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Results for “multigene typing”

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PubMed2002

Evolution of NK receptors: a single Ly49 and multiple KIR genes in the cow.

Natural killer (NK) cell receptors for classical MHC class I molecules are encoded by the killer Ig-like receptor (KIR) multigene family in humans and other primates. Mouse NK cells, however, employ a completely different multigene family, the C-type lectin-like Ly49 genes, to perform the same function. This example of functional convergent evolution raises the question of what type of receptors are found in non-primate and non-rodent mammals. By screening a bovine spleen cDNA library, we isolated an Ly49 gene from the cow (Bos Taurus) and show by genomic Southern blotting that it is likely a single copy gene in this species. The coding region is intact and has an immunoreceptor tyrosine-based inhibition motif (ITIM) in the cytoplasmic domain, suggesting a role as an inhibitory receptor. We have also identified several bovine cDNA clones related to KIR and show that at least one has an intact open reading frame with two ITIM. Evidence for multiple KIR-like genes in the cow was obtained by Southern blotting and we found that at least two of these genes contain an ancient retro-element present in all human KIR genes. These results suggest that the cow and primate KIRgene families arose from a common ancestral gene but amplified independently. Furthermore, these findings indicate that the existence of multiple Ly49 genes may be a phenomenon unique to rodents.

Amino Acid Motifs↗

PubMed1987

Human collagen genes encoding basement membrane alpha 1 (IV) and alpha 2 (IV) chains map to the distal long arm of chromosome 13.

At least 20 genes encode the structurally related collagen chains that comprise greater than 10 homo- or heterotrimeric types. Six members of this multigene family have been assigned to five chromosomes in the human genome. The two type I genes, alpha 1 and alpha 2, are located on chromosomes 17 and 7, respectively, and the alpha 1 (II) gene is located on chromosome 12. Our recent mapping of the alpha 1 (III) and alpha 2 (V) genes to the q24.3----q31 region of chromosome 2 provided the only evidence that the collagen genes are not entirely dispersed. To further determine their organization, we and others localized the alpha 1 (IV) gene to chromosome 13 and in our experiments sublocalized the gene to band q34 by in situ hybridization. Here we show the presence of the alpha 2 type IV locus also on the distal long arm of chromosome 13 by hybridizing a human alpha 2 (IV) cDNA clone to rodent-human hybrids and to metaphase chromosomes. To our knowledge, these studies represent the only demonstration of linkage between genes encoding both polypeptide chains of the same collagen type.

Amino Acid Sequence↗

PubMed1993

Nature and possible functions of interferons secreted by the preimplantation pig blastocyst.

In several ungulate species, the preimplantation trophoblast, among various secretions, produces large amounts of antiviral activity that was identified as interferon (IFN). IFNs (types I and II) are pleiotropic cytokines, which in addition to a potent antiviral activity, exert multiple effects on cell growth and differentiation, in particular on the cells of the immune system. In ruminants, trophoblastic IFN, or trophoblast protein-1 (TP-1), was found to consist of a multigenic family related to type I IFN-omega. These IFNs exert hormone-like effects through receptors present on the endometrium, leading to the prolongation of luteal life-span and hence to sustained progesterone secretion. In pigs, a species in which the maternal recognition of pregnancy is controlled by conceptus-derived oestrogens, two IFNs have been found in the preimplantation trophoblast. The major species is IFN-gamma (type II), that so far had been found only in activated T lymphocytes and natural killer (NK) cells. Transcription of the IFN-gamma gene in the pig trophoblast differs from that in mature lymphocytes, since two mRNAs are present. The other component with antiviral activity is a novel type I IFN, distant in sequence from IFN-alpha, beta, omega, and containing seven cysteines in its deduced mature protein. These two unrelated IFNs are temporally co-induced, with maximal secretion at day 16 of pregnancy. Specific receptors for both IFNs have been found on endometrial epithelial cells, but not on the preimplantation trophoblast, suggesting a paracrine effect on the uterus. Different hypotheses as to their role(s) in the establishment or maintenance of implantation are discussed. Whereas an indirect anti-infectious (antiviral) protection of the conceptus by IFNs cannot be ruled out, arguments are presented that do not favour a role in the immune tolerance of the conceptus.

Animals↗

PubMed1993

Two yeast chromosomes are related by a fossil duplication of their centromeric regions.

