Subunit-specific surface mobility of differentially labeled AMPA receptor subunits

Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Simple Summary

Common sole (Solea solea) is an important species for the aquaculture industry. Defects in pigmentation of the species are very common in farmed conditions. Differences in gene expression between normally pigmented juveniles and those that present both sides full pigmented, ocular and blind, were investigated. Differentially expressed transcripts were functionally annotated, and gene ontology was carried out. The results indicated that ambicolorated juveniles showed a significant upregulation of genes involved in the signal transmission at the synaptic level and regulation of ion channels, affecting the plasticity and the development of the synapses, as well as the transmission of signals or ions through channels.

Abstract

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.

Regulation of coenzyme A levels by degradation: the 'Ins and Outs'

Coenzyme A (CoA) is the predominant acyl carrier in mammalian cells and a cofactor that plays a key role in energy and lipid metabolism. CoA and its thioesters (acyl-CoAs) regulate a multitude of metabolic processes at different levels: as substrates, allosteric modulators, and via post-translational modification of histones and other non-histone proteins. Evidence is emerging that synthesis and degradation of CoA are regulated in a manner that enables metabolic flexibility in different subcellular compartments. Degradation of CoA occurs through distinct intra- and extracellular pathways that rely on the activity of specific hydrolases. The pantetheinase enzymes specifically hydrolyze pantetheine to cysteamine and pantothenate, the last step in the extracellular degradation pathway for CoA. This reaction releases pantothenate in the bloodstream, making this CoA precursor available for cellular uptake and de novo CoA synthesis. Intracellular degradation of CoA depends on specific mitochondrial and peroxisomal Nudix hydrolases. These enzymes are also active against a subset of acyl-CoAs and play a key role in the regulation of subcellular (acyl-)CoA pools and CoA-dependent metabolic reactions. The evidence currently available indicates that the extracellular and intracellular (acyl-)CoA degradation pathways are regulated in a coordinated and opposite manner by the nutritional state and maximize the changes in the total intracellular CoA levels that support the metabolic switch between fed and fasted states in organs like the liver. The objective of this review is to update the contribution of these pathways to the regulation of metabolism, physiology and pathology and to highlight the many questions that remain open.

The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life

Covering: up to 2013. Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from identification, characterization, structure determination, mutagenesis, inhibition, and engineering in synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of enzymes that post-translationally install a 4'-phosphopantetheine arm on various carrier proteins.

Integrated electroosmotic perfusion of tissue with online microfluidic analysis to track the metabolism of cystamine, pantethine, and coenzyme A

We have developed an approach that integrates electroosmotic perfusion of tissue with a substrate-containing solution and online microfluidic analysis of products, in this case thiols. Using this approach we have tracked the metabolism of cystamine, pantethine and CoA in the extracellular space of organotypic hippocampal slice cultures (OHSCs). Currently, little is known about coenzyme A (CoA) biodegradation and even less is known about the regulation and kinetic characteristics for this sequential multienzyme reaction. We found that the steady state percentage yields of cysteamine from cystamine and pantethine during the transit through OHSCs were 91% ± 4% (SEM) and 0.01%-0.03%, respectively. The large difference in the yields of cysteamine can be used to explain the drugs' different toxicities and clinical effectiveness against cystinosis. The kinetic parameters of the enzyme reaction catalyzed by the ectoenzyme pantetheinase are KM,C/α = 4.4 ± 1.1 mM and Vmax,C = 29 ± 3 nM/s, where α is the percentage yield of pantethine to pantetheine through disulfide exchange. We estimate that the percentage yield of pantethine to pantetheine through disulfide exchange is approximately 0.5%. Based on the formation rate of cysteamine in the OHSCs, we obtained the overall apparent Michaelis constant and maximum reaction rate for sequential, extracellular CoA degradation in an in situ environment, which are K'M = 16 ± 4 μM, V'max = 7.1 ± 0.5 nM/s. Kinetic parameters obtained in situ, although difficult to measure, are better representations of the biochemical flux in the living organism than those from isolated enzymes in vitro.

Phosphorylation and assembly of glutamate receptors after brain ischemia

BACKGROUND AND PURPOSE

Overassembly of synaptic glutamate receptors leads to excitotoxicity. The goal of this study is to investigate phosphorylation and assembly of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid and N-methyl-D-aspartate receptors after brain ischemia with reperfusion (I/R).

METHODS

Rats were subjected to 15 minutes of global ischemia followed by 0.5, 4, and 24 hours of reperfusion. Phosphotyrosine peptides of glutamate receptors in synaptosomal fraction after I/R were identified and quantified by state-of-the-art immuno-affinity purification of phosphotyrosine peptides followed by liquid chromatography/mass spectrometry/mass spectrometry analysis (immunoaffinity purification-coupled liquid chromatography/mass spectrometry/mass spectrometry). Glutamate receptor phosphorylation and synaptic assembly after I/R were studied by biochemical methods.

RESULTS

Numerous phosphotyrosine-sites of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid and N-methyl-D-aspartate were upregulated by approximately 2- to 37-fold after I/R. A core glutamate receptor kinase, Src kinase, was significantly activated. GluR2/3 and NR2A/B were rapidly clustered from extrasynaptic to synaptic membrane fractions after I/R. GluR2/3 was then translocated into the intracellular pool, whereas NR2A/B remained in the synaptic fraction for as long as 24 hours. Consistently, trafficking-related phosphorylation of GluR2/3-S880 was significantly but transiently upregulated, whereas NR2A/B-Y1246 and NR2A/B-Y1472 were significantly and persistently upregulated after I/R.

