Comparative analysis of the polycystic kidney disease 1 (PKD1) gene reveals an integral membrane glycoprotein with multiple evolutionary conserved domains

PKD1 is the major locus of the common genetic disorder autosomal dominant polycystic kidney disease (ADPKD). Analysis of the predicted protein sequence of the human PKD1 gene, polycystin, shows a large molecule with a unique arrangement of extracellular domains and multiple putative transmembrane regions. The precise function of polycystin remains unclear with a paucity of mutations to define key structural and functional domains. To refine the structure of this protein we have cloned the genomic region encoding the Fugu PKD1 gene. Fugu PKD1 spans 36 kb of genomic DNA and has greater complexity with 54 exons compared with 46 in man. Comparative analysis of the predicted protein sequences shows a lower level of homology than in similar studies with identity of 40 and 59% similarity. However key structural motifs including leucine rich repeats (LRR), a C-type lectin and LDL-A like domains and 16 PKD repeats are maintained. A region of homology with the sea urchin REJ protein was also confirmed in Fugu but found to extend over 1000 amino acids. Several highly conserved intra- and extra-cellular regions, with no known sequence homologies, that are likely to be of functional importance were detected. The likely structure of the membrane associated region has been refined with similarity to the PKD2 protein and voltage gated Ca2+ and Na+ channels highlighted over part of this area. The overall protein structure has therefore been clarified and this comparative analysis derived structure will form the basis for the functional study of polycystin and its individual domains.

Histopathologic findings in drug-induced pemphigus

Drug-induced pemphigus represents a diagnostic challenge, as usually no clinical feature differentiates it from its idiopathic counterpart. It was suggested recently that some histologic features may assist in diagnosing drug-associated diseases. The purpose of the study was to determine whether the histologic criteria suggested in the literature are specific enough to arouse suspicion of drug-induced pemphigus. Biopsy specimens of drug-induced and idiopathic pemphigus were reviewed by five dermatologists with no clinical data available about the patients. The sections were assessed to the presence of spongiosis with eosinophils, vacuolar degeneration, and the degree of acantholysis and cleavage level. Using the suggested criteria, the reviewers were unable to confirm a diagnosis of drug-induced pemphigus. It is advisable to consider drug etiology in every case of newly diagnosed pemphigus based on clinical criteria an detailed drug consumption history, as histologic features do not differentiate between drug-associated and idiopathic disease.

Paraneoplastic pemphigus associated with pancreatic carcinoma

A case of paraneoplastic pemphigus associated with pancreatic carcinoma is presented. The histopathological and immunological features of the case, which are consistent with and differ from the accepted diagnostic criteria, are discussed.

Molecular cloning of 5-hydroxytryptamine (5-HT) type 1 receptor genes from the Japanese puffer fish, Fugu rubripes

To characterize the structure of Fugu G-protein coupled receptor family and its evolutionary divergence, we have cloned and sequenced the Fugu 5-HT type 1 receptor genes by Polymerase Chain Reaction (PCR) with degenerate primers followed by phage library screening. The analysis of the deduced amino acid sequences showed that F1A alpha and F1A beta have the highest homology to the human 5-HT1A receptor (71.5% and 63.7%, respectively). Another clone, F1D, showed highest (70.5%) homology to the human type 1D receptor. The amino acid residues that are important for ligand binding have been conserved in these Fugu genes. The phylogenetic tree analysis suggests that the duplication event of the Fugu type 1A receptor may have occurred after the divergence of Fugu and the tetrapod lineage.

Recognition of pemphigus antigens in drug-induced pemphigus vulgaris and pemphigus foliaceus

BACKGROUND

The clinical appearance and biologic behavior of drug-induced pemphigus depend on the type of inducing drug.

OBJECTIVE

Our purpose was to investigate patients with drug-induced pemphigus vulgaris and pemphigus foliaceus antigens and compare results of studies to detect antibody reactivity in sera of these patients with the serology of patients with idiopathic pemphigus.

METHODS

Ten patients with drug-induced pemphigus were studied. Antibody reactivity was determined against the pemphigus vulgaris antigen, desmoglein 3, and against desmoglein 1.

