Evolution of EF-hand calcium-modulated proteins. V. The genes encoding EF-hand proteins are not clustered in mammalian genomes

Proteins with calmodulin-like domains: structures and functional roles

The appearance of modular proteins is a widespread phenomenon during the evolution of proteins. The combinatorial arrangement of different functional and/or structural domains within a single polypeptide chain yields a wide variety of activities and regulatory properties to the modular proteins. In this review, we will discuss proteins, that in addition to their catalytic, transport, structure, localization or adaptor functions, also have segments resembling the helix-loop-helix EF-hand motifs found in Ca2+-binding proteins, such as calmodulin (CaM). These segments are denoted CaM-like domains (CaM-LDs) and play a regulatory role, making these CaM-like proteins sensitive to Ca2+ transients within the cell, and hence are able to transduce the Ca2+ signal leading to specific cellular responses. Importantly, this arrangement allows to this group of proteins direct regulation independent of other Ca2+-sensitive sensor/transducer proteins, such as CaM. In addition, this review also covers CaM-binding proteins, in which their CaM-binding site (CBS), in the absence of CaM, is proposed to interact with other segments of the same protein denoted CaM-like binding site (CLBS). CLBS are important regulatory motifs, acting either by keeping these CaM-binding proteins inactive in the absence of CaM, enhancing the stability of protein complexes and/or facilitating their dimerization via CBS/CLBS interaction. The existence of proteins containing CaM-LDs or CLBSs substantially adds to the enormous versatility and complexity of Ca2+/CaM signaling.

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.

Factors triggering type III secretion in Pseudomonas aeruginosa

The type III secretion system of Pseudomonas aeruginosa is tightly regulated by various environmental signals, such as low calcium and contact with the host cell. However, the exact signals triggering type III secretion are unknown. The present study describes the finding that secretion of P. aeruginosa type III effector molecules requires protein factors from serum and L broth, designated type III secretion factors (TSFs), in addition to the low-calcium environment. In the absence of TSF or calcium chelator EGTA, basal levels of type III effector molecules are accumulated intracellularly. Addition of TSF and EGTA together effectively triggers the secretion of pre-existing effector molecules in a short time, even before the active expression of type III genes; thus, active type III gene expression does not seem to be a prerequisite for type III secretion. A search for TSF molecules in serum and L broth resulted in the identification of albumin and casein as the functional TSF molecules. Although there is no clear sequence similarity between albumin and casein, both proteins are known to have a low-affinity, high-capacity calcium-binding property. Tests of well-studied calcium-binding proteins seemed to indicate that low-affinity calcium-binding proteins have TSF activity, although the requirement of low-affinity calcium-binding ability for the TSF activity is not clear. P. aeruginosa seems to have evolved a sensing mechanism to detect target cells for type III injection through host-derived proteins in combination with a low-calcium signal. Disruption of the bacterial ability to sense low calcium or TSF might be a valid avenue to the effective control of this bacterial pathogen.

Unipolar brush cells in marmoset cerebellum and cochlear nuclei express calbindin

Unipolar brush cells (UBCs) are excitatory neurons in the mammalian cerebellum and cochlear nuclei (CN), including the CN of primates, as shown only recently. UBCs are readily identified by their expression of the calcium-binding protein calretinin (CR), except for those of the primate CN that hardly immunostain for CR. The present findings corroborate the existence of UBCs in the CN of a primate, Callithrix. Furthermore, evidence is presented for UBCs, in the cerebellum and a small subpopulation of UBCs in the CN of Callithrix to express the calcium-binding protein calbindin (CB). This may be unique for Callithrix as CB-expressing UBCs have not been recognized in any other mammal. Presence of CB but not CR in UBCs of the Callithrix CN may indicate a certain interchangeability between these two calcium-binding proteins.

