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Results for “multigene typing”

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PubMed1999

Genetic polymorphism of murine tissue plasminogen activator associated with antiphospholipid syndrome.

In a subset of patients with systemic lupus erythematosus (SLE), antiphospholipid syndrome characterized by thrombocytopenia, thrombosis, recurrent abortion and antiphospholipid antibodies develops. Male (NZW x BXSB) F1 mice are widely used as a model for SLE-associated antiphospholipid syndrome. Our earlier genetic studies showed that one susceptibility allele for thrombocytopenia and associated IgG platelet-binding autoantibodies in male (NZW x BXSB) F1 mice was linked to the BXSB-type polymorphic microsatellite D8Mit96, located in proximity to the gene Plat for tissue-type plasminogen activator (t-PA). In the present studies, sequence analyses for structural and promoter regions of Plat revealed a single nucleotide polymorphism encoding a catalytic domain of t-PA, with an amino acid substitution of anionic Glu366 in NZW for a cationic Lys in BXSB. Progeny studies using NZW x (NZW x BXSB) F1 male backcross mice showed that the BXSB Plat allele was significantly associated with high levels of both platelet-binding antibodies and thrombocytopenia. Furthermore, these two traits appeared to be regulated by a complementary effect of two BXSB alleles; one is linked to Plat and the other to the H-2 complex and the gene for plasminogen. Thus, the BXSB-type Plat may be one susceptibility allele for the multigenic antiphospholipid syndrome seen in (NZW x BXSB) F1 mice. Potential mechanisms are discussed.

Amino Acid Sequence↗

PubMed2004

Comparison of the genome sequence of FP9, an attenuated, tissue culture-adapted European strain of Fowlpox virus, with those of virulent American and European viruses.

The 266 kbp genome sequence of plaque-purified, tissue culture-adapted, attenuated European Fowlpox virus FP9 has been determined and compared with the 288 kbp sequence of a pathogenic US strain (FPVUS). FP9 carries 244 of the 260 reported FPVUS ORFs (both viruses also have an unreported orthologue of conserved poxvirus gene A14.5L). Relative to FPVUS, FP9 differed by 118 mutations (26 deletions, 15 insertions and 77 base substitutions), affecting FP9 equivalents of 71 FPVUS ORFs. To help to identify mutations involved in adaptation and attenuation, the virulent parent of FP9, HP1, was sequenced at positions where FP9 differed from FPVUS. At 68 positions, FP9 and HP1 sequences were identical, reflecting differences between American and European lineages. Mutations at the remaining 50 positions in FP9 relative to FPVUS and HP1, involving 46 ORFs, therefore accounted for adaptation and attenuation. ORFs deleted during passage included those encoding members of multigene families: 12 ankyrin repeat proteins, three C-type lectin-like proteins, two C4L/C10L-like proteins, one G-protein coupled receptor protein, one V-type Ig domain protein, two N1R/p28 proteins and one EFc family protein. Tandem ORFs encoding Variola virus B22R orthologues were fused by a 5.8 kbp deletion. Single-copy genes disrupted or deleted during passage included those encoding a homologue of murine T10, a conserved DNA/pantothenate metabolism flavoprotein, photolyase, the A-type inclusion protein and an orthologue of vaccinia A47L. Gene assignments have been updated for DNase II/DLAD, binding proteins for IL-18 and interferon-gamma, phospholipid hydroperoxide glutathione peroxidase (PHGPX/GPX-4) and for a highly conserved homologue of ELOVL4.

Adaptation, Physiological↗

PubMed1986

Differential order of replication of Xenopus laevis 5S RNA genes.

In Xenopus laevis there are two multigene families of 5S RNA genes: the oocyte-type 5S RNA genes which are expressed only in oocytes and the somatic-type 5S RNA genes which are expressed throughout development. The Xenopus 5S RNA replication-expression model of Gottesfeld and Bloomer (Cell 28:781-791, 1982) and Wormington et al. (Cold Spring Harbor Symp. Quant. Biol. 47:879-884, 1983) predicts that the somatic-type 5S RNA genes replicate earlier in the cell cycle than do the oocyte-type genes. Hence, the somatic-type 5S RNA genes have a competitive advantage in binding the transcription factor TFIIIA in somatic cells and are thereby expressed to the exclusion of the oocyte-type genes. To test the replication-expression model, we determined the order of replication of the oocyte- and somatic-type 5S RNA genes. Xenopus cells were labeled with bromodeoxyuridine, stained for DNA content, and then sorted into fractions of S phase by using a fluorescence-activated cell sorter. The newly replicated DNA containing bromodeoxyuridine was separated from the lighter, unreplicated DNA by equilibrium centrifugation and was hybridized with DNA probes specific for the oocyte- and somatic-type 5S RNA genes. In this way we found that the somatic-type 5S RNA genes replicate early in S phase, whereas the oocyte-type 5S RNA genes replicate late in S phase, demonstrating a key aspect of the replication-expression model.