RESULTS

The patient with pemphigus foliaceus and low levels of autoantibodies precipitated neither antigen. One patient with pemphigus vulgaris and high levels of antibody also failed to precipitate any specific antigen. Sera from eight patients with drug-induced pemphigus vulgaris had circulating autoantibodies directed to either the pemphigus vulgaris or pemphigus foliaceus antigen. Low levels of antibody in two of these eight patients precipitated only the pemphigus foliaceus antigen. High levels of antibody in five of the eight patients precipitated the pemphigus vulgaris antigen; two of these also reacted with the pemphigus foliaceus antigen.

CONCLUSION

The autoantibody response was similar in both spontaneous and drug-related disease. A similar molecular mechanism in the two types of pemphigus is suggested.

Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes

The clustered organization of Hox genes provides a powerful opportunity to examine gene gain and loss in evolution because physical linkage is a key diagnostic feature which allows homology to be established unambiguously. Furthermore, Hox genes play a key role in determination of axial and appendicular skeletal morphology and may be a key component of the evolution of diverse metazoan body forms. Despite suggestions that changes in Hox gene number played a role in evolution of metazoan body plans, there has been a general lack of evidence for such variation amongst gnathostomes (or indeed any vertebrate) and it has therefore been widely assumed that differential regulation may be the key element in all vertebrate Hox evolution. We have studied the Hox gene clusters of a teleost fish, Fugu rubripes, to test the possibility that Hox organization may have varied since the origin of jawed vertebrates. We have identified four Hox complexes in Fugu and found an unprecedented degree of variation when compared with tetrapod clusters. Our data show that: Fugu clusters are widely variant with respect to length; at least nine genes have been lost; there is a new group-2 paralogue; and pseudo-gene remnants of group-1 and group-3 paralogues were found in the Hoxc complex, when compared with the present mammalian clusters. We show that gene loss after duplication of the prototypical vertebrate Hox clusters is a key feature of both tetrapod and fish evolution.

Genomic structure and sequence of the pufferfish (Fugu rubripes) growth hormone-encoding gene: a comparative analysis of teleost growth hormone genes

A nested polymerase chain reaction (PCR) technique for amplifying a fragment of the gene (GH) encoding teleost growth hormone has been developed. Using this technique, a fragment of the pufferfish, Fugu rubripes and Arothron maculatus, dwarf gourami, Colisa lalia; guppy, Poecilia reticulata; and goldfish, Carassius auratus GH genes were cloned. The Fugu rubripes (Fugu) gene fragment was used to isolate the GH gene from a Fugu genomic library. The complete nucleotide sequence of a 8.5-kb SacI genomic fragment containing the Fugu GH gene has been determined. The GH gene spans 2.5 kb from the first codon to polyadenylation signal, and contains six exons and five introns similar to the GH genes of salmonids, tilapia, barramundi, flounder and yellowtail. The GH introns contain microsatellite and satellite sequences. The microsatellites found in the fifth intron of the GH gene are also present in the corresponding introns of tilapia, barramundi and flounder GH genes. Southern analysis revealed that the GH gene is a single-copy gene in the Fugu. The promoter region of the Fugu GH gene contains conserved sequences that are likely to be involved in the pituitary-specific expression of the gene. A phylogenetic tree of nucleotide (nt) sequences of all known teleost GH genes has been inferred using the distance matrix method. The topology of this tree reflects the major phylogenetic groupings of teleosts. The intron patterns and repetitive sequences of GH genes can serve as useful natural markers for the classification and phylogenetic studies of teleosts.

A novel bacterial vector system for monitoring protein-protein interactions in the cAMP-dependent protein kinase complex

