Raalin, a transcript enriched in the honey bee brain, is a remnant of genomic rearrangement in Hymenoptera

We identified a predicted compact cysteine-rich sequence in the honey bee genome that we called 'Raalin'. Raalin transcripts are enriched in the brain of adult honey bee workers and drones, with only minimum expression in other tissues or in pre-adult stages. Open-reading frame (ORF) homologues of Raalin were identified in the transcriptomes of fruit flies, mosquitoes and moths. The Raalin-like gene from Drosophila melanogaster encodes for a short secreted protein that is maximally expressed in the adult brain with negligible expression in other tissues or pre-imaginal stages. Raalin-like sequences have also been found in the recently sequenced genomes of six ant species, but not in the jewel wasp Nasonia vitripennis. As in the honey bee, the Raalin-like sequences of ants do not have an ORF. A comparison of the genome region containing Raalin in the genomes of bees, ants and the wasp provides evolutionary support for an extensive genome rearrangement in this sequence. Our analyses identify a new family of ancient cysteine-rich short sequences in insects in which insertions and genome rearrangements may have disrupted this locus in the branch leading to the Hymenoptera. The regulated expression of this transcript suggests that it has a brain-specific function.

Anxiety induced by prenatal stress is associated with suppression of hippocampal genes involved in synaptic function

Exposure of pregnant women or animals to stress during a critical period of foetal brain development increases the likelihood of anxiety, depression and learning deficits that are associated with structural alterations in the offspring hippocampus. In this study, we report the effect of gestational stress in rats on anxiogenic behaviour and hippocampal gene expression of their 23-day-old female offspring. As the rat brain continues to develop after birth, we also used the procedure of handling (H) during the first 10 days of life to reverse the anxiogenic behaviour of prenatally stressed (PS) rats. By means of micro-array analysis on hippocampal extracts, we found that the expression of about 6.1% of 9505 valid genes was significantly altered by prenatal stress (p<0.05). Of these, 48% were over-expressed and 52% under-expressed. The latter included approximately 300 genes that participate in axonal growth, regulation of ion channels and transporters, trafficking of synaptic vesicles and neurotransmitter release. About 30% of the genes that were down-regulated in PS rats were restored to control levels by H. These include genes that play a role in pre-synaptic organization and function. Our results provide a possible relationship between hippocampal gene expression and changes in behaviour resulting from prenatal stress.

SUVi and BACH1: a new subfamily of mammalian helicases?

The RecQ family of DNA helicases have been shown to be important for the maintenance of genomic integrity in prokaryotes and eukaryotes. Members of this family are genes responsible for cancer predisposition disorders like Bloom's syndrome, Werner's syndrome and Rothmund-Thomson syndrome. Here, we show the sequence homologies between two recently identified mammalian helicases, namely SUVi and BACH1. These two genes also share strong homologies with other members of the RecQ family. On the basis of published data and sequence analysis we suggest that SUVi/BACH1 may represent a novel subfamily of mammalian helicases, functioning in the processing of lesions induced by different genotoxic agents.

Using Bayesian networks to analyze expression data

DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a "snapshot" of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graph-based model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998).

Direct interaction of a brain voltage-gated K+ channel with syntaxin 1A: functional impact on channel gating

Presynaptic voltage-gated K(+) (Kv) channels play a physiological role in the regulation of transmitter release by virtue of their ability to shape presynaptic action potentials. However, the possibility of a direct interaction of these channels with the exocytotic apparatus has never been examined. We report the existence of a physical interaction in brain synaptosomes between Kvalpha1.1 and Kvbeta subunits with syntaxin 1A, occurring, at least partially, within the context of a macromolecular complex containing syntaxin, synaptotagmin, and SNAP-25. The interaction was altered after stimulation of neurotransmitter release. The interaction with syntaxin was further characterized in Xenopus oocytes by both overexpression and antisense knock-down of syntaxin. Direct physical interaction of syntaxin with the channel protein resulted in an increase in the extent of fast inactivation of the Kv1.1/Kvbeta1.1 channel. Syntaxin also affected the channel amplitude in a biphasic manner, depending on its concentration. At low syntaxin concentrations there was a significant increase in amplitudes, with no detectable change in cell-surface channel expression. At higher concentrations, however, the amplitudes decreased, probably because of a concomitant decrease in cell-surface channel expression, consistent with the role of syntaxin in regulation of vesicle trafficking. The observed physical and functional interactions between syntaxin 1A and a Kv channel may play a role in synaptic efficacy and neuronal excitability.

Involvement of extracellular signal-regulated kinase (ERK) in pardaxin-induced dopamine release from PC12 cells

Pardaxin (PX), an ionophore-peptide neurotoxin isolated from the fish Pardachirus marmoratus, induces neurotransmitter release from neuronal preparations by both calcium-dependent and calcium-independent mechanisms. The aim of the present study was to investigate the role of extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) in pardaxin-induced dopamine (DA) release. The experiments were performed on variants of the PC12 cell line, an established cellular model for investigating DA release. Time course experiments indicated that PX, at nontoxic concentrations, stimulated ERK1 and ERK2 within 5 to 15 min, measured with a dual phospho-ERK antibody. PX stimulation of ERK activity was calcium (Ca(2+))-dependent and followed by ERK translocation to the nucleus. This effect was temporally related to PX-induced exocytosis, and measured by [(3)H]dopamine release as well as by a vesicle fusion-based enzyme-linked immunosorbent assay. Blocking ERK activity with the specific mitogen-activated protein kinase kinase inhibitors PD98059 (50 microM for 45 min) and UO126 (30 microM for 30 min) inhibited PX-induced exocytosis in the presence but not in the absence of extracellular Ca(2+). These results suggest the essential role of ERKs in PX-induced DA release under physiological conditions and support the hypothesis that ERKs are involved in regulating exocytosis.