Animals↗

PubMed1998

FROM VACUOLAR GS-X PUMPS TO MULTISPECIFIC ABC TRANSPORTERS.

While the concept of H+-coupling has dominated studies of energy-dependent organic solute transport in plants for over two decades, recent studies have demonstrated the existence of a group of organic solute transporters, belonging to the ATP-binding cassette (ABC) superfamily, that are directly energized by MgATP rather than by a transmembrane H+-electrochemical potential difference. Originally identified in microbial and animal cells, the ABC superfamily is one of the largest and most widespread protein families known. Competent in the transport of a broad range of substances including sugars, peptides, alkaloids, inorganic anions, and lipids, all ABC transporters are constituted of one or two copies each of an integral membrane sector and cytosolically oriented ATP-binding domain. To date, two major subclasses, the multidrug resistance-associated proteins (MRPs) and multidrug resistance proteins (MDRs) (so named because of the phenotypes conferred by their animal prototypes), have been identified molecularly in plants. However, only the MRPs have been defined functionally. This review therefore focuses on the functional capabilities, energetics, organization, and regulation of the plant MRPs. Otherwise known as GS-X pumps, or glutathione-conjugate or multispecific organic anion Mg2+-ATPases, the MRPs are considered to participate in the transport of exogenous and endogenous amphipathic anions and glutathionated compounds from the cytosol into the vacuole. Encoded by a multigene family and possessing a unique domain organization, the types of processes that likely converge and depend on plant MRPs include herbicide detoxification, cell pigmentation, the alleviation of oxidative damage, and the storage of antimicrobial compounds. Additional functional capabilities might include channel regulation or activity, and/or the transport of heavy metal chelates. The identification of the MRPs, in particular, and the demonstration of a central role for ABC transporters, in general, in plant function not only provide fresh insights into the molecular basis of energy-dependent solute transport but also offer the prospect for manipulating and investigating many fundamental processes that have hitherto evaded analysis at the transport level.

Journal Article↗

PubMedDate not supplied

Molecular cloning and sequence analysis of two distinct types of Xenopus laevis protein kinase C.

Two distinct types of protein kinase C cDNA clones were isolated from a Xenopus laevis oocyte cDNA library, and the complete nucleotide sequences were determined. The sequences encode a single open reading frame with a domain structure that consists of four constant (designated C1-C4) and five variable (designated V1-V5) regions. Comparison of the two sequences shows good homology at the nucleotide and deduced amino acid level. The differences reside primarily in the variable regions. Each clone encodes 671 and 676 amino acids, respectively, having extensive homology with published sequences of human, rat, and bovine protein kinase C. These results provide evidence that these two distinct types of protein kinase C are members of a multigene family in amphibian and mammalian species.

Amino Acid Sequence↗

PubMed1991

Chicken major histocompatibility complex-encoded B-G antigens are found on many cell types that are important for the immune system.

B-G antigens are a polymorphic multigene family of cell surface molecules encoded by the chicken major histocompatibility complex (MHC). They have previously been described only on cells of the erythroid lineage. By using flow cytometry, section staining, and immunoprecipitation with monoclonal antibodies and rabbit antisera to B-G molecules and by using Northern blots with B-G cDNA clones, we demonstrate here that B-G molecules and RNA are present in many other cell types: thrombocytes, peripheral B and T lymphocytes, bursal B cells and thymocytes, and stromal cells in the bursa, thymus, and caecal tonsil of the intestine. The reactions also identify at least one polymorphic B-G determinant encoded by the B-F/B-L region of the chicken MHC. The serology and tissue distribution of B-G molecules are as complex as those of mammalian MHC class I and class II molecules. These facts, taken with certain functional data, lead us to suggest that B-G molecules have an important role in the selection of B cells in the chicken bursa.

Animals↗

PubMed1975

Electrophoretic study of human ribosomal core proteins: evidence for selection against variation.

Ten human ribosomal core proteins examined electrophoretically showed significantly less polymorphic variation than expected on the basis of other protein systems studied. This implies that selective forces may restrict variation at these loci. Variation in common multigenic traits must be determined by a combination of common alleles. If there is restriction of variation at certain types of loci, a limit is placed on the number of loci which can play a role in multigenic inheritance. Surveys for polymorphism in groups of proteins with similar structural or functional roles will further define these limits.

