The evolutionary divergence of neurotransmitter receptors and second-messenger pathways

Members of the superfamily of G-protein-coupled neurotransmitter receptors have a conserved secondary structure, a moderate and reasonably steady rate of sequence change, and usually lack introns within the coding sequence. These properties are advantageous for evolutionary studies. The duplication and divergence of the genes in this gene family led to the formation of distinct neurotransmitter pathways and may have facilitated the evolution of complex nervous systems. I have analyzed this evolutionary divergence by quantitative multiple sequence alignment, bootstrap resampling, and statistical analysis of 49 adrenergic, muscarinic cholinergic, dopamine, and octopamine receptor sequences from 12 animal species. The results indicate that the first event to occur within this gene family was the divergence of the catecholamine receptors from the muscarinic acetylcholine receptors, which occurred prior to the divergence of the arthropod and vertebrate lineages. Subsequently, the ability to activate specific second-messenger pathways diverged independently in both the muscarinic and the catecholamine receptors. This appears to have occurred after the divergence of the arthropod and vertebrate lineages but before the divergence of the avian and mammalian lineages. However, the second-messenger pathways activated by adrenergic and dopamine receptors did not diverge independently. Rather, the ability of the catecholamine receptors to bind to specific ligands, such as epinephrine, norepinephrine, dopamine, or octopamine, was repeatedly modified in evolutionary history, and in some cases was modified after the divergence of the second-messenger pathways.     

A communication network within the cytoplasmic domain of toll-like receptors has remained conserved during evolution

Toll/IL-1R (TIR) domain, that is, the cytoplasmic domain, in toll-like receptors (TLRs) from different species showed high sequence conservation in stretches spread across the surface as well as the core of the domain. To probe the structure–function significance of these residues, especially those coming from the core of TIR domains, we analyzed molecular dynamics trajectories of sequence similarity based models of human TIR domains. This study brought forth that N-terminal of the TIR domain simultaneously interacts with the flanking residues of the BB loop and central β-sheets. At the same time, residues of the central β-strands form favorable contacts with the DD loop and C-terminal, thus forming a two-way circuit between the N- and C-termini. In this work, the array of intradomain interactions is termed as communication network. Importantly, the “hubs” of this communication network were found to be conserved in all human TLRs. Earlier mutagenesis–function correlation work brought forth that certain mutations in the “core” of the TIR domain of TLR4 (e.g. in IFI767–769AAA and L815A) led to almost complete abrogation of signaling and reasoning for this dramatic loss-of-function has remained unclear, since these sites are not surface exposed. Using MD studies, we show here that this communication network gets disrupted in mutants of human TLR4 which were earlier reported to be functionally compromised. Extension of MD studies to heterodimer of TLR1/2 suggested that this evolutionarily conserved communication network senses the interactions formed upon dimerization and relays it to surfaces which are not involved in direct interdomain contacts.     

Targeted trafficking of neurotransmitter receptors to synaptic sites

Emerging data are sheding light on the critical task for synapses to locally control the production of neurotransmitter receptors ultimately leading to receptor accumulation and modulation at postsynaptic sites. By analogy with the epithelial-cell paradigm, the postsynaptic compartment may be regarded as a polarized domain favoring the selective recruitment and retention of newly delivered receptors at synaptic sites. Targeted delivery of receptors to synaptic sites is facilitated by a local organization of the exocytic pathway, likely resulting from spatial cues triggered by the nerve. This review focuses on the various mechanisms responsible for regulation of receptor assembly and trafficking. A particular emphasis is given to the role of synaptic anchoring and scaffolding proteins in the sorting and routing of their receptor companion along the exocytic pathway. Other cellular components such as lipidic microdomains, the docking and fusion machinery, and the cytoskeleton also contribute to the dynamics of receptor trafficking at the synapse.     

突触前代谢型谷氨酸受体调节神经递质的释放

谷氨酸通过激活离子型受体（iGluR)介导快速兴奋性突触传递,参与脑内几乎所有生理过程。谷氨酸过量释放可导致与脑缺血,缺氧及变性疾病有关的兴奋毒作用,最终引起神经元的死亡。代谢型谷氨酸受体（mGluRs)是一个与G－蛋白偶联的受体家族,分三型共八个亚型。其中Ⅱ和Ⅲ型mGluRs主要位于突触前,发挥对谷氨酸释放的负反馈调节。Ⅲ型mGluRs中的mGluR7位于谷氨酸能末梢突触前膜的活性区,发挥自身受体的作用,对正常情况下突触传递过程的谷氨酸释放进行负反馈调节;而属于Ⅱ型的mGluR2及属于Ⅲ型的mGluR4和mGluR8,则位于远离突有膜活性区的外突触区,因而正常突触传递过程中释放的谷氨酸量不能激活它们。只有在突触传递增强的情况下才被激活,抑制递质的释放。国外,mGluRs还分布在GABA能纤维末梢,通过突触前机制抑制GABA的释放。对突触前膜受体尤其是位于外突触区的mGluRs受体的研究,将有可能开发出理想的工具药,从而预防和阻止谷氨酸过量释放引起的神经毒及神经元的死亡。     

