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Mutations dislocate caspase-12 from the endoplasmatic reticulum to the cytosol.

Mouse AKR-2B cells express two forms of caspase-12: the full-length form coding for a protein of 47.8 kDa and a new splice variant of 40.2 kDa which is devoid of the CARD domain. In addition, three point mutations were disclosed: I/L-15, E/D-46 and P/L-105. A major portion of the two protein variants was found in the cytosol. Immunofluorescence studies showed an even distribution of caspase-12 within the cell, indicative for a cytoplasmatic localization. Transfection of AKR-2B cells with wild-type caspase-12 showed a colocalization of this protein with the endoplasmic reticulum (ER). Unlike mouse embryonal fibroblasts (MEF) which contain wild-type caspase-12, AKR-2B cells were largely resistant against treatment with the endoplasmatic reticulum stressing reagents brefeldin and tunicamycin. In AKR-2B cells, cytoplasmatic caspase-12 is bound to high molecular weight complexes of >1000 kDa [Cell Death Differ. 9 (2001) 125] and serum depletion leads to cleavage and detachment of caspase-12 from this high molecular weight complex. Cleavage of caspase-12 and -3 occurred almost simultaneously reaching a maximum 3-5 h after serum deprivation at which time also maximum apoptosis is found. Analysis of caspase-12 cleavage in vitro in comparison with fragmentation in vivo suggests that during death in AKR-2B cells induced by starvation, cleavage was brought about by caspase-3 at positions D24 and D94. Thus, mutated caspase-12 is differently integrated in signaling pathways of cell death and has lost its function as initiator caspase upon ER-stress. Instead, it is turned into a substrate of effector caspases. The implication of these findings in the pathological phenotype of ARK-2B mice is discussed.

Alternative Splicing↗

Identification of two novel human genes, DIPLA1 and DIPAS, expressed in placenta tissue.

Here we report the identification and expression analysis of two novel human genes--DIPLA1 (Differentially expressed in placenta 1) and DIPAS (DIPLA1 Antisense). These genes are located at chromosomal region 9q33.1, in opposite orientations, and are flanked by the pregnancy-associated plasma protein-A (PAPP-A) and astrotactin 2 (ASTN2) genes. The mRNA sequences of both genes contain several upstream AUGs (uAUG) and various potential open reading frames (ORFs). DIPLA1 mRNA is 1.8 kb long and contains a 285 nt ORF coding for a polypeptide designated as replicative senescence up-regulated (RSU) protein. Antisense DIPAS mRNA is 2.7 kb long and contains a 309 nt ORF coding for a protein with partial similitude to the gamma isoform variant of the human Ca(2+)/calmodulin (CaM)-dependent protein kinase II. Both genes are conserved in placental-species and are presumably transcribed from initiator (Inr) promoter elements located at opposite strands. In 20 human normal tissues tested, DIPLA1 mRNA expression was placenta-specific, whereas DIPAS mRNA expression was higher in placenta, brain, kidney and testis. In addition, DIPAS mRNA hybridizes with the 3'UTR region from PAPP-A mRNA, which spans over 4 kb more than previously reported, forming a potential sense-antisense double stranded RNA (dsRNA) duplex. Our results are of interest for placenta gene expression regulation and for the identification of novel genes in the human genome.

Alternative Splicing↗

Characterization of Xenopus Phox2a and Phox2b defines expression domains within the embryonic nervous system and early heart field.

The closely related homeodomain containing genes, Phox2a and Phox2b, are essential for neuronal specification and differentiation within discrete subsets of neurons during vertebrate embryogenesis. We have isolated Xenopus Phox2 homologs, termed Xphox2a and Xphox2b, and characterized their expression during early development. In addition, we have characterized a Phox2a splice variant, termed Xphox2a.2, which lacks homeo- and C-terminal protein coding domains. Xphox2a, Xphox2a.2 and Xphox2b transcripts are expressed in dynamic temporal and regional patterns during nervous system development. The expression of Xphox2a and Xphox2b is only partially overlapping and includes cranial motor and interneuron populations as well as peripheral sympathetic and cranial ganglion neurons, sites linked to Phox2 expression in other species. In addition, we have identified an early domain of Xphox2a and subsequent Xphox2b expression in ventral regions of the embryo, within the developing heart field. XPhox2 expression within this domain is preceded by the gastrula-stage expression of the proneural basic helix-loop-helix transcription factor, Xash1, pointing to a new region of action for this group transcription factors during vertebrate development.

