CBP7 Interferes with the Multicellular Development of Dictyostelium Cells by Inhibiting Chemoattractant-Mediated Cell Aggregation

Calcium ions are involved in the regulation of diverse cellular processes. Fourteen genes encoding calcium binding proteins have been identified in Dictyostelium. CBP7, one of the 14 CBPs, is composed of 169 amino acids and contains four EF-hand motifs. Here, we investigated the roles of CBP7 in the development and cell migration of Dictyostelium cells and found that high levels of CBP7 exerted a negative effect on cells aggregation during development, possibly by inhibiting chemoattractant-directed cell migration. While cells lacking CBP7 exhibited normal development and chemotaxis similar that of wild-type cells, CBP7 overexpressing cells completely lost their chemotactic abilities to move toward increasing cAMP concentrations. This resulted in inhibition of cellular aggregation, a process required for forming multicellular organisms during development. Low levels of cytosolic free calcium were observed in CBP7 overexpressing cells, which was likely the underlying cause of their lack of chemotaxis. Our results demonstrate that CBP7 plays an important role in cell spreading and cell-substrate adhesion. cbp7 null cells showed decreased cell size and cell-substrate adhesion. The present study contributes to further understanding the role of calcium signaling in regulation of cell migration and development.

Identification of caleosin and two oleosin isoforms in oil bodies of pine megagametophytes

Numerous oil bodies of 0.2-2 μm occupied approximately 80% of intracellular space in mature pine (Pinus massoniana) megagametophytes. They were stably isolated and found to comprise mostly triacylglycerols as examined by thin layer chromatography analysis and confirmed by both Nile red and BODIPY stainings. Fatty acids released from the triacylglycerols of pine oil bodies were mainly unsaturated, including linoleic acid (60%), adrenic acid (12.3%) and vaccenic acid (9.7%). Proteins extracted from pine oil bodies were subjected to immunological cross-recognition, and the results showed that three proteins of 28, 16 and 14 kDa were detected by antibodies against sesame seed caleosin, sesame oleosin-L and lily pollen oleosin-P, respectively. Complete cDNA fragments encoding these three pine oil-body proteins, tentatively named caleosin, oleosin-L and oleosin-G, were obtained by PCR cloning and further confirmed by mass spectrometric analysis. Consistently, phylogenetic tree analyses showed that pine caleosin was closely-related to the caleosin of cycad megagametophyte among known caleosin sequences. While pine oleosin-L was found clustered with seed oleosin isoforms of angiosperm species, oleosin-G was distinctively grouped with the oleosin-P of lily pollen. The oleosin-G identified in pine megagametophytes seems to represent a new class of seed oleosin isoform evolutionarily close to the pollen oleosin-P.

Expression and characterization of the calcium-activated photoprotein from the ctenophore Bathocyroe fosteri: insights into light-sensitive photoproteins

Calcium-binding photoproteins have been discovered in a variety of luminous marine organisms [1]. Recent interest in photoproteins from the phylum Ctenophora has stemmed from cloning and expression of several photoproteins from this group [2-5]. Additional characterization has revealed unique biochemical properties found only in ctenophore photoproteins, such as inactivation by light. Here we report the cloning, expression, and characterization of the photoprotein responsible for luminescence in the deep-sea ctenophore Bathocyroe fosteri. This animal was of particular interest due to the unique broad color spectrum observed in live specimens [6]. Full-length sequences were identified by BLAST searches of known photoprotein sequences against Bathocyroe transcripts obtained from 454 sequencing. Recombinantly expressed Bathocyroe photoprotein (BfosPP) displayed an optimal coelenterazine-loading pH of 8.5, and produced calcium-triggered luminescence with peak wavelengths closely matching the 493 nm peak observed in the spectrum of live B. fosteri specimens. Luminescence from recombinant BfosPP was inactivated most efficiently by UV and blue light. Primary structure alignment of BfosPP with other characterized photoproteins showed very strong sequence similarity to other ctenophore photoproteins and conservation of EF-hand motifs. Both alignment and structural prediction data provide more insight into the formation of the coelenterazine-binding domain and the probable mechanism of photoinactivation.