A 15 kbp fragment of the Saccharomyces cerevisiae genome was cloned and localised to the centromeric region of chromosome XIV by genetic linkage and DNA sequencing. It had a strong sequence similarity and a conserved gene linkage and transcriptional orientation relatively to the centromeric region of chromosome III, indicating a fossil interchromosomal duplication of several linked genes. On chromosome XIV, the duplicated fragment included the centromere, four genes (FUN34, CIT1 and two tDNAs), one open reading frame (DOM34) and a truncated delta element. Additional inserts bearing unique genes were present on the centromeric region of chromosome III. The level of silent substitutions indicated a relatively ancient genetic separation, pre-dating the emergence of S. cerevisiae and S. douglasii as distinct species. The ensuing evolution of the duplicated regions retained strict sequence identity for the two tDNAs pairs, but was partially divergent for CIT1 and FUN34, and generated a probable pseudogenic equivalent of DOM34 on chromosome III. Extant multigenic duplications of this type might play an important role in the evolution of eukaryotic genomes.

Centromere↗

PubMed2000

Pathogenesis of type 2 diabetes: the relative contribution of insulin resistance and impaired insulin secretion.

Type 2 diabetes is characterised by both impaired insulin secretion and insulin resistance but their relative contribution to the development of hyperglycaemia may differ due to heterogeneity of the disease. Under most circumstances, insulin resistance is the earliest detectable defect in pre-diabetic individuals but it is not known whether this is the primary defect or secondary to other abnormalities such as abdominal obesity with excessive free fatty acid turnover and increased lipid deposits in muscle. Initially, enhanced insulin secretion can compensate for the insulin resistance but early phase insulin secretion is impaired. In the transition from normal to impaired and diabetic glucose tolerance, insulin sensitivity deteriorates about 40% whereas insulin secretion deteriorates 3-4 fold. In addition to insulin resistance, the metabolic syndrome includes hypertension, dyslipidaemia, obesity and microalbuminuria. In patients with manifest diabetes, chronic hyperglycaemia can result in further deterioration of insulin sensitivity and secretion (glucotoxicity), which is aggravated by elevated free fatty acids (lipotoxicity). Abdominal obesity and insulin resistance are strongly correlated and studies have aimed at understanding the genetic basis. Candidate genes for the metabolic syndrome include those for the beta 3-adrenergic receptor, lipoprotein lipase, hormone sensitive lipase, peroxisome proliferator-activated receptor-gamma, insulin receptor substrate-1 and glycogen synthase. Therefore, type 2 diabetes is multigenic and appears to represent a collision between thrifty genes and an affluent society. Successful management will require treatments targeted at defects of both insulin secretion and insulin resistance.

Diabetes Mellitus↗

PubMed1995

Plasmodium falciparum: typing of malaria parasites based on polymorphism of a novel multigene family.

Pf60.1, a marker recently isolated from the human malaria parasite Plasmodium falciparum, defines a large multigene family encoding antigens of 60 kDa, expressed by the blood stages (Carcy et al., Molecular and Biochemical Parasitology, 1994, 68, 221-233). Southern blotting showed that DNA from all strains and field isolates analyzed contained a large number of Pf60.1 copies. Considerable RFLP was observed. This diversity could be likewise visualized by analyzing PCR fragments amplified using primers derived from the Pf60.1 insert. Specific, multiple-band patterns were generated from laboratory strains, cloned lines, or wild isolates. This was further outlined after RsaI digestion of the PCR products. The sensitivity of this amplification was such that products could be visualized using a DNA amount representing less than one genome equivalent. Moreover, amplification was observed in some strains using a single primer, suggesting that some members of the Pf60.1 family are adjacent in an inverted orientation. This analysis confirmed the genetic similarity of a subset of laboratory strains. The results described here show that the extended diversity of this P. falciparum gene family provides a useful and sensitive PCR approach for strain typing.

Animals↗

PubMed2004

Rapid expansion of the Ly49 gene cluster in rat.

The cytotoxic activity of mouse natural killer cells is regulated in part through cell surface molecules belonging to the Ly49 multigene family. In mice, the genomic sequence of the Ly49 gene cluster has been examined in detail and this analysis provided a model of the expansion of this multigene family. In the present study, we have analyzed a 1.8-Mb region of the draft rat genome revealing surprising differences in size and gene content between the mouse and the rat Ly49 clusters. The rat cluster contains at least 36 Ly49 genes, including pseudogenes, while dot-plot analysis of the cluster reveals an equidistant spacing of genes, suggesting that duplication of genes in the cluster occurred through a mechanism similar to that in the mouse. Phylogenetic analysis of the predicted rat genes reveals a number of distinct gene clusters and indicates that the majority of gene duplication events occurred after the divergence of mice and rats. Thus, the rodent Ly49 locus is subject to extremely rapid gene amplification and diversification.

