Editorial overview: Molecular neuroscience

Neuroscience as a field tries to understand the mechanistic principles by which the nervous system can carry out its complex sets of tasks. Individual neurons, of which ~80 billion collectively make up the central nervous system in a human, are unlike most cells of the body. Most live for the lifespan of the animal without dividing, extend their axons over distances from 50 to 1000 times the diameter of the cell body where they will form synaptic contacts with between 1000 and 10 000 other neurons and receive inputs from as many other cells that form synaptic contacts along their dendritic tree, cell soma and axon. Additionally, neurons interact closely with glial cells and form an essential partnership with these cells throughout the lifespan of the animal. The molecular basis of how the cellular biochemistry is harnessed to allow neurons to grown, communicate, renew their machinery, respond to appropriate cues and dispose of the machinery at the end of its lifespan are all frontier topics in molecular neuroscience. Molecular neuroscience got its start with traditional biochemical purification approaches, but over fifty years ago molecular genetics vastly expanded the repertoire of genes identified to be critical for nervous system function. Today new clues often emerge from human genetics as links between neurological disorders and genetic mutations reveal our many gaps in fundamental understanding of biological processes within neurons and glia.

This issue brings together reviews that span a gamut of cutting-edge topics in molecular neuroscience. Details of the functioning of critical machinery at synapses, how synapses are guided to form at the correct time and place, how proteins are locally synthesized and when they turnover, how entire organelles are maintained are a few of the topics that are crucial to how the nervous system survives and are discussed in the reviews below.

How neurons form synapses with the correct partners and how synapses are maintained throughout lifetime of an organism remain the long-standing questions. Synaptogenesis is a multi-step process, leading to the establishment of synaptic vesicle release machinery on the presynaptic side, clustering of neurotransmitter receptors and signal transduction machinery on the postsynaptic side, and precise registration of the two subcellular specifications across the synaptic cleft, a specialized extracellular matrix made of molecules secreted from glia, neurons or other cells. In the absence of synaptic partners, each specialization has the intrinsic capacity to assemble morphological rudimentary structures. Which side initiates synaptic cross-talk in vivo depends on the neuronal types and specific synapses. Cell-surface proteins, such as neurexin and neuroligins, and secreted proteins, such as laminins, have long been studied for their roles in specifying synaptic connectivity. Four reviews in this series cover recent advance in understanding the molecular complexity of synaptogenetsis and synapse maintenance, and present complementary insights on the same molecule in distinct neuronal circuits and from different model organisms. Kurshan and Shen emphasize the progress on the molecular composition and dynamics in pre-synaptic and post-synaptic compartments, and highlight the roles of γ-neurexin, a newly discovered short and conserved isoform of neurexin, in synapse formation in Caenorhabditis elegans. This γ-neurexin lacks trans-synaptic binding domains, and is capable to amplify presynaptic assembly pathways through its intracellular PDZ-binding motif. Apóstolo and de Wit cover new findings revealing the compartmentalized distribution and function of various cell surface molecules in mammalian brain. They further discuss how numerous glial-derive factors interact with neuronal cell surface proteins, and how secreted proteins, such as complement proteins C1ql2 and C1ql3, modulate excitatory synapse connections and function. Sakers and Eroglu focus on the neuroligin protein family, which are ligands for neurexins and were previously thought to be only produced from neurons and reside in postsynaptic compartment. However, a series of recent papers have demonstrated that astrocytes produce neuroligin 2 and that the glial produced neuroligins not only regulate synaptogenesis and synapse transmission but also contribute to disease pathogenesis and glioma. Lastly, Connor et al. provide a comprehensive review on how the vertebrate-specific immunoglobulin superfamily proteins known as MDGAs interact with neuroligins to suppress synapse development. MDGAs are tethered to the membrane through a GPI anchor, and MDGA–neuroligin interactions occlude neuroligin–neurexin binding. As accumulating evidence links mutations in these molecules to various neurodevelopmental and neuropsychiatric disorders, these reviews are timely and point to many questions for future investigation.