Adaptations to endosymbiosis in a cnidarian-dinoflagellate association: differential gene expression and specific gene duplications

Trophic endosymbiosis between anthozoans and photosynthetic dinoflagellates forms the key foundation of reef ecosystems. Dysfunction and collapse of symbiosis lead to bleaching (symbiont expulsion), which is responsible for the severe worldwide decline of coral reefs. Molecular signals are central to the stability of this partnership and are therefore closely related to coral health. To decipher inter-partner signaling, we developed genomic resources (cDNA library and microarrays) from the symbiotic sea anemone Anemonia viridis. Here we describe differential expression between symbiotic (also called zooxanthellate anemones) or aposymbiotic (also called bleached) A. viridis specimens, using microarray hybridizations and qPCR experiments. We mapped, for the first time, transcript abundance separately in the epidermal cell layer and the gastrodermal cells that host photosynthetic symbionts. Transcriptomic profiles showed large inter-individual variability, indicating that aposymbiosis could be induced by different pathways. We defined a restricted subset of 39 common genes that are characteristic of the symbiotic or aposymbiotic states. We demonstrated that transcription of many genes belonging to this set is specifically enhanced in the symbiotic cells (gastroderm). A model is proposed where the aposymbiotic and therefore heterotrophic state triggers vesicular trafficking, whereas the symbiotic and therefore autotrophic state favors metabolic exchanges between host and symbiont. Several genetic pathways were investigated in more detail: i) a key vitamin K-dependant process involved in the dinoflagellate-cnidarian recognition; ii) two cnidarian tissue-specific carbonic anhydrases involved in the carbon transfer from the environment to the intracellular symbionts; iii) host collagen synthesis, mostly supported by the symbiotic tissue. Further, we identified specific gene duplications and showed that the cnidarian-specific isoform was also up-regulated both in the symbiotic state and in the gastroderm. Our results thus offer new insight into the inter-partner signaling required for the physiological mechanisms of the symbiosis that is crucial for coral health.

CBL-mediated targeting of CIPKs facilitates the decoding of calcium signals emanating from distinct cellular stores

During adaptation and developmental processes cells respond through nonlinear calcium-decoding signaling cascades, the principal components of which have been identified. However, the molecular mechanisms generating specificity of cellular responses remain poorly understood. Calcineurin B-like (CBL) proteins contribute to decoding calcium signals by specifically interacting with a group of CBL-interacting protein kinases (CIPKs). Here, we report the subcellular localization of all 10 CBL proteins from Arabidopsis and provide a cellular localization matrix of a plant calcium signaling network. Our findings suggest that individual CBL proteins decode calcium signals not only at the plasma membrane and the tonoplast, but also in the cytoplasm and nucleus. We found that distinct targeting signals located in the N-terminal domain of CBL proteins determine the spatially discrete localization of CBL/CIPK complexes by COPII-independent targeting pathways. Our findings establish the CBL/CIPK signaling network as a calcium decoding system that enables the simultaneous specific information processing of calcium signals emanating from different intra- and extracellular stores, and thereby provides a mechanism underlying the specificity of cellular responses.

Calponin in non-muscle cells

Calponin is an actin filament-associated regulatory protein expressed in smooth muscle and non-muscle cells. Calponin is an inhibitor of the actin-activated myosin ATPase. Three isoforms of calponin have been found in the vertebrates. Whereas the role of calponin in regulating smooth muscle contractility has been extensively investigated, the function and regulation of calponin in non-muscle cells is much less understood. Based on recent progresses in the field, this review focuses on the studies of calponin in non-muscle cells, especially its regulation by cytoskeleton tension and function in cell motility. The ongoing research has demonstrated that calponin plays a regulatory role in non-muscle cell motility. Therefore, non-muscle calponin is an attractive target for the control of cell proliferation, migration and phagocytosis, and the treatment of cancer metastasis.

Gene Duplication and the Evolution of Vertebrate Skeletal Mineralization

The mineralized skeleton is a critical innovation that evolved early in vertebrate history. The tissues found in dermal skeletons of ancient vertebrates are similar to the dental tissues of modern vertebrates; both consist of a highly mineralized surface hard tissue, enamel or enameloid, more resilient body dentin, and basal bone. Many proteins regulating mineralization of these tissues are evolutionarily related and form the secretory calcium-binding phosphoprotein (SCPP) family. We hypothesize here the duplication histories of SCPP genes and their common ancestors, SPARC and SPARCL1. At around the same time that Paleozoic jawless vertebrates first evolved mineralized skeleton, SPARCL1 arose from SPARC by whole genome duplication. Then both before and after the split of ray-finned fish and lobe-finned fish, tandem gene duplication created two types of SCPP genes, each residing on the opposite side of SPARCL1. One type was subsequently used in surface tissue and the other in body tissue. In tetrapods, these two types of SCPP genes were separated by intrachromosomal rearrangement. While new SCPP genes arose by duplication, some old genes were eliminated from the genome. As a consequence, phenogenetic drift occurred: while mineralized skeleton is maintained by natural selection, the underlying genetic basis has changed.