Methodologies for target selection in structural genomics

As the number of complete genomes that have been sequenced keeps growing, unknown areas of the protein space are revealed and new horizons open up. Most of this information will be fully appreciated only when the structural information about the encoded proteins becomes available. The goal of structural genomics is to direct large-scale efforts of protein structure determination, so as to increase the impact of these efforts. This review focuses on current approaches in structural genomics aimed at selecting representative proteins as targets for structure determination. We will discuss the concept of representative structures/folds, the current methodologies for identifying those proteins, and computational techniques for identifying proteins which are expected to adopt new structural folds.

Culturing neuronal cells on surfaces coated by a novel polyethyleneimine-based polymer

Maintaining cells in culture is essential for studying many aspects of cell biology and physiology. Cell culturing is dependent on proper anchorage of cells to the growth surfaces. For most cell lines, and especially for post-mitotic neurons, coated tissue culture plates are prerequisite for seeding. The most commonly used coating reagents are positively charged polymers such as poly-L-lysine or biologically purified adhesive molecules such as collagen. In this report, we present a simple procedure for synthesizing and for coating cell culture surfaces. The reagent is a biologically inert hydrophobized polyethyleneimine (PEI), which provides adequate adhesive properties for cultured cell lines including those of neuronal lineage. The hydrophobized PEI is branched PEI modified by octadecanyl groups bound to 2 mol% of the amino groups of the PEI. Unlike the native PEI that is water soluble, the modified PEI is soluble in ethanol, and thus resistant to solubilization in biological media. The protocol of coating was optimized for tissue culture plates as well as glass surfaces and in many respects this polymer outperformed other routinely used coating reagents. Neuronal cell lines, plated on the polymer-treated surfaces are resistant to manipulations including repeated media changes and extensive washing. The advantage of coating surfaces with the developed PEI-based polymer compared to other commonly used coating reagents is discussed.

Why aren't foamy viruses pathogenic?

Foamy viruses are complex retroviruses that lead to either highly cytopathic or persistent infections in vitro, but to non-pathogenic lifelong infections in naturally or accidentally infected hosts. Factors that could contribute to these benign persistent infections include regulated transcription from the two viral promoters, the functions of the Bet accessory protein and the host immune response.

Estimating the probability for a protein to have a new fold: A statistical computational model

Structural genomics aims to solve a large number of protein structures that represent the protein space. Currently an exhaustive solution for all structures seems prohibitively expensive, so the challenge is to define a relatively small set of proteins with new, currently unknown folds. This paper presents a method that assigns each protein with a probability of having an unsolved fold. The method makes extensive use of protomap, a sequence-based classification, and scop, a structure-based classification. According to protomap, the protein space encodes the relationship among proteins as a graph whose vertices correspond to 13,354 clusters of proteins. A representative fold for a cluster with at least one solved protein is determined after superposition of all scop (release 1.37) folds onto protomap clusters. Distances within the protomap graph are computed from each representative fold to the neighboring folds. The distribution of these distances is used to create a statistical model for distances among those folds that are already known and those that have yet to be discovered. The distribution of distances for solved/unsolved proteins is significantly different. This difference makes it possible to use Bayes' rule to derive a statistical estimate that any protein has a yet undetermined fold. Proteins that score the highest probability to represent a new fold constitute the target list for structural determination. Our predicted probabilities for unsolved proteins correlate very well with the proportion of new folds among recently solved structures (new scop 1.39 records) that are disjoint from our original training set.

ProtoMap: automatic classification of protein sequences and hierarchy of protein families

The ProtoMap site offers an exhaustive classification of all proteins in the SWISS-PROT database, into groups of related proteins. The classification is based on analysis of all pairwise similarities among protein sequences. The analysis makes essential use of transitivity to identify homologies among proteins. Within each group of the classification, every two members are either directly or transitively related. However, transitivity is applied restrictively in order to prevent unrelated proteins from clustering together. The classification is done at different levels of confidence, and yields a hierarchical organization of all proteins. The resulting classification splits the protein space into well-defined groups of proteins, which are closely correlated with natural biological families and superfamilies. Many clusters contain protein sequences that are not classified by other databases. The hierarchical organization suggested by our analysis may help in detecting finer subfamilies in families of known proteins. In addition it brings forth interesting relationships between protein families, upon which local maps for the neighborhood of protein families can be sketched. The ProtoMap web server can be accessed at http://www.protomap.cs.huji.ac.il

