Building functional modules from molecular interactions

The main reaction pathways in the living cell are carried out by functional modules--namely, macromolecular machines with compact structure or ensembles that change their composition and/or organization during function. Modules define themselves by spatial sequestration, chemical specificity and a characteristic time domain within which their function proceeds. On receiving a specific input, modules go through functional cycles, with phases of increasing and decreasing complexity of molecular interactions. Here, we discuss how such modules are formed and the experimental and theoretical approaches that can be used to investigate them, using examples from polynucleotide-protein interactions, vesicle transport and signal transduction to illustrate the underlying principles. Further progress in this field, where systems biology and biochemistry meet, will depend on iterative validation of the experimental and theoretical approaches.     

Masters of manipulation: Viral modulation of the immunological synapse

In order to thrive, viruses have evolved to manipulate host cell machinery for their own benefit. One major obstacle faced by pathogens is the immunological synapse. To enable efficient replication and latency in immune cells, viruses have developed a range of strategies to manipulate cellular processes involved in immunological synapse formation to evade immune detection and control T‐cell activation. In vitro, viruses such as human immunodeficiency virus 1 and human T‐lymphotropic virus type 1 utilise structures known as virological synapses to aid transmission of viral particles from cell to cell in a process termed trans‐infection. The formation of the virological synapse provides a gateway for virus to be transferred between cells avoiding the extracellular space, preventing antibody neutralisation or recognition by complement. This review looks at how viruses are able to subvert intracellular signalling to modulate immune function to their advantage and explores the role synapse formation has in viral persistence and cell‐to‐cell transmission.     

Physiology and pathology of endosome-to-Golgi retrograde sorting

Bidirectional traffic between the Golgi apparatus and the endosomal system sustains the functions of the trans-Golgi network (TGN) in secretion and organelle biogenesis. Export of cargo from the TGN via anterograde trafficking pathways depletes the organelle of sorting receptors, processing proteases, SNARE molecules, and other factors, and these are subsequently retrieved from endosomes via the retrograde pathway. Recent studies indicate that retrograde trafficking is vital to early metazoan development, nutrient homeostasis, and for processes that protect against Alzheimer's and other neurological diseases.     

Neural substrates of memory: from synapse to system

One of the fundamental challenges of modern neuroscience is to understand how memories are acquired, stored, and retrieved by the brain. In the broadest terms, attempts to dissect memory can be broken down into four experimental disciplines: (1) identification of molecular components, (2) ex vivo and in vivo cellular analysis of neuronal function, (3) theoretical modeling approaches of neural systems, and (4) organismal-level behavioral analyses. Our objective here is to offer a conceptually unifying perspective and to discuss this perspective in relation to an experiment analysis of memory in Drosophila.     

Copper at synapse: Release,binding and modulation of neurotransmission

Over the last decade, a piece of the research studying copper role in biological systems was devoted to unravelling a still elusive, but extremely intriguing, aspect that is the involvement of copper in synaptic function. These studies were prompted to provide a rationale to the finding that copper is released in the synaptic cleft upon depolarization. The copper pump ATP7A, which mutations are responsible for diseases with a prominent neurodegenerative component, seems to play a pivotal role in the release of copper at synapses. Furthermore, it was found that, when in the synaptic cleft, copper can control, directly or indirectly, the activity of the neurotransmitter receptors (NMDA, AMPA, GABA, P2X receptors), thus affecting excitability. In turn, neurotransmission can affect copper trafficking and delivery in neuronal cells. Furthermore, it was reported that copper can also modulate synaptic vesicles trafficking and the interaction between proteins of the secretory pathways. Interestingly, proteins with a still unclear role in neuronal system though associated with the pathogenesis of neurodegenerative diseases (the amyloid precursor protein, APP, the prion protein, PrP, α-synuclein, α-syn) show copper-binding domains. They may act as copper buffer at synapses and participate in the interplay between copper and the neurotransmitters receptors.Given that copper dysmetabolism occurs in several diseases affecting central and peripheral nervous system, the findings on the contribution of copper in synaptic transmission, beside its more consolidate role as a neuronal enzymes cofactor, may open new insights for therapy interventions.     

