Evolution of the EF-hand calcium-binding protein family: evidence for exon shuffling and intron insertion

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.

Characterization of the X-linked murine centrin Cetn2 gene

A multi-gene family (Cetn1, Cetn2, and Cetn3) encodes the calcium-binding protein, centrin, in the mouse. This work characterizes the Cetn2 gene. Structurally, Cetn2 consists of five exons and four introns, and contains a classical TATA-less promoter. Cetn2 has two alternate transcription start sites, and a single length 3' untranslated region. Fluorescence in situ hybridization demonstrates that Cetn2 is an X-linked gene whose alleles replicate asynchronously during S-phase. Cetn2 encodes a 172 amino acid protein, with a predicted molecular mass of 19,795 Da (pI=4.71), that contains all of the defining characteristics of centrin. Northern blot analysis indicates that Cetn2 is ubiquitously expressed in the tissues of adult mice. RT-PCR shows that Cetn2 and Cetn3, but not Cetn1, are expressed in NIH 3T3 cells. Immunofluorescence microscopy demonstrates that mouse centrin 2 protein localizes to the region immediately surrounding the centrioles in the centrosome of NIH 3T3 cells.

Molecular characterization of a calmodulin-like dictyostelium protein CalB

A gene named calB was cloned and characterized in Dictyostelium. A relationship to calmodulin (CaM) is suggested by sequence identity (50%), similar exon-intron structure and cross-reactivity with anti-CaM sera. The level of calB mRNA is developmentally regulated with maxima during aggregation and in spores. CalB null cells grow normally, develop and produce viable spores. We demonstrated the capacity of tagged CalB to bind Ca(2+) using the (45)Ca(2+) overlay assay and showed that its mobility on SDS-PAGE is dependent on Ca(2+)/EGTA pretreatment.

Calbrain, a novel two EF-hand calcium-binding protein that suppresses Ca2+/calmodulin-dependent protein kinase II activity in the brain

A cDNA clone that encodes a novel Ca2+-binding protein was isolated from a human brain cDNA library. The gene for this clone, termed calbrain, encodes a 70-amino acid polypeptide with a predicted molecular mass of 8.06 kDa. The analysis of deduced amino acid sequence revealed that calbrain contains two putative EF-hand motifs that show significantly high homology to those of the calmodulin (CaM) family rather than two EF-hand protein families. By Northern hybridization analysis, an approximate 1.5-kilobase pair transcript of calbrain was detected exclusively in the brain, and in situ hybridization study revealed its abundant expression in the hippocampus, habenular area in the epithalamus, and in the cerebellum. A recombinant calbrain protein showed a Ca2+ binding capacity, suggesting the functional potency as a regulator of Ca2+-mediated cellular processes. Ca2+/calmodulin-dependent kinase II, the most abundant protein kinase in the hippocampus and strongly implicated in the basic neuronal functions, was used to evaluate the physiological roles of calbrain. Studies in vitro revealed that calbrain competitively inhibited CaM binding to Ca2+/calmodulin-dependent kinase II (Ki = 129 nM) and reduced its kinase activity and autophosphorylation.

A unique exon-intron organization of a porcine S100C gene: close evolutionary relationship to calmodulin genes

We found a unique exon-intron structure of the porcine S100C gene, a member of the S100 family, in which all other genes characterized to date have common exon-intron organization. The genomic DNA encoding the porcine S100C was cloned and the entire nucleotide sequence of the gene was analyzed. The gene is present as a single copy and consists of three exons and two introns with a total size of 5.3 kb. The first intron is located after the ATG translation initiation codon. Such an intron has never been found in other S100 genes, but is found in almost all calmodulin genes. The gene structural similarity suggests a close evolutionary relationship between the S100C gene and calmodulin genes.