Amino Acid Sequence↗

Expression and purification of human antimicrobial peptide, dermcidin, in Escherichia coli.

Human dermcidin, an anionic antimicrobial peptide expressed in the pons of the brain and the sweat glands, displays antimicrobial activity against pathogenic microorganisms such as Staphylococcus aureus and Candida albicans. Here, we describe the recombinant production of a 48 amino acid dermcidin variant with C-terminal homoserine lactone (DCD-1Hsl). Dermcidin coding sequence was cloned downstream of a 125 amino acid ketosteroid isomerase gene and upstream of a His6Tag sequence in pET-31b(+) vector and transformed into Escherichia coli. The fusion protein was expressed in the form of inclusion bodies, purified on His Bind Resin, and cleaved by CNBr to release recombinant DCD-1Hsl. Purification of rDCD-1Hsl was achieved by solid-phase extraction that yielded milligram amounts of peptide with more than 95% purity. Recombinant peptide showed antimicrobial activities against E. coli ML-35p, Salmonella typhimurium 5156, Listeria monocytogenes 264, S. aureus 29/58 (clinical isolate), and C. albicans K2 (clinical strain). The application of this expression/purification approach represents a fast and efficient method to prepare milligram quantities of dermcidin in its biologically active form.

Amino Acid Sequence↗

Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci.

Most genetic loci linked to polygenic traits are in non-coding regions, with complex regulation and linkage disequilibrium (LD), complicating causal variant and gene prioritization. We used multiplexed single-cell CRISPR interference and activation perturbations to investigate cis-regulatory element (CRE) and gene expression relationships within tight LD in the endogenous chromatin context. We demonstrated the prevalence of multiple causality in perfect LD (pLD) for independent expression quantitative trait loci (eQTLs) and uncovered fine-grained genetic effects on gene expression within pLD, which are difficult to decipher using traditional eQTL fine-mapping or existing computational methods. We found that over one-third of the causal CREs lack classical epigenetic markers prior to perturbation, and we functionally validated one of these hidden regulatory mechanisms. Leveraging Multiome single-cell epigenetic and sequence perturbations, we highlighted the regulatory plasticity of the human genome. Our study will guide the exploration of missing causal mechanisms underlying molecular trait regulation and disease development.

Humans↗

[Bart syndrome associated to lethal junctional epidermolysis bullosa (Herlitz form)].

We present the case of a newborn with congenital absence of skin in the anterior part of the left leg that shortly after developed bulla and erosions in hands, feet, ears, buttocks and mouth. The cutaneous biopsy and ultrastructural and immunohistochemical studies showed a subepidermal bulla in the lamina lucida, absence of hemidesmosomes and marked decrease of laminin 5, thus establishing the diagnosis of Bart syndrome associated to the Herlitz form of lethal junctional epidermolysis bullosa. Bart syndrome consists of congenital and localized absence of skin, nail abnormalities and mucoc-cutaneous bullae. It is usually associated to dystrophic epidermolysis bullosa. The Herlitz form of junctional epidermolysis bullosa is a rare variant, usually lethal that is produced by mutations in the genes coding for the anchor protein laminin 5. To our knowledge this is the second case that reports an association between Bart syndrome and lethal junctional epidermolysis bullosa and the first in which the results of immunofluorescence mapping are published.

Collagen Type VII↗

Expressional analysis of the cardiac Na-Ca exchanger in rat development and senescence.