Rapid chemical reaction techniques developed for use in investigations of membrane-bound proteins (neurotransmitter receptors)

New techniques for investigating chemical reactions on cell surfaces in the microsecond-to-millisecond time region are described. Reactions mediated by membrane-bound neurotransmitter receptors that control signal transmission between 10¹² cells of the nervous system are taken as an example. Cells with receptors on their plasma membrane are equilibrated with photolabile, biologically inactive precursors of the neurotransmitters. Photolysis of these compounds releases free neurotransmitter that interacts with the receptors, leading to the transient opening of transmembrane receptor-formed channels that are permeant to small inorganic ions. The current thus induced can be measured. The technique can be used to measure the elementary steps of the receptor-mediated reactions. To illustrate the approach it was shown that an understanding of the mechanism of inhibition of the nicotinic acetylcholine receptor by the drug cocaine was obtained and led to the first proof that compounds exist that alleviate the inhibition.     

Autoantibodies and monoclonal antibodies in the purification and molecular characterization of neurotransmitter receptors

The combination of immunological advances with membrane receptor research has promoted rapid progress in the molecular characterization of neurotransmitter receptor molecules. We have to date produced monoclonal antibodies to β₁-, β₂-, and β₁-adrenergic, D₂-dopaminergic, and muscarinic receptors. In addition we have discovered that some allergic respiratory disease patients possess circulating autoantibodies to β₂-adrenergic receptors. These antireceptor antibodies in conjunction with specific receptor affinity reagents have allowed us to isolate, purify, and begin to characterize α- and β-adrenergic, dopaminergic, and muscarinic receptors. For example, immunoprecipitation of turkey erythrocyte β₁ receptors with monoclonal antibodies yields a single polypeptide M_r 65–70 K. In contrast, purification of β₂-adrenergic receptors using either autoantibodies or monoclonal antibodies yields a receptor species with a subunit of M_r 55–59 K. Autoantibodies to β₂ receptors demonstrate a 50–100% homology among β₂ receptors from humans to rats, whereas monoclonal antibody FV-104 recognizes a determinant in the ligand binding site of all β₁ and β₂ receptors tested to date. These data suggest that β₁- and β₂-adrenergic receptors may have evolved from a common ancestor, perhaps by gene duplication.     

A comparative computational analysis of protein sequences and literature mining classify 'orphan' neurotransmitter transporters

Various sources of protein data, such as knowledgebases and scientific literature, are currently available, as are numerous tools for their analysis. The matter becomes one of choosing the tools that are most appropriate for the specific task and for the specific proteins. A combination of standard and alternative tools may lead to biologically significant results.Here, a computational classification of proteins is made using standard multiple sequence alignment in combination with an alternative method for analysis of hydropathy distribution in proteins. Both of these methods are applied to the Na⁺/Cl⁻-dependent neurotransmitter symporters (NSSs), resulting in two alternative classifications. The classifications are validated and interpreted biologically by literature and knowledgebase annotation mining, producing a consensus classification. The classification leads to the identification and functional characterization of three families of largely structurally and functionally uncharacterized orphan NSSs. The literature and knowledgebase annotations are mined to functionally characterize the NSSs in these families. The presented work also demonstrates that, in specific cases, the analysis of the hydropathy distribution in proteins is capable of revealing functional properties of proteins.     

The molecular basis of adaptive evolution of squirrelfish rhodopsins

The wavelengths of maximal absorption (lambdamax) of the rhodopsins of nine squirrelfishes (N. sammara, N. argenteus, S. punctatissimum, S. microstoma, S. diadema, S. xantherythrum, S. spiniferum, N. aurolineatus, and S. tiere) and two soldierfishes (M. violacea and M. berndti) vary between 481 and 502 nm. Phylogenetic and mutagenesis analyses suggest that the common ancestor of these pigments had a lambdamax value of approximately 493 nm, and the contemporary lambdamax values were generated mostly by amino acid replacements E122M, F261Y, and A292S. The probability of observing all these amino acid replacements at specific branches of the phylogenetic tree is only 2.5 x 10(-9); it is highly unlikely that these changes have occurred by neutral evolution. Because of a close association between the lambdamax values of these pigments and the wavelengths of light available to the corresponding species, the excess number of amino acid changes at specific branches in the phylogenetic tree strongly suggests that the rhodopsins have undergone adaptive changes at various stages of the holocentrid evolution.     