CONCLUSIONS

Phosphorylation of glutamate receptors at synapses may lead to overassembly of glutamate receptors, probably via activation of Src family kinases, after I/R. This study provides global proteomic information about glutamate receptor tyrosine phosphorylation after brain ischemia.

Neurexin-neuroligin adhesions capture surface-diffusing AMPA receptors through PSD-95 scaffolds

The mechanisms governing the recruitment of functional glutamate receptors at nascent excitatory postsynapses following initial axon-dendrite contact remain unclear. We examined here the ability of neurexin/neuroligin adhesions to mobilize AMPA-type glutamate receptors (AMPARs) at postsynapses through a diffusion/trap process involving the scaffold molecule PSD-95. Using single nanoparticle tracking in primary rat and mouse hippocampal neurons overexpressing or lacking neuroligin-1 (Nlg1), a striking inverse correlation was found between AMPAR diffusion and Nlg1 expression level. The use of Nlg1 mutants and inhibitory RNAs against PSD-95 demonstrated that this effect depended on intact Nlg1/PSD-95 interactions. Furthermore, functional AMPARs were recruited within 1 h at nascent Nlg1/PSD-95 clusters assembled by neurexin-1β multimers, a process requiring AMPAR membrane diffusion. Triggering novel neurexin/neuroligin adhesions also caused a depletion of PSD-95 from native synapses and a drop in AMPAR miniature EPSCs, indicating a competitive mechanism. Finally, both AMPAR level at synapses and AMPAR-dependent synaptic transmission were diminished in hippocampal slices from newborn Nlg1 knock-out mice, confirming an important role of Nlg1 in driving AMPARs to nascent synapses. Together, these data reveal a mechanism by which membrane-diffusing AMPARs can be rapidly trapped at PSD-95 scaffolds assembled at nascent neurexin/neuroligin adhesions, in competition with existing synapses.

Regulation of AMPA receptor surface diffusion by PSD-95 slots

Excitatory synaptic transmission is largely mediated by AMPA receptors (AMPARs) present at the postsynaptic density. Recent studies in single molecule tracking of AMPAR has revealed that extrasynaptic AMPARs are highly mobile and thus might serve as a readily available pool for their synaptic recruitment during synaptic plasticity events such as long-term potentiation (LTP). Because this hypothesis relies on the cell's ability to increase the number of diffusional traps or 'slots' at synapses during LTP, we will review a number of protein-protein interactions that might impact AMPARs lateral diffusion and thus potentially serve as slots. Recent studies have identified the interaction between the AMPAR-Stargazin complex and PSD-95 as the minimal components of the diffusional trapping slot. We will overview the molecular basis of this critical interaction, its activity-dependent regulation and its potential contribution to LTP.

How to obtain labeled proteins and what to do with them

We review new and established methods for the chemical modification of proteins in living cells and highlight recent applications. The review focuses on tag-mediated protein labeling methods, such as the tetracysteine tag and SNAP-tag, and new developments in this field such as intracellular labeling with lipoic acid ligase. Recent promising advances in the incorporation of unnatural amino acids into proteins are also briefly discussed. We describe new tools using tag-mediated labeling methods including the super-resolution microscopy of tagged proteins, the study of the interactions of proteins and protein domains, the subcellular targeting of synthetic ion sensors, and the generation of new semisynthetic metabolite sensors. We conclude with a view on necessary future developments, with one example being the selective labeling of non-tagged, native proteins in complex protein mixtures.

Covalent quantum dot receptor linkage via the acyl carrier protein for single-molecule tracking, internalization, and trafficking studies

Here we describe a labeling technique for the covalent linkage of quantum dots to transmembrane receptors for single-molecule tracking. Our method combines the acyl carrier protein (ACP) technique with coenzyme A (CoA)—functionalized quantum dots to covalently attach quantum dots to ACP fusions of receptor proteins. The advantages of this approach include: (i) the use of a smaller attachment linker than in many other quantum dot—labeling systems; (ii) the ability to achieve a reliable 1:1 fluorophore-to-receptor labeling stoichiometry; (iii) the specificity of the method; and (iv) the covalent nature of the quantum dot linkage. We demonstrate the general suitability of this technique in single-molecule tracking, internalization, and trafficking studies by imaging two different transmembrane receptors in living cells.

GluR2/3 label expression of the AMPA-type glutamate receptor in the hippocampal formation of the homing pigeon stabilizes just after birth

The compositions of the glutamate AMPA-type receptors influence the neural response and the subunits GluR2/3 has been referred to as essential for receptor trafficking and synapse consolidation. We investigate the GluR2/3 occurrence and expression in the hippocampal formation of newly born homing pigeons by a semi-quantitative approach, the Western-blotting technique and by immunohistochemistry. Immunoreactivity for GluR2/3 occurs before hatching has been evident in neuropil that was fully dispersed over the hippocampus proper (HP) and the area parahippocampalis (APH). Although many HP cells are NeuN-positives, a specific neuronal protein indicating that they are already differentiated as neurons while not one contains GluR2/3 at the hatching day (P0). Few neurons at the APH seem to express GluR2/3 at P0, but 3 days later (P3) the GluR2/3 labeling can be recognized in many HP neurons, showing a distribution pattern that resembles the adult, gradually increasing in intensity until P10. Also, the Western-blot shows an augment between P0 and P3, remaining stable after that. The enhancement of the neuronal label at P3 coincides with the retraction of the GluR2/3 label in neuropil, reducing their occurrence during the maturational period to become restricted to the dorsomedial portion as reported for adults. As the HP GluR2/3-containing cells are supposedly projecting neurons, taking together, the results signalize the relevance of the GluR2/3 in post-hatch formation of avian hippocampal circuitry in which the third day seems to be the critical period.