The cardiac Na-Ca exchanger (NCX) serves as the main calcium extrusion mechanism in heart muscle and is important in maintaining intracellular calcium homeostasis. The accumulations of NCX RNA and protein are known to be regulated in cardiac hypertrophy, by thyroid hormone and during postnatal development. In this study the temporal and spatial patterns of NCX mRNA and protein accumulations were examined, and nuclear run-on assays performed. NCX is highly expressed in late fetal and neonatal rat hearts, decreasing to adult levels by 20 days after birth for RNA (P < 0.05, fetal and 1 neonatal day old (1 ND) versus 20 day old (20 ND)). Maximal protein expression is seen in 19 embryonic day (ED) old hearts, and reaches adult levels sometime after 20 neonatal days. (P < 0.05, fetal versus adult). Spatially, NCX is homogenously expressed in early embryonic and fetal heart, followed by a decline after birth. The protein levels decline more slowly suggesting a long protein half-life. The lowest level of mRNA accumulation is seen in 6 and 18 month old animals (P < 0.05 for all time points before 10 neonatal days). In the 24 month old senescent rat, NCX transcripts are increased by almost 50% above that seen at 6 and 18 months (P < 0.05) but are not different from those at 15 neonatal days. Perinatal NCX expression is regulated transcriptionally: late fetal and neonatal hearts have high transcriptional activity but by 20 postnatal days, no detectable transcriptional activity can be demonstrated. Throughout development, at least five transcription start sites are used, and no significant difference in the 5' untranslated or 3' coding splice sites could be demonstrated, although several new cardiac splicing variants were identified. We also report the cloning of a 3.7 kb fragment containing the cardiac NCX1 promoter which is transcriptionally active in neonatal cardiomyocytes.

Aging↗

Regulation of cAMP phosphodiesterase mRNAs expression in rat brain by acute and chronic fluoxetine treatment. An in situ hybridization study.

Changes in brain cyclic AMP (cAMP) have been suggested to underlie the clinical action of antidepressant treatments. Also, a regionally-selective regulation of cAMP-specific phosphodiesterases (PDEs) has been demonstrated for some antidepressants. To further investigate the effects of antidepressant treatments on PDEs, we examined the expression of different cAMP-specific PDEs in the brain of rats treated (1 and 14 days) with fluoxetine 3 mg/kg day. The mRNAs coding for PDE4A, PDE4B, PDE4D, and the five known PDE4D splice variants were analyzed by in situ hybridization on 45 brain structures of acute and chronic fluoxetine-treated rats. We also examined the binding sites for the putative antidepressant drug [(3)H]rolipram, a PDE4-selective inhibitor. In some brain areas single fluoxetine administration increased the density of the mRNA of all PDE4 isozymes, except PDE4D and PDE4D5. Chronic fluoxetine treatment increased PDE4A mRNA levels and decreased those for PDE4B, PDE4D and PDE4D1 mRNAs in some brain regions. The study was complemented with the analysis of the expression of the transcripts of BDNF. Chronic fluoxetine treatment down-regulated the expression of BDNF. These results show that the expression of PDE4 isozymes is modulated by a clinically relevant fluoxetine dose. The significance of these changes in PDE4 expression to the antidepressant effect of fluoxetine is discussed.

3',5'-Cyclic-AMP Phosphodiesterases↗

Lung cancer susceptibility in relation to combined polymorphisms of microsomal epoxide hydrolase and glutathione S-transferase P1.