Calbindin-D9k and calbindin-D28k expression in rat mineralized tissues in vivo

Following their terminal differentiation, highly specialized cells, ameloblasts, odontoblasts, and osteoblasts sequentially elaborate mineralized tissues. While the developmental expression pattern of matrix proteins has been studied extensively, less attention has been paid to the molecules involved in calcium handling, such as calcium-binding proteins. This shortcoming, as well as previous conflicting data, led us to conduct studies on calbindin-D9k and calbindin-D28k in rat mandibular bone and incisor based on several methods established on rat ameloblasts in vivo. Radioimmunoassays showed that calbindin-D28k accounts for approximately 0.1% of cytosolic proteins in the ectomesenchymal fraction and 1% in the epithelial fraction of the rat incisor and is 100-fold more concentrated than calbindin-D9k in both tissue types. Western blot analysis confirmed that the anticalbindin-D28k reactive species corresponded to the well characterized renal calbindin-D28k in the ectomesenchyme. In this tissue, calbindin-D28k was ultrastructurally immunolocalized in the odontoblasts. Quantitative immunocytochemistry showed that labeling was distributed throughout their nucleus and cytoplasm. The similar cytoplasmic distribution of both calbindin-D proteins and mRNAs suggests that their expression is regulated at the subcellular level. In particular, immunoreactive calbindin-D28k appeared to be associated with rough endoplasmic reticulum. Calbindin-D9k antisense probe showed negligible labeling in odontoblasts, in parallel with the protein quantities measured (approximately 10 ng/mg of total protein). Finally, in situ hybridization showed transcripts for both calbindins-D in ameloblasts and also in osteoblasts. In summary, the present results support the concept that an elevated expression of these vitamin D-dependent calcium-binding proteins may characterize the phenotype of cells directly involved in the elaboration of mineralized tissues, enamel, dentine, and bone.

The nuclear matrix: a structural milieu for genomic function

While significant progress has been made in elucidating molecular properties of specific genes and their regulation, our understanding of how the whole genome is coordinated has lagged behind. To understand how the genome functions as a coordinated whole, we must understand how the nucleus is put together and functions as a whole. An important step in that direction occurred with the isolation and characterization of the nuclear matrix. Aside from the plethora of functional properties associated with these isolated nuclear structures, they have enabled the first direct examination and molecular cloning of specific nuclear matrix proteins. The isolated nuclear matrix can be used for providing an in vitro model for understanding nuclear matrix organization in whole cells. Recent development of high-resolution and three-dimensional approaches for visualizing domains of genomic organization and function in situ has provided corroborative evidence for the nuclear matrix as the site of organization for replication, transcription, and post-transcriptional processing. As more is learned about these in situ functional sites, appropriate experiments could be designed to test molecular mechanisms with the in vitro nuclear matrix systems. This is illustrated in this chapter by the studies of nuclear matrix-associated DNA replication which have evolved from biochemical studies of in vitro nuclear matrix systems toward three-dimensional computer image analysis of replication sites for individual genes.

A calcineurin-B-encoding gene expressed during differentiation of the amoeboflagellate Naegleria gruberi contains two introns

One of two similar genes in the unicellular eukaryote Naegleria gruberi is shown to encode calcineurin B (CnB), the regulatory subunit of calcium-calmodulin-regulated protein phosphatase 2B. Over a span of 156 amino acids, excluding divergent N-termini, the encoded sequence shows 62% identity with vertebrate CnB, and also shows sequence elements specific, among calcium-binding proteins, to CnB. In contrast, the sequence shows only 23% identity with N. gruberi flagellar calmodulin. CNB mRNA is readily detected in amoebae; its abundance increases fourfold during differentiation to flagellates, reaches a peak at 50-70 min, when flagella are forming, and then declines. A genomic clone matches an expressed cDNA, except that it is interrupted by two phase I introns. The position of one intron, which separates the divergent N-terminal domain from the four calcium-binding domains (EF hands), is shared with a yeast CNB gene; the other is located in the central helix between the two pairs of calcium-binding loops; features that support an ancient origin. These introns, the first found in protein-coding genes of Naegleria, are flanked by characteristic splice junction sequences. N. gruberi CnB also shares similarities with recoverins. The finding in a protist of a CNB gene that contains two introns separating functional domains, shares similarities to recoverins and shows increased expression during differentiation is provocative. If the phylogeny of major groups derived from ribosomal RNA is accepted, Naegleria is among the earliest branching eukaryotes known to contain canonical pre-mRNA introns.

