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Identification and partial characterization of a variant of human CXCR3 generated by posttranscriptional exon skipping.

Chemokines are recognized as functionally important in many pathological disorders, which has led to increased interest in mechanisms related to the regulation of chemokine receptor (CKR) expression. Known mechanisms for regulating CKR activity are changes in gene expression or posttranslational modifications. However, little is known about CKR with respect to a third regulatory mechanism, which is observed among other seven-transmembrane receptor subfamilies, the concept of differential splicing or processing of heteronuclear RNA. We now report on the discovery of a variant human CKR, CXCR3, resulting from alternative splicing via exon skipping. The observed RNA processing entails a drastically altered C-terminal protein sequence with a predicted four- or five-transmembrane domain structure, differing from all known functional CKR. However, our data indicate that that this splice variant, which we termed CXCR3-alt, despite its severe structural changes still localizes to the cell surface and mediates functional activity of CXCL11.

Alternative Splicing↗

Identification of an antigenic and genetic variant of dengue-4 virus from the Caribbean.

Twenty-one dengue (DEN) viruses isolated from the Caribbean (Dominica and Jamaica) during the 1981-1982 epidemic year were distinct serological and genetic variants of DEN-4 virus. These isolates were clearly identified as DEN-4 viruses using type-specific monoclonal antibodies in indirect immunofluorescence assays. However, they either were not neutralized, or were neutralized poorly using hyperimmune mouse ascitic fluids (HMAF) or rhesus monkey serum directed against the H-241 prototype strain of DEN-4 virus isolated in the Philippines in 1956. HMAF prepared against a representative Caribbean isolate, however, neutralized with similar effectiveness the homologous virus, the H-241 prototype strain, and virus strains isolated from the Pacific and Southeast Asian areas from 1973 to 1984. The Caribbean isolate exhibited no more than 30% and 16% oligonucleotide spot homology with the H-241 and Bangkok viruses, respectively, by RNA fingerprint analysis, while demonstrating 82% and 89% homology with the Gilbert and Niue Island isolates, respectively. The isolation of dengue viruses which are serologically and genetically distinct from the prototype virus emphasizes the need for continued dengue virus surveillance. The recognition of unique dengue isolates should allow the selection of reference strains and vaccine candidate strains which will induce antibodies that are equally effective in neutralizing viruses from all geographic areas.

Aedes↗

Characterization of the 13q14 tumor suppressor locus in CLL: identification of ALT1, an alternative splice variant of the LEU2 gene.

Chromosome 13q14 deletions constitute the most common genetic abnormality in chronic lymphocytic leukemia (CLL). To identify the putative tumor suppressor gene targeted by 13q14 genomic loss, we completely sequenced and characterized a segment of 790 kb at 13q14 spanning the minimal region of loss in CLL. Transcribed sequences in the region were identified through database homology searches and exon-prediction analysis. Two-hundred kb at the centromeric end of the sequence contain five CpG islands, three previously identified genes LEU5/RFP2, LEU2, and LEU1, seven of seven EST clusters composed of >10 ESTs, and a large number of predicted exons. Homology searches against the mouse EST database have allowed us to identify a highly conserved alternative first exon of the LEU2 gene, giving rise to a novel transcript, ALT1 (GenBank accession no. AF380424), which originates within a G+C region in the vicinity of the D13S272 marker. Two novel 3' exons of LEU2 were also identified and are present in both LEU2 and ALT1 transcripts. However, we have not identified any mutations in leukemia cases, or alterations in expression of mRNAs in the region, that might directly implicate these mRNAs in the pathology of CLL. The centromeric end of the sequence, where all reported genes are located, contains twice the expected amount of ALU repeats, whereas the telomeric end is LINE1 rich and contains four LINE1 elements longer than 4 kb, including two full-length LINE1 sequences. This feature of the sequence may favor the occurrence of chromosomal rearrangements and may confer instability to the region, resulting in deletions that may inactivate an as yet unidentified tumor suppressor.

Alternative Splicing↗

Genomic organization and identification of a novel alternative splicing variant of mouse mitochondrial thioredoxin reductase (TrxR2) gene.