Among all types of cells within an organism, neurons display most exquisite complexity not only in cellular morphology but also compartmentalized proteomes. The microtubule cytoskeleton sculpts neuronal structure and mediates the transport of vesicles, proteins, RNAs, and organelles that sustain neuronal activity. While the molecular constitutes of microtubules are seemingly simple and many in vitro reconstitution assays are well established for quantitative measurement of microtubule-mediated functions, a central challenge remains to translate the biochemically defined activity of many microtubule-associated-proteins (MAPs), such as motor proteins, into understanding their function and regulation in neurons in vivo. For example, microtubules in axons and dendrites are distinguished by their polarity, organization, posttranslational modifications (PTM), and microtubule-binding proteins. Kelliher et al. review how microtubule function in neuronal activity is locally controlled by different PTM patterns, such as the acetylation of a-tubulin lysine 40 in mechanosensation and axono-morphogenesis and dendrito-morphogenesis. Vanhauwaert et al. cover recent findings on mitochondria transport in neurons, which is dependent on microtubules. Falk et al. highlight many roles of the GTP-binding Septin proteins. Originally discovered in yeast for their roles in cytokinesis, Septins can oligomerize in proto-filaments and can associate with membranes and also with microtubules and actin cytoskeletons. In higher mammals Septins include >10 genes, many of which are now shown to be important for neuronal development, maintenance and function, leading to the proposal that combinations of different Septin complexes, or ‘dynamic Septin code’, could enable simultaneous morphological remodelling at distinct locations within a single neuron. Moreover, mis-regulation of Septins is likely linked to autism and schizophrenia (also see Caldeira et al.) Thus, understanding of how Septin codes could switch from long-lasting structures to plastic state will be an important to the diversity of neuronal morphologies.

The vast majority of neurons and their synapses must sustain their function over the lifetime of an animal, therefore, neuronal and synaptic proteins need to be continually replaced. A quantitative understanding of neuronal proteome, especially those providing compartmental specificity, is necessary for understanding the metabolic load imposed on neurons to sustain synaptic protein homeostasis. Cohen and Ziv review the approaches that have been used to measure neuronal and synaptic protein lifetimes. Metabolic labeling using SILAC (Stable Isotope Labeling with Amino acids) and mass-spectrometry enables measurement of protein half-life, and newly synthesized proteins can be measured with BONCAT (biorthogonal noncanonical amino acid tagging). Cumulated data show that neuronal and synaptic proteins have unusually long half-lifetimes, typically on the order of days to weeks, and even longer. Long-lived proteins include histones, mitochondrial, nuclear pore, myelin-associated, and extracellular matrix proteins; short-lived proteins tend to include proteins related to nucleic acid processing, membrane-associated proteins, secreted proteins, signaling proteins, and chaperones. Synaptic proteins might be selectively stabilized at synapses, yet, half-lives of specific proteins belonging to the same complexes can deviate significantly. Lysosomal-mediate protein degradation is a major cellular pathway regulating protein turnover Boecker and Holtzbaur review how autophagy and endo-lysosomal degradation, both converging at the point of cargo delivery to lysosomes, regulate vesicular protein turnover, and highlight specific protein targets of bulk autophagy and selective autophagy in axons, dendrites, and pre-synaptic and post-synaptic compartments. Vanhauwaert et al. offer additional insights on protein turnover control in quality control of mitochondria.

Although our understanding of the biochemical under-pinnings of synapse function has made significant strides, detailed mechanistic understanding of the biochemical machinery remains at the frontier of molecular neuroscience. As chemical synaptic transmission is usually triggered by an abrupt change in local membrane potential, the details of how different ion channels sculpt the action potential as it travels down the axon is an exciting new area reviewed by Alpazar et al. Unc13, a protein discovered in the original and most powerful genetic screen in C. elegans, is crucial for all known forms of chemical synaptic transmission. Dittman reviews the many mysteries that have emerged in understanding exactly how this protein controls the exocytic protein machinery. Of the many types of neurotransmitter used in the brain, dopamine has a privileged role, particularly in the striatum. The machineries responsible for controlling dopamine secretion is reviewed by Liu and Kaeser. The conversion of the secreted chemical signal back into an electrical one is carried out in dendrites. The initial detection of a given neurotransmitter on the postsynaptic dendrite is usually handled by ionotropic receptors, assembled into complexes that determine the precise localization and turnover of these ion channels. Tomita reviews what is currently understood regarding GABA receptor assemblies and how this impacts function. For excitatory transmission the depolarization of the dendritic membrane often triggers Ca²⁺ entry through voltage-gated Ca²⁺ channels. Sather and Ditmer discuss how these channels are also controlled by the endoplasmic reticulum in dendrites through novel regulator processes. Understanding mal-adaptive changes in synapse function in response to chronic exposure to drugs of abuse has been an important goal that lies at the intersection of synapse biology and addiction research. Stellwagen et al. review the new appreciation for astrocytes and microglia in contributing to adaptive and mal-adaptive responses. Recently the concept of ‘membrane-less’ organelles has emerged in many areas of cell biology, where protein assemblies can be driven by numerous weak multi-valent interactions through intrinsically disordered protein domains. Feng et al. review evidence for the presence of these novel protein-phases in both the pre-synaptic and post-synaptic compartments. A key but relatively recently appreciated aspect of synapse function is the constant need for fuel to keep the machinery running. Rossi and Pekkurnaz review how mitochondria at synapses are able to change their behavior in response to changes in energetic requirements.

