Structural biology of ionotropic glutamate delta receptors and their crosstalk with metabotropic glutamate receptors.

Enigmatic orphan glutamate delta receptors (GluD) are one of the four classes of the ionotropic glutamate receptors (iGluRs) that play key roles in synaptic transmission and plasticity. While members of other iGluR families viz AMPA, NMDA, and kainate receptors are gated by glutamate, the GluD receptors neither bind glutamate nor evoke ligand-induced currents upon binding of glycine and D-serine. Thus, the GluD receptors were considered to function as structural proteins that facilitate the formation, maturation, and maintenance of synapses in the hippocampus and cerebellum. Recent work has revealed that GluD receptors have extensive crosstalk with metabotropic glutamate receptors (mGlus) and are also gated by their activation. The latest development of a novel optopharamcological tool and the cryoEM structures of GluD receptors would help define the molecular and chemical basis of the GluD receptor's role in synaptic physiology. This article is part of the special Issue on "Glutamate Receptors - Orphan iGluRs".

The architecture of GluD2 ionotropic delta glutamate receptor elucidated by cryo-EM.

GluD2 receptor belongs to the orphan delta family of glutamate receptor ion channels. These receptors play key roles in synaptogenesis and synaptic plasticity and are associated with multiple neuronal disorders like schizophrenia, autism spectrum disorder, cerebellar ataxia, intellectual disability, paraplegia, retinal dystrophy, etc. Despite the importance of these receptors in CNS, insights into full-length GluD2 receptor structure is missing till-date. Here we report cryo-electron microscopy structure of the rat GluD2 receptor in the presence of calcium ions and the ligand 7-chlorokynurenic acid, elucidating its 3D architecture. The structure reveals a non-swapped architecture at the extracellular amino-terminal (ATD), and ligand-binding domain (LBD) interface similar to that observed in GluD1; however, the organization and arrangement of the ATD and LBD domains in GluD2 are unique. While our results demonstrate that non-swapped architecture is conserved in the delta receptor family, they also highlight the differences that exist between the two member receptors; GluD1 and GluD2.

The structural bases for agonist diversity in an Arabidopsis thaliana glutamate receptor-like channel.

Arabidopsis thaliana glutamate receptor-like (GLR) channels are amino acid-gated ion channels involved in physiological processes including wound signaling, stomatal regulation, and pollen tube growth. Here, fluorescence microscopy and genetics were used to confirm the central role of GLR3.3 in the amino acid-elicited cytosolic Ca2+ increase in Arabidopsis seedling roots. To elucidate the binding properties of the receptor, we biochemically reconstituted the GLR3.3 ligand-binding domain (LBD) and analyzed its selectivity profile; our binding experiments revealed the LBD preference for l-Glu but also for sulfur-containing amino acids. Furthermore, we solved the crystal structures of the GLR3.3 LBD in complex with 4 different amino acid ligands, providing a rationale for how the LBD binding site evolved to accommodate diverse amino acids, thus laying the grounds for rational mutagenesis. Last, we inspected the structures of LBDs from nonplant species and generated homology models for other GLR isoforms. Our results establish that GLR3.3 is a receptor endowed with a unique amino acid ligand profile and provide a structural framework for engineering this and other GLR isoforms to investigate their physiology.

Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy.

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of >100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25-60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABAA receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions.SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows that inhibitory synapses contain uniform thin sheet-like postsynaptic densities (PSDs), while excitatory synapses contain previously known mesh-like PSDs. We discovered "discus-shaped" ellipsoidal synaptic vesicles, and their distributions along with regular spherical vesicles in synaptic types are characterized. High-resolution tomograms further allowed identification of putative neurotransmitter receptors and their heterogeneous interaction with synaptic scaffolding proteins. The specificity and resolution of our approach enables precise in situ analysis of ultrastructural organization underlying distinct synaptic functions.

Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation.