ProtoMap: automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space

We investigate the space of all protein sequences in search of clusters of related proteins. Our aim is to automatically detect these sets, and thus obtain a classification of all protein sequences. Our analysis, which uses standard measures of sequence similarity as applied to an all-vs.-all comparison of SWISSPROT, gives a very conservative initial classification based on the highest scoring pairs. The many classes in this classification correspond to protein subfamilies. Subsequently we merge the subclasses using the weaker pairs in a two-phase clustering algorithm. The algorithm makes use of transitivity to identify homologous proteins; however, transitivity is applied restrictively in an attempt to prevent unrelated proteins from clustering together. This process is repeated at varying levels of statistical significance. Consequently, a hierarchical organization of all proteins is obtained. The resulting classification splits the protein space into well-defined groups of proteins, which are closely correlated with natural biological families and superfamilies. Different indices of validity were applied to assess the quality of our classification and compare it with the protein families in the PROSITE and Pfam databases. Our classification agrees with these domain-based classifications for between 64.8% and 88.5% of the proteins. It also finds many new clusters of protein sequences which were not classified by these databases. The hierarchical organization suggested by our analysis reveals finer subfamilies in families of known proteins as well as many novel relations between protein families.

Depolarization affects the binding properties of muscarinic acetylcholine receptors and their interaction with proteins of the exocytic apparatus

Membrane depolarization is the signal that triggers release of neurotransmitter from nerve terminals. As a result of depolarization, voltage-dependent Ca(2+) channels open, level of intracellular Ca(2+) increases. and release of neurotransmitter commences. Previous study had shown that in rat brain synaptosomes, muscarinic acetylcholine (ACh) receptors (mAChRs) interact with soluble NSF attachment protein receptor proteins of the exocytic machinery in a voltage-dependent manner. It was suggested that this interaction might control the rapid, synchronous release of acetylcholine. The present study investigates the mechanism for such a voltage-dependent interaction. Here we show that depolarization shifts mAChRs, specifically the m2 receptor subtype, to a low affinity state toward its agonists. At resting potential, mAChRs are in a high affinity state (K(d) of approximately 20 nM) and they shift to a low affinity state (K(d) of tens of microM) upon membrane depolarization. In addition, interaction between m2 receptor subtype and the exocytic machinery increases with receptor occupancy. Both phenomena are independent of Ca(2+) influx. We propose that these results may explain control of ACh release from nerve terminals. At resting potential the exocytic machinery is clamped due to its interaction with the occupied mAChR and depolarization relieves this interaction. This, together with Ca(2+) influx, enables release of ACh to commence.

Nonlinear optical measurement of membrane potential around single molecules at selected cellular sites

Membrane potential around single molecules has been measured by using the nonlinear optical phenomenon of second harmonic generation. This advance results from the interaction between a highly dipolar molecule with a selectively directed highly polarizable 1-nm gold particle. With this approach, a second harmonic signal, which is enhanced by the nanoparticle, is detected from a volume of nanometric dimensions. This present work clearly shows that functional cellular imaging around single molecules is possible by selectively directing an antibody with a 1-nm gold label to a specific membrane protein. The results of this work open the way for three-dimensional, high resolution functional imaging of membrane electrophysiology in cells and cellular networks.

Ca2+-dependent exocytosis in mast cells is stimulated by the Ca2+ sensor, synaptotagmin I

Mast cells secrete a variety of biologically active substances that mediate inflammatory responses. Synaptotagmin(s) (Syts) are a gene family of proteins that are implicated in the control of Ca2+-dependent exocytosis. In the present study, we investigated the possible occurrence and functional involvement of Syt in the control of mast cell exocytosis. Here, we demonstrate that both connective tissue type and mucosal-like mast cells express Syt-immunoreactive proteins, and that these proteins are localized almost exclusively to their secretory granules. Furthermore, expression of Syt I, the neuronal Ca2+ sensor, in rat basophilic leukemia cells (RBL-2H3), a tumor analogue of mucosal mast cells, resulted in prominent potentiation and acceleration of Ca2+-dependent exocytosis. Therefore, these findings implicate Syt as a Ca2+ sensor that mediates regulated secretion in mast cells to calcium ionophore.

A map of the protein space--an automatic hierarchical classification of all protein sequences

We investigate the space of all protein sequences. We combine the standard measures of similarity (SW, FASTA, BLAST), to associate with each sequence an exhaustive list of neighboring sequences. These lists induce a (weighted directed) graph whose vertices are the sequences. The weight of an edge connecting two sequences represents their degree of similarity. This graph encodes much of the fundamental properties of the sequence space. We look for clusters of related proteins in this graph. These clusters correspond to strongly connected sets of vertices. Two main ideas underlie our work: i) Interesting homologies among proteins can be deduced by transitivity. ii) Transitivity should be applied restrictively in order to prevent unrelated proteins from clustering together. Our analysis starts from a very conservative classification, based on very significant similarities, that has many classes. Subsequently, classes are merged to include less significant similarities. Merging is performed via a novel two phase algorithm. First, the algorithm identifies groups of possibly related clusters (based on transitivity and strong connectivity) using local considerations, and merges them. Then, a global test is applied to identify nuclei of strong relationships within these groups of clusters, and the classification is refined accordingly. This process takes place at varying thresholds of statistical significance, where at each step the algorithm is applied on the classes of the previous classification, to obtain the next one, at the more permissive threshold. Consequently, a hierarchical organization of all proteins is obtained. The resulting classification splits the space of all protein sequences into well defined groups of proteins. The results show that the automatically induced sets of proteins are closely correlated with natural biological families and super families. The hierarchical organization reveals finer sub-families that make up known families of proteins as well as many interesting relations between protein families. The hierarchical organization proposed may be considered as the first map of the space of all protein sequences. An interactive web site including the results of our analysis has been constructed, and is now accessible through http:/(/)www.protomap.cs.huji.ac.il

