The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour

Abstract

Neuronal synapses play fundamental roles in information processing, behaviour and disease. Neurotransmitter receptor complexes, such as the mammalian N ‐methyl‐d‐aspartate receptor complex (NRC/MASC) comprising 186 proteins, are major components of the synapse proteome. Here we investigate the organisation and function of NRC/MASC using a systems biology approach. Systematic annotation showed that the complex contained proteins implicated in a wide range of cognitive processes, synaptic plasticity and psychiatric diseases. Protein domains were evolutionarily conserved from yeast, but enriched with signalling domains associated with the emergence of multicellularity. Mapping of protein–protein interactions to create a network representation of the complex revealed that simple principles underlie the functional organisation of both proteins and their clusters, with modularity reflecting functional specialisation. The known functional roles of NRC/MASC proteins suggest the complex co‐ordinates signalling to diverse effector pathways underlying neuronal plasticity. Importantly, using quantitative data from synaptic plasticity experiments, our model correctly predicts robustness to mutations and drug interference. These studies of synapse proteome organisation suggest that molecular networks with simple design principles underpin synaptic signalling properties with important roles in physiology, behaviour and disease. ### Synopsis We present an integrated analysis of molecular organisation, signal transduction, physiology and diseases of a neurotransmitter receptor signalling complex as a step toward synapse systems biology. We also present a new model for understanding the molecular complexity of the synapse proteome and its relationship to synapse physiology. Within the brain, neurons encode information as patterns of electrical activity in the form of action potentials. Communication between neurons occurs at specialised junctions (synapses), where information is transferred via chemical messengers (neurotransmitters). Neurotransmitters released from the presynaptic cell cross the synaptic cleft and bind to receptors embedded in the postsynaptic membrane. Different receptors play different roles: while AMPA receptors are responsible for the onward transmission of electrical signals, NMDA and metabotropic glutamate (mGluR) receptors process the information contained in patterns of neurotransmitter release, activating intracellular biochemical pathways that lead to changes in the properties of the neuron. Changes in synaptic properties in response to patterns of stimulation (experience), collectively known as synaptic plasticity, are commonly thought to form the basis of memory and learning. Receptors, signalling enzymes and scaffolding molecules are assembled into complexes embedded in the postsynaptic density (PSD), a dense layer of proteins associated with the intracellular surface of the postsynaptic membrane. Proteomic studies have identified over 1000 different proteins in the PSD, making it one of the most complex molecular structures known to cell biology ([Husi et al , 2000][1]; [Husi and Grant, 2001][2]; [Farr et al , 2004][3]; [Collins et al , 2005][4]). These studies have also shown that receptors associate with specific subclusters of the PSD. Of interest here, the NMDA and mGluR receptors are linked within large subcomplexes referred to as MASC (MAGUK‐Associated Signalling Complex) that comprise some 186 proteins. Given the fundamental role of the synapse in information processing, behaviour and disease, it is important to understand the functional organization of the PSD and the macromolecular complexes within it. As a first step towards unravelling the functional complexities of the synaptic proteome, we have made a detailed analysis of the MASC complex. Our approach consisted of three stages ([Figure 1][5]). The first stage, in which proteins present in the complex were isolated and identified, has been reported elsewhere ([Husi et al , 2000][1]; [Collins et al , 2005][4]). Briefly, the complexes were biochemically isolated from mouse brain and their protein composition identified using antibodies and mass spectrometry. Proteomic profiling was followed by systematic annotation, involving extensive literature searching and manual data curation. To investigate the involvement of proteins in biochemical pathways, they were annotated for structure and function. MASC proteins were highly enriched for domains associated with key elements of synaptic signalling such as calcium binding, scaffolding and phosphorylation. The functional roles of proteins reflected the presence of diverse signalling pathways, suggesting that these are co‐ordinated within the complex. To investigate the evolutionary conservation of MASC proteins, we searched for orthologues in yeast and fruit fly. While all protein families represented in the complex are evolutionarily conserved from yeast, most show significant expansion associated with the emergence of multicellularity. This clearly reflects specialisation of the complex for intercellular signalling. To evaluate the role of the complex in synaptic function, behaviour and disease, an array of phenotypic data was collated from the scientific literature. This comprised of physiological data obtained from rodent studies, where mutations or drugs that specifically interfere with a given protein were tested for their effects on synapse electrophysiology or behaviour. Reports on the involvement of specific molecules in human diseases were also collated. A complete summary of the curated information and its provenance is provided in the supplementary material, allowing verification and reuse by other studies. In total, almost a quarter of MASC proteins were known to be essential for normal synaptic plasticity, with approximately the same number involved in rodent behaviour. Nearly a third of MASC proteins were...