Female↗

PubMed2005

Characterization of the pufferfish Takifugu rubripes apolipoprotein multigene family.

We have characterized the apolipoprotein multigene family of the pufferfish Takifugu rubripes. The pufferfish mainly contains 28-kDa, 27-kDa, and 14-kDa apolipoproteins in its plasma and was designated apo-28 kDa, apo-27 kDa, and apo-14 kDa, respectively. N-terminal amino acid sequencing revealed that pufferfish apo-28 kDa and apo-27 kDa have an identical amino acid sequence except an additional propeptide in the former; and both are homologues of apoA-I from other animals. The sequence of pufferfish apo-14 kDa is homologous to that of eel apo-14 kDa previously reported, both being apparently specific to fish. In silico screening, using the publicly available Fugu genome database confirmed the pufferfish apoA-I and apo-14 kDa genes. The database further contained the genes encoding four types of apoA-IV, one apoC-II and two types of apoE. Thus, pufferfish contains nine genes encoding apolipoprotein multigene family. Two apoA-IV and one apoE genes were tandemly arrayed and located on one scaffold. Thus two sets of these genes formed two gene clusters. The apoC-II and apo-14 kDa genes are also located on a single scaffold. apoA-I and apo-14 kDa gene transcripts were mainly expressed in liver and less abundantly in brain. The transcripts of the former gene were also observed in intestine. In contrast, the transcripts encoding four apoA-IVs, one apoC-II, and two apoEs were mainly expressed in intestine. These structural details of pufferfish apolipoproteins and tissue distribution of their gene transcripts provide a novel evidence for better understanding of evolutionary relationships of apolipoprotein multigene family.

Amino Acid Sequence↗

PubMed2006

IGF-I receptor gene activation enhanced the expression of monocarboxylic acid transporter 1 in hepatocarcinoma cells.

The present study aims to investigate the effect of IGF-I receptor (IGF-IR) gene activation on the expression of monocarboxylic acid transporters (MCTs) in hepatocarcinoma cells. In order to reflect malignant hepatoma, H4IIE cells (a rat hepatoma cell line) stably expressing IGF-IR (IGF-IR-H4IIE cells) have been established by retroviral infection and then the effect of IGF-IR gene up-regulation on the modulation of MCT expression was determined in IGF-IR-H4IIE cells. Immunoblot assay indicated that the expression level of MCT1 was 3.3-fold higher in IGF-IR-H4IIE cells compared to that in control cells, implying that IGF-IR signaling is coupled with the process of MCT1 expression. In contrast, the expression level of MCT2 was not affected by the IGF-IR activation, suggesting that MCT1 and MCT2 are regulated by the distinct type of signals. Furthermore, the cellular uptake of benzoic acid, a representative substrate of MCT1, was significantly (p<0.05) enhanced following the activation of IGF-IR via the pre-incubation with IGF-I (10 ng/ml). In conclusion, MCT1 expression was up-regulated in hepatocarcinoma cells and the IGF-IR signaling appeared to be coupled with the modulation of MCT1 expression.

Animals↗

PubMed1990

Overexpression of wild-type and dominant negative mutant vimentin subunits in developing Xenopus embryos.

Vimentin belongs to the diverse multigene family of intermediate filament proteins, each member of which is expressed in a tissue-specific and developmentally regulated pattern. The existence of vimentin filaments has been documented in oocytes, eggs, and early embryos of Xenopus laevis, but the role of these cytoskeletal components remains unknown. To investigate the functions of vimentin during early development in Xenopus, we induced the overexpression of wild-type and deletion mutant subunits in most of the cells of embryos by injecting synthetic RNA into fertilized eggs. Wild-type vimentin subunits, as well as subunits lacking most of the amino-terminal head piece, assembled into normal appearing filaments in vivo. Deletion mutants of the fourth alpha-helical rod domain were assembly incompetent and dominantly inhibited the polymerization of wild-type subunits when both types of subunit were co-expressed in cells. Expression of at least a tenfold excess of wild-type or mutant subunits within cells of embryos did not lead to any detectable morphological or developmental abnormalities, suggesting that the presence and proper regulation of vimentin expression is not essential during the initial stages of embryogenesis in Xenopus.

Amino Acid Sequence↗

PubMed2002

Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family.