Highly sensitive ELISA-based assay for quantifying protein levels in neuronal cultures

A simple assay for quantifying the expression level of proteins in situ is presented. The assay is performed directly in culture plates and simply requires incubating the cells (either fixed or in live cultures) with the appropriate antibody against the desired protein. Cells are then incubated with a peroxidase-conjugated secondary antibody followed by incubation with the soluble peroxidase substrate-tetramethylbenzidine. Antibody binding levels are quantified in an ELISA-based protocol by reading optical density at 450 nm. The assay is applicable for any surface-attached cell culture. The assay is highly sensitive, allowing detection of expressed proteins in a monolayer of cell cultured in a 96 well plate. The assay was optimized for a neuronal cell-line-P19. These are embryonal carcinoma cells which differentiate into neurons after treatment with retinoic acid. The neurons do not survive well in 96 well plates and are thus plated in 24 or 48 well plates. We demonstrate the use of the method for an in vivo labeling of neurons by quantifying epitopes which are exposed upon nerve stimulation. Advantages of a routine ELISA protocol in quantification over wide range of sensitivity and in performing simultaneous large number of repetitions and different controls are thus fully extended to live cell cultures.

Expression and localization of muscarinic receptors in P19-derived neurons

The muscarinic acetylcholine receptors are important in a variety of physiological processes such as induction of secretion from various glands and regulation of pacemaker activity, muscle tone, and neurotransmission. To date, the muscarinic receptor family includes five members (designated m1-m5), of which m1-m4 are abundant in brain and in peripheral tissues, and m5 is found exclusively in brain, and even there at very low levels. The expression of m1-m5 receptor subtypes was studied in neurons derived from the murine embryonal carcinoma cell line P19. These cells serve as a model system for differentiation and maturation of neurons resembling CNS neurons. Our results show that P19 neurons express mainly the m2, m3, and m5 subtypes. Low levels of m1 receptors are also detected and m4 subtype is practically absent. Furthermore, muscarinic receptors in P19 neurons are functional in activating second messenger signaling pathways. The localization of m2 receptors is predominantly presynaptic, whereas the m5 subtype is mainly postsynaptic. Consequently, P19 cells provide a model system for the study of pre- and postsynaptic muscarinic acetylcholine-receptor subtypes in a proper neuronal context. This is particularly valid for the rare m5 receptors.

SNARE proteins--why so many, why so few?

Both trafficking and secretion critically depend on accurate and specific membrane recognition and fusion. A key step in these processes is the assembly of a complex consisting of a small number of proteins, i.e., the exocytic core complex. In nerve terminals, this set consists of VAMP and synaptotagmin, which reside at membranes of synaptic vesicles, and syntaxin and SNAP-25 at the plasma membrane. In this survey, different secretory systems that depend on the exocytic core proteins are considered. The possibility that specificity in membrane recognition and fusion is achieved by the numerous variants of proteins of the exocytic core is discussed. Variability of the core complex proteins is determined by the complexity of gene families, isoform-specific localization, and posttranslational modifications. Basic biochemical properties depend on specific isoforms, and the possible protein-protein interactions are determined, in turn, by the compatibility of different isoforms. A correlation between specific variants and distinct biochemical or cellular properties is shown. The outcome of this survey is that heterogeneity in secretion may be dictated by the large number of possible combinations of variants of only a few proteins.

Voltage-dependent interaction between the muscarinic ACh receptor and proteins of the exocytic machinery

1. Release of neurotransmitter into the synaptic cleft is the last step in the chain of molecular events following the arrival of an action potential at the nerve terminal. The neurotransmitter exerts negative feedback on its own release. This inhibition would be most effective if exerted on the first step in this chain of events, i.e. a step that is mediated by membrane depolarization. Indeed, in numerous studies feedback inhibition was found to be voltage dependent. 2. The purpose of this study is to investigate whether the mechanism underlying feedback inhibition of transmitter release resides in interaction between the presynaptic autoreceptors and the exocytic apparatus, specifically the soluble NSF-attachment protein receptor (SNARE) complex. 3. Using rat synaptosomes we show that the muscarinic ACh autoreceptor (mAChR) is an integral component of the exocytic machinery. It interacts with syntaxin, synaptosomal-associated protein of 25 kDa (SNAP-25), vesicle-associated membrane protein (VAMP) and synaptotagmin as shown using both cross-linking and immunoprecipitation. 4. The interaction between mAChRs and both syntaxin and SNAP-25 is modulated by depolarization levels; binding is maximal at resting potential and disassembly occurs at higher depolarization. 5. This voltage-dependent interaction of mAChRs with the secretory core complex appears suitable for controlling the rapid, synchronous neurotransmitter release at nerve terminals.