S100 protein expression in subpopulations of neurons of rat brain

Available data are conflicting as regards the occurrence of Ca2+ and Zn2+ binding S100 proteins in neurons of mammalian brain. Here the localization and expression of S100 was re-investigated using several different antibodies and in situ hybridization. A map is provided for the distribution of two classes of S100-positive neuron populations in the adult rat CNS. "Persistently S100-positive" neurons had large size, were strongly immunoreactive and were mainly distributed in the nuclei of the lower brainstem and cerebellum. "Variably S100-positive" neurons were preferentially found in the forebrain of rats older than 90 days and were especially numerous in limbic regions. The S100-immunoreactivity in these neurons was moderately intense, occurred with high interindividual variation and appeared related to function as suggested by variations due to anesthesia. The expression of S100 mRNA in neurons was re-investigated at high spatial resolution with non-radioactive in situ hybridization using an oligonucleotide specific for S100 beta-mRNA. Expression of S100 was demonstrated in astrocytes and in those neuron populations which were also strongly S100-immunoreactive. No expression of S100 beta message was seen in weakly immunoreactive neurons, b but this may be due to low sensitivity of the techniques used. The data suggest that the S100 proteins are synthesized in all astrocytes and in distinct subpopulations of neurons in rat brain. These neurons show a characteristic topography and vary in S100 expression probably due to their function and maturation.

Alternative splicing of calretinin mRNA leads to different forms of calretinin

cDNA clones for calretinin, a member of the troponin-C family of calcium-binding proteins, were isolated from a cDNA library of the human colon carcinoma cell line WiDr. Sequence analysis revealed two forms of alternatively spliced calretinin mRNAs encoding C-terminally truncated proteins. Exon 7 was either spliced to exon 9 (delta 8) or to exon 10 (delta 8,9); both resulted in a frame shift and a translational stop at the second codon of exon 9 (delta 8), or at codon 15 of exon 10 (delta 8,9), respectively. The presence of delta 8 and delta 8,9 calretinin mRNA in WiDr cells was confirmed using reverse-transcriptase PCR and sequence analysis of the amplicon, as well as by a ribonuclease protection assay. Co115/3 and three other human colon carcinoma cell lines were found, by reverse-transcriptase PCR to also contain delta 8,9 calretinin mRNA. The truncated proteins were able to bind calcium, as evidenced by a calcium blot of the delta 8 form (calretinin-20k) and delta 8,9 form (calretinin-22k) expressed in Escherichia coli. Immunohistochemical staining using an antiserum specific for the novel C-terminus of calretinin-22k confirmed its presence in WiDr, Co115/3 and three additional colon carcinoma cell lines. The fact that alternative splicing of calretinin was found in five different cell lines suggests that alternatively spliced calretinins fulfill a physiological function.

Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21: rationale for a new nomenclature of the S100 calcium-binding protein family

S100 proteins are low-molecular-weight calcium-binding proteins of the EF-hand superfamily and appear to be involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. More than 10 members of the S100 protein family have been described from human sources so far. We have now isolated a YAC clone from human chromosome 1q21, on which 9 different genes coding for S100 calcium-binding proteins could be localized. Moreover, we have mapped the gene coding for S100P to human chromosome 4p16 and thereby completed the chromosomal assignments of all known human S100 genes. The clustered organization of S100 genes in the 1q21 region allows us to introduce a new logical nomenclature for these genes, which is based on the physical arrangement on the chromosome. The new nomenclature should facilitate and further the understanding of this protein family and be easily expandable to other species.

Structure of the gene encoding anchorin CII (chick annexin V)

Anchorin CII (annexin V) was first characterized as a collagen-binding protein and later identified as the chick homologue of human endonexin II, a member of the annexin gene family. Its gene (anx5) structure and sequence have been investigated to provide insight into the evolution and regulation of this important protein, and to elucidate its putative role in signal transduction and cellular differentiation. Four chick genomic clones encoding anchorin CII were isolated and characterized by restriction analysis, Southern blotting and sequencing. The anchorin CII-encoding gene spans about 24 kb and consists of 13 exons ranging in length from 50 to 561 bp, interrupted by 12 introns of 94 bp to 7 kb. Its promoter sequence contained no TATA box, but did display a high G+C content and multiple Sp1-binding sites typical of 'housekeeping' genes. Potential binding sites for transcription factors in the 5'-upstream region are consistent with regulation of anx5 expression by mitogens, oncoproteins, steroids and possibly metals. Genomic Southern blotting confirmed that chick anx5 is present as a single-copy gene.

Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins

In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin dendrograms computed from DNA and from protein sequences. In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family. Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3'-tail sequence, intron sequences, and intron positions all show significant differences.