In some species, histone gene clusters consist of tandem arrays of each type of histone gene, whereas in other species the genes may be clustered but not arranged in tandem. In certain species, however, histone genes are found scattered across several different chromosomes. This study examines the evolution of histone 3 (H3) genes that are not arranged in large clusters of tandem repeats. Although H3 amino acid sequences are highly conserved both within and between species, we found that the nucleotide sequence divergence at synonymous sites is high, indicating that purifying selection is the major force for maintaining H3 amino acid sequence homogeneity over long-term evolution. In cases where synonymous-site divergence was low, recent gene duplication appeared to be a better explanation than gene conversion. These results, and other observations on gene inactivation, organization, and phylogeny, indicated that these H3 genes evolve according to a birth-and-death process under strong purifying selection. Thus, we found little evidence to support previous claims that all H3 proteins, regardless of their genome organization, undergo concerted evolution. Further analyses of the structure of H3 proteins revealed that the histones of higher eukaryotes might have evolved from a replication-independent-like H3 gene.

Amino Acid Sequence↗

PubMed1995

Human REG family genes are tandemly ordered in a 95-kilobase region of chromosome 2p12.

Reg, first isolated from a rat regenerating islet cDNA library, is expressed in regenerating islet beta-cells. Recently, it has been revealed that Reg and Reg-related genes constitute a multigene family, the Reg family. In human, the four REG family genes, i.e., REG 1 alpha, REG 1 beta, REG-related sequence (RS) and HIP/PAP, have so far been isolated. In this study, we analyzed YAC clones containing the four genes and performed two-color FISH to determine the map order of the genes. The human REG family genes are tandemly ordered in the 95-kbp DNA region of chromosome 2p12 as follows: 2cen-HIP/PAP-RS-REG I alpha-REG I beta-ptel.

Acute-Phase Proteins↗

PubMed2002

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗

PubMed2006

Molecular genetic analysis of the Idd4 locus implicates the IFN response in type 1 diabetes susceptibility in nonobese diabetic mice.

High-resolution mapping and identification of the genes responsible for type 1 diabetes (T1D) has proved difficult because of the multigenic etiology and low penetrance of the disease phenotype in linkage studies. Mouse congenic strains have been useful in refining Idd susceptibility loci in the NOD mouse model and providing a framework for identification of genes underlying complex autoimmune syndromes. Previously, we used NOD and a nonobese diabetes-resistant strain to map the susceptibility to T1D to the Idd4 locus on chromosome 11. Here, we report high-resolution mapping of this locus to 1.4 megabases. The NOD Idd4 locus was fully sequenced, permitting a detailed comparison with C57BL/6 and DBA/2J strains, the progenitors of T1D resistance alleles found in the nonobese diabetes-resistant strain. Gene expression arrays and quantitative real-time PCR were used to prioritize Idd4 candidate genes by comparing macrophages/dendritic cells from congenic strains where allelic variation was confined to the Idd4 interval. The differentially expressed genes either were mapped to Idd4 or were components of the IFN response pathway regulated in trans by Idd4. Reflecting central roles of Idd4 genes in Ag presentation, arachidonic acid metabolism and inflammation, phagocytosis, and lymphocyte trafficking, our combined analyses identified Alox15, Alox12e, Psmb6, Pld2, and Cxcl16 as excellent candidate genes for the effects of the Idd4 locus.

Animals↗

PubMed2000

Intermediate filaments and their associates: multi-talented structural elements specifying cytoarchitecture and cytodynamics.

The assembly of intermediate filament (IF) arrays involves the recruitment of a complex set of cell-type-specific IF-associated proteins. Some of them are integral membrane proteins, others act as crosslinking proteins with vectorial binding activities, and yet others comprise motor proteins. In vivo IFs appear to be predominantly heteropolymers, although in vitro several IF proteins (e.g. vimentin, desmin, neurofilament (NF)-L and the nuclear lamins) do self-assemble into IF-like polymers. In contrast, NF-M, NF-H, nestin, synemin and paranemin, all bona fide IF proteins, are unable to self-assemble into IFs either in vitro or in vivo. The individual IF proteins of this large multigene family are chemically heterogeneous, exhibiting different assembly kinetics and yielding discrete types of filaments. The unique physical properties and interaction capabilities of these distinct IF molecular building blocks, in combination with accessory proteins, mediate the generation of a highly dynamic and interconnected, cell-type-specific cytoarchitecture.

Actin Cytoskeleton↗

PubMed1998

Characterization and developmentally regulated expression of four annexins in the killifish medaka.