Biochemical characterization of a truncated penta-EF-hand Ca2+ binding protein from maize

Plants possess multiple genes encoding calcium sensor proteins that are members of the penta-EF-hand (PEF) family. Characterized PEF proteins such as ALG-2 (apoptosis-linked gene 2 product) and the calpain small subunit function in diverse cellular processes in a calcium-dependent manner by interacting with their target proteins at either their N-terminal extension or Ca2+ binding domains. We have identified a previously unreported class of PEF proteins in plants that are notable because they do not possess the hydrophobic amino acid rich N-terminal extension that is typical of these PEF proteins. We demonstrate that the maize PEF protein without the N-terminal extension has the characteristics of known PEF proteins; the protein binds calcium in the 100 nM range and, as a result of calcium binding, displays an increase in hydrophobicity. Characterization of the truncated maize PEF protein provides insights into the role of the N-terminal extension in PEF protein signaling. In the context of the current model of how PEF proteins are activated by calcium binding, these results demonstrate that this distinctive class of PEF proteins could function as calcium sensor proteins in plants even in the absence of the N-terminal extension.

The anatomical relationships between the serotonergic afferents and the neurons containing calcium-binding proteins in the rat claustrum

Claustrum is a telencephalic structure integrating information of various modalities. Proper functioning of this structure depends on the presence of a network of intrinsic connections. This includes GABA-ergic neuronal populations that also contain calcium-binding proteins (CaBPs). The goal of this study was to analyze qualitative and quantitative the 5-HT-containing fibers in the rat claustrum and to assess the relationships between these fibers and the populations of claustral neurons expressing CaBPs. We used the methods of immunocytochemistry and morphometry. The serotonergic fibers in the claustrum are heterogeneous, both with respect to their morphology and spatial distribution. Thin varicose fibers are more numerous and are homogeneously distributed within the claustrum. Remaining fibers were thicker and possessed larger varicosities. They were present mainly in the ventral part of the claustrum. Although the serotonergic fibers are found in the vicinity of claustral cells containing CaBPs, direct contacts between these fibers and cells are rare. Other mechanisms, including volume transmission, may possibly mediate serotonergic influences.

Calcium Homeostasis in Human Placenta: Role of Calcium‐Handling Proteins

The human placenta is a transitory organ, representing during pregnancy the unique connection between the mother and her fetus. The syncytiotrophoblast represents the specialized unit in the placenta that is directly involved in fetal nutrition, mainly involving essential nutrients, such as lipids, amino acids, and calcium. This ion is of particular interest since it is actively transported by the placenta throughout pregnancy and is associated with many roles during intrauterine life. At term, the human fetus has accumulated about 25-30 g of calcium. This transfer allows adequate fetal growth and development, since calcium is vital for fetal skeleton mineralization and many cellular functions, such as signal transduction, neurotransmitter release, and cellular growth. Thus, there are many proteins involved in calcium homeostasis in the human placenta.

Expression of calcium-binding proteins in the proliferative zones around the corticostriatal junction of rabbits during pre- and postnatal development

Herein we asked whether cells expressing calcium-binding proteins around the corticostriatal junction are of pallial or subpallial origin. Brains of rabbit embryos between embryonic day E18 and E28 and postnatal day 0-P22 were immunoreacted with monoclonal antibodies raised against calretinin, calbindin and parvalbumin. At E18-E21, calbindin- and calretinin-immunoreactive cells were seen in distinct proliferative zones in the vicinity of the corticostriatal junction. Whereas calbindin-immunoreactive neurons were in the ventricular zone of the ventral pallium (the medial wall of the lateral ventricular angle), calretinin-immunoreactive cells were, nearby, in the subventricular zone of the subpallium at the lateral edge of the lateral ganglionic eminence. From E25 to P22, both calbindin- and calretinin-immunoreactive cells appeared in the pallial ventricular and subventricular zones around the lateral ventricular angle. Some of these cells resembled migratory neuroblasts. Parvalbumin-immunoreactive cells appeared at P5-P10, albeit they were almost negligible in the proliferative zones around the corticostriatal junction and the lateral ventricular angle. The results suggest that a number of the calbindin-expressing neurons that are generated in mid-gestation and postnatally are of pallial origin. They also indicate that only a few of the late-generated calretinin-immunoreactive cells may have a pallial source. The origin of the parvalbumin-immunoreactive cells was not ascertained in the present study.