Human microsomal epoxide hydrolase (mEH) catalyzes a key step in the biotransformation of benzo[a]pyrene that yields the highly mutagenic (+)-anti-7,8-diol-9,10 epoxide (BPDE). Two polymorphisms have been described in the coding region of the mEH gene (EPHX1) that produce two protein variants: 113Tyr-->113His (exon 3) and 139His-->139Arg (exon 4). We performed a case-control study among Northwestern Mediterranean Caucasians to investigate a possible association between these EPHX1 variants and lung cancer risk. Both EPHX1 polymorphisms were analyzed in a group of lung cancer patients (n=176) and in a control group of healthy smokers (n=187). The results showed a significantly decreased risk for the rare homozygous 113His/113His (adjusted odds ratio (OR): 0.44, 95% confidence interval (CI): 0.27-0.71) and 139Arg/139Arg (adjusted OR: 0.55, 95% CI: 0.33-0.91) compared with the major wild-types 113Tyr/113Tyr and 139His/139His, respectively, as the references. Thereafter, we analyzed the EPHX1 variants in combination with three glutathione S-transferase polymorphic genes (GSTM1, GSTT1, and GSTP1) and we found a significant overepresentation of cancer patients with a combination of exon 3 113Tyr/113Tyr EPHX1 and exon 5 105Ile/105Ile GSTP1 (adjusted OR: 2.34, 95% CI: 1.21-4.52). The polymorphic site within the exon 5 of GSTP1 results in a Ile-->Val substitution, and the isoleucine GSTpi isoform has been found in vitro to be less active than the valine isoform towards the conjugation of BPDE. The 113 Tyr/Tyr EPHX1 encodes for a high-activity mEH. Our results agree with these observations in vitro and suggest that a genetically determined combination of a high-activity mEH and a low-activity GSTpi may increase lung cancer risk among smokers.

Adult↗

Novel ABCA1 compound variant associated with HDL cholesterol deficiency.

The recent discovery of an ATP-binding cassette transporter, ABCA1, as an important regulator of high density lipoprotein (HDL) metabolism and reverse cholesterol transport has facilitated the identification of novel variants associated with HDL cholesterol deficiency states. We identified a subject with HDL cholesterol deficiency (4 mg/dl) who developed and died of complications related to cerebral amyloid angiopathy (CAA). The proband had a compound heterozygous mutation. One mutation was a G3295T substitution with conversion of asparagine to tyrosine (D1099Y) in ABCA1. The single-base substitution at codon 1099 resulted in the abolition of an RsaI cleavage site. The proband and affected individuals having another mutation were heterozygotes for T5966C with phenylalanine converted to serine (F2009S). The presence of the T5966C mutation was detected by restriction digestion with HinfI. These variants were not identified in over 400 chromosomes of healthy subjects. In the kindred, family members heterozygous for the ABCA1 variant exhibited low levels of HDL cholesterol. Direct sequencing of all coding regions and splice site junctions of other HDL candidate genes revealed no additional mutations, indicating that combined defective ABCA1 alleles may result in familial HDL deficiency.

ATP Binding Cassette Transporter 1↗

HPC2/ELAC2 polymorphisms and prostate cancer risk: analysis by age of onset of disease.

The candidate prostate cancer susceptibility gene HPC2/ELAC2 has two common coding polymorphisms: (Ser-->Leu 217) and (Ala-->Thr 541). The Thr541 variant in the HPC2/ELAC2 gene has previously been reported to be at an increased frequency in prostate cancer cases. To evaluate this hypothesis we genotyped 432 prostate cancer patients (including 262 patients diagnosed 55 years (OR=1.27, 95% CI 0.59-2.74). We conclude that any association between the Thr541 variant and prostate cancer is likely to be weak.

Adult↗

Serum Gm allotype development during childhood.

