Functional analysis of the promoters of the human CaMIII calmodulin gene and of the intronless gene coding for a calmodulin-like protein

Optimization and Corroboration of the Regulatory Pathway of p42.3 Protein in the Pathogenesis of Gastric Carcinoma

AIMS

To optimize and verify the regulatory pathway of p42.3 in the pathogenesis of gastric carcinoma (GC) by intelligent algorithm.

METHODS

Bioinformatics methods were used to analyze the features of structural domain in p42.3 protein. Proteins with the same domains and similar functions to p42.3 were screened out for reference. The possible regulatory pathway of p42.3 was established by integrating the acting pathways of these proteins. Then, the similarity between the reference proteins and p42.3 protein was figured out by multiparameter weighted summation method. The calculation result was taken as the prior probability of the initial node in Bayesian network. Besides, the probability of occurrence in different pathways was calculated by conditional probability formula, and the one with the maximum probability was regarded as the most possible pathway of p42.3. Finally, molecular biological experiments were conducted to prove it.

RESULTS

In Bayesian network of p42.3, probability of the acting pathway "S100A11→RAGE→P38→MAPK→Microtubule-associated protein→Spindle protein→Centromere protein→Cell proliferation" was the biggest, and it was also validated by biological experiments.

CONCLUSIONS

The possibly important role of p42.3 in the occurrence of gastric carcinoma was verified by theoretical analysis and preliminary test, helping in studying the relationship between p42.3 and gastric carcinoma.

Emanuel Strehler’s work on calcium pumps and calcium signaling

Cells are equipped with mechanisms to control tightly the influx, efflux and resting level of free calcium (Ca²⁺). Inappropriate Ca²⁺ signaling and abnormal Ca²⁺ levels are involved in many clinical disorders including heart disease, Alzheimer’s disease and stroke. Ca²⁺ also plays a major role in cell growth, differentiation and motility; disturbances in these processes underlie cell transformation and the progression of cancer. Accordingly, research in the Strehler laboratory is focused on a better understanding of the molecular “toolkit” needed to ensure proper Ca²⁺ homeostasis in the cell, as well as on the mechanisms of localized Ca²⁺ signaling. A long-term focus has been on the plasma membrane calcium pumps (PMCAs), which are linked to multiple disorders including hearing loss, neurodegeneration, and heart disease. Our work over the past 20 years or more has revealed a surprising complexity of PMCA isoforms with different functional characteristics, regulation, and cellular localization. Emerging evidence shows how specific PMCAs contribute not only to setting basal intracellular Ca²⁺ levels, but also to local Ca²⁺ signaling and vectorial Ca²⁺ transport. A second major research area revolves around the calcium sensor protein calmodulin and an enigmatic calmodulin-like protein (CALML3) that is linked to epithelial differentiation. One of the cellular targets of CALML3 is the unconventional motor protein myosin-10, which raises new questions about the role of CALML3 and myosin-10 in cell adhesion and migration in normal cell differentiation and cancer.

Multiple calmodulin genes exhibit systematically differential responses to chronic ethanol treatment and withdrawal in several regions of the rat brain

Ethanol induces profound alterations in the neuronal signaling systems, including the calcium (Ca(2+)) signaling. Prolonged exposure to ethanol evokes adaptive changes in the affected systems as they strive to restore the normal neuronal function. We investigated the involvement of calmodulin (CaM) genes, coding for the major mediator protein of intracellular Ca(2+) signals, in these adaptive processes at the mRNA level. The changes induced in the regional abundances of the CaM I, II, and III mRNA classes by chronic ethanol treatment and withdrawal were examined by means of quantitative in situ hybridization, employing gene-specific [35S]cRNA probes on rat brain cryostat sections. Regional analysis of the resulting changes in mRNA levels highlighted brain areas that belong in neuronal systems known to be especially sensitive to the action of ethanol. The results revealed systematically differential regulation for the three mRNA classes: the CaM I and CaM III mRNA levels displayed increases, and CaM II levels decreases in the affected brain regions, in both chronic ethanol- and withdrawal-treated animals. As regards the numbers of brain regions undergoing significant alterations in mRNA content, the CaM I mRNA levels exhibited changes in most brain areas, the CaM II levels did so in a lower number of brain regions, and the CaM III levels changed in only a few brain areas. These results suggest a differential regulation for the CaM genes in the rat brain and may help towards elucidation of the functional significance of the multiple CaM genes in the mammalian genome.