Acceleration of neuronal maturation of P19 cells by increasing culture density

P19 embryonal carcinoma cells differentiate into neurons, astrocytes, and fibroblast-like cells following induction with retinoic acid. The mature neurons are capable of neurotransmitter release, and from functional synapses. We have previously shown that high culture density suppresses the cholinergic phenotype of P19 neurons. Here we demonstrate that increasing culture density accelerates the maturation of P19 neurons in a continuous manner. This is manifested by several criteria: increased efficiency of evoked [3H]aspartate release; decreased level of basal release; up-regulation of synaptic vesicle proteins; increased neurite outgrowth rate; and earlier segregation of axons and dendrites. While glutamate release is enhanced in dense cultures, the efficiency of [3H]GABA release is hardly affected, suggesting that P19 GABAergic neurons are not affected by culture density. The acceleration of neuronal maturation in dense cultures is also exhibited by the ability of dense, but not sparse cultures to release [3H]aspartate at an earlier day of differentiation. Furthermore, density effects are monitored already a few hours after plating the cultures, when neurite length in dense cultures is several fold higher than in sparse cultures. This indicates that commitment to a faster and coordinated maturation process occurs already very early during P19 neuronal differentiation.

Differential expression pattern of Rab-GDI isoforms during the parotid gland secretion cycle

Rab GDP dissociation inhibitor (GDI) plays an important role in regulating the GDP/GTP cycle of small GTP binding proteins of the Rab family. It also regulates their association to membranes. The small family of Rab-GDI consists of several closely related isoforms, the functional differences between which are still unknown. Here we show that multiple GDI isoforms are expressed in rat parotid gland and that the individual GDI isoforms have a characteristic expression both at the RNA and at the protein level, during the parotid secretory cycle. GDIalpha, the major isoform in brain, is expressed throughout the secretory process and is equally distributed between cytoplasmic and membranous fractions. In contrast, an isoform related to, but different from GDIbeta is found predominantly in the cytoplasmic fraction and its expression is detected only after beta-adrenergic stimulation of the gland, at the end of the secretion phase, when exocytosis is already completed. The induction of such a GDI isoform at the beginning of the recovery stage correlates with the expression pattern of Rab1 and Rab5, but not Rab2 and Rab4. Our results suggest different functional roles for multiple GDI isoforms along the secretion and recovery phases in rat parotid gland.

Global self-organization of all known protein sequences reveals inherent biological signatures

A global classification of all currently known protein sequences is performed. Every protein sequence is partitioned into segments of 50 amino acid residues and a dynamic programming distance is calculated between each pair of segments. This space of segments is initially embedded into Euclidean space. The algorithm that we apply embeds every finite metric space into Euclidean space so that (1) the dimension of the host space is small, (2) the metric distortion is small. A novel self-organized, cross-validated clustering algorithm is then applied to the embedded space with Euclidean distances. We monitor the validity of our clustering by randomly splitting the data into two parts and performing an hierarchical clustering algorithm independently on each part. At every level of the hierarchy we cross-validate the clusters in one part with the clusters in the other. The resulting hierarchical tree of clusters offers a new representation of protein sequences and families, which compares favorably with the most updated classifications based on functional and structural data about proteins. Some of the known families clustered into well distinct clusters. Motifs and domains such as the zinc finger, EF hand, homeobox, EGF-like and others are automatically correctly identified, and relations between protein families are revealed by examining the splits along the tree. This clustering leads to a novel representation of protein families, from which functional biological kinship of protein families can be deduced, as demonstrated for the transporter family. Finally, we introduce a new concise representation for complete proteins that is very useful in presenting multiple alignments, and in searching for close relatives in the database. The self-organization method presented is very general and applies to any data with a consistent and computable measure of similarity between data items.

Expression and localization of synaptotagmin I in rat parotid gland

Synaptotagmins are a gene family of membrane proteins with distinct expression patterns. Synaptotagmin I is an abundant protein of the synaptic vesicle membrane and was implicated as the Ca2+ sensor in fast responding synapses. Yet, its precise role along the synaptic vesicle life cycle is not fully understood. In this report we show that synaptotagmin I is not exclusively confined to neuronal and neuroendocrine systems, rather, it is also expressed in the exocrine system of the parotid gland. The gene for synaptotagmin I was isolated and sequenced from rat parotid cDNA. The identity of synaptotagmin I protein was further confirmed by several independent antibodies. The protein is exclusively found in the membranous fraction of purified granules, similarly to VAMP-2, another major integral membrane protein of synaptic vesicles. Synaptotagmin I represents 0.4% of the total membrane protein mass of the granule. Using immunoelectron microscopy the two proteins were also localized primarily to the granules' membranes. These findings suggest that synaptotagmin I which regulates Ca(2+)-dependent neurotransmitter release also plays a role which is common to all secretory organelles-neuronal, endocrine and exocrine. A role for synaptotagmin I in integrating signals with protein secretion in the parotid gland is suggested.

Culture density regulates both the cholinergic phenotype and the expression of the CNTF receptor in P19 neurons

The P19 embryonal carcinoma cells differentiate into neurons, astrocytes, and fibroblast-like cells following induction with retinoic acid. The cells mature into functional neurons, as determined by their ability to release neurotransmitters in a Ca(2+)- and depolarization-dependent manner. P19 neurons in culture represent a mixed population in terms of their neurotransmitter phenotype. The cholinergic phenotype of these neurons is modulated by culture density. Cholinergic markers, such as the vesicular acetylcholine transporter, acetyl cholinesterase, and choline acetyltransferase, are expressed in about 85% of the cells in sparse cultures and are largely suppressed at high cell densities. In contrast, glutamate release is enhanced in dense P19 neuronal cultures. The factor mediating the density effect is concentrated exclusively on the cell membrane of P19 neurons and not on the nonneuronal cells, which also differentiate from P19 embryonal carcinoma cells. This membrane-associated component retains its functionality, even after membrane fixation. The downregulation of the cholinergic properties in dense cultures is paralleled by a downregulation of the alpha subunit of the ciliary neurotrophic factor (CNTF) receptor. Thus, it is suggested that the membrane-associated factor, which mediates the density effect, downregulates the cholinergic phenotype by inhibiting the responsiveness of these neurons to CNTF. We further suggest that the P19 cell line can serve as a model system for the study of neurotransmitter phenotype acquisition and plasticity throughout neuronal differentiation.

