015).…”

“…(C) Heat map of EEF2, demonstrating increased expression in soluble fraction of synaptoneurosomes with brief mTORC1 inhibition. Data obtained from Niere et al, 2015 and (Aragam et al, 2011; De Vry et al, 2016; Dekker et al, 2012; Dlugos et al, 2009; Fatemi et al, 2001; Galeotti and Ghelardini, 2011; Gatt et al, 2015; Gray et al, 2015; Lee et al, 2010b; Liu et al, 2015; Luo et al, 2010; Ogawa and Kunugi, 2015; Ray et al, 2014; Rietschel et al, 2010; Sakaida et al, 2013; Shyn et al, 2011; Skoog et al, 2015; Stachowicz et al, 2015; Tadic et al, 2007; Unschuld et al, 2009; Wagner et al, 2015; Yoshimasu et al, 2015) for bioinformatics analysis.…”

Neuroproteomics: How Many Angels can be Identified in an Extract from the Head of a Pin?

“…Changes in gene expression and protein expression have long been linked to long-term synaptic plasticity. The work from Niere et al (10) in this issue demonstrates that inhibition of neuronal mTOR, the inactivation of which typically decreases overall protein synthesis, can also increase translation of specific proteins such as postsynaptic PARK7 that has been linked to Parkinson's disease. In this case, a proteomics study of normal synaptic functions provides insights on new roles for neurodegeneration-associated proteins.…”