Differential regulation of calmodulin content and calmodulin messenger RNA levels by acute and repeated, intermittent amphetamine in dopaminergic terminal and midbrain areas

Repeated doses of psychoactive drugs often produce adaptive responses that differ from the initial drug application and additional adaptive processes occur following cessation of the drug. The relationship between alterations in calmodulin protein and messenger RNA produced by an initial versus a repeated dose of amphetamine was examined, as well as changes following drug cessation. Calmodulin protein and messenger RNA of the three individual calmodulin genes were measured in rat dopaminergic cell body and terminal areas following acute or repeated amphetamine. Rats were either injected once with 2.5mg/kg amphetamine or saline and decapitated after 3h, or given 10 injections of amphetamine three to four days apart and decapitated 3h after the final injection. Calmodulin messenger RNA and protein were also measured three and seven days after ceasing drug treatment. Acute amphetamine increased calmodulin 1.7-fold in the striatum and threefold in the ventral mesencephalon, with corresponding elevations in calmodulin messenger RNAs. In response to the 10th dose of amphetamine, however, the degree of increase in calmodulin was diminished in the striatum and ablated in the ventral mesencephalon. Correspondingly, select species of calmodulin messenger RNA were decreased from control levels. In the frontal cortex or nucleus accumbens, calmodulin levels were basically unaltered by the first or 10th doses of amphetamine, but both calmodulin and its messenger RNA were altered with time upon cessation of the drug. Three days later, both calmodulin protein and messenger RNA were decreased in select brain areas. By seven days after the 10th injection, calmodulin content was altered compared to saline controls in all areas, but the change in messenger RNA no longer paralleled the change in protein.Our findings demonstrate that both calmodulin protein and select species of calmodulin messenger RNA are altered by acute amphetamine, but this effect is attenuated after repeated, intermittent amphetamine. There are further time-dependent changes after cessation of repeated amphetamine, which may reflect compensatory neuronal responses. The alterations in calmodulin content and synthesis could contribute to changes in patterns or duration of behaviors that occur upon cessation of repeated amphetamine.

The calmodulin multigene family as a unique case of genetic redundancy: multiple levels of regulation to provide spatial and temporal control of calmodulin pools?

Calmodulin (CaM) is a ubiquitous, highly conserved calcium sensor protein involved in the regulation of a wide variety of cellular events. In vertebrates, an identical CaM protein is encoded by a family of non-allelic genes, raising questions concerning the evolutionary pressure responsible for the maintenance of this apparently redundant family. Here we review the evidence that the control of the spatial and temporal availability of CaM may require multiple regulatory levels to ensure the proper localization, maintenance and size of intracellular CaM pools. Differential transcription of the CaM genes provides one level of regulation to meet tissue-specific, developmental and cell-specific needs for altered CaM levels. Post-transcriptional regulation occurs at the level of mRNA stability, perhaps dependent on alternative polyadenylation and differences in the untranslated sequences of the multiple gene transcripts. Recent evidence indicates that trafficking of specific CaM mRNAs may occur to specialized cellular locales such as the dendrites of neurons. This could allow local CaM synthesis and thereby help generate local pools of CaM. Local CaM activity may be further regulated by post-translational mechanisms such as phosphorylation or storage of CaM in a 'masked' form. The spatial resolution of CaM activity is enhanced by the limited free diffusion of CaM combined with differential affinity for and availability of target proteins. Preserving multiple CaM genes with divergent noncoding sequences may be necessary in complex organisms to ensure that the many CaM-dependent processes occur with the requisite spatial and temporal resolution. Transgenic mouse models and studies on mice carrying single and double gene 'knockouts' promise to shed further light on the role of specificity versus redundancy in the evolutionary maintenance of the vertebrate CaM multigene family.