N-methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B receptor in the absence or presence of the GluN2B-specific allosteric modulator Ro 25-6981 (Ro), determined by cryogenic electron microscopy (cryo-EM). In the absence of Ro, the GluN2A and GluN2B amino-terminal domains (ATDs) adopt "closed" and "open" clefts, respectively. Upon binding Ro, the GluN2B ATD clamshell transitions from an open to a closed conformation. Consistent with a predominance of the GluN2A subunit in ion channel gating, the GluN2A subunit interacts more extensively with GluN1 subunits throughout the receptor, in comparison with the GluN2B subunit. Differences in the conformation of the pseudo-2-fold-related GluN1 subunits further reflect receptor asymmetry. The triheteromeric NMDAR structures provide the first view of the most common NMDA receptor assembly and show how incorporation of two different GluN2 subunits modifies receptor symmetry and subunit interactions, allowing each subunit to uniquely influence receptor structure and function, thus increasing receptor complexity.

Automatic cryo-EM particle selection for membrane proteins in spherical liposomes.

Random spherically constrained (RSC) single particle reconstruction is a method to obtain structures of membrane proteins embedded in lipid vesicles (liposomes). As in all single-particle cryo-EM methods, structure determination is greatly aided by reliable detection of protein "particles" in micrographs. After fitting and subtraction of the membrane density from a micrograph, normalized cross-correlation (NCC) and estimates of the particle signal amplitude are used to detect particles, using as references the projections of a 3D model. At each pixel position, the NCC is computed with only those references that are allowed by the geometric constraint of the particle's embedding in the spherical vesicle membrane. We describe an efficient algorithm for computing this position-dependent correlation, and demonstrate its application to selection of membrane-protein particles, GluA2 glutamate receptors, which present very different views from different projection directions.

Structure and mechanism of glutamate receptor ion channel assembly, activation and modulation.

Ionotropic glutamate receptors (iGluRs) are ligand gated ion channels that mediate excitatory synaptic transmission in the brain of vertebrates. A rapidly growing body of crystal structures for isolated iGluR extracellular domains, and more recently a full length AMPA receptor, combined with data from electrophysiological experiments and MD simulations, provides a framework that makes it possible to investigate the molecular basis for assembly, gating and modulation. These unprecedented advances in structural biology are constantly challenged by novel functional properties that emerge despite decades of functional analysis, and by a growing family of auxiliary proteins that modulate iGluR activity and assembly.

Drosophila neuroligin 1 promotes growth and postsynaptic differentiation at glutamatergic neuromuscular junctions.

Precise apposition of presynaptic and postsynaptic domains is a fundamental property of all neuronal circuits. Experiments in vitro suggest that Neuroligins and Neurexins function as key regulatory proteins in this process. In a genetic screen, we recovered several mutant alleles of Drosophila neuroligin 1 (dnlg1) that cause a severe reduction in bouton numbers at neuromuscular junctions (NMJs). In accord with reduced synapse numbers, these NMJs show reduced synaptic transmission. Moreover, lack of postsynaptic DNlg1 leads to deficits in the accumulation of postsynaptic glutamate receptors, scaffold proteins, and subsynaptic membranes, while increased DNlg1 triggers ectopic postsynaptic differentiation via its cytoplasmic domain. DNlg1 forms discrete clusters adjacent to postsynaptic densities. Formation of these clusters depends on presynaptic Drosophila Neurexin (DNrx). However, DNrx binding is not an absolute requirement for DNlg1 function. Instead, other signaling components are likely involved in DNlg1 transsynaptic functions, with essential interactions organized by the DNlg1 extracellular domain but also by the cytoplasmic domain.

Organization of the core structure of the postsynaptic density.

Much is known about the composition and function of the postsynaptic density (PSD), but less is known about its molecular organization. We use EM tomography to delineate the organization of PSDs at glutamatergic synapses in rat hippocampal cultures. The core of the PSD is dominated by vertically oriented filaments, and ImmunoGold labeling shows that PSD-95 is a component of these filaments. Vertical filaments contact two types of transmembrane structures whose sizes and positions match those of glutamate receptors and intermesh with two types of horizontally oriented filaments lying 10-20 nm from the postsynaptic membrane. The longer horizontal filaments link adjacent NMDAR-type structures, whereas the smaller filaments link both NMDA- and AMPAR-type structures. The orthogonal, interlinked scaffold of filaments at the core of the PSD provides a structural basis for understanding dynamic aspects of postsynaptic function.