Chromosomal localization, genomic organization and evolution of the genes encoding human phosphatidylinositol transfer protein membrane-associated (PITPNM) 1, 2 and 3

Eukaryotic proteins containing a phosphatidylinositol transfer (PITP) domain can be divided into two groups, one consisting of small soluble 35-kDa proteins and the other those that are membrane-associated and show sequence similarities to the Drosophila retinal degeneration B (rdgB) protein. The rdgB protein consists of four domains, an amino terminal PITP domain, a Ca2+-binding domain, a transmembrane domain and a carboxyl terminal domain that interacts with the protein tyrosine kinase PYK2. Three mammalian phosphatidylinositol transfer protein membrane-associated genes (PITPNM1, 2 and 3) with homology to Drosophila rdgB have previously been described and shown to be expressed in the mammalian retina. These findings and the demonstration that the rdgB gene plays a critical role in the invertebrate phototransduction pathway have led to the mammalian genes being considered as candidate genes for human eye diseases. In order to facilitate the analysis of these genes we have used radiation hybrid mapping and fluorescence in situ hybridization to localize the PITPNM2 and 3 genes to human chromosomes 12p24 and 17p13 respectively and hybrid mapping to confirm the localization of PITPNM1 to chromosome 11q13. We have also determined the genomic organization of both the soluble and membrane-associated Drosophila and human PITP domain-containing genes. Phylogenetic analysis indicates that the two groups arose by gene duplication that occurred very early in animal evolution.

Basal body duplication and maintenance require one member of the Tetrahymena thermophila centrin gene family

Centrins, small calcium binding EF-hand proteins, function in the duplication of a variety of microtubule organizing centers. These include centrioles in humans, basal bodies in green algae, and spindle pole bodies in yeast. The ciliate Tetrahymena thermophila contains at least four centrin genes as determined by sequence homology, and these have distinct localization and expression patterns. CEN1's role at the basal body was examined more closely. The Cen1 protein localizes primarily to two locations: one is the site at the base of the basal body where duplication is initiated. The other is the transition zone between the basal body and axoneme. CEN1 is an essential gene, the deletion of which results in the loss of basal bodies, which is likely due to defects in both basal body duplication and basal body maintenance. Analysis of the three other centrins indicates that two of them function at microtubule-rich structures unique to ciliates, whereas the fourth is not expressed under conditions examined in this study, although when artificially expressed it localizes to basal bodies. This study provides evidence that in addition to its previously known function in the duplication of basal bodies, centrin is also important for the integrity of these organelles.

GANESH: software for customized annotation of genome regions

GANESH is a software package designed to support the genetic analysis of regions of human and other genomes. It provides a set of components that may be assembled to construct a self-updating database of DNA sequence, mapping data, and annotations of possible genome features. Once one or more remote sources of data for the target region have been identified, all sequences for that region are downloaded, assimilated, and subjected to a (configurable) set of standard database-searching and genome-analysis packages. The results are stored in compressed form in a relational database, and are updated automatically on a regular schedule so that they are always immediately available in their most up-to-date versions. A Java front-end, executed as a stand alone application or web applet, provides a graphical interface for navigating the database and for viewing the annotations. There are facilities for importing and exporting data in the format of the Distributed Annotation System (DAS), enabling a GANESH database to be used as a component of a DAS configuration. The system has been used to construct databases for about a dozen regions of human chromosomes and for three regions of mouse chromosomes.

Calcium-regulated protein kinases of plants

The importance of calcium ions in coupling physiological responses to external and developmental signals in plants has been well documented. Recently, Plieth and Trewavas (Plant Physiology, 2002, 129: 786-796) have shown that gravistimulation, too, elicits changes in the concentration of cytoplasmic Ca2+ in Arabidopsis plants. Cytoplasmic calcium brings about responses by interacting with target proteins, many of which contain EF-hand calcium-binding motifs. In plants there are at least five classes of protein kinases, all of which are in the CDPK/SnRK family, that either contain EF-hands within their structure or interact with proteins that contain EF-hands. Calcium-dependent protein kinases (CDPKs) and calcium and calmodulin-activated protein kinases (CCaMKs) both contain EF hands in their C-terminal domains and are activated by the binding of calcium. SnRK3s (Group 3 of the SNF-1 related kinases) bind to proteins that contain three EF hands, and some are activated by calcium. Members of two other protein kinase classes, plant calmodulin-dependent protein kinase (CaMK) and CDPK-related kinase (CRK), bind to calmodulin, but it remains to be seen whether the activity of these enzymes is regulated by calcium/calmodulin. This paper will review what is known about the structure and the regulation of these protein kinases and address the question of why there is such a plethora of calcium-regulated kinases in plants.