An optical submicrometer calcium sensor with conductance sensing capability

The identification of chemical species and the measurement of their concentrations with high (submicrometer) spatial resolution are of considerable importance in cell biology. In this article we report the first successful development of a > or = 0.1-micron Ca2+ sensor based on a pulled micropipet, filled with a conducting porous sol-gel glass which was doped with the fluorescent calcium green 1 Ca2+ indicator. Such sensors are potentially capable of measuring Ca2+ concentrations as low as 10(-8) M, in confined volumes, with a three-dimensional resolution which exceeds approximately 0.1 micron. A major advantage of the sensor is its capability to be integrated into a multifunctional probe which will measure chemical analyte concentrations and ion conductance.

Cholinergic properties of neurons differentiated from an embryonal carcinoma cell-line (P19)

P19 is a mouse-derived embryonal carcinoma cell-line capable of differentiation toward ectodermal, mesodermal and endodermal lineages. Following treatment with retinoic acid these cells differentiate into neurons, astrocytes and fibroblast-like cells. We induced P19 differentiation under conditions which lead to a homogeneous neuronal culture (> 95% neurons). Under these conditions, most cells (approximately 85%) express high levels of the cholinergic markers acetyl cholinesterase and choline acetyltransferase while approximately 10% of cells express the GABAergic marker glutamic acid decarboxylase. While the proportion of the GABAergic neurons is constant at different culture conditions, the cholinergic phenotype is suppressed at high cell densities. The cholinergic nature of P19 neurons is also evident in their ability to form contacts with a muscle cell-line--C2. At day 10 of differentiation cells are capable of depolarization-dependent acetylcholine release. The release is Ca2+ dependent, and drops to baseline levels at 0.5 mM Ca2+. The cells also respond to sub-nM levels of alpha-latrotoxin by acetylcholine release. All major proteins implicated in synapse functionality are expressed prior to day 10 at both at RNA and protein levels. However, the expression pattern of each gene is unique. The genes include cytoskeletal proteins, synaptic vesicle proteins and terminal specific proteins. We suggest that this cell-line can serve as an in-vitro model system for the study of neuronal phenotype acquisition. Under our conditions, the P19 cells can also provide a system in which to study the differentiation of functional cholinergic neurons.

Bacterial neurotoxins--a thousand years later

Clostridium bacteria are responsible for the neuroparalysis in tetanus and in botulism by producing potent neurotoxins. Here we review the current developments in understanding the toxins' mode of action by deciphering the molecular basis for their function. The active forms of tetanus and botulinum neurotoxins block neurotransmitter release via a zinc-dependent protease activity. All known tetanus and botulinum toxins cleave only three key components in the synaptic vesicle docking and fusion protein complex. While tetanus and botulinum types B, D, F and G cleave VAMP/synaptobrevin, an integral membrane protein of the synaptic vesicles, two other synaptic proteins from the plasma membrane, SNAP-25 and syntaxin, are cleaved by botulinum types A and E and botulinum type C, respectively. We discuss the mechanism by which the proteolytic activity of these toxins causes a block in vesicle fusion.

alpha-latrotoxin is a potent inducer of neurotransmitter release in Torpedo electric organ--functional and morphological characterization

In this report we show that alpha-latrotoxin from black widow spider venom is a potent activator of neurotransmitter release in synaptosomes from the Torpedo electric organ. Binding of the purified toxin (5 nM) to the synaptosomal fraction occurs already at 4 degrees C and is dependent on the presence of divalent ions. However, neurotransmitter release commences only after temperature elevation (22 degrees C) and is completed within 2 min. The effect of alpha-latrotoxin on release is achieved at 1 nM and is already saturated at 5 nM. The release is stimulated by the presence of Ca2+ ions. Activation of release by alpha-latrotoxin is accompanied by morphological changes in electric organ synaptosomes. The synaptosomes swell, resulting in a 55% increase in section area. Moreover, the number of synaptic vesicles per unit area decreases about three-fold, and rows of docked synaptic vesicles are rarely detected as opposed to control synaptosomes. These morphological changes indicate that the massive release is mainly due to synaptic vesicle fusion. alpha-Latrotoxin binding sites are highly concentrated in the innervated face of the electrocytes. Immunoelectron microscopy on electric organ sections reveals alpha-latrotoxin binding sites over the entire plasma membrane at release sites and facing Schwann cells surrounding Torpedo nerve terminals. Surprisingly, a high concentration of binding sites is also found at structures surrounding branching unmyelinated axons. This staining is in close proximity to Schwann cell envelopes and to the basal lamina around axonal tips. The mode of action of alpha-latrotoxin in view of the localization of its binding sites is discussed.