EMBOSS软件包序列分析程序应用实例

本文介绍欧洲分子生物学开放软件包EMBOSS序列分析程序应用实例.第1节简单介绍EMBOSS软件包的概况和基本用法.第2节介绍格式转换、序列提取、序列变换和序列显示等常用序列处理程序.第3节介绍序列比对程序,包括双序列比对、多序列比对和点阵图程序.第4节介绍常用核酸序列分析程序,可用于核苷酸组分统计、开放读码框分析、C...     

"In vivo" intraneuronal trafficking of G protein coupled receptors in the striatum: regulation by dopaminergic and cholinergic environment

We have studied "in vivo" neurochemically identified striatal neurons to analyze the localisation and the trafficking of dopamine and acetylcholine G protein coupled receptors (GPCR) (D1R, D2R, m2R and m4R) under the influence of neurotransmitter environment. We have identified receptors in tissue sections through immunohistochemical detection at the light and electron microscopic level. We have identified receptors in normal animals and after acute and chronic stimulations. We have quantified receptors through image analysis at the electron microscopic level in relation to various subcellular compartments. Our results demonstrate that, in normal conditions, GPCRs are mostly associated with plasma membrane of the striatal neurons, mostly at extra-synaptic sites. In certain instances (m4R; D2R), receptors have prominent localisation inside the rough endoplasmic reticulum. Our results also show that two distinct receptors for a same neurotransmitter may have distinct subcellular localisation in a same neuronal population (m2R versus m4R) and that the same neurotransmitter receptor (m4R) can have distinct localisation in distinct neuronal populations (cytoplasm versus cell surface). After acute stimulation, cell surface receptors undergo dramatic subcellular changes that involve plasma membrane depletion, internalisation in endosomes and in multivesicular bodies. Such changes are reversible after the end of the stimulation and are blocked by antagonist action. Chronic stimulation also provokes changes in subcellular localisation with specific pattern: plasma membrane depletion, and exaggerated storage of receptors in rough endoplasmic reticulum and eventually Golgi complex (D1R; m2R and m4R). Decreasing chronic receptor stimulation reverses such changes. These results demonstrate that, "in vivo", in the striatum, GPCRs undergo complex intraneuronal trafficking under the influence of neurochemical environment in conditions that dramatically modulate the number of cell surface receptors available for interaction with neurotransmitters or drugs. This confirms that "in vivo", the trafficking and the subcellular compartmentalization of GPCRs may contribute to regulate neuronal sensitivity and neuronal interactions in physiological, experimental and pathological conditions, including in therapeutic conditions.     

Regulation of neurotransmitter release by metabotropic glutamate receptors

The G protein-coupled metabotropic glutamate (mGlu) receptors are differentially localized at various synapses throughout the brain. Depending on the receptor subtype, they appear to be localized at presynaptic and/or postsynaptic sites, including glial as well as neuronal elements. The heterogeneous distribution of these receptors on glutamate and nonglutamate neurons/cells thus allows modulation of synaptic transmission by a number of different mechanisms. Electrophysiological studies have demonstrated that the activation of mGlu receptors can modulate the activity of Ca(2+) or K(+) channels, or interfere with release processes downstream of Ca(2+) entry, and consequently regulate neuronal synaptic activity. Such changes evoked by mGlu receptors can ultimately regulate transmitter release at both glutamatergic and nonglutamatergic synapses. Increasing neurochemical evidence has emerged, obtained from in vitro and in vivo studies, showing modulation of the release of a variety of transmitters by mGlu receptors. This review addresses the neurochemical evidence for mGlu receptor-mediated regulation of neurotransmitters, such as excitatory and inhibitory amino acids, monoamines, and neuropeptides.     

Topological characterization of neuronal arbor morphology via sequence representation: II - global alignment

Background

The increasing abundance of neuromorphological data provides both the opportunity and the challenge to compare massive numbers of neurons from a wide diversity of sources efficiently and effectively. We implemented a modified global alignment algorithm representing axonal and dendritic bifurcations as strings of characters. Sequence alignment quantifies neuronal similarity by identifying branch-level correspondences between trees.