A bacterial expression vector is described for investigation of protein-protein interactions. Important features of the vector include partition of the cI repressor of bacteriophage lambda into two functional domains separated by a multicloning site, and low level auto-regulated expression of human genes as C-terminal fusions to the DNA-binding domain of cI. Two different reporter systems have been employed; expression of either a suppressor tRNA or the alkaline phosphatase gene is dependent in both cases on the extent of repression of the major leftward promoter of lambda (lambdaP(L)). The cAMP-dependent protein kinase (PKA) has been used as a model protein complex because both homodimer and heterodimer interactions are known to occur and because cAMP acts as a modulator of these interactions. It has been shown that the product of the repressor gene with newly incorporated expressed polylinker restriction sites still functions as a repressor. Substitution of the dimerisation domain of the cI repressor with the regulatory subunit of PKA does not diminish the ability of a cI fusion protein to repress expression of the reporter gene from lambdaP(L), indicating that the regulatory subunit of PKA dimerises the fusion protein in the Escherichia coli cytoplasm. Substitution instead with the catalytic subunit of PKA destroys the repression ability of cI, which is partially restored by separate expression of the regulatory subunit within the same cell. Complete restoration is achieved using a host E. coli strain which has lost its ability to synthesise cAMP and again this can be reversed by the addition of exogenous cAMP to these cells. Human PKA has been reconstituted in the E. coli cytoplasm, where all subunit interactions appear functional and respond as expected to the allosteric modulator cAMP.

Circulating pemphigus IgG in families of patients with pemphigus: comparison of indirect immunofluorescence, direct immunofluorescence, and immunoblotting

BACKGROUND

Patients with pemphigus vulgaris (PV) are genetically linked to two alleles of the HLA subgroup, and circulating antibodies were found in first-degree relatives of these patients, thus showing genetic predisposition.

OBJECTIVE

Our purpose was to determine the occurrence of circulating true PV-IgG in patients' relatives.

METHODS

Circulating PV-IgG was determined in 21 first-degree relatives of 12 patients with PV by indirect immunofluorescence on monkey esophagus, carcinoma A431 cultures, and Western immunoblotting. Direct immunofluorescence was performed on skin biopsy specimens of 20 relatives.

RESULTS

Circulating PV-IgG was detected in 15 relatives (71%) by all methods tested. Good correlation was found between immunoblot reactivity and immunofluorescence. Of the 15 "positive" relatives, only five showed fixation of IgG to epidermal cells in vivo.

CONCLUSION

The permeability of the epidermis or epidermal cell reactivity in vivo probably controls the expression of disease in patients' relatives.

Genomic structure and sequence analysis of the valyl-tRNA synthetase gene of the Japanese pufferfish, Fugu rubripes

The genomic sequence and exon-intron organisation of the valyl-tRNA synthetase gene in the Japanese pufferfish, Fugu rubripes, have been determined. This single-copy Fugu gene spans 8.5 kb, about 2.5 times smaller than that in man (21 kb). It contains 29 exons, with the largest intron being 1008 bp. The predicted polypeptide consists of 1217 amino acids, with a molecular weight of 138 kD and an isoelectric point of 7.27. It shares 40% identity in the overlapping region with its homolog in bacteria, 47% with yeast, and 67% with man. The Fugu gene has an additional N-terminal sequence which shows strong similarity to elongation factory-1gamma, a feature it shares only with the human sequence, but not with any other lower eukaryote or prokaryote studied so far. This N-terminal segment is encoded in the first six exons, suggesting their capture by a translocation through introns. Indeed, the acquisition of extra domains to perform related functions in RNA splicing and translation of polypeptides has already been observed in other aminoacyl-tRNA synthetases. Two cDNA sequences of human valyl-tRNA synthetase have been published, with discrepancies between them. Aided by comparisons with the Fugu gene, three of these discrepancies have been resolved, involving the elucidation of the sequence and positions of two introns. This compact vertebrate genome has demonstrated its value as a tool for the analysis of genes at the genomic level.

Diclofenac: a new trigger of pemphigus vulgaris?

Many drugs have been shown to induce pemphigus, including thiol and nonthiol drugs. We present a case of pemphigus vulgaris where a nonsteroidal anti-inflammatory medication, diclofenac in suppositories and topical gel preparations, is suspected of having triggered the disease. The temporal relationship between drug and outbreak of disease together with the positive migration inhibition factor test to diclofenac point to the possible involvement of this drug in triggering pemphigus vulgaris.

Paraneoplastic subacute cutaneous lupus erythematosus: report of a case associated with cancer of the lung

A case of subacute cutaneous lupus erythematosus (SCLE) associated with lung carcinoma is presented. A review of the literature revealed only 5 other cases of SCLE associated with internal malignancy. The tumor in the described case most probably developed before the appearance of the eruption. Cancer chemotherapy was followed by shrinkage of tumor mass and regression of the skin lesions. The sequence of these events corresponds to the definition of paraneoplastic dermatoses.