Gm allotypes are genetic variants of the immunoglobulin heavy G chains (IGHG) of IgG molecules, coded from chromosome 14q32, characterized by differences in amino acid epitopes of the constant heavy G chains and inherited in the Mendelian manner. Gm allotypes have influence on IgG subclass levels, and serum Gm allotype levels have been given for different Gm genotypes in adults. Four hundred and thirty healthy children, aged 1-15 years, were examined for serum Gm allotypes and IgG subclasses from the six most common Gm genotypes and different age groups were measured using competitive enzyme-linked immunosorbant assay and radial immunodiffusion methods. Quantities (in g/l) of G1m(a) and G1m(f) of IgG1, G2m(n) and G2m(-n) of IgG2 and G3m(g), and G3m(b) of IgG3 are given. Different maturation rates of the alternative Gm allotypes within IgG1, IgG2 and IgG3 were shown. G2m(n) development was strikingly retarded compared with G2m(-n) from the gamma2 locus. This was found comparing IgG2 levels from homozygous G2m(-n-n) and G2m(nn) individuals, but was also seen in heterozygous G2m(n-n) genotypes. From the gamma1 locus G1m(f) levels dominated significantly, but inconstantly, over G1m(a) levels in heterozygous G1m(af) individuals. In homozygous G1m genotypes, G1m(aa) compared with G1m(ff) of the same age, one or the other dominated, sometimes significantly. Serum levels of G3m(b) from the gamma3 locus of homozygous G3m(bb) individuals were increased significantly compared with G3m(g) levels of homozygous G3m(gg) individuals, in ages over 3 years. However, in heterozygous G3m(gb) individuals G3m(b) dominance was not evident. There is a relatively rapid development of G1m(f) molecules and a retarded development of G2m(n) in the Gm(f;n;b) haplotype. In comparison, G1m(a) is retarded and G2m(-n) is enhanced in the Gm(a;-n;g) haplotype. The retarded serum G2m(n) development is comparable with serum IgA development during childhood. Different maturation rates of Gm allotypes within the same IgG subclass provide further explanation for the variation of the antibody response during childhood. Quantitative Gm allotype determinations give information of the activity from IGHG genes. The genetic variation constitutes an additional basis for evaluation of IgG antibodies in different diseases in childhood.

Adolescent↗

Mechanism of action of a pestivirus antiviral compound.

We report here the discovery of a small molecule inhibitor of pestivirus replication. The compound, designated VP32947, inhibits the replication of bovine viral diarrhea virus (BVDV) in cell culture at a 50% inhibitory concentration of approximately 20 nM. VP32947 inhibits both cytopathic and noncytopathic pestiviruses, including isolates of BVDV-1, BVDV-2, border disease virus, and classical swine fever virus. However, the compound shows no activity against viruses from unrelated virus groups. Time of drug addition studies indicated that VP32947 acts after virus adsorption and penetration and before virus assembly and release. Analysis of viral macromolecular synthesis showed VP32947 had no effect on viral protein synthesis or polyprotein processing but did inhibit viral RNA synthesis. To identify the molecular target of VP32947, we isolated drug-resistant (DR) variants of BVDV-1 in cell culture. Sequence analysis of the complete genomic RNA of two DR variants revealed a single common amino acid change located within the coding region of the NS5B protein, the viral RNA-dependent RNA polymerase. When this single amino acid change was introduced into an infectious clone of drug-sensitive wild-type (WT) BVDV-1, replication of the resulting virus was resistant to VP32947. The RNA-dependent RNA polymerase activity of the NS5B proteins derived from WT and DR viruses expressed and purified from recombinant baculovirus-infected insect cells confirmed the drug sensitivity of the WT enzyme and the drug resistance of the DR enzyme. This work formally validates NS5B as a target for antiviral drug discovery and development. The utility of VP32947 and similar compounds for the control of pestivirus diseases, and for hepatitis C virus drug discovery efforts, is discussed.

Animals↗

Genetic variation in natural populations: problem of electrophoretically cryptic alleles.

Electrophoretic studies have shown that the average frequency of heterozygous loci per individual is about 12% in Drosophila and other invertebrates and about 6% in vertebrates. It is estimated that only about two-thirds of all amino acid substitutions change net electric charge; hence, a large fraction of all genetic variation may be undetected by electrophoresis. Peptide mapping of 11 independent alleles coding for alcohol dehydrogenase in Drosophila melanogaster has uncovered one cryptic variant; thus, the frequency of electrophoretically cryptic variation is apparently low, about 9% in this sample. Nevertheless, with a simple model it is shown that this degree of cryptic variation, if it is typical of other loci, would substantially change our current estimates of genetic variation: the average heterozygosity would increase from about 12% to about 25% for invertebrates and from about 6% to 21% for vertebrates. A variety of techniques--including sequential electrophoresis and heat or urea denaturation--have been used by various investigators to detect electrophoretically cryptic variation. These techniques appear to be less effective than peptide mapping for detecting cryptic variation, but, like peptide mapping, they suggest that standard electrophoresis may detect most of the protein variation present in natural populations. The charge-state model of protein variation proposes that the "alleles" detected by electrophoresis are extremely diverse classes consisting of many electrophoretically cryptic alleles. The alcohol dehydrogenase peptide-mapping results are inconsistent with the charge-state model.