Animals↗

PubMed1990

cDNA sequence, tissue-specific expression, and chromosomal mapping of the human slow-twitch skeletal muscle isoform of troponin I.

Troponin I (TnI) is a myofibrillar protein involved in the calcium-mediated regulation of striated muscle contraction. Three isoforms of TnI are known and each is expressed in a muscle fiber-type-specific manner. TnI-fast and TnI-slow are expressed exclusively in fast-twitch and slow-twitch skeletal muscle myofibers, respectively, while a third isoform, TnI-card, is expressed in both the atrium and the ventricle of the heart. An explanation of the myofiber-type-restricted expression of the troponin I multigene family will further aid in understanding how various types of striated muscle fibers are established. To initiate the study of TnI isoform gene expression, we have isolated a full-length cDNA representing the human slow-twitch skeletal muscle isoform of troponin I. Sequence comparisons demonstrate that the TnI-slow protein is highly conserved between species. Therefore, the cDNA was used as a probe to investigate the tissue-specific and developmental regulation of the TnI-slow gene in both rodent and human myogenic cells. TnI-slow message appears to be restricted to muscle tissue containing slow-twitch skeletal muscle myofibers. TnI-slow gene expression is induced in differentiated cultures of primary human muscle cells and several (but not all) myogenic cell lines. In addition, a human-specific probe prepared from the 3' untranslated region of the cDNA has been used to probe a panel of human/mouse somatic cell hybrid lines, resulting in the assignment of the human TnI-slow gene to the q12----qter region of chromosome 1. The locus is designated TNNI1.

Amino Acid Sequence↗

PubMed2004

Differential levels of diabetogenic stress in two new mouse models of obesity and type 2 diabetes.

The genetic basis for the more common forms of human obesity predisposing to insulin resistance and development of type 2 diabetes is multigenic rather than monogenic in origin. New mouse "diabesity" models have been created by combining independent diabetes risk-conferring quantitative trait loci from two unrelated parental strains: New Zealand Obese (NZO/HlLt) and Nonobese Nondiabetic (NON/Lt). F1 hybrid males, heterozygous at all polymorphic autosomal loci distinguishing the two parental strains, are driven to obesity-induced diabetes (diabesity) at high frequencies. This review focuses on two new recombinant congenic strains (RCSs) developed by introgressing multiple NZO/HlLt chromosomal segments into the nominally diabesity-resistant NON/Lt strain background. Both RCSs gain more weight than NON animals. Although exhibiting comparable weight gain and adiposity, only one of the two RCSs develops diabetes. Hence, these two RCSs will be instructive in elucidating genetic and pathophysiological differences underlying uncomplicated obesity syndromes versus diabetogenic obesity (diabesity) syndromes. Unlike mice with null mutations in a single gene producing morbid obesity, the new models develop a more moderate obesity produced by the interaction of numerous genes with relatively small effects. These RCSs are differentially sensitive to adverse side effects of thiazolidinediones and thus should be particularly useful for pharmacogenetic analyses.

Animals↗

PubMed2025

Modularization of the type II secretion gene cluster from Xanthomonas euvesicatoria facilitates the identification of a structurally conserved XpsCLM assembly platform complex.

Many bacterial pathogens depend on a type II secretion (T2S) system to secrete virulence factors from the periplasm into the extracellular milieu. T2S systems consist of an outer membrane secretin channel, a periplasmic pseudopilus and an inner membrane-associated assembly platform including a cytoplasmic ATPase. The components of T2S systems are often conserved in different bacterial species, however, the architecture of the assembly platform is largely unknown. Here, we analysed predicted assembly platform components of the Xps-T2S system from the plant-pathogenic bacterium Xanthomonas euvesicatoria. To facilitate these studies, we generated a modular xps-T2S gene cluster by Golden Gate assembly of single promoter and gene fragments. The modular design allowed the efficient deletion and replacement of T2S genes and the insertion of reporter fusions. Mutant approaches as well as interaction and crosslinking studies showed that the predicted assembly platform components XpsC, XpsL and XpsM form a trimeric complex which is essential for T2S and associates with the cytoplasmic ATPase XpsE and the secretin XpsD. Structural modeling revealed a similar trimeric architecture of XpsCLM homologs from Pseudomonas, Vibrio and Klebsiella species, despite overall low amino acid sequence similarities. In X. euvesicatoria, crosslinking and fluorescence microscopy studies showed that the formation of the XpsCLM complex is independent of the secretin and vice versa, suggesting that the assembly of the T2S system is a dynamic process which involves the association of preformed subcomplexes.