Molecular cloning, sequence and structure analysis of hamster apurinic/apyrimidinic endonuclease (chAPE1) gene

We have cloned a 13 kb genomic DNA fragment from the Chinese hamster ovary cell line, CHO-KI, and determined the nucleotide sequence of a 4 kb stretch of DNA which encompasses the complete sequence (2.277 kb) of the hamster apurinic/apyrimidinic endonuclease (chAPE1) gene. The intron/exon boundaries, identified by RT-PCR, follow GT/AG rule. The structure of the chAPE1 gene is similar to other mammalian apurinic/apyrimidinic (AP) endonuclease (hAPE1, BAP1, rAPEN and mAPE1) genes in that it has five exons and four introns with the first exon unexpressed. This structure, however, differs from one of the two structures that have been proposed for mAPE1 gene. Three transcription start sites (TSS) for the chAPE1 gene were identified by primer extension analysis at +1, +14 and +18 positions. The sequence also includes 1.72 kb of the upstream region of the chAPE1 gene. In this region, a CCAAT box but no TATA box that could initiate the transcription at the initiation sites was identified. The upstream region also includes the binding sites for a variety of other transcription factors. A polyadenylation site, 13 nucleotides downstream to the polyadenylation signal, was identified by 3'-RACE analysis. The observed 1.28 kb transcript of the chAPE1 gene is smaller than the 1.5 kb transcript of the human AP endonuclease gene. The translation of chAPE1 gene starts within the second exon with ATG and terminates in the fifth exon with UGA codons, 318 and 2121 nucleotides downstream to the first TSS, respectively. The encoded peptide of 317 amino acid residues is similar in size and is highly homologous in its amino acid sequence to mouse, rat, human, and bovine AP endonucleases.

Effect of antisense oligodeoxynucleotides directed to individual calmodulin gene transcripts on the proliferation and differentiation of PC12 cells

Calmodulin (CaM) is encoded by three different genes that collectively give rise to five transcripts. In the present study, we used antisense oligodeoxynucleotides targeted to unique sequences in the transcripts from the individual CaM genes to selectively block the expression of the different genes and to investigate the roles these individual genes play in the proliferation and nerve growth factor (NGF)-induced differentiation of PC12 cells. Culturing PC12 cells in the presence of oligodeoxynucleotide antisense to the transcripts from CaM genes I and II caused a significant decrease in the proliferation and a significant delay in the NGF-induced differentiation of PC12 cells when compared with untreated cells and with cells treated with the corresponding randomized oligodeoxynucleotides. However, an oligodeoxynucleotide antisense to CaM gene III did not significantly alter the proliferation or the NGF-induced differentiation of PC12 cells. The inhibition of cell proliferation could be reversed by washing out the antisense oligodeoxynucleotides. The levels of CaM in cells treated with oligodeoxynucleotides antisense to CaM genes I or II were reduced 52% or 63%, respectively, of the levels found in the control cells. However, the levels of CaM were not significantly reduced in PC12 cells treated with CaM gene III antisense oligodeoxynucleotide. None of the randomized oligodeoxynucleotides had any effect on the levels of CaM in PC12 cells. The reduced levels of CaM in PC12 cells treated with an oligodeoxynucleotide antisense to CaM gene I were accompanied by a reduction in the levels of the CaM gene I mRNAs, supporting a true antisense mechanism of action for these oligodeoxynucleotides. These results suggest that altering the level of CaM by using antisense oligodeoxynucleotides targeted to the dominant CaM transcripts in a particular cell type will specifically inhibit their proliferation and, in the case of neuronal cells, alter the course of their differentiation.

Characterization of the human CALM2 calmodulin gene and comparison of the transcriptional activity of CALM1, CALM2 and CALM3

Human calmodulin is encoded by three genes CALM1, CALM2 and CALM3 located on different chromosomes. To complete the characterization of this family, the exon-intron structure of CALM2 was solved by a combination of genomic DNA library screening and genomic PCR amplification. Intron interruptions were found at identical positions in human CALM2 as in CALM1 and CALM3; however, the overall size of CALM2 (16 kb) was almost twice that of the other two human CALM genes. Over 1 kb of the 5' flanking sequence of human CALM2 were determined, revealing the presence of a TATA-like sequence 27 nucleotides upstream of the transcriptional start site and several conserved sequence elements possibly involved in the regulation of this gene. To determine if differential transcriptional activity plays a major role in regulating cellular calmodulin levels, we directly measured and compared the mRNA abundance and transcriptional activity of the three CALM genes in proliferating human teratoma cells. CALM3 was at least 5-fold more actively transcribed than CALM1 or CALM2. CALM transcriptional activity agreed well with the mRNA abundance profile in the teratoma cells. In transient transfections using luciferase reporter genes driven by 1 kb of the 5' flanking DNA of the three CALM genes, the promoter activity correlated with the endogenous CALM transcriptional activity, but only when the 5' untranslated regions were included in the constructs. We conclude that the CALM gene family is differentially active at the transcriptional level in teratoma cells and that the 5' untranslated regions are necessary to recover full promoter activation.