Calbindin-D28K (CaBP28k)-like Immunoreactivity in Ascending Projections

This study concerns the involvement of calbindin-D28K (CaBP28k)-containing neurons in the efferent projections of both the trigeminal nucleus caudalis and the dorsal vagal complex (nucleus of the solitary tract and area postrema) in rats. Recent evidence has shown that these projections are particularly important for the processing of visceroception and/or nociception at central levels. The trigeminal nucleus caudalis has dense projections to both the nucleus of the solitary tract and the parabrachial area; the dorsal vagal complex is intimately connected to the parabrachial area. CaBP28k is a calcium-binding protein the function of which could be a determining factor in controlling the excitability of cells by acting on intrinsic calcium metabolism. CaBP28k content of projections was ascertained using a double labelling approach that combined the retrograde transport of a protein - gold complex to identify projection cells and immunocytochemistry to identify CaBP28k-positive cells. The trigeminal nucleus caudalis is rich in both CaBP28k-immunoreactive cells and cells projecting to the parabrachial area or the nucleus of the solitary tract. Cells containing both the protein and the retrograde tracer, however, were mostly restricted to the superficial layers (laminae I and outer II) and to their rostral extensions, the dorsal paramarginal and paratrigeminal nuclei. These trigeminal subdivisions are targets for nociceptive, visceroceptive and thermal inputs of peripheral origins. The dorsal vagal complex is rich in CaBP28k. Dense populations of immunoreactive cells are observed in the ventrolateral part of the area postrema and all of the three main subdivisions of the nucleus of the solitary tract (rostral gustatory, ventrolateral respiratory and medial cardiovascular subregions). The subnucleus commissuralis, subnucleus centralis and dorsal subnuclei are particularly densely stained. The subnucleus centralis, which is involved in regulating food and water intake, does not project to the parabrachial area. The area postrema, subnucleus commissuralis and dorsal subnuclei, which are implicated in cardiovascular and/or ingestive behaviours, have dense projections to the parabrachial area, many of which contain CaBP28k. The present results demonstrate that CaBP28k-containing cells form a major part of the solitary and trigeminal projection systems, including subregions that are involved in visceroception and/or nociception processing. The location of solitary nucleus projection cells overlaps those of some neuropeptidergic projecting populations, suggesting colocalization. Consequently, certain neuropeptidergic actions may be CaBP28k-dependent.

Isolation of human retinal genes: recoverin cDNA and gene

A human retina cDNA library enriched for retina-specific clones was prepared by subtraction with a non-retina population of cDNA in combination with polymerase chain reaction (PCR) amplifications. A highly retina-specific cDNA clone (1190 bp) was obtained through this library encoding a 200 amino acid protein with three calcium binding sites and 87% homology to the bovine photoreceptor protein, recoverin, which has been shown to mediate the recovery of the dark current after photoactivation, and 58% homology to the calcium-binding chick cone protein, visinin. Analysis of the gene indicated a 9-10 kb single-copy gene with at least three exons and two introns. The three exons contained the entire coding sequence, and all of the calcium-binding EF-hand regions were in putative exon 1. The recoverin gene was mapped to human chromosome 17 by hybridization to a panel of human-rodent hybrid DNAs.

Differential expression of calbindin-D 28 kDa in rat incisor ameloblasts throughout enamel development

Calbindin-D 28 kDa (CaBP 28 kDa), a vitamin D-dependent calcium-binding protein, has been associated with calcium handling by cells. We have investigated the expression of this protein in the rat incisor enamel organ, an epithelium interposed between a mineralizing matrix and connective tissue rich in blood vessels, by radioimmunoassay (RIA), Western blotting, and quantitative protein A-gold immunocytochemistry with antibodies to rat kidney CaBP 28 kDa. RIA of cytosolic extracts showed that enamel organs contained relatively high concentrations of CaBP 28 kDa (compared to kidney; see review by Christakos S., C. Gabrielides, and W.B. Rhoten 1989 Endocr. Rev., 10:3-25). Immunoblotting of proteins extracted from enamel organ strips revealed an intensely-stained band near 28 kDa throughout amelogenesis following ameloblast differentiation. Immunocytochemically, CaBP 28 kDa was localized exclusively within ameloblasts. The density of labelling increased from the presecretory stage to the secretory stage and fluctuated across the maturation stage in relation to ameloblast modulation. Ruffle-ended ameloblasts consistently showed the most intense immunoreaction. Gold particles were present throughout the cytoplasm and nuclei of ameloblasts but regions rich in rough endoplasmic reticulum or cell webs showed a higher immunolabelling. Some gold particles were also associated with the external face of the rough endoplasmic reticulum. Multivesicular bodies in maturation stage ameloblasts were occasionally immunoreactive. These data suggest that the intracellular concentration of CaBP 28 kDa is regulated throughout amelogenesis reflecting a stage-specific control of calcium homeostasis in ameloblasts.