Annexins are Ca2+-regulated membrane binding proteins implicated in a wide range of membrane-related and signal transduction events, including the endocytosis of membrane receptors and Ca2+-regulated as well as constitutive secretion. To date, 10 unique members of this multigene family have been identified in a variety of cell types and tissues of higher vertebrates, with different members showing distinct tissue distributions in the adult organisms. To establish whether annexins also function in embryonic development, we analyzed the expression pattern during vertebrate morphogenesis using the medaka fish Oryzias latipes as a model system. From a larval medaka cDNA library, we isolated four types of clones, which were shown by sequence analysis to encode four different annexins (herein referred to as max 1-4). A comparison with known annexin sequences in the databases revealed that two medaka annexins (max 1 and 2) are highly similar in sequence to mammalian annexins V and IV, respectively, whereas the other two medaka annexins (max 3 and 4) are probably novel members of the family most closely related to mammalian annexins I and XI. Using whole-mount RNA in situ hybridization, we showed that the expression of the different medaka annexins during embryogenesis was strictly regulated at both the spatial and the temporal level. High levels of max 1, 2, and 3 transcripts were present in the developing stomach, gut, liver, air-bladder, and rectum during somitogenesis, thus identifying the digestive tract as the prime region of annexin expression. Interestingly, two structures playing crucial roles in neuronal patterning showed a distinct expression of annexins. The mesendoderm of the anterior prechordal plate of neurula-stage embryos was a site of max 4 transcription, and the floor plate of somitogenesis-stage embryos showed expression of max 2 and 3 to differing rostrocaudal extends along the brain and spinal cord. These results suggest specific functions of different annexins during vertebrate morphogenesis.

Aging↗

PubMed1999

The divergence-homogenization duality in the evolution of the b1 mating type gene of Coprinus cinereus.

The A mating type locus of the fungus Coprinus cinereus is a complex, multigenic locus which regulates compatibility and subsequent sexual development. Genes within the A locus such as the b1 gene studied here exhibit extreme sequence variation. In this work, we asked how b1 alleles have evolved high levels of variation and, at the same time, conserved function. We compared sequence variation in 17 alleles characterized as belonging to seven different compatibility classes. Comparison of sequence variation between representatives of these seven classes shows that different regions of the b1 gene have been subject to varying levels of substitution, recombination, and structural/functional constraints. The N-terminal region of the encoded protein, which has been previously demonstrated to govern self/nonself recognition, exhibited hypervariability with levels of amino acid identity as low as 41%. We used a novel analysis of neutral mutations accumulating in this gene to rule out the possibility that the N-terminal region is hypermutable. In contrast, the C-terminal region displayed heterogeneous levels of variation, with functional motifs being better conserved. In fact, there is a duality in the b1 gene between variability and conservation; recombination events have homogenized the C-terminal region, while recombination events are undetectable in the N-terminal region. The ability to regulate sexual development is maintained in all of the mating compatibility alleles studied, and these data suggest that some functional motifs may tolerate high levels of substitution.

Alleles↗

PubMed2004

Molecular cloning, expression and chromosomal localization of a novel human REG family gene, REG III.

Regenerating gene (Reg), first isolated from a regenerating islet cDNA library, encodes a secretory protein with a growth stimulating effect on pancreatic beta cells that ameliorates the diabetes of 90% depancreatized rats and non-obese diabetic mice. Reg and Reg-related genes have been revealed to constitute a multigene family, the Reg family, which consists of four subtypes (types I, II, III, IV) based on the primary structures of the encoded proteins of the genes [Diabetes 51(Suppl. 3) (2002) S462]. Plural type III Reg genes were found in mouse and rat. On the other hand, only one type III REG gene, HIP/PAP (gene expressed in hepatocellular carcinoma-intestine-pancreas/gene encoding pancreatitis-associated protein), was found in human. In the present study, we found a novel human type III REG gene, REG III. This gene is divided into six exons spanning about 3 kilobase pairs (kb), and encodes a 175 amino acid (aa) protein with 85% homology with HIP/PAP. REG III was expressed predominantly in pancreas and testis, but not in small intestine, whereas HIP/PAP was expressed strongly in pancreas and small intestine. IL-6 responsive elements existed in the 5'-upstream region of the human REG III gene indicating that the human REG III gene might be induced during acute pancreatitis. All the human REG family genes identified so far (REG Ialpha, REG Ibeta, HIP/PAP, REG III and REG IV) have a common gene structure with 6 exons and 5 introns, and encode homologous 158-175-aa secretory proteins. By database searching and PCR analysis using a yeast artificial chromosome clone, the human REG family genes on chromosome 2, except for REG IV on chromosome 1, were mapped to a contiguous 140 kb region of the human chromosome 2p12. The gene order from centromere to telomere was 5' HIP/PAP 3'-5' RS 3'-3' REG Ialpha 5'-5' REG Ibeta 3'-3' REG III 5'. These results suggest that the human REG gene family is constituted from an ancestor gene by gene duplication and forms a gene cluster on the region.

5' Flanking Region↗