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PubMed1977

Effect of polyploidy on phosphoglucose isomerase diversity in Festuca microstachys.

Studies of the inheritance of electrophoretic banding patterns in Festuca microstachys support the hypothesis that three closely related loci, one located in each of the three ancestral genomes, code the multiple phosphoglucose isomerase (glucosephosphate isomerase; D-glucose-6-phosphate ketol-isomerase, EC 5.3.1.9) variants found in this hexaploid species. The close relationship among the three loci is indicated by the observation that hybrid enzymes of intercistronic origin form when the loci in different genomes carry alleles coding homodimers with unlike migration rates. Homozygous individuals fixed for different alleles in different genomes produce hybrid enzymes and, when self-fertilized, they breed true for isozyme patterns normally found only in the heterozygotes of diploid species. Biochemical diversity due to this "fixed heterozygosity" is high in F. microstachys; although this species is more than 99% self-fertilized the proportion of individuals with at least one heterodimer exceeded 61% in all of the 16 natural populations studied and it exceeded 92% in 11 of the populations. This great biochemical diversity may contribute to the ability of F. microstachys to survive in the wide range of habitats in which it is found over western North America.

Alleles↗
PubMed1991

Molecular characterization of erythrocyte glycophorin C variants.

Human erythrocyte glycophorin C plays a functionally important role in maintaining erythrocyte shape and regulating membrane mechanical stability. Immunochemical and serologic studies have identified a number of glycophorin C variants that include the Yus, Gerbich, and Webb phenotypes. We report here the molecular characterization of these variants. Amplification of glycophorin C mRNA from the Yus phenotype, using two oligonucleotide primers that span the coding domain, generated a 338-bp fragment compared with a 395-bp fragment generated by amplification of normal glycophorin C mRNA. Sequencing of the mutant 338-bp fragment identified a 57-bp deletion that corresponds to exon 2 of the glycophorin C gene. Similar analysis showed deletion of 84-bp exon 3 in the Gerbich phenotype. In contrast to the generation of shorter than normal DNA fragments from mRNA amplification in the Yus and Gerbich phenotypes, amplification of mRNA from the Webb phenotype generated a normal-sized fragment. Sequencing of this DNA fragment showed an A----G substitution at nucleotide 23 of the coding sequence, resulting in the substitution of asparagine by serine. This modification accounts for the altered glycosylation of glycophorin C seen in this phenotype. These results have enabled us to characterize glycophorin C variants in three different phenotypes that involve deletions of exons 2 and 3 of the glycophorin C gene, as well as a point mutation in exon 1 that results in altered glycosylation of this protein.

Amino Acid Sequence↗
PubMedDate not supplied

Two splice variants derived from a Drosophila melanogaster candidate ClC gene generate ClC-2-type Cl- channels.

Members of the ClC family of membrane proteins have been found in a variety of species and they can function as Cl- channels or Cl-/H+ antiporters. Three potential ClC genes are present in the Drosophila melanogaster genome. Only one of them shows homology with a branch of the mammalian ClC genes that encode plasma membrane Cl- channels. The remaining two are close to mammalian homologues coding for intracellular ClC proteins. Using RT-PCR we have identified two splice variants showing highest homology (41% residue identity) to the mammalian ClC-2 chloride channel. One splice variant (DmClC-2S) is expressed in the fly head and body and an additional, larger variant (DmClC-2L) is only present in the head. Both putative Drosophila channels conserve key features of the ClC channels cloned so far, including residues conforming the selectivity filter and C-terminus CBS domains. The splice variants differ in a stretch of 127 aa at the intracellular C-terminal portion separating cystathionate beta synthase (CBS) domains. Expression of either Drosophila ClC-2 variant in HEK-293 cells generated inwardly rectifying Cl- currents with similar activation and deactivation characteristics. There was great similarity in functional characteristics between DmClC-2 variants and their mammalian counterpart, save for slower opening kinetics and faster closing rate. As CBS domains are believed to be sites of regulation of channel gating and trafficking, it is suggested that the extra amino acids present between CBS domains in DmClC-2L might endow the channel with a differential response to signals present in the fly cells where it is expressed.

Alternative Splicing↗
PubMed2003

Survival to adulthood and dominant inheritance of platyspondylic skeletal dysplasia, Torrance-Luton type.

We present a second family with survival to adulthood and dominant transmission of the Torrance-Luton type of platyspondylic chondrodysplasia, and demonstrate the radiographs at different ages together with radiographs and further data of the first family which was published in the Journal of Pediatrics (J Pediatr 136:411-413). Two families are described with survival to adulthood and dominant transmission of the Torrance-Luton type of platyspondylic chondrodysplasia. Although lethality is increased in patients with this disorder, mild expressions of the genetic defect are compatible with survival into