Alleles↗

Coinfection with multiple strains of the Epstein-Barr virus in human immunodeficiency virus-associated hairy leukoplakia.

Epstein-Barr virus DNA was analyzed from specimens of hairy leukoplakia, an oral lesion that occurs in patients infected with the human immunodeficiency virus. The simultaneous presence of both type 1 and type 2 Epstein-Barr virus was demonstrated by Southern blot analysis and polymerase chain reaction assay. Restriction fragment length polymorphisms in the BamHI WYH region and in clones of the EcoRI C region suggested the presence of multiple strains of type 1 and type 2 viruses. The demonstration of multiple variably sized BamHI H fragments on Southern blot analysis and cloning of the EBNA-2 gene coding region also suggested the presence of multiple viral strains or variants coinfecting hairy leukoplakia. Recombination of the viral genome in and around the EBNA-2 gene apparently generated viral variants that replicated efficiently, one of which appeared to increase in abundance in a lesion over time. These data indicate that hairy leukoplakia involves coinfection with multiple strains of replicating Epstein-Barr virus and the endogenous generation of viral variants, some of which have mutations of the EBNA-2 gene.

Antigens, Viral↗

Functional studies on native and mutated forms of perilipins. A role in protein kinase A-mediated lipolysis of triacylglycerols.

Perilipin A coats the lipid storage droplets in adipocytes and is polyphosphorylated by protein kinase A (PKA); the fact that PKA activates lipolysis in adipocytes suggests a role for perilipins in this process. To assess whether perilipins participate directly in PKA-mediated lipolysis, we have expressed constructs coding for native and mutated forms of the two major splice variants of the perilipin gene, perilipins A and B, in Chinese hamster ovary fibroblasts. Perilipins localize to lipid droplet surfaces and displace the adipose differentiation-related protein that normally coats the droplets in these cells. Perilipin A inhibits triacylglycerol hydrolysis by 87% when PKA is quiescent, but activation of PKA and phosphorylation of perilipin A engenders a 7-fold lipolytic activation. Mutation of PKA sites within the N-terminal region of perilipin abrogates the PKA-mediated lipolytic response. In contrast, perilipin B exerts only minimal protection against lipolysis and is unresponsive to PKA activation. Since Chinese hamster ovary cells contain no PKA-activated lipase, we conclude that the expression of perilipin A alone is sufficient to confer PKA-mediated lipolysis in these cells. Moreover, the data indicate that the unique C-terminal portion of perilipin A is responsible for its protection against lipolysis and that phosphorylation at the N-terminal PKA sites attenuates this protective effect.

Animals↗

Regulation of the NEDD8 conjugation system by a splicing variant, NUB1L.

NEDD8 is a ubiquitin-like protein that controls vital biological events through its conjugation to target proteins. We previously identified a negative regulator of the NEDD8 conjugation system, NUB1, which works by recruiting NEDD8 and its conjugates to the proteasome for degradation. Recently, we found its splicing variant, NUB1L. It possesses an insertion of 14 amino acids that codes for a UBA domain. Structural study revealed that NUB1 has a NEDD8-binding site at the C terminus, whereas NUB1L has an additional site at the newly generated UBA domain. Interestingly, the sequence A(X4)L(X10)L(X3)L was conserved in these NEDD8-binding sites among human and other mammals. Mutational studies revealed that at least three Leu residues in the conserved sequence are required for binding with NEDD8. Functional study suggested that the NEDD8-binding ability at the C terminus of NUB1 and NUB1L is mainly involved in the down-regulation of NEDD8, but the NEDD8-binding ability at the UBA2 domain of NUB1L is minimally or not involved at all. The NEDD8-binding ability at the UBA2 domain might be required for an unknown function of NUB1L.

Adaptor Proteins, Signal Transducing↗

MRBAYES: Bayesian inference of phylogenetic trees.

SUMMARY: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. AVAILABILITY: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.

Algorithms↗