High-resolution quantitative visualization of glutamate and GABA receptors at central synapses.

Glutamate and GABA are the main transmitters in the central nervous system and their effects are mediated by ionotropic and metabotropic receptors. Immunogold electron microscopy has revealed the quantitative localization of these receptors at 20-30nm resolution. SDS-digested freeze-fracture replica labeling (SDS-FRL), a newly developed immunogold method, provides an accurate estimate of molecule numbers. Here, we summarize the recent advances in quantitative receptor localization, including use of SDS-FRL analyses to determine numbers of AMPA-type glutamate receptors in the cerebellum. The two-dimensional view and high sensitivity of SDS-FRL have revealed small, irregularly shaped AMPA receptor clusters within cerebellar synapses.

Non-NMDA-type glutamate receptors are essential for maturation but not for initial assembly of synapses at Drosophila neuromuscular junctions.

The assembly of glutamatergic postsynaptic densities (PSDs) seems to involve the gradual recruitment of molecular components from diffuse cellular pools. Whether the glutamate receptors themselves are needed to instruct the structural and molecular assembly of the PSD has hardly been addressed. Here, we engineered Drosophila neuromuscular junctions (NMJs) to express none or only drastically reduced amounts of their postsynaptic non-NMDA-type glutamate receptors. At such NMJs, principal synapse formation proceeded and presynaptic active zones showed normal composition and ultrastructure as well as proper glutamate release. At the postsynaptic site, initial steps of molecular and structural assembly took place as well. However, growth of the nascent PSDs to mature size was inhibited, and proteins normally excluded from PSD membranes remained at these apparently immature sites. Intriguingly, synaptic transmission as well as glutamate binding to glutamate receptors appeared dispensable for synapse maturation. Thus, our data suggest that incorporation of non-NMDA-type glutamate receptors and likely their protein-protein interactions with additional PSD components triggers a conversion from an initial to a mature stage of PSD assembly.

Glutamate and GABA receptors and transporters in the basal ganglia: what does their subsynaptic localization reveal about their function?

GABA and glutamate, the main transmitters in the basal ganglia, exert their effects through ionotropic and metabotropic receptors. The dynamic activation of these receptors in response to released neurotransmitter depends, among other factors, on their precise localization in relation to corresponding synapses. The use of high resolution quantitative electron microscope immunocytochemical techniques has provided in-depth description of the subcellular and subsynaptic localization of these receptors in the CNS. In this article, we review recent findings on the ultrastructural localization of GABA and glutamate receptors and transporters in monkey and rat basal ganglia, at synaptic, extrasynaptic and presynaptic sites. The anatomical evidence supports numerous potential locations for receptor-neurotransmitter interactions, and raises important questions regarding mechanisms of activation and function of synaptic versus extrasynaptic receptors in the basal ganglia.

Ultrastructural quantification of glutamate receptors at excitatory synapses in hippocampus of synapsin I+II double knock-out mice.

Previous findings, mainly in in vitro systems, have shown that the density of vesicles and the synaptic efficacy at excitatory synapses are reduced in the absence of synapsins, despite the fact that transgenic mice lacking synapsins develop an epileptic phenotype. Here we study glutamate receptors by quantitative immunoblotting and by quantitative electron microscopic postembedding immunocytochemistry in hippocampus of perfusion fixed control wild type and double knock-out mice lacking synapsins I and II. In wild type hippocampus the densities of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunits were higher (indicated for glutamate receptor subunit 1, highly significant for glutamate receptor subunits 2/3) in mossy fiber-to-cornu ammonis 3 pyramidal cell synapses than in the Schaffer collateral/commissural-to-cornu ammonis 1 pyramidal cell synapses, the two synapse categories that carry the main excitatory throughput of the hippocampus. The opposite was true for N-methyl-D-aspartate receptors. The difference in localization of glutamate receptor subunit 1 receptor subunits was increased in the double knock-out mice while there was no change in the overall expression of the glutamate receptors in hippocampus as shown by quantitative Western blotting. The increased level of glutamate receptor subunit 1 at the mossy fiber-to-cornu ammonis 3 pyramidal cell synapse may result in alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors with reduced proportions of glutamate receptor subunit 2, and hence increased Ca2+ influx, which could cause increased excitability despite of impaired synaptic function (cf. [Krestel HE, Shimshek DR, Jensen V, Nevian T, Kim J, Geng Y, Bast T, Depaulis A, Schonig K, Schwenk F, Bujard H, Hvalby O, Sprengel R, Seeburg PH (2004) A genetic switch for epilepsy in adult mice. J Neurosci 24:10568-10578]), possibly underlying the seizure proneness in the synapsin double knock-out mice. In addition, the tendency to increased predominance of N-methyl-d-aspartate receptors at the main type of excitatory synapse onto cornu ammonis 1 pyramidal cells might contribute to the seizure susceptibility of the synapsin deficient mice. The results showed no significant changes in the proportion of 'silent' Schaffer collateral/commissural synapses lacking alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors or in the synaptic membrane size, indicating that plasticity involving these parameters is not preferentially triggered due to lack of synapsins.