Subcellular co-localization and co-variations of two vitamin D-dependent proteins in rat ameloblasts

The immunocytochemical patterns of calbindin-D9k (CaBP 9k) and calbindin-D28k (CaBP 28k) were compared by light and electron microscopy throughout amelogenesis. Labelling on serial sections and co-localization of CaBPs confirmed that the two proteins were restricted to a single cell type, the ameloblasts. Their quantity increased during presecretion, was stable during secretion and alternately high and low during the cyclic modulation of ameloblasts which occurs during maturation. Ruffle-ended ameloblasts contained the highest apparent concentration. Investigations with several fixatives indicated that the CaBPs were present in the cytosol and the nucleus, although there were slight differences with various fixatives by light microscopy. Their concentrations in these compartments varied in parallel throughout amelogenesis. However, mitochondria contained only immunoreactive CaBP 9k. While the distribution of CaBP 9k in zones containing Golgi apparatus and rough endoplasmic reticulum was similar, CaBP 28k concentration has, in another paper, been shown to be higher near the rough endoplasmic reticulum.

Related calcium-binding proteins map to the same subregion of chromosome 1q and to an extended region of synteny on mouse chromosome 3

The serum protein cystic fibrosis-associated antigen (CFAG), present at elevated levels in CF homozygotes and heterozygotes, is now known to consist of two distinct but related subunits (calgranulins A (CAGA) and B (CAGB)). Both show similarity to the S100-related calcium-binding proteins. We have previously assigned CAGA to human chromosome 1q12-q21 and demonstrate here that the cDNA probe for CAGB cosegregates with it in our somatic cell hybrid panel. cDNA probes for the related genes calcyclin (CACY) and a mouse placental protein (18A2, suggested name Capl) enabled us to confirm and refine the in situ hybridization result assigning CACY to chromosome 1q21-25 and to demonstrate that both genes cosegregate with CAGA and CAGB. Capl was mapped to a region of chromosome 3 in the mouse using the BXD recombinant inbred strain mice where the p11 protein (calpactin light chain Cal1l), another S100 family member, has been localized. Cacy is shown to be within 8 kb of Capl in the mouse genome.

The role of introns in evolution

What are the roles of 'classical' introns in the evolution of nuclear genes, and what was the origin of these introns? Exon shuffling has been important in the evolution of cell surface and extracellular proteins, but the evidence for it in respect of intracellular proteins is weak. Intron distributions imply that some introns have been removed while others have been inserted in the course of evolution: ancestral patterns of introns may thus have been obscured. Recent evidence on the self-splicing and reverse-splicing abilities of Group II introns supports the hypothesis that these could have been the ancestors of classical introns.

Evolution of EF-hand calcium-modulated proteins. I. Relationships based on amino acid sequences

The relationships among 153 EF-hand (calcium-modulated) proteins of known amino acid sequence were determined using the method of maximum parsimony. These proteins can be ordered into 12 distinct subfamilies--calmodulin, troponin C, essential light chain of myosin, regulatory light chain, sarcoplasmic calcium binding protein, calpain, aequorin, Stronglyocentrotus purpuratus ectodermal protein, calbindin 28 kd, parvalbumin, alpha-actinin, and S100/intestinal calcium-binding protein. Eight individual proteins--calcineurin B from Bos, troponin C from Astacus, calcium vector protein from Branchiostoma, caltractin from Chlamydomonas, cell-division-cycle 31 gene product from Saccharomyces, 10-kd calcium-binding protein from Tetrahymena, LPS1 eight-domain protein from Lytechinus, and calcium-binding protein from Streptomyces--are tentatively identified as unique; that is, each may be the sole representative of another subfamily. We present dendrograms showing the relationships among the subfamilies and uniques as well as dendrograms showing relationships within each subfamily. The EF-hand proteins have been characterized from a broad range of organismal sources, and they have an enormous range of function. This is reflected in the complexity of the dendrograms. At this time we urge caution in assigning a simple scheme of gene duplications to account for the evolution of the 600 EF-hand domains of known sequence.