Expansive data from single-cell sequencing and neuronal type and compartmental proteomic studies indicates that neuronal identity is strongly linked to its pattern of connectivity. The roles of local protein synthesis have been continuously examined as technology improves in detection sensitivity and specificity. The use of RiboTag mouse, combined with ribosome profiling, is powerful in identifying in vivo local transcriptome. mRNAs encoding a number of transmembrane proteins, including ion channels, are found within the presynaptic transcriptome and protein translation machinery is present in mature axons. Biever et al. review recent evidence supporting presynaptic translation and intra-axonal synthesis of transmembrane proteins. The complexity of localized translational control lies in the dynamic interaction between regulatory elements embedded in the transcript and a rich toolbox of transacting factors, including translational machinery components, RNA binding proteins and miRNAs. Heterogenity of ribosomes may underlie compartmental-specific local translation. Improvements in imaging technology has enabled tracking of mRNPs, which are made of higher-order assemblies of RNAs and proteins with unprecedented temporal resolution Das et al. review both visualization and bioinformatic methodologies for analyzing neuronal mRNPs. For example, an algorithm based on Bayesian model selection and Hidden single-molecule detection Markov Modeling helps to characterize the transient transition states of individual mRNA transporting granules, and captures the real-time dynamics of protein synthesis in living neurons. Current studies demonstrate that composition of mRNPs is dynamic across space and time. The generation of new reagents, such as transgenic mice expressing PP7 stem-loops knocked-in to the 3′UTR of the activity-regulated gene Arc, offers a promising tool to address in vivo how neuronal activity regulates local proteomes. The main action in the generation of neuronal proteome diversity remains in the nucleus. Soto and Lipscombe review recently publications on the cellular mechanisms that regulate alternative splicing, highlighting the specific action of select RNA splicing factors in regulating neuronal membrane protein isoforms. They also discuss how the mechanistic dissection of the SMN (Survival of Motor Neuron) protein in alternative splicing leads to the development of therapeutic strategies in treating human patients.

Throughout the lifetime, neurons need to protect themselves from acute damage and chronic stress or disease, and fight against cellular destruction. Ding and Hammarlund highlight the recent findings on injury induced-axon degeneration, focusing on the signaling network involving the axon survival factors NMNAT2. Emerging studies from C. elegans also uncover a unique form of axon degeneration, due to absence of mitochondria. Vanhauwaert et al. also cover how quality control of mitochondria is linked to chronic neurodegeneration in mammals. All together, these studies point to critical understanding of energy regulation and cytoskeleton integrity to be key steps in protecting damaged axons and stressed neurons from self-destruction. The theme of dysregulation of neuronal proteins in human diseases is further stressed in the review by Caldeira et al. Additionally, emerging evidence for non-coding RNAs points to their powers in tuning neuronal network, and mis-regulation of network activity contributes to neuropsychiatric disorders, as reviewed in Zampa et al. The brain is intimately involved in correct regulation of all of the body’s vital organs through an constant exchange of information informing on critical physiological parameters like blood pressure and fluid balances. In some cases dedicated neuronal circuits play a key role in determining vital parameters such as thirst and satiety as discussed by Ichiki et al. One critical interface between the brain and the rest of the body is the blood-brain barrier formed by specialized endothelial cells whose cell biology controls the detailed exchange of macromolecules into and out of the cerebrospinal fluids. Ayloo and Gu discuss recent progress in showing the critical importance of transcytosis across this epithelium and how it is regulated.

The set of reviews encompassed in this issue exemplifies how molecular neuroscience spans a wide set of problems from atomic level resolution of protein function to who animal physiology.