Results

The space generated from pairwise similarities is capable of classifying neuronal arbor types as well as, or better than, traditional topological metrics. Unsupervised cluster analysis produces groups that significantly correspond with known cell classes for axons, dendrites, and pyramidal apical dendrites. Furthermore, the distinguishing consensus topology generated by multiple sequence alignment of a group of neurons reveals their shared branching blueprint. Interestingly, the axons of dendritic-targeting interneurons in the rodent cortex associates with pyramidal axons but apart from the (more topologically symmetric) axons of perisomatic-targeting interneurons.

Conclusions

Global pairwise and multiple sequence alignment of neurite topologies enables detailed comparison of neurites and identification of conserved topological features in alignment-defined clusters. The methods presented also provide a framework for incorporation of additional branch-level morphological features. Moreover, comparison of multiple alignment with motif analysis shows that the two techniques provide complementary information respectively revealing global and local features.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0605-1) contains supplementary material, which is available to authorized users.     

Insilco analysis of functionally important residues in folate receptors

Lack of crystal structure data of folate binding proteins has left so many questions unanswered (for example, important residues in active site, binding domain, important amino acid residues involved in interactions between ligand and receptor). With sequence alignment and PROSITE motif identification, we attempted to answer evolutionarily significant residues that are of functional importance for ligand binding and that form catalytic sites. We have analyzed 46 different FRs and FBP sequences of various organisms obtained from Genbank. Multiple sequence alignment identified 44 highly conserved identical amino acid residues with 10 cysteine residues and 12 motifs including ECSPNLGPW (which might help in the structural stability of FR).     

Microglial neurotransmitter receptors trigger superoxide production in microglia; consequences for microglial-neuronal interactions

Microglia express three isoforms of the NADPH oxidase, Nox1, Nox2 and Nox4, with the potential to produce superoxide (O(2) ˙(-) ). Microglia also express neurotransmitter receptors, which can modulate microglial responses. In this study, microglial activity of Nox1, Nox2 and Nox4 in primary rat cultured microglia or the rodent BV2 cell line were altered by microglial neurotransmitter receptor modulation. Glutamate, GABA or ATP triggered microglial O(2) ˙(-) production via Nox activation. Nox activation was elicited by agonists of metabotropic mGlu3 receptors and by group III receptors, by GABA(A) but not GABA(B) receptors, and by purinergic P2X(7) or P2Y(2/4) receptors but not P2Y(1) receptors, and inhibited by metabotropic glutamate receptor 5 antagonists. The neurotransmitters also modulated Nox mRNA expression and NADPH activity. The activation of Nox by BzATP or GABA promoted a neuroprotective phenotype whilst the activation of Nox by glutamate promoted a neurotoxic phenotype. Taken together, these data indicate that microglial neurotransmitter receptors can signal via Nox to promote neuroprotection or neurotoxicity. This has implications for the subsequent neurotoxic profile of microglia when neurotransmitter levels may become skewed in neurodegeneration.     

The distribution of P2X<Subscript>5</Subscript> purinergic receptors in the enteric nervous system of mouse

The distribution of the P2X₅ purinoceptor in the enteric nervous system of the mouse was studied by immunohistochemistry. P2X₅ receptor immunoreactivity was widely distributed in myenteric and submucosal plexuses throughout the gastrointestinal tract. In myenteric plexuses, immunoreactivity for the P2X₅ receptor was observed in nerve fibres that enveloped ganglion cell bodies, and possibly on glial cell processes. P2X₅ receptor immunoreactivity was colocalised with vasoactive intestinal peptide and surrounded ganglion cells that contained calretinin, calbindin or nitric oxide synthase. In the submucous plexus, P2X₅ receptor immunoreactivity occurred throughout the cytoplasm and on the surface membranes of the nerve cells. Double-labelling studies showed that 22%, 9%, 6% and 68% of P2X₅ receptor-immunoreactive neurones were also immunoreactive for calretinin, calbindin, nitric oxide synthase and vasoactive intestinal peptide, respectively. Thus, the P2X₅ receptor subunit is expressed in specific functional groups of neurones. P2X₂ and P2X₃ receptors were also present in the mouse enteric plexuses but no immunoreactivity for P2X₁, P2X₄ or P2X₆ receptors was found.     

Prediction of pi-turns in proteins using PSI-BLAST profiles and secondary structure information

Due to the structural and functional importance of tight turns, some methods have been proposed to predict gamma-turns, beta-turns, and alpha-turns in proteins. In the past, studies of pi-turns were made, but not a single prediction approach has been developed so far. It will be useful to develop a method for identifying pi-turns in a protein sequence. In this paper, the support vector machine (SVM) method has been introduced to predict pi-turns from the amino acid sequence. The training and testing of this approach is performed with a newly collected data set of 640 non-homologous protein chains containing 1931 pi-turns. Different sequence encoding schemes have been explored in order to investigate their effects on the prediction performance. With multiple sequence alignment and predicted secondary structure, the final SVM model yields a Matthews correlation coefficient (MCC) of 0.556 by a 7-fold cross-validation. A web server implementing the prediction method is available at the following URL: http://210.42.106.80/piturn/.     