Nucleotide binding by the synapse associated protein SAP90

The rat synapse associated protein SAP90 is a member of a superfamily of potential guanylate kinases localized at cell-cell contact sites. This superfamily includes the synapse associated protein SAP97, a close relative of SAP90, the Drosophila tumor suppressor gene product dlg-Ap, the mammalian zonula occludens proteins ZO-1 and ZO-2 and the erythrocyte protein p55. Here we show that SAP90 specifically binds GMP in the micromolar range while binding to ATP, GDP and ADP is at a much lower affinity (10-25 mM), whether or not binding is detected for other guanine and adenine nucleotides. No guanylate kinase activity of SAP90 was detected under our experimental conditions. The importance of the GMP binding capacity per se and an evolutionary role for conserving of the guanylate kinase domain in this superfamily are discussed.

The effect of calcium levels on synaptic proteins. A study on VAT-1 from Torpedo

In this study we compare major synaptic proteins from Torpedo electric organ to their homologues from mammalian brain. Most of these proteins are members of small gene families. We demonstrate a high degree of evolutionary conservation of most synaptic proteins. However, in the electric organ each gene family is represented only by a single member. We focus on VAT-1, a major protein of the vesicle membrane in Torpedo. VAT-1 is located on the synaptic vesicle membrane and is highly concentrated on the plasma membrane following the application of alpha-latrotoxin. Taking advantage of the relative simplicity of Torpedo synapses, we performed an in vitro study on the properties of VAT-1 affected by changes in Ca2+ levels. VAT-1 is a low affinity Ca2+ binding protein whose ability to bind Ca2+ resides mainly, but not entirely, on the carboxy-terminal domain of the protein. In the presence of Ca2+, the protein is organized in a high molecular mass complex, which is destabilized by depleting Ca2+. This effect occurs only by chelating Ca2+ ions, but not with other divalent ions. VAT-1 is not complexed to any of the proteins which were implicated in the docking/fusion complex such as VAMP, synaptophysin or syntaxin, regardless of Ca2+ levels. Dependence of the stability of protein complexes on Ca2+ levels is also demonstrated on Torpedo n-Sec1. The possible physiological implications of such Ca2+ dependence are discussed.

Proline clustering in proteins from synaptic vesicles

Synaptic vesicle proteins share a specialized and common fate throughout the life cycle of the vesicle, and thus may need to respond to some common signals. It is therefore expected that these proteins will share some common motifs. However, sequence comparison among many of these proteins has not revealed any obvious motifs. Such a motif may be formed by the relative abundance of proline residues, which are not randomly distributed along the sequence but rather are clustered at the cytoplasmatic face of vesicular proteins. We propose that proline clusters serve as structural spacers between functional domains as well as potential target sites for protein-protein interactions. In view of the proline-rich nature of SH3 binding proteins, some of the proline-rich synaptic vesicle proteins may also participate in SH3 binding. Such binding may modulate certain signalling pathways in nerve terminals. Surprisingly, the consensus sequence between the proline clusters of synaptic vesicle proteins is found in a large family of abundant proline-rich proteins of the secretory organelles of the parotid exocrine gland.

VAT-1 from Torpedo synaptic vesicles is a calcium binding protein: a study in bacterial expression systems

1. Calcium binding properties were examined in VAT-1, an abundant 41-kDa membrane protein expressed in the cholinergic cynaptic vesicles of Torpedo. 2. An overlay assay, using 45Ca2+ as a tracer, demonstrated the ability of a recombinant VAT-1 produced from the IPTG-inducible pKK223-3 expression vector to bind calcium. 3. A high yield of recombinant VAT-1 was obtained from the glutathione S-transferase (GST) expression system. The fusion product enabled VAT-1 purification via affinity chromatography. Subsequent cleavage by thrombin resulted in its separation from the GST carrier protein. 4. A direct Ca(2+)-binding study was performed with purified VAT-1 by a quick-spin column technique, in the presence of 45Ca2+. Quantitative analysis revealed a 1:1 molar stoichiometry for binding of Ca2+ to VAT-1, with a dissociation constant of 130 microM. 5. A GST-linked truncated protein consisting of 13 kDa from the VAT-1 carboxy-terminal domain was found to retain the capacity to bind Ca2+. 6. A data search for homologies between VAT-1 and known Ca(2+)-binding proteins revealed considerable similarity to members of the annexin family in a 140-amino acid region from the carboxy terminal of VAT-1, which overlaps two tandem Ca(2+)-binding domains of the annexin proteins.

VAT-1 from Torpedo electric organ forms a high-molecular-mass protein complex within the synaptic vesicle membrane

VAT-1 is an abundant 41-kDa protein from Torpedo cholinergic synaptic vesicles. Most of VAT-1 immunoreactivity (70%) is localized to the synaptic vesicle membrane while the rest (30%) copurifies with larger membranous fragments. VAT-1 forms a high-molecular-mass complex within the synaptic vesicle membrane. The Stokes radius of the VAT-1 complex is 4.85 nm and the sedimentation coefficient is 8.0 x 10(-13) S. Using these values, the calculated apparent mass of the VAT-1 complex is 176 kDa and the friction coefficient is consistent with that for a globular protein. Electrophoresis of solubilized synaptic vesicle proteins following cross-linking resulted in a 40-kDa ladder which was detected by VAT-1 antibodies. This is in accord with VAT-1 protein complex being composed primarily of VAT-1 subunits. The hydrodynamic characteristics of the VAT-1 protein complex suggest that it is composed of three or four VAT-1 subunits. Synaptophysin, an abundant component of Torpedo synaptic vesicle membranes, which has a similar apparent size as VAT-1, is not part of the VAT-1 protein complex. Interactions between the subunits within the protein complex do not depend on disulfide bonds or on lowering the ionic strength. However, partial dissociation of VAT-1 subunits from the complex occurs by chelating calcium ions.