Eukaryotic mitochondria are equipped with a complete thioredoxin system, composed of thioredoxin and thioredoxin reductase, which has been implicated in the protection against the reactive oxygen intermdiates generated during the respiratory process in this organelle. Like its cytosolic counterpart, mammalian mitochondrial thioredoxin reductase is a homodimeric selenoprotein. We report here the genomic organization of the mouse mitochondrial thioredoxin gene (TrxR2) that spans 53 kb and consists of 18 exons ranging from 20 to 210 bp. All splicing sites conformed to the GT/AG rule with the exon-intron boundaries located exactly at the same position as the human TrxR2 gene, the only mammalian mitochondrial thioredoxin reductase gene whose genomic structure has been elucidated to date. In addition, we have identified a novel mRNA splicing variant lacking intron 14 resulting in a protein subunit with a shorter interface domain. This new splicing variant provides a framework for further analysis of this important enzyme as its predicted homodimeric conformation can now be expanded to a putative heterodimeric structure as well as a small subunit homodimer with the obvious implications at the regulatory level.

Alternative Splicing↗

Identification of 127 amino acid substitution variants in screening 37 DNA repair genes in humans.

The repair of damaged DNA requires the function of multiple proteins in generally damage-specific, nonredundant pathways. The relationship of DNA repair to cancer susceptibility is obvious in "cancer families," in which low frequency, high penetrance, loss-of-function variant alleles of genes with roles in the repair of damaged DNA have been associated with a high risk of disease. More important for the cancer incidence in the general population, many individuals exhibit reduced (60-75% of normal) repair capacity phenotypes that have been associated with several-fold increases in individual cancer risk. In a program to identify the molecular basis for the variation in repair capacity and the elevated cancer susceptibility, we have identified 127 amino acid substitution variants in resequencing 37 DNA repair genes in 36-164 unrelated individuals. Over 50% of the substitutions are exchanges of amino acid residues with dissimilar physical or chemical properties, at sites at which the common residue is identical in the human and mouse proteins. Five additional sequence changes resulting in proteins with altered termination of translation and one amino acid insertion variant were detected. The variant allele frequencies average 0.047, with individual variant allele frequencies ranging from <0.01 to 0.43. Homozygous variant individuals and individuals with multiple amino acid substitutions in a gene were observed. Most individuals exhibited variation in multiple genes in a repair pathway. Ten variant alleles accounted for 52% of the genetic variation among individuals, but a striking 23% of the total variation is associated with 108 variants with allele frequencies of less than 5%. Screening generally healthy individuals generates a catalogue of common variants that is a resource for molecular epidemiology studies endeavoring to use a genotype to phenotype paradigm to estimate the role of genetic variation and individual susceptibility in disease risk from environmental and lifestyle exposures in the general population of the United States.

Amino Acid Substitution↗

Identification of a novel alternatively spliced variant endothelin converting enzyme-1 lacking a transmembrane domain.

Endothelin-converting enzyme (ECE)-1 cleaves big endothelins, as well as bradykinin and beta-amyloid peptide. Several isoforms of ECE-1 (ECE-1a, 1b, 1c, and 1d) have been identified to date, they differ only in their amino terminus and share the catalytic domain located in the C-terminal end. In addition to full-length ECE-1 forms, we identified novel, alternatively spliced messenger RNAs (mRNAs) of ECE-1b, 1c, and 1d. These splice variants (SVs) lack exon 3', which codes for the transmembrane (TM) region and is present in full-length forms. SV mRNAs were highly expressed in endothelial cells (EC) derived from macrovascular and microvascular beds. Analyses of ECE-1d and its SV forms in stably transfected human embryonic kidney (HEK)-293 cells revealed that both proteins were recognized by antibodies to C-terminal ECE-1, but an antibody to the N-terminal only bound ECE-1d. The novel protein, designated ECE-1sv, has an apparent molecular weight of 75 kDa. ECE-1sv lacks the TM sequence (or signal peptide) and, therefore, is expected to remain cytosolic. Presence of ECE-1sv in different cellular compartments than the full-length forms of the ECE-1 may suggest a distinct physiologic role for these proteins.