Effects of electroacupuncture with different frequencies on spinal ionotropic glutamate receptor expression in complete Freund's adjuvant-injected rat.

We investigated expressional changes of spinal glutamate receptors by electroacupuncture (EA) in an inflammatory animal model. Inflammation was induced by an intraplantar injection of complete Freund's adjuvant (CFA) into the hindpaw of male Sprague-Dawley rats. Bilateral EA stimulation at 2, 15 and 120 Hz was applied at those acupoints corresponding to Zusanli and Sanyinjiao in man using needles with 3-day intervals for 30 days. Paw edema and mechanical thresholds were measured by a water displacement plethysmometer and Analgesy-Meter, respectively. Edema and mechanical sensitivity of the hindpaw induced by CFA-injection were strongly inhibited by EA stimulation. At 30 days after CFA-injection, effects of EA on ionotropic glutamate receptor (NR-1, NR-2A, GluR-1 and GluR-2/3) expression in association with c-fos and calcitonin gene-related peptide (CGRP) expression were observed in the dorsal horn of the spinal cord using immunohistochemistry. The number of c-fos-like immunostained cells was decreased significantly in the superficial laminae of the dorsal horn by 2Hz EA, but CGRP expression also showed a marked decrease in the same region using the other types of EA stimulation. N-methyl-D-aspartate receptor (NR-1 and NR-2A) expression was attenuated in all regions of the dorsal horn by all types of EA. Of the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor (GluR-1 and -2/3), only GluR-1 expression was prevented by EA treatment in the superficial laminae and the neck of the dorsal horn. It is concluded that EA treatment can attenuate inflammatory edema and mechanical thresholds in CFA-injected rats through modulating expression of ionotropic glutamate receptors, and especially N-methyl-D-aspartate receptors, in the dorsal horn of the spinal cord.

The Three-dimensional Structure of an Ionotropic Glutamate Receptor Reveals a Dimer-of-dimers Assembly.

The ionotropic glutamate receptors (iGluRs) represent a major family of ion channels whose quaternary structure has not yet been defined. Here, we present the three-dimensional structure of a fully assembled iGluR, determined at approximately 20A resolution by electron microscopy. Analysis of negatively stained single-particle images reveals the presence of 2-fold, but not 4-fold, symmetry for these tetrameric channels, providing the first direct structural evidence for a dimer-of-dimers assembly. The receptor appears elongated, measuring approximately 170Ax140Ax110A, with the 2-fold symmetry centered on its longitudinal axis. The overall molecular shape and symmetry suggest an orientation relative to the membrane and permit the identification of a putative transmembrane domain. Internal cavities located along the longitudinal axis may represent components of the ion conduction pathway.

Expression of zebrafish glutamate receptor delta2 in neurons with cerebellum-like wiring.