Synapsins: from synapse to network hyperexcitability and epilepsy

The synapsin family in mammals consists of at least 10 isoforms encoded by three distinct genes and composed by a mosaic of conserved and variable domains. Synapsins, although not essential for the basic development and functioning of neuronal networks, are extremely important for the fine-tuning of SV cycling and neuronal plasticity.Single, double and triple synapsin knockout mice, with the notable exception of the synapsin III knockout mice, show a severe epileptic phenotype without gross alterations in brain morphology and connectivity. However, the molecular and physiological mechanisms underlying the pathogenesis of the epileptic phenotype observed in synapsin deficient mice are still far from being elucidated. In this review, we summarize the current knowledge about the role of synapsins in the regulation of network excitability and about the molecular mechanism leading to epileptic phenotype in mouse lines lacking one or more synapsin isoforms. The current evidences indicate that synapsins exert distinct roles in excitatory versus inhibitory synapses by differentially affecting crucial steps of presynaptic physiology and by this mean participate in the determination of network hyperexcitability.     

TorsinA and dystonia: from nuclear envelope to synapse

A GAG deletion in the DYT1 gene is responsible for the autosomal dominant movement disorder, early onset primary torsion dystonia, which is characterised by involuntary sustained muscle contractions and abnormal posturing of the limbs. The mutation leads to deletion of a single glutamate residue in the C-terminus of the protein torsinA, a member of the AAA+ ATPase family of proteins with multiple functions. Since no evidence of neurodegeneration has been found in DYT1 patients, the dystonic phenotype is likely to be the result of neuronal functional defect(s), the nature of which is only partially understood. Biochemical, structural and cell biological studies have been performed in order to characterise torsinA. These studies, together with the generation of several animal models, have contributed to identify cellular compartments and pathways, including the cytoskeleton and the nuclear envelope, the secretory pathway and the synaptic vesicle machinery where torsinA function may be crucial. However, the role of torsinA and the correlation between the dysfunction caused by the mutation and the dystonic phenotype remain unclear. This review provides an overview of the findings of the last ten years of research on torsinA, a critical evaluation of the different models proposed and insights towards future avenues of research.     

Activity-dependent switch from synapse formation to synapse elimination during development of neuromuscular junctions

The embryonic development of neuromuscular junctions consists of two successive epochs, an early period marked by exuberant synapse formation and a later period marked by synapse elimination. In the frog muscles we have studied, myogenesis is protracted and overlaps the periods of synapse formation and elimination. Thus, the formative and regressive events of synaptic development do not occur in synchrony across different fibers in the muscle. We propose that local activity orchestrates a shift from synaptogenesis to synapse elimination at the level of single muscle fibers. We also present evidence that perisynaptic Schwann cells and the expression of ion channels in the sarcolemma play important roles in the development of neuromuscular junctions. Questions for future study are outlined.     

Making space for rats: from synapse to place code

The formation of spatial memories is believed to depend on long-term potentiation (LTP) of synapses within the hippocampal network. In this issue of Neuron, Dragoi et al. demonstrate that LTP can cause changes in the hippocampal representation of space without disrupting network dynamics. These results help define the elusive relationship between cellular-level synaptic plasticity and systems-level neural coding.     

Connecting the dots: from actin polymerization to synapse formation

Protrusive behavior of dendritic spines on developing neurons has been previously suggested to mediate the formation of new axodendritic synaptic contacts. A study by Zito et al. in this issue of Neuron links actin polymerization in dendritic spines with the motility that the spines exhibit and the synapses that they form.     