Spatial and temporal regulation of the rat calmodulin gene III directed by a 877-base promoter and 103-base leader segment in the mature and embryonal central nervous system of transgenic mice

Three non-allelic rat calmodulin (CaM) genes CaMI, CaMII and CaMIII, which share no homology in their 5'-upstream regions, are coordinately expressed in neurons of the central nervous system (CNS). Deletion analysis of the CaMIII promoter showed that the upstream segments longer than 700 bases functioned as efficient promoters, and that the sequence from -133 to -65 was required for the activity of house-keeping type promoter in transient expression assays on a mouse glioma cell line C6. However, the transient expression seemed not to be cell type specific. To determine the temporal and spatial specificity of the promoter function, we produced transgenic mice carrying a fusion gene of the CaMIII segment from -877 to +103 and the lacZ reporter gene. In CNS of the adult transgenic mice, the localization of transgene expression was similar to that of endogenous CaMIII transcripts analyzed by in situ hybridization. The transgene was expressed prominently in pyramidal cells of the cerebral neocortex and the hippocampal regions CA1 to CA3, in Purkinje cells of the cerebellar cortex, and in neurons of the spinal cord, and moderately in granule cells of the dentate gyrus and the cerebellar cortex. In the developing CNS, the overall profiles of neuron-specific expression were also similar for both transgene and endogenous CaMIII that were expressed in the mantle layer and the dorsal root ganglia of the embryonal spinal cord. These results indicated that the neuron-specific expression of rat CaMIII was directed by this 877-base promoter sequence. The CaMIII segment used for the promoter of transgene contained a 29-bp sequence at -410, namely H3, which was conserved in the upstream regions of vertebrate CaMII and CaMIII. H3 seemed to play a pivotal role in the temporal and spatial expression of transgene in CNS, although the deletion of H3 did not decrease CAT activity in the transient expression. The transgene expression was not observed in the external granular cells of the developing cerebellum and in some neurons of the embryonic sensory ganglia in which the endogenous CaMIII was obviously expressed. Therefore, the other cis-acting element(s) located outside of this 877-bp segment seemed to be required for the temporal regulation of CaMIII in certain rudimentary neurons.

Cloning and characterization of allograft inflammatory factor-1: a novel macrophage factor identified in rat cardiac allografts with chronic rejection

The development of arteriosclerotic lesions in the Lewis to F344 rat model of chronic cardiac rejection is characterized by macrophage adhesion to the vessel lumen and macrophage infiltration in the neointima prior to smooth muscle cell accumulation. We report the cloning and characterization of allograft inflammatory factor-1 (AIF-1), a novel cDNA that is expressed early and persistently in chronically rejecting cardiac allografts but is absent in cardiac syngrafts and host hearts. The full-length cDNA codes for a hydrophilic polypeptide of 17 kD that contains a 12-amino acid region similar to an EF-hand (calcium-binding) domain. In cardiac allografts AIF-1 transcripts and protein localized to infiltrating mononuclear cells. Analysis of isolated cell populations confirmed that AIF-1 was selectively expressed in macrophages and neutrophils and demonstrated that AIF-1 transcripts could be upregulated by sixfold after stimulation with the T cell-derived cytokine IFN-gamma. Treatment with a diet deficient in essential fatty acids (which attenuates arteriosclerosis) or CTLA-4 Ig (which blocks lymphocyte activation) significantly decreased AIF-1 transcript levels. Upregulation of AIF-1 in the setting of T cell activation suggests that it may play a role in macrophage activation and function.

Cloning and sequencing of an intronless mouse S-adenosylmethionine decarboxylase gene coding for a functional enzyme strongly expressed in the liver