Alternative Splicing↗

Protein chemical identification and characterization of the human variants of far upstream element binding protein in medulloblastoma DAOY cell line.

The assembly of trans-acting proteins on sequence-specific DNA cis-elements is crucial in the regulation of eukaryotic gene expression. Far upstream element binding proteins (FAB) are proteins that regulate the expression of the c-myc oncogene by binding to the far upstream element of the c-myc gene. The present study unambiguously identified the two human variants of FAB (FAB1, FAB2) in the medulloblastoma DAOY cell line and characterized their structure for the first time by tandem mass spectrometry independent of antibody availability and specificity. The study also tentatively assigned the third variant (FAB3) at the level of mass spectrometry, although tandem mass spectrometric analysis failed to corroborate the result. These findings open up an exciting possibility for discerning the cellular roles of FAB in tumor biology.

Amino Acid Sequence↗

Active arginine residues in beta-hexosaminidase. Identification through studies of the B1 variant of Tay-Sachs disease.

Lysosomal beta-hexosaminidase (EC 3.2.1.52) occurs as two major isoenzymes, hexosaminidases A (alpha beta) and B (beta beta). The alpha- and beta-subunits are encoded by the HEXA and HEXB genes, respectively. Extensive homology in both the gene structures and deduced primary sequences demonstrate their common evolutionary origin. Defects in the alpha- or beta-subunits lead to Tay-Sachs of Sandhoff disease, respectively. The B1 variant of Tay-Sachs disease is characterized by an unusual phenotype. Patient samples contain both isoenzymes; however, hexosaminidase A lacks activity toward alpha-specific substrates. In a previous report, we analyzed the biochemical consequences of an Arg178----His substitution in the alpha-subunit, causing the B1 phenotype, by in vitro mutagenesis of the homologous codon for Arg211 in the beta-subunit to produce His. We found that the substitution did not affect dimer formation or cellular targeting but caused a near total loss of activity toward a common alpha- and/or beta-substrate. Additional effects were also noted that suggested a perturbation had occurred to the protein's secondary structure. In this report, we investigate further the role of Arg in the catalysis of hexosaminidase substrates. The introduction of more or less conservative amino acid substitutions at the beta-Arg211 site were evaluated in terms of their effects on the protein's catalytic activity and susceptibility to the arginine-specific reagents and on its stability and rate of maturation in the cell's lysosome. These data demonstrate that the changes in the in vivo stability and rate of maturation, previously noted with the Arg211----His substitution, are independent of the loss in enzymatic activity. Whereas treatment of purified normal human placental hexosaminidases A and B with arginine-specific modifying reagents produced a time-dependent loss of enzymatic activity toward both alpha-specific and common substrates, these reagents failed to significantly decrease the residual activities of mutant proteins lacking Arg at position 211. Kinetic analysis of the residual enzyme activity from our most conservative construct, Arg211----Lys, determined an apparent Vmax approximately 400-fold reduced from that of the wild type enzyme but detected no change in the apparent Km. Additionally, the pH optimum of this mutant enzyme was narrower and slightly more basic than that of the normal enzyme. Thus, Arg211 in the beta-subunit and, by extrapolation, the Arg178 in the alpha-subunit of beta-hexosaminidase are "active" residues, i.e. part of the catalytic sites, but do not participate in substrate binding.

Arginine↗

Identification of haptoglobin alpha-2FF variants in mid-trimester maternal serum as potential markers for Down syndrome.

Exploratory protein analysis in mid-trimester maternal sera by 2-dimensional electrophoresis and image analysis was performed to determine the differences between mothers carrying fetuses with Down syndrome (DS) and control mothers. Nine haptoglobin alpha-1 and alpha-2 (Hp1 and Hp2) variants were detected. Three apparent isoforms of the Hp2FF protein having the same relative charge but different Mr's were detected, with the two smaller variants--Hp2FF (-0.7k) and Hp2FF (-1.3k)--believed to be first reported here. Ninety-two percent of the cases (n = 83) had the Hp2FF (-0.7k) protein, and 61% had Hp2FF (-1.3k). The geometric mean concentration of Hp2FF (Mr = 18.0 kd) was found to be significantly increased (P less than 0.01) in mid-trimester sera from cases (n = 27) compared to controls (n = 56). When the concentrations of the three Hp2FF isoforms were added, the cases had larger sums on average than controls (P less than 0.01).