P-glycoprotein-ATPase modulation: the molecular mechanisms

P-glycoprotein-ATPase is an efflux transporter of broad specificity that counteracts passive allocrit influx. Understanding the rate of allocrit transport therefore matters. Generally, the rates of allocrit transport and ATP hydrolysis decrease exponentially with increasing allocrit affinity to the transporter. Here we report unexpectedly strong down-modulation of the P-glycoprotein-ATPase by certain detergents. To elucidate the underlying mechanism, we chose 34 electrically neutral and cationic detergents with different hydrophobic and hydrophilic characteristics. Measurement of the P-glycoprotein-ATPase activity as a function of concentration showed that seven detergents activated the ATPase as expected, whereas 27 closely related detergents reduced it significantly. Assessment of the free energy of detergent partitioning into the lipid membrane and the free energy of detergent binding from the membrane to the transporter revealed that the ratio, q, of the two free energies of binding determined the rate of ATP hydrolysis. Neutral (cationic) detergents with a ratio of q = 2.7 ± 0.2 (q > 3) followed the aforementioned exponential dependence. Small deviations from the optimal ratio strongly reduced the rates of ATP hydrolysis and flopping, respectively, whereas larger deviations led to an absence of interaction with the transporter. P-glycoprotein-ATPase inhibition due to membrane disordering by detergents could be fully excluded using ²H-NMR-spectroscopy. Similar principles apply to modulating drugs.     

Plant apocarotenoids: from retrograde signaling to interspecific communication

Carotenoids are isoprenoid compounds synthesized by all photosynthetic and some non-photosynthetic organisms. They are essential for photosynthesis and contribute to many other aspects of a plant's life. The oxidative breakdown of carotenoids gives rise to the formation of a diverse family of essential metabolites called apocarotenoids. This metabolic process either takes place spontaneously through reactive oxygen species or is catalyzed by enzymes generally belonging to the CAROTENOID CLEAVAGE DIOXYGENASE family. Apocarotenoids include the phytohormones abscisic acid and strigolactones (SLs), signaling molecules and growth regulators. Abscisic acid and SLs are vital in regulating plant growth, development and stress response. SLs are also an essential component in plants’ rhizospheric communication with symbionts and parasites. Other apocarotenoid small molecules, such as blumenols, mycorradicins, zaxinone, anchorene, β-cyclocitral, β-cyclogeranic acid, β-ionone and loliolide, are involved in plant growth and development, and/or contribute to different processes, including arbuscular mycorrhiza symbiosis, abiotic stress response, plant–plant and plant–herbivore interactions and plastid retrograde signaling. There are also indications for the presence of structurally unidentified linear cis-carotene-derived apocarotenoids, which are presumed to modulate plastid biogenesis and leaf morphology, among other developmental processes. Here, we provide an overview on the biology of old, recently discovered and supposed plant apocarotenoid signaling molecules, describing their biosynthesis, developmental and physiological functions, and role as a messenger in plant communication.     

Signaling from synapse to nucleus: the logic behind the mechanisms

Signaling from synapse to nucleus is vital for activity-dependent control of neuronal gene expression and represents a sophisticated form of neural computation. The nature of specific signal initiators, nuclear translocators and effectors has become increasingly clear, and supports the idea that the nucleus is able to make sense of a surprising amount of fast synaptic information through intricate biochemical mechanisms. Information transfer to the nucleus can be conveyed by physical translocation of messengers at various stages within the multiple signal transduction cascades that are set in motion by a Ca(2+) rise near the surface membrane. The key role of synapse-to-nucleus signaling in circadian rhythms, long-term memory, and neuronal survival sheds light on the logical underpinning of these signaling mechanisms.     

Spermidine boosts autophagy to protect from synapse aging

All animals form memories to adapt their behavior in a context-dependent manner. With increasing age, however, forming new memories becomes less efficient. While synaptic plasticity promotes memory formation, the etiology of age-induced memory formation remained enigmatic. Previous work showed that simple feeding of polyamine spermidine protects from age-induced memory impairment in Drosophila. Most recent work now shows that spermidine operates directly at synapses, allowing for an autophagy-dependent homeostatic regulation of presynaptic specializations. How exactly autophagic regulations intersect with synaptic plasticity should be an interesting subject for future research.