A genomic clone for a mouse S-adenosylmethionine decarboxylase (AdoMetDC) gene was isolated from a cosmid library. Surprisingly, the gene proved to be intronless. With the exception of three base substitutions (changing 2 amino acids in the deduced protein), the 1002-nucleotide sequence of the open reading frame was identical to that of mouse AdoMetDC cDNA. Moreover, the gene contained a poly(dA) tract at the 3' end and was flanked by 13-base pair direct repeats. Our findings suggest that this gene has arisen by retroposition, in which a fully processed AdoMetDC mRNA has been reverse transcribed into a DNA copy and inserted into the genome. By polymerase chain reaction, we positively identified the intronless gene in the mouse genome, and, by primer extension analysis, we proved the gene to be functional. Thus, its transcripts were found in many cell lines and tissues of the mouse and were particularly abundant in the liver. When the open reading frame of the intronless gene was expressed in Escherichia coli HT551, a strain with no AdoMetDC activity, it was found to encode a 38-kDa protein, corresponding to AdoMetDC proenzyme. Although the change of methionine 70 to isoleucine was close to the cleavage site at serine 68, this protein underwent proenzyme processing, generating a 31-kDa alpha subunit and an 8-kDa beta subunit. Importantly, the protein encoded by the intronless gene was functional, i.e. it catalyzed the decarboxylation of S-adenosylmethionine, and its specific activity was comparable with that of recombinant human AdoMetDC purified according to the same procedure.

Computer-aided analysis of potential transcription-factor binding sites in the rabbit beta-casein gene promoter

Computer analysis of putative cis- and trans-regulatory sequences in the promoter region of the rabbit beta-casein gene is described. Nucleotide sequences up to 2096 bp upstream of the initiation site were compared to known consensus sequences of both ubiquitous and specific transcription factor motifs as well as to those described as characteristic for milk protein genes. Our analysis demonstrated that 5 independent motifs described for milk protein gene promoters exist. Four of them--'Groenen structure', 'Yu-Lee' 1 and 6 sequence and 'Oka box A'--were found in the beta-casein gene promoter; surprisingly, no typical milk box was found. More than one hundred and fifty putative binding motifs were found, representing 56 various consensus sequences. These sequences are located both inside and outside structures typical of milk protein gene promoters and include sequences homologous to mammary gland specific, hormone specific and ubiquitous transcription factors. Our analysis suggests that milk protein gene promoters can bind many transcription factors and assure complex regulation by hormonal and tissue specific factors.

Structure, promoter analysis and chromosomal assignment of the human APEX gene

APEX nuclease is a mammalian DNA repair enzyme having apurinic/apyrimidinic endonuclease, 3'-5'-exonuclease, DNA 3' repair diesterase and DNA 3'-phosphatase activities. This report describes the organization of the gene (APEX gene) for human APEX nuclease. Human APEX gene was cloned using human APEX cDNA and a human leukocyte genomic library in bacteriophage vector EMBL-3. We proved that human APEX gene consists of 5 exons spanning 2.64 kilobases and suggested that the gene exists as a single copy in the haploid genome. The boundaries between exon and intron follow the GT/AG rule. The major transcription initiation site was assigned by primer extension analysis to C at 515 nucleotides upstream from the ATG initiation codon. The translation initiation and termination sites locate in the exon II and V, respectively. The 5' flanking region (0.89 kilobase) sequenced lacks typical TATA and CAAT boxes, but contains TATA- and CAAT-like sequences and putative cis-acting regulatory elements such as binding sites for Sp1, AP2 and ATF. A part of the 5' flanking region belongs to a CpG island, which extends to the intron II. The CpG island is thought to be a transcription regulatory region of APEX gene, a housekeeping gene. The promoter activity of the 5' upstream region was analyzed by introducing the region in HeLa cells in an expression construct containing luciferase gene as a reporter gene, and the region from position 130 bp upstream to position 205 bp downstream of the major transcription initiation site was shown to be enough for high promoter activity. Northern hybridization experiments suggested that the gene is expressed ubiquitously in human cells. The locus of APEX gene was mapped to human chromosome 14q11.2-q12 using the in situ hybridization technique.

Localization of the intronless gene coding for calmodulin-like protein CLP to human chromosome 10p13-ter

The functional intronless gene coding for a calmodulin-like protein (CLP) has been localized to human chromosome 10p13-ter. Chromosomal assignment was performed by Southern blot analysis of DNA from human-rodent somatic cell hybrids and amplification of a CLP gene-specific 1090-bp DNA fragment by the polymerase chain reaction (PCR) on DNA from human-hamster cell hybrids. Chromosomal sublocalization was carried out by in situ hybridization of human chromosome metaphase spreads. The CLP gene is the first member of the human calmodulin/calmodulin-like gene family to be chromosomally sublocalized. Its presence near the telomeric end of the short arm of chromosome 10 may be of significance with respect to its highly (epithelial) cell-type restricted expression in vivo and strong downregulation upon malignant transformation. The generation of a human CLP gene-specific sequence tag site specified by the two primers used for PCR should prove useful for future linkage studies.