Mammalian glutamate receptor (GluR) delta2 is selectively expressed in cerebellar Purkinje cells and plays key roles in cerebellar plasticity, motor learning, and neural wiring. Here, we isolated cDNA encoding the zebrafish ortholog of mammalian GluRdelta2. We found that in adult zebrafish brain, glurdelta2 mRNA was expressed not only in cerebellar Purkinje cells, but also in the crest cells of the medial octavolateral nucleus (MON) and the type I neurons of the optic tectum. Immunohistochemical analysis revealed that zebrafish GluRdelta2 proteins were selectively localized in the apical dendrites of these neurons. Interestingly, the crest cells of the MON and the type I neurons of the optic tectum receive large numbers of parallel fiber inputs at the apical dendrites and sensory inputs at the proximal or basal dendrites. These results suggest that the expression of zebrafish GluRdelta2 is selective for cerebellum-like neural wiring with large numbers of parallel fiber inputs.

The postsynaptic scaffold proteins ProSAP1/Shank2 and Homer1 are associated with glutamate receptor complexes at rat retinal synapses.

The postsynaptic density (PSD) at glutamatergic synapses is a macromolecular complex of various molecules that organize the different glutamate receptors spatially and link them to their appropriate downstream signaling pathways and to the cytoskeleton. Recently, a new family of multidomain proteins called Shanks or ProSAPs (proline-rich synapse-associated proteins) has been identified. They are suggested to be central adaptor proteins of the PSD of glutamatergic synapses, bridging different types of glutamate receptor complexes. With immunocytochemistry and light and electron microscopy, we examined the cellular, synaptic, and postnatal developmental expression of ProSAP1/Shank2 at the synapses of rat retina. With double-labeling experiments and confocal microscopy, we analyzed the association of ProSAP1/Shank2 with proteins specific for glutamatergic, glycinergic, and gamma-aminobutyric acid (GABA)ergic synapses and with proteins known to be involved in the structural and functional organization of PSDs containing N-methyl-D-aspartate receptors [95-kDa postsynaptic density protein (PSD-95)], group I metabotropic glutamate receptors (Homer1), and alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors [glutamate receptor-interacting protein (GRIP)]. ProSAP1/Shank2 was present postsynaptically at the glutamatergic ribbon synapses of photoreceptor and bipolar cells, and it was absent from glycinergic and GABAergic amacrine cell synapses. The double-labeling experiments revealed a high rate of colocalization of ProSAP1/Shank2 with Homer1 and PSD-95, and little colocalization with GRIP. These data suggest that ProSAP1/Shank2 acts as an organizer at PSDs of different glutamatergic retinal synapses.

NCAM180 and glutamate receptor subtypes in potentiated spine synapses: an immunogold electron microscopic study.

Activity-dependent changes in expression and localization of the largest major isoform of the neural cell adhesion molecule NCAM180 and three subtypes of glutamate receptors predominantly expressed in the outer part of the molecular layer of the dentate gyrus of adult rats-the NMDA receptor NR2A, the AMPA receptor GluR2/3, and the metabotropic glutamate receptor mGluR1 - were investigated using postembedding immunogold labeling, and electron microscopy. In synaptic membranes of nonstimulated spine synapses, NCAM180 and NR2A accumulated in the center of the postsynaptic density, whereas GluR2/3 and mGluR1 were distributed evenly. Twenty-four hours following induction of long-term potentiation in vivo, NCAM180 and NR2A accumulated at the edges of postsynaptic densities, whereas GluR2/3 was localized more centrally. Also, the distribution of gold particles per synapse significantly changed for NCAM180, NR2A, and mGluR1. Thus, changes in synaptic strength are associated with concomitant changes in the expression and distribution of NCAM180 and glutamate receptors, particularly of the NR2A subtype.

Structure and molecular organization of dendritic spines.

Dendritic spines mediate most excitatory synapses in the CNS and are therefore likely to be of major importance for neural processing. We review the structural aspects of dendritic spines, with particular emphasis on recent advances in the characterization of their molecular components. Spine morphology is very diverse and spine size is correlated with the strength of the synaptic transmission. In addition, the spine neck biochemically isolates individual synapses. Therefore, spine morphology directly reflects its function. A large number of molecules have been described in spines, involving several biochemical families. Considering the small size of a spine, the variety of molecules found is astounding, suggesting that spines are paramount examples of biological nanotechnology. Single-molecular studies appear necessary for future progress. The purpose of this rich molecular diversity is still mysterious but endows synapses with a diverse and flexible biochemical machinery.