The protein VAT-1 from Torpedo electric organ exhibits an ATPase activity

VAT-1 is an abundant protein in Torpedo electric organ which copurifies with a major ATPase activity from synaptic vesicles. VAT-1 was expressed in E. coli and the product was purified and analyzed. The protein binds specifically to an ATP column and displays an ATPase activity as measured by the kinetics of [32P]phosphate release. The activity is dependent on divalent ions, with both Mg2+ and Ca2+ supporting the reaction. The apparent Km for ATP is 18 microM. This ATPase activity is not affected by known inhibitors of the vesicular V- and P-type ATPases such as vanadate and N-ethylmaleimide. We suggest that VAT-1 activity may affect ATP-dependent reactions in Torpedo nerve terminals, such as phosphorylation and dephosphorylation of proteins.

Brain contains two forms of synaptic vesicle protein 2

Molecular cloning of a cDNA encoding synaptic vesicle protein 2 (SV2) revealed that it is homologous to a family of proton cotransporters from bacteria and fungi and to a related family of glucose transporters found in mammals. The similarity to proton cotransporters raised the possibility that SV2 might mediate the uptake of neurotransmitters into vesicles, an activity known to require a proton gradient. To determine whether SV2 is a member of a family of vesicular proteins, we used the SV2 clone to screen for similar cDNAs in rat brain. We characterized 42 clones, 25 of which encode SV2 and 4 of which encode a protein, SV2B, that is 65% identical and 78% similar to SV2. The protein encoded by SV2B cDNA is recognized by the monoclonal antibody that defines the SV2 protein. When SV2B is expressed in COS cells, antibody labeling is reticular in nature, suggesting that SV2B, like SV2 (hence, SV2A), is segregated to intracellular membranes. The expression of SV2B is limited to neural tissue. While both forms of SV2 are expressed in all brain regions, SV2B is expressed at highest levels in the cortex and hippocampus, whereas the highest level of expression of SV2A is in subcortical regions. Therefore, the SV2 proteins, like other characterized synaptic vesicle proteins, comprise a small gene family.

VAT-1 from Torpedo is a membranous homologue of zeta crystallin

VAT-1 is a major protein from Torpedo synaptic vesicles. A protein data-base search revealed a striking homology to zeta crystallin from guinea pig lens. The overall amino-acid identity is 27%, and 58% similarity is reached by including conserved substitutions. The highest similarity (60% to 85%) between the two proteins is observed in five discrete domains, which are also conserved in zinc-dependent dehydrogenases, particularly in the alcohol dehydrogenase family. The cofactor-binding domain of oxidoreductases is conserved in VAT-1 and in zeta crystallin. VAT-1 preferably binds NADPH in the presence of zinc. In contrast with its homologous proteins, VAT-1 is an integral membrane protein of synaptic vesicles.

Structure and chromosomal localization of the mammalian agrin gene

Agrin, a component of the synaptic basal lamina, has been shown to induce clustering of ACh receptors on the surface of muscle fibers. Analysis of cDNAs isolated from a rat embryonic spinal cord library demonstrated that agrin contains domains similar to regions of protease inhibitors, laminin and epidermal growth factor. The domain structure of agrin is further revealed here in an analysis of the agrin gene. Two additional internal repeated sequences are defined: one rich in cysteine residues with no homology to other proteins, and another similar to the laminin G domain, which is involved in heparin binding. Alternative RNA splicing at two positions in the gene predicts up to eight possible forms of the agrin protein. The gene (symbol AGRN/Agrn) has been assigned to chromosome 1 region pter-p32 in human and to mouse chromosome 4.

Sharing of antigenic epitopes between synaptophysin and granulophysin

The immunological crossreactivity between the two granule-specific membrane glycoproteins, synaptophysin and granulophysin, was studied using a series of site-specific monoclonal and polyclonal antibodies. The epitope relatedness of six monoclonal antibodies against granulophysin was examined by competitive ELISA. The antibodies are shown to recognize distinct, but overlapping epitopes within a compact region that is constructed by the three-dimensional configuration of the molecule. All these antibody clones also recognize rat neuronal synaptophysin. Two monoclonal antibodies against synaptophysin, of which one is the well-characterized SY38 antibody, directed against the carboxy terminal of the molecule, are also shown to react with granulophysin. Characterized polyclonal antibodies against different peptide antigens of synaptophysin failed to recognize granulophysin. Synaptophysin and granulophysin are distinctly recognized in brain cell (white matter) and the pituitary both qualitatively and quantitatively. Based on these and other observations, it is suggested that the repeat motif in the cytoplasmic tail of synaptophysin represents an immunodominant construct that is the target for the observed crossreactive antibodies and that a similar tertiary construct has been preserved in granulophysin and in other transmembrane proteins.