Age Factors↗

Identification of an apoC-II variant (apoC-IIBethesda) in a kindred with apoC-II deficiency and type I hyperlipoproteinemia.

Apolipoprotein (apo) C-II deficiency is characterized by elevated plasma triglycerides, chylomicrons, and very low density lipoproteins, as well as reduced levels of low density and high density lipoproteins. A subject with apoC-II deficiency has been identified with an apoC-II plasma level of less than 0.05 mg/dl. The plasma apoC-II in the proband was immunochemically similar to apoC-II in normal subjects when analyzed by Ouchterlony immunodiffusion, however the apoC-II had an apparently lower molecular weight and higher pI when analyzed by two-dimensional gel electrophoresis. This apoC-II variant, designated apoC-IIBethesda, was not affected by neuraminidase treatment or reduction. Two-dimensional gel electrophoresis of the plasma of the mother of the proband revealed both normal apoC-II and apoC-IIBethesda, whereas analysis of the father and two siblings revealed apoC-II of normal electrophoretic mobility. These results were interpreted as indicating that the proband was a compound heterozygote with one allele for apoC-IIBethesda inherited from the mother and an allele coding for an abnormality which results in the virtual or complete absence of plasma apoC-II from the father. This proband represents the first example of a compound heterozygote for an apolipoprotein defect associated with a dyslipoproteinemia.

Apolipoprotein C-II↗

Population genetic studies of the Philippine Negritos. III. Identification of the carbonic anhydrase-1 variant with CA1 Guam.

Investigation of blood samples from 277 Mamanwas of northeastern Mindanao, Philippines, confirmed the concentration of the variant carbonic anhydrase-1 (CA1 3N) in this group. The frequency for the variant allele was estimated at .217 +/- .017. It occurs also in the Manobos, the Mongoloid indigenous inhabitants of the same district, although the frequency is low (.019 +/- .008). Survey of samples from other Philippine populations, including the Aeta and the Ifugao of Luzon, failed to find variants. This findings suggests different origins of the Aeta and the Mamanwa, although both are usually referred to as Negritos. The Ca1 3N protein was purified by affinity chromatography using azosulfonamide and rechromatography on a DEAE-Sephadex column. The tryptic peptide pattern of CA1 3N was similar to that of CA1 Guam already reported. Furthermore, amino acid analyses of the tryptic peptides indicated that CA1 3N is characterized by the substitution 253 Gly leads to Arg, confirming the identity of this variant with CA1 Guam. The widespread occurrence of CA1 3 variants in the Western Pacific suggests that this variant was once common in an aboriginal population of this region, from which it was scattered by gene flow.

Black People↗

Identification of H-2-controlled structural variants of the murine Slp protein and demonstration of cis-regulation of its expression.

H-2 haplotype-related structural variation in Slp beta-chains was detected by the limited proteolysis peptide mapping technique. Two distinct peptide patterns were distinguished: Slp.1 was found in strains carrying the S regions of the H-2d and H-2s haplotypes, and Slp.2 was found in strains bearing the S region of H-2w7. These different patterns were expressed codominantly in male (Sd X Sw7)F1 hybrids, whereas only the Slp.2 pattern was expressed in female heterozygotes. The 2 beta-chains are most likely the products of alleles of the Slp structural gene, which must then be located in the murine major histocompatibility complex, very probably in the S region.

Animals↗

Identification of alternatively spliced mRNAs encoding variants of MDK1, a novel receptor tyrosine kinase expressed in the murine nervous system.