Xanthomonas↗

PubMed1994

Characterization of a hair (wool) keratin intermediate filament gene domain.

In epithelial differentiation keratin intermediate filament genes are expressed in multifarious tissue-specific and stage-specific patterns. Pairs of type I and type II intermediate filament genes, belonging to multigene families, are coordinately regulated, and 4-5 genes of each type are expressed in the hair follicle. Accumulating chromosomal mapping data points to a major locus for each intermediate filament multigene family on separate chromosomes. In this report we describe the isolation of a sheep hair keratin cosmid by chromosome walking that overlaps two previously described cosmids and establishes a continuous 100-kb segment of cloned DNA containing three hair and three hair-like type II intermediate filament keratin genes. A new hair keratin type II intermediate filament gene, KRT2.11, is located in the middle of the cluster, and partial sequence data reveal a striking conservation of its predicted N-terminal region with other sheep hair keratin type II intermediate filament proteins. Expression analyses demonstrate the presence of a 2.4-kb KRT2.11 transcript in wool follicle RNA and show that expression occurs in the follicle cortical keratinocytes above the dermal papilla. The three hair genes are clustered within about 40 kb and flanked by hair-like genes that are not expressed in the hair follicle, thereby demarcating a hair keratin gene domain.

Amino Acid Sequence↗

PubMed1993

Regional sublocalization of the human CD69 gene to chromosome bands 12p12.3-p13.2, the predicted region of the human natural killer cell gene complex.

The early activation antigen CD69 is a member of a supergene family of type II integral membrane proteins with a C-type lectin domain. In recent reports the genes encoding the natural killer (NK) cell-related molecules of this supergene family, NKR-P1, NK1.1 and Ly-49, were shown to be clustered in a chromosomal region in mouse, termed the NK gene complex. The human homologue of this complex is likely to reside on chromosome 12 near the PRP locus (12p13.2). By analyzing T cell hybrids, the CD69 gene was previously mapped to human chromosome 12. Here we report the regional sublocalization of the human CD69 gene to chromosome bands 12p12.3-p13.2, suggesting that CD69 belongs to one linkage group together with different cell surface molecules on NK cells.

Animals↗

PubMed1992

Expression of carcinoembryonic antigen and related genes in lung and gastrointestinal cancers.

Carcinoembryonic antigen (CEA), a tumor marker for lung cancers of small cell (SCLC) and non-small cell (NSCLC) types, belongs in a multigene family which includes non-specific cross-reacting antigen (NCA) and biliary glycoprotein 1 (BGP). We used specific cDNA probes and a CEA immunoassay to determine the pattern of expression in normal and malignant lung and gastrointestinal (GI) tissues. Normal lung contained high amounts of NCA and a low concentration of CEA. All 3 genes were expressed discordantly in lung tumors and cell lines. In contrast, all three genes were expressed in most G1 tumor cell lines. In both lung and colorectal cell lines expression of NCA RNA was relatively high, while BGP RNA was relatively low, and the median concentrations of CEA were greater than in corresponding non-malignant tissues. While CEA protein concentrations in lung cell lines were similar to those present in G1 cell lines, the ratio of NCA:CEA RNA was significantly higher in lung cancer lines than in colorectal lines. Thus, NCA constitutes most of the "CEA-like" immunoreactivity previously described in lung cancers. There was excellent concordance between expression of CEA RNA and CEA protein, as well as between concentrations of CEA protein in cell line pellets and supernatant fluids. Of interest, significantly higher rates of CEA expression were present in lung cancers expressing neuroendocrine (NE) markers. The association between CEA expression and NE cell properties is intriguing and may prove to be of clinical interest.

Antigens, CD↗

PubMed1990

The developmental fate of fission yeast cells is determined by the pattern of inheritance of parental and grandparental DNA strands.