GnRH and GnRH receptors: distribution,function and evolution

Gonadotropin‐releasing hormone (GnRH) was originally identified because of its essential role in regulating reproduction in all vertebrates. Since then, three phylogenetically related GnRH decapeptides have been characterized in vertebrates and invertebrates. Almost all tetrapods investigated have at least two GnRH forms (GnRH1 and GnRH2) in the central nervous system. From distributional and functional studies in vertebrates, GnRH1 in the hypothalamus projects predominantly to the pituitary and regulates reproduction via gonadotropin release. GnRH2, which is located in the midbrain, projects to the whole brain and is thought to be involved in sexual behaviour and food intake. GnRH3, located in the forebrain, has only been found in teleost fish and appears to be involved in sexual behaviour, as well as, in some fish species, gonadotropin release. Multiple GnRH receptors (GnRH‐Rs), G‐protein‐coupled receptors regulate endocrine functions and neural transmissions in vertebrates. Phylogenetic and structural analyses of coding sequences show that all vertebrate GnRH‐Rs cluster into two main receptor types comprised of four subfamilies. This suggests that at least two rounds of GnRH receptor gene duplications may have occurred in different groups within each lineage. Functional studies suggest that two particular subfamilies of GnRH receptors have independently evolved to act as species‐specific endocrine modulators in the pituitary, and these show the greatest variety in regulating neuron networks in the brain. Given the long evolutionary history of the GnRH system, it seems likely that much more remains to be understood about its roles in behaviour and function of vertebrates.     

ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach

Background

Obtaining an accurate sequence alignment is fundamental for consistently analyzing biological data. Although this problem may be efficiently solved when only two sequences are considered, the exact inference of the optimal alignment easily gets computationally intractable for the multiple sequence alignment case. To cope with the high computational expenses, approximate heuristic methods have been proposed that address the problem indirectly by progressively aligning the sequences in pairs according to their relatedness. These methods however are not flexible to change the alignment of an already aligned group of sequences in the view of new data, resulting thus in compromises on the quality of the deriving alignment. In this paper we present ReformAlign, a novel meta-alignment approach that may significantly improve on the quality of the deriving alignments from popular aligners. We call ReformAlign a meta-aligner as it requires an initial alignment, for which a variety of alignment programs can be used. The main idea behind ReformAlign is quite straightforward: at first, an existing alignment is used to construct a standard profile which summarizes the initial alignment and then all sequences are individually re-aligned against the formed profile. From each sequence-profile comparison, the alignment of each sequence against the profile is recorded and the final alignment is indirectly inferred by merging all the individual sub-alignments into a unified set. The employment of ReformAlign may often result in alignments which are significantly more accurate than the starting alignments.

Results

We evaluated the effect of ReformAlign on the generated alignments from ten leading alignment methods using real data of variable size and sequence identity. The experimental results suggest that the proposed meta-aligner approach may often lead to statistically significant more accurate alignments. Furthermore, we show that ReformAlign results in more substantial improvement in cases where the starting alignment is of relatively inferior quality or when the input sequences are harder to align.

Conclusions

The proposed profile-based meta-alignment approach seems to be a promising and computationally efficient method that can be combined with practically all popular alignment methods and may lead to significant improvements in the generated alignments.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-265) contains supplementary material, which is available to authorized users.     

东方蜜蜂气味受体基因Or1和Or2的克隆与序列分析

本研究采用自行设计的引物对东方蜜蜂Apis cerana Fabricius气味受体(odorant receptors)Or1、Or2的部分基因组序列(GenBank登录号为:JN544932,JN544931)进行了克隆、测序和分析,以探寻传统气味受体(AcOr1)和非典型气味受体(AcOr2)基因在近缘种昆虫间的进化差异。试验所得的东方蜜蜂气味受体基因Or1、Or2的序列长度分别为1247bp和1138bp,各包含4个和2个内含子,编码区序列长度分别为682、686 bp。经序列比对发现,两气味受体DNA序列在东、西方蜜蜂及熊蜂间差异较大,最低相似性仅为56%(AcOr1—BtOr82a-like),差异的主要来源为内含子长度及其碱基的变异,而编码区氨基酸序列相似性较高,均达85%以上;从整体分析来看,在膜翅目昆虫中,非典型气味受体AcOr2较传统气味受体AcOr1是相对保守的气味受体基因。