Characterization of the spasmin 1 gene in Zoothamnium arbuscula strain Kawagoe (protozoa, ciliophora) and its relation to other spasmins and centrins

Zoothamnium arbuscula strain Kawagoe is a giant sessile peritrich ciliated protozoa that possesses a contractile organelle called a spasmoneme. We report here on the molecular characterization and provide an opportunity to discuss the evolutionary relationships of the Z. arbuscula spasmin; spasmins belong to the calmodulin superfamily and are the major components of spasmoneme filaments. We analysed and obtained the whole sequence of the spasmin 1 gene and a partial sequence of the spasmin 2 gene. It is surprising that the sequence of spasmin 1 does not contain introns and encodes an open reading frame of 531 bp. It predicts a product of 177 amino acids with a calculated molecular mass of 19659 Da and a pI of 4.68. The amino acid sequence has two putative calcium-binding domains. One of them is a functional domain, as defined by the EF-hand consensus. The varieties of spasmins were revealed by comparison with amino acid components and molecular relationships of spasmin 1 protein and other spasmins. A comparison of the amino acid sequence between the Z. arbuscula spasmin and known centrins indicates that spasmins have a one residue deletion in the EF-hand domain-2 and four residue insertions in domain-4, as does the Vorticella spasmin. However, there are large variations in the amino acid sequence at domain-4 within spasmin 1, spasmin 2 and the Vorticella spasmin.

Distribution of calcium-binding proteins in the cerebellum

Calcium plays a fundamental role in the cell as second messenger and is principally regulated by calcium-binding proteins. Although these proteins share in common their ability to bind calcium, they belong to different subfamilies. They present, in general, specific developmental and distribution patterns. Most Purkinje cells express the fast and slow calcium buffer proteins calbindin-D28k and parvalbumin, whereas basket, stellate and Golgi cells the slow buffer parvalbumin only. They are, almost all, calretinin negative. Granule, Lugaro and unipolar brush cells present an opposite immunoreactivity profile, most of them being calretinin positive while lacking calbindin-D28k and parvalbumin. The developmental pattern of appearance of these proteins seems to follow the maturation of neurons. Calbindin-D28k appears early, shortly after cessation of mitosis when neurons become ready to start migration and differentiation while parvalbumin is expressed later in parallel with an increase in neuronal activity. The other proteins are generally detected later. During development, some of these proteins, like calretinin, are transiently expressed in specific cellular subpopulations. The function of these proteins is not fully understood, although strong evidence supports a prominent role in physiological settings with altered calcium concentrations. These proteins regulate and are regulated by intracellular calcium level. For example, they may directly or indirectly enable sensitization or desensitization of calcium channels, and may further block calcium entry into the cells, like the calcium-sensor proteins, that have been shown to be potent and specific modulators of ion channels, which may allow for feedback control of current function and hence signaling. The absence of calcium buffer proteins results in marked abnormalities in cell firing; with alterations in simple and complex spikes or transformation of depressing synapses into facilitating synapses. Calcium-binding protein implication in resistance to degeneration is still a controversial issue. Neurons rich in calcium-binding proteins, especially calbindin-D28k and parvalbumin, seem to be relatively resistant to degeneration in a variety of acute and chronic disorders. However other data support that an absence of calcium-binding proteins may also have a neuroprotective effect. It is not unlikely that neurons may face a dual action mechanism where a decrease in calcium-binding proteins has a first short-term beneficial effect while it becomes detrimental for the cell over the long term.

Calcium-binding proteins: intracellular sensors from the calmodulin superfamily

In all eukaryotic cells, and particularly in neurons, Ca(2+) ions are important second messengers in a variety of cellular signaling pathways. In the retina, Ca(2+) modulation plays a crucial function in the development of the visual system's neuronal connectivity and a regulatory role in the conversion of the light signal received by photoreceptors into an electrical signal transmitted to the brain. Therefore, the study of retinal Ca(2+)-binding proteins, which frequently mediate Ca(2+) signaling, has given rise to the important discovery of two subfamilies of these proteins, neuronal Ca(2+)-binding proteins (NCBPs) and calcium-binding proteins (CaBPs), that display similarities to calmodulin (CaM). These and other Ca(2+)-binding proteins are integral components of cellular events controlled by Ca(2+). Some members of these subfamilies also play a vital role in signal transduction outside of the retina. The expansion of the CaM-like protein family reveals diversification among Ca(2+)-binding proteins that evolved on the basis of the classic molecule, CaM. A large number of NCBP and CaBP subfamily members would benefit from their potentially specialized role in Ca(2+)-dependent cellular processes. Pinpointing the role of these proteins will be a challenging task for further research.