A novel member of the eck/eph family of receptor tyrosine kinases (RTKs), termed mouse developmental kinase 1 (MDK1), was identified and shown to be closely related to the Eek, Ehk1/Cek7, Ehk2, Cek4/Mek4/hek and Sek/Cek8 subfamily. Northern blot analysis revealed MDK1 mRNA transcripts of 6.8, 5.7, 4.0, 3.2 and 2.6 kb that encode apparent splice variants. Sequence analyses of MDK1 cDNA clones from adult mouse brain predict the existence of at least five isoforms, including two truncated receptor variants lacking the kinase domain. Northern blot and in situ hybridization analysis indicate that in the adult mouse MDK1 RNA expression is restricted to brain, testes and spleen. The distinct patterns of MDK1 gene expression during mouse development suggest an important role in the formation of neuronal structures and possibly other morphogenic processes.

Alternative Splicing↗

Identification of tumor-associated protein variants during rat hepatocarcinogenesis. Aldose reductase.

Tumor-associated protein variants were detected by two-dimensional gel electrophoresis (2-DE) in soluble proteins from chemically induced rat hepatomas and transformed rat liver cell lines. Among them, a series of 8 protein variants was found localized at similar sites in 2-DE gels (33-35 kDa, with different pI values). We characterized four of them. In situ peptide mapping with limited proteolysis disclosed a significant relationship between these four individual protein spots. Their different position in 2-DE gels might be due to posttranslational modifications: one of the variants was phosphorylated, three others were modified by glycosylation. The most prominent tumor-associated protein variant of this series (spot 17) was further studied by amino acid analysis and internal amino acid microsequencing. It became evident that this variant is identical to aldose reductase (EC 1.1.1.21). This enzyme of the sorbitol pathway is expressed in the liver during embryogenesis, but is absent in adult rat liver. Our results suggest that it is reexpressed and functionally active during liver carcinogenesis.

Aldehyde Reductase↗

Serological and molecular identification of an HLA-B8 variant, HLA-B8Jon (B*0802).

The serological and molecular characteristics of the first HLA-B8 variant (B8Jon), located on a haplotype bearing HLA-A1, -B8Jon, -Cw*07, DRB1*0301, DQA1*05, DQB1*0201, BfS, C4AQ0, C4B1 and the microsatellite alleles D6S265-3, 258-11, 105-8, 299-1 and 202-2 are identified and described. This new HLA-B antigen was distinguished from the usual B8 by its lack of reactivity with Bw6 and most Bw4 antisera, together with its failure to react with most antisera cross-reactive with HLA-B8. B8Jon gives a 'weaker' response than HLA-B8 in titration studies with B8 antisera. It cannot be differentiated from the usual B8 by one-dimensional iso-electric focusing. Time course studies, absorption analyses and serological tests on 17 Bw4 antibodies suggest that B8Jon possesses an unusually 'weak' Bw4 epitope. Studies on the Bw4 sequence motif by PCR, using sequence-specific primers, indicate that B8Jon has a Bw4 sequence in common with other HLA-B alleles, including B*4402-B*4405, rather than the Bw6 motif found on the familiar HLA-B8 molecule.

DNA↗

Identification of two novel Mycobacterium avium allelic variants in pig and human isolates from Brazil by PCR-restriction enzyme analysis.

Mycobacterium avium complex (MAC) is composed of environmental mycobacteria found widely in soil, water, and aerosols that can cause disease in animals and humans, especially disseminated infections in AIDS patients. MAC consists of two closely related species, M. avium and M. intracellulare, and may also include other, less-defined groups. The precise differentiation of MAC species is a fundamental step in epidemiological studies and for the evaluation of possible reservoirs for MAC infection in humans and animals. In this study, which included 111 pig and 26 clinical MAC isolates, two novel allelic M. avium PCR-restriction enzyme analysis (PRA) variants were identified, differing from the M. avium PRA prototype in the HaeIII digestion pattern. Mutations in HaeIII sites were confirmed by DNA sequencing. Identification of these isolates as M. avium was confirmed by PCR with DT1-DT6 and IS1245 primers, nucleic acid hybridization with the AccuProbe system, 16S ribosomal DNA sequencing, and biochemical tests. The characterization of M. avium PRA variants can be useful in the elucidation of factors involved in mycobacterial virulence and routes of infection and also has diagnostic significance, since they can be misidentified as M. simiae II and M. kansasii I if the PRA method is used in the clinical laboratory for identification of mycobacteria.

Alleles↗