Protein folds in the all-beta and all-alpha classes

Analysis of the structures in the Protein Databank, released in June 1996, shows that the number of different protein folds, i.e. the number of different arrangements of major secondary structures and/or chain topologies, is 327. Of these folds, approximately 25% belong to the all-alpha class, 20% belong to the all-beta class, 30% belong to the alpha/beta class, and 25% belong to the alpha + beta class. We describe the types of folds now known for the all-beta and all-alpha classes, emphasizing those that have been discovered recently. Detailed theories for the physical determinants of the structures of most of these folds now exist, and these are reviewed.

Short-range linkage relationships of the valyl-tRNA synthetase gene in Fugu rubripes

The class III region of the human major histocompatibility complex (MHC) is gene-dense, averaging one gene every 10-20 kilobases (kb). Its gene order has been compared with other organisms. To extend this analysis further in another non-mammalian vertebrate, the compact genome of Fugu rubripes was investigated for the existence of orthologues of these class III genes and their relative arrangements. Orthologues of the Mr 70000 heat shock protein (HSP70) and valyl-tRNA synthetase genes have been isolated. They do not seem to be closely physically linked as compared with mammals (supported by longer-range analysis using pulsed field gel electrophoresis). Random shotgun sequencing of the two Fugu cosmids containing the gene encoding valyl-tRNA synthetase revealed sequences resembling genes encoding tenascin-X, the nuclear antigen A/Ro of Sjogren's syndrome, and the Landsteiner-Wiener blood group glycoprotein. These linkage relationships recapitulate some mammalian data, albeit imperfectly. Tenascin-X has been located both in the human and mouse Mhc class III regions. Three copies of a sequence found in the gene encoding Sjogren's syndrome nuclear antigen A/Ro have been identified in the human Mhc class I region; the mouse Mhc class I region contains one copy. It is postulated that a fragmented gene pattern had existed prior to convergence in the ancestral mammalian immune response-related Mhc region, and that some of these genes had belonged to the same linkage group.

G protein alpha subunit multigene family in the Japanese puffer fish Fugu rubripes: PCR from a compact vertebrate genome

We compare the complexity and organization of the G protein alpha subunit multigene family in the vertebrate genomes of mammals and the Japanese puffer fish Fugu rubripes. Fourteen Fugu G alpha genes were identified of the 16 genes characterized previously in mammals, including Fugu genes from the four classes of alpha subunits Gs, Gi, Gq, and G12. Fugu and mammalian G alpha coding sequences are highly homologous, and the intron/exon structure of the fish and mammalian orthologs is identical throughout the coding regions. A novel G alpha gene, G alpha p1, was also identified in Fugu rubripes and two other species of puffer fish. The complete sequence of Gnaz and the tandemly duplicated genes Gnai2 and Gnat1 were obtained from a Fugu genomic cosmid library. Introns in the puffer fish G alpha genes lacked repeat DNA sequences, other than simple sequence length repeats, and most introns were significantly shorter in Fugu than in mammalian orthologs. The compact genome of puffer fish provides a unique vertebrate model for characterizing multigene families and identifying novel genes directly from genomic DNA by PCR amplification with degenerate primers. The fact that Fugu encodes most, if not all, of the G protein alpha subunits identified in mammals strongly supports Fugu as a model organism for vertebrate genome research.

Fugu intron oversize reveals the presence of U15 snoRNA coding sequences in some introns of the ribosomal protein S3 gene

We present here the analysis of the genomic organization of the Fugu gene coding for ribosomal protein S3 and its intron encoded U15 RNA, and compare it with the homologous human and Xenopus genes. Only two of the six Fugu S3 gene introns do not contain the U15 sequence and are in fact shorter than 100 nucleotides, as most Fugu introns. The other four introns are somewhat longer and contain sequences homologous to U15 RNA; two of these represent functional copies, as shown by microinjections of Fugu transcripts into Xenopus oocytes, whereas the other two appear to be nonfunctional pseudocopies. Thus Fugu turns out to be ideal for the study of intron encoded snoRNAs, partly because of the reduced cloning and sequencing workload, and partly because the intron length per se can be an indication of the presence of a snoRNA coding sequence.