An Arabidopsis SNF1-related protein kinase, AtSR1, interacts with a calcium-binding protein, AtCBL2, of which transcripts respond to light

AtSR1 is a protein kinase of Arabidopsis thaliana, which belongs to the SNF1-related protein kinase subfamily 3. We previously showed accumulation of its transcripts to be responsive to light. In this study, we examined the interaction between AtSR1 and six calcineurin B like proteins of Arabidopsis and found that AtSR1 prominently interacts with one of them, AtCBL2, by yeast two-hybrid assay. Interaction between AtSR1 and AtCBL2 could also be directly confirmed in vitro by pull down assay. RNA blot and reverse transcription-polymerase chain reaction analyses showed that transcripts of AtCBL2, and also of AtCBL1, another CBL, increased upon illumination of leaves. The physiological meaning of the interaction of AtSR1and AtCBL2 is not clear, but they presumably function in signal transduction of light.

Matrix Gla protein in Xenopus laevis: molecular cloning, tissue distribution, and evolutionary considerations

Matrix Gla protein (MGP) belongs to the family of vitamin K-dependent, Gla-containing proteins and in higher vertebrates, is found in the extracellular matrix of mineralized tissues and soft tissues. MGP synthesis is highly regulated at the transcription and posttranscription levels and is now known to be involved in the regulation of extracellular matrix calcification and maintenance of cartilage and soft tissue integrity during growth and development. However, its mode of action at the molecular level remains unknown. Because there is a large degree of conservation between amino acid sequences of shark and human MGP, the function of MGP probably has been conserved throughout evolution. Given the complexity of the mammalian system, the study of MGP in a lower vertebrate might be advantageous to relate the onset of MGP expression with specific events during development. Toward this goal, MGP was purified from Xenopus long bones and its N-terminal amino acid sequence was determined and used to clone the Xenopus MGP complementary DNA (cDNA) by a mixture of reverse-transcription (RT)- and 5'- rapid amplification of cDNA ends (RACE)-polymerase chain reaction (PCR). MGP messenger RNA (mRNA) was present in all tissues analyzed although predominantly expressed in Xenopus bone and heart and its presence was detected early in development at the onset of chondrocranium development and long before the appearance of the first calcified structures and metamorphosis. These results show that in this system, as in mammals, MGP may be required to delay or prevent mineralization of cartilage and soft tissues during the early stages of development and indicate that Xenopus is an adequate model organism to further study MGP function during growth and development.

Identification and characterization of two penta-EF-hand Ca(2+)-binding proteins in Dictyostelium discoideum

Penta-EF-hand (PEF) proteins such as ALG-2 (apoptosis-linked gene 2 product) and the calpain small subunit are a newly classified family of Ca(2+)-binding proteins that possess five EF-hand-like motifs. We identified two mutually homologous PEF proteins, designated DdPEF-1 and DdPEF-2 (64% amino acid residue identities), in the cellular slime mold Dictyostelium discoideum. Both PEF proteins showed a higher similarity to mammalian ALG-2 and peflin (Group I PEF proteins) than to calpain and sorcin subfamily (Group II PEF proteins) in the first EF-hand (EF-1) regions. Northern blot analyses revealed that DdPEF-1 and DdPEF-2 were constitutively expressed throughout development of Dictyostelium, but their levels of expression were developmentally regulated. In situ hybridization analyses demonstrated that DdPEF-1 was expressed in both the anterior prestalk and the posterior prespore regions of the tipped aggregate, slugs and early culminants. On the other hand, DdPEF-2 was dominantly expressed in the anterior tip region of these multicellular structures. Both PEF proteins were detected as 22-23-kDa proteins in soluble fractions in the presence of EGTA but in particulate fractions in the presence of Ca(2+) by Western blotting using specific monoclonal antibodies. Together with the finding of PEF-like sequences in DNA databases of plants, fungi and protists, our results strongly suggest that Group I PEF proteins are ubiquitously present in all eukaryotes and play important roles in basic cellular functions.