A key feature for development consists of producing sister cells that differ in their potential for cellular differentiation. Following two cell divisions, a haploid Schizosaccharomyces pombe cell produces one cell in four 'granddaughters' with a changed mating cell type, implying nonequivalence of sister cells in each of two consecutive cell divisions. The observed pattern of switching is analogous to the mammalian 'stem cell' lineage by which a cell produces one daughter like itself while the other daughter is advanced in its developmental program. It is tested here whether sisters differ because of unequal distribution of cytoplasmic and/or nuclear components to them or due to inheriting a specific parental DNA chain at the mating type locus. Only the DNA strand-segregation model predicts that those cells engineered to contain an inverted tandem duplication of the mating type locus should produce equivalent sisters. Consequently, two 'cousins' in four related granddaughter cells should switch. The results verified the prediction, thus establishing that all cells otherwise fully possess the potential to switch. Therefore, the program of cell type change in S.pombe cell lineages is determined by the pattern of DNA strand inheritance at the mating type locus. A specific DNA sequence present at the mating type locus is postulated to be the cause of developmental asymmetry between sister cells. A general model for cellular differentiation is proposed in which the act of DNA replication itself is hypothesized to produce developmentally nonequivalent sister genomes.

DNA, Fungal↗

PubMed2002

Differential effects of osteogenic protein-1 (BMP-7) on gene expression of BMP and GDF family members during differentiation of the mouse MC615 chondrocyte cells.

The mRNA expression patterns of several bone morphogenetic proteins (BMPs) and growth differentiation factors (GDFs) in long-term cultures of the clonal mouse chondrocyte cell line MC615 were examined. Distinct spatial and temporal patterns of expression of BMPs and GDFs were observed. The temporal orders of expression were correlated with those of several biochemical markers characteristic of chondrocytic cell differentiation. BMP-1, -2, -5, and -6 mRNA expression increased throughout the chondrogenic process and BMP-4 mRNA expression was not changed. GDF-1 and -3 mRNA expression increased throughout the chondrogenic process, and GDF-5, -6, -8, and -9 mRNA expressions were not changed. Effects of osteogenic protein-1 (OP-1, BMP-7) on the expression patterns of several other members of the BMP family and of the GDF family were also examined. OP-1 downregulated the BMP-1, -4, -5, and -6 mRNA expression by a maximal 3-, 5-, 2.5-, and 3-fold, respectively. The BMP-2 mRNA expression was not changed significantly by a low concentration of OP-1, but was increased at 200 ng/ml at day 7 of treatment. In contrast to the BMPs, OP-1 upregulated significantly the six GDF members examined (GDF-1, -3, -5, -6, -8, and -9) by three- to four-fold. Our findings demonstrate that OP-1 differentially regulates the mRNA expression of several related members of the BMP family and upregulates the mRNA expression of several members of the GDF family. The observations suggest that OP-1 action on cartilage differentiation involves a complex regulation of gene expression of several members of the BMP and the GDF family.

Aggrecans↗

PubMed2006

Transcriptional regulation of NK cell receptors.

The stochastic expression of individual members of NK cell receptor gene families on subsets of NK cells has attracted considerable interest in the transcriptional regulation of these genes. Each receptor gene can contain up to three separate promoters with distinct properties. The recent discovery that an upstream promoter can function as a probabilistic switch element in the Ly49 gene family has revealed a novel mechanism of variegated gene expression. An important question to be answered is whether or not the other NK cell receptor gene families contain probabilistic switches. The promoter elements currently identified in the Ly49, NKR-P1, CD94, NKG2A, and KIR gene families are described.

Animals↗

PubMed1988

Apolipoprotein gene cluster on chromosome 19. Definite localization of the APOC2 gene and the polymorphic Hpa I site associated with type III hyperlipoproteinemia.

Recently, using an APOE cDNA probe, we discovered an Hpa I restriction fragment length polymorphism (RFLP) that appeared to be strongly associated with the expression of type III hyperlipoproteinemia (Klasen et al. 1987). In the present report it is shown that the same Hpa I RFLP can be revealed with both the APOC1 and APOC2 cDNA probes. This enabled us to localize the polymorphic Hpa I site between the APOE and APOC1 genes and to localize the APOC2 gene approximately 22 kb 3' of the APOC1 pseudogene on chromosome 19.

Apolipoproteins↗

PubMed1994

Characterization of the mouse gene encoding the neuronal intermediate filament protein alpha-internexin.

We have determined the complete nucleotide (nt) sequence of the coding region of the mouse gene encoding the neuronal intermediate filament protein, alpha-internexin (alpha INX). The mouse alpha INX gene (m alpha INX) contains three exons and two introns, and may be classified as a member of the type-IV intermediate filament multigene family. The nt sequence of the transcribed region of m alpha INX shows high homology to that of the rat gene. Comparison of the deduced amino-acid sequences between the mouse and rat gene products reveals that the head and rod domains are highly conserved. However, the tail domains show significant differences which may make it possible to raise specific antibodies that can distinguish the alpha INX of mouse from that of rat.

Amino Acid Sequence↗