Parvalbumin genes from human and rat are identical in intron/exon organization and contain highly homologous regulatory elements and coding sequences

The structural organization of the chromosomal gene for human parvalbumin was determined mostly by sequencing exons and intron exon junctions of a 7500 base-pair (bp) long genomic clone derived from a chromosome 22-specific gene library. Four exons coding for 100 from a total of 109 amino acids were detected in this clone and 472 bp of the 5'-flanking region were sequenced. The region corresponding to the C-terminal amino acids 101 to 109 of human parvalbumin was determined by sequencing a cDNA fragment derived from human brain mRNA after amplification by the polymerase chain reaction. The first intron is placed 7 bp upstream from the ATG translation start signal, whereas all other splice sites divide putative Ca2+-binding domains. All intron positions coincide exactly with those reported for the rat parvalbumin gene. The 5' mRNA leader sequence has a similarity of 57%, the coding region of 91% and the 3' non-coding region of 83% to the corresponding rat sequences. Only nine conservative amino acid replacements were observed between human and rat parvalbumins. The predicted secondary structures for human, rat, mouse and rabbit parvalbumins are very similar, indicating a strong structural relationship among mammalian parvalbumins. Several elements with potential transcription regulatory activities were found in the region immediately 5' to the transcription start site including a TATA box (TATATA) and a CAAT box (CCAAAAT). Several regions in the putative promoter are strongly conserved between the human and rat parvalbumin genes. One of these with a length of 32 bp is identical with the rat counterpart and has a high degree of homology to a promoter region in the myosin light chain 3F gene, which is expressed in fast contracting/relaxing muscle fibers (anaerobic/type IIb), the cell type that also exhibits highest levels of parvalbumin expression. The human parvalbumin mRNA contains the putative polyadenylation signal AATAAA 13 nucleotides upstream from the polyadenylation site. A 700-nucleotide long parvalbumin mRNA is synthesized at low levels in the human cerebellum as well as in the neuroblastoma cell line SK-N-BE.

Primary structure and functional expression of the inositol 1,4,5-trisphosphate-binding protein P400

Cloning and expression of functional P400 protein from cerebellar Purkinje neurons shows that this protein is a receptor for inositol 1,4,5-trisphosphate, a second messenger that mediates the release of intracellular calcium.

Cloning and analysis of calbindin-D28K cDNA and its expression in the central nervous system

The vitamin D-dependent calcium-binding protein (CaBP), calbindin-D28K (CaBP28K), is present in the central nervous system (CNS), the sensory system, and kidneys of mammals and birds. Recent studies have indicated that several other CaBPs of very similar Mrs are also present in the CNS. This study was carried out to establish the relationship between CaBP28K and other CaBP, particularly spot 35, to provide a basis for further studies on the tissue-specific regulation and distribution of CaBP28K. A cloned pC28 cDNA was isolated from a rat brain expression library using synthetic oligodeoxyribonucleotides (oligos) complementary to rat spot-35 mRNA. This pC28 cDNA had an open reading frame (ORF) of 783 nucleotides (nt) coding for a 261-aa, 30-kDa protein. There was 100% homology between the pC28 sequence and that of the CaBP28K isolated from rat brain cDNA library using a chicken intestinal CaBP28K probe (Hunziker and Schrickel, 1988). Thus the aa and nt sequences of rat CaBP28K and spot 35 are identical. Primer extension studies and Northern analyses show that the major species of CaBP28K mRNA contains a 5'-untranslated region of 132 nt, a coding region of 261 codons and a 3'-untranslated region of 804 nt without the poly(A) tail. The rat CaBP28K probe hybridizes to one major RNA species (1.9 kb) and two minor ones (2.8 and 3.2 kb) in the cerebellum, hippocampus, retina and kidney. This distribution correlates well with the distribution of CaBP28K itself in these organs. Comparison of the genomic organization of the CaBP28K gene with that of other members of the 'EF-hand' CaBP family emphasizes that the CaBP28K gene diverged from the others at the first duplication of the gene encoding one CaBP domain. All the members of the 'EF-hand' gene CaBP family evolved by exon shuffling and specific genomic rearrangements.

Bovine myeloperoxidase and lactoperoxidase each contain a high affinity site for calcium

Both bovine myeloperoxidase and lactoperoxidase contain one calcium per iron with no other metal present in significant amount. Calcium is bound with high affinity and is removed upon exposure to 6 M guanidine hydrochloride/EGTA which results in precipitation of protein. Computer amino acid sequence analyses of human myeloperoxidase reveal two plausible calcium binding sites. This is the first evidence for the presence of calcium in these peroxidases.