Synaptotagmin 13: structure and expression of a novel synaptotagmin

Synaptotagmins represent a family of putative vesicular trafficking proteins. With synaptotagmin 13, we have now identified a novel synaptotagmin, making this one of the largest families of trafficking proteins. Similar to synaptotagmins 3, 4, 6, 7, 9, and 11, synaptotagmin 13 is expressed at highest levels in brain but is also detectable at lower levels in non-neuronal tissues. Synaptotagmin 13 is composed of the canonical domains of synaptotagmins that include an N-terminal transmembrane region and two C-terminal cytoplasmic C2-domains (C2A- and C2B-domain) and a connecting sequence between the transmembrane region and the C2-domains. Different from most other synaptotagmins, however, synaptotagmin 13 does not have an N-terminal sequence preceding the transmembrane region, and features an unusually long connecting sequence that is proline-rich. Furthermore, the C2-domains of synaptotagmin are degenerate and lack almost all of the residues involved in Ca2+ binding, suggesting that synaptotagmin 13 is not a Ca2+-binding protein unlike most other synaptotagmins. Our data demonstrate that synaptotagmins represent a larger and more complex gene family than previously envisioned.

Classification and evolution of EF-hand proteins

Forty-five distinct subfamilies of EF-hand proteins have been identified. They contain from two to eight EF-hands that are recognizable by amino acid sequence as being statistically similar to other EF-hand domains. All proteins within one subfamily are congruent to one another, i.e. the dendrogram computed from one of the EF-hand domains is similar, within statistical error, to the dendrogram computed from another(s) domain. Thirteen subfamilies--including Calmodulin, Troponin C, Essential light chain, Regulatory light chain--referred to collectively as CTER, are congruent with one another. They appear to have evolved from a single ur-domain by two cycles of gene duplication and fusion. The subfamilies of CTER subsequently evolved by gene duplications and speciations. The remaining 32 subfamilies do not show such general patterns of congruence; however, some--such as S100, intestinal calcium binding protein (calbindin 9 kd), and trichohylin--do not form congruent clusters of subfamilies. Nearly all of the domains 1, 3, 5, and 7 are most similar to other ODD domains. Correspondingly the EVEN numbered domains of all 45 subfamilies most closely resemble EVEN domains of other subfamilies. Many sequence and chemical characteristics do not show systemic trends by subfamily or species of host organisms; such homoplasy is widespread. Eighteen of the subfamilies are heterochimeric; in addition to multiple EF-hands they contain domains of other evolutionary origins.

Psoriasin binds calcium and is upregulated by calcium to levels that resemble those observed in normal skin

Recently, we described a small molecular weight protein termed psoriasin that showed sequence similarity with the S100 calcium-binding proteins and that is highly upregulated in psoriatic epidermis as well as in primary human keratinocytes undergoing abnormal differentiation. Here we present evidence showing that natural and recombinant psoriasin binds calcium, as judged by the calcium overlay assay, and that it contains all the sequence features characteristic of the S100 family. Furthermore, [35S]-methionine labeling experiments showed that psoriasin synthesis is upregulated by 2 mM Ca++ (ratio Ca++/control at 88 h = 2.56) to levels that resemble those observed in unfractionated keratinocyte populations obtained from normal skin.

Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories

In the first report in this series we described the relationships and evolution of 152 individual proteins of the EF-hand subfamilies. Here we add 66 additional proteins and define eight (CDC, TPNV, CLNB, LPS, DGK, 1F8, VIS, TCBP) new subfamilies and seven (CAL, SQUD, CDPK, EFH5, TPP, LAV, CRGP) new unique proteins, which we assume represent new subfamilies. The main focus of this study is the classification of individual EF-hand domains. Five subfamilies--calmodulin, troponin C, essential light chain, regulatory light chain, CDC31/caltractin--and three uniques--call, squidulin, and calcium-dependent protein kinase--are congruent in that all evolved from a common four-domain precursor. In contrast calpain and sarcoplasmic calcium-binding protein (SARC) each evolved from its own one-domain precursor. The remaining 19 subfamilies and uniques appear to have evolved by translocation and splicing of genes encoding the EF-hand domains that were precursors to the congruent eight and to calpain and to SARC. The rates of evolution of the EF-hand domains are slower following formation of the subfamilies and establishment of their functions. Subfamilies are not readily classified by patterns of calcium coordination, interdomain linker stability, and glycine and proline distribution. There are many homoplasies indicating that similar variants of the EF-hand evolved by independent pathways.

Prokaryotic calcium-binding protein of the calmodulin superfamily. Calcium binding to a Saccharopolyspora erythraea 20 kDa protein

The EF-hand calcium-binding protein from Saccharopolyspora erythraea has been shown, using 113Cd NMR, to possess three Cd(2+)-ion binding sites. This indicates that of the four EF-hand motifs in the molecule, one (probably site 2) is unable to bind Cd(2+)-ions. Data from the titration of the protein with Ca2+, in the presence of Quin2, were fitted to a curve calculated on the assumption that the protein contains three high affinity Ca2+ binding sites, two of which (pK1 = 8.0, pK2 = 9.0) are strongly cooperative, and one single site (pK3 = 7.5). Preliminary 1H NMR experiments indicate marked structural changes upon Ca(2+)-binding.

A series of annexins from human placenta and their characterization by use of an endogenous phospholipase A2

Membranes from human placenta contain proteins which inhibit the activity of phospholipases A2 by binding to phospholipid thus impeding substrate availability. We used unilamellar mixed liposomes and a partially purified cytosolic phospholipase A2 from placenta for characterizing this substrate-depleting activity. A major portion of these inhibitory proteins was released by extracting washed membranes with a Ca+(+)-chelator. Biochemical fractionation and systematic analysis resulted in the unequivocal identification of a series of annexin proteins. We describe a straightforward procedure which allows to obtain 8 annexins from placenta either in pure form or as a mixture of two annexins. One of them was obtained in two forms which had the same molecular mass of 68 kDa but differed in charge. We also present suggestive evidence for a novel annexin I-related polypeptide of Mr 45,000 which is an excellent in vitro substrate for protein kinase C. We estimate that about 2% of the total placental membrane proteins are annexins. For achieving half inhibition of phospholipase A2 activity with pure annexins, up to a 6.5-fold difference in the amounts of protein was observed when calculated on a molar basis. This suggests specificity of individual annexin species.

Calcium-binding proteins: an overview

In order to understand the mechanism of the various responses evoked by calcium in the cell, the identification and characterization of a number of calcium receptors were undertaken within the past two decades. Advances in amino acid sequence and protein three-dimensional structure led to the description of two families of calcium-binding proteins, the EF-hand homolog family and the annexin family. The EF-hand motif consists of two alpha helices, "E" and "F", joined by a Ca(2+)-binding loop. EF-hands have been identified in numerous Ca(2+)-binding proteins by similarity of amino acid sequence and confirmed in some crystal structures. Functional EF-hands seem always to occur in pairs. To date, the EF-hand homolog family contains more than 160 different Ca(2+)-modulated proteins which have a broad range of functions. Among them, are the calmodulin, the troponin C, the myosin regulatory light chain, the parvalbumin, the S-100 proteins and the calbindins 9- and 28 kDa. The most striking feature of the EF-hand family is the ability to modulate the activity of a number of enzymes. Several groups have identified proteins from various tissues that show calcium-dependent binding to membranes. These proteins, termed annexins have a molecular weight of 35- or 67 kDa. The amino acid sequences of the members of the annexin family show that each protein contains conserved internal repeats of about 70 amino acids each. The 35 kDa annexins contain four repeats, which show a high degree of homology with each other and with the repeat sequences of the other proteins. These repeats correspond to structural domains with a similar fold.(ABSTRACT TRUNCATED AT 250 WORDS)

The EF-hand family of calcium-modulated proteins

The EF-hand homolog proteins bind calcium (Ca2+) with dissociation constants in the micromolar range and are modulated by stimulus-induced increases in cytosolic free Ca2+. We have grouped over 160 different EF-hand homolog proteins into ten subfamilies and ten unique categories. Except for troponin-C, all subfamilies and unique EF-hand homologs represented in vertebrates can be found in the CNS. In this review, structural and functional characteristics of these proteins are discussed, with special emphasis on the multifunctional regulatory protein, calmodulin. The possible function of bending within the central helix of calmodulin is considered and is illustrated with a model calmodulin--target complex.

Identification of bovine brain calcium binding proteins

Three peaks of calcium binding activity have been identified by the Chelex-100 calcium binding assay of the fractions from DEAE cellulose chromatography of 100,000 X g supernatant of bovine brain. These calcium binding activity peaks have been subjected to extensive purification and three novel calcium binding proteins (Mr 27,000, Mr 48,000 and Mr 63,000) and two previously characterized proteins (calcineurin and calmodulin) have been identified as components of calcium binding activity peaks. Analysis of the calcium binding properties of the novel proteins by equilibrium dialysis suggests these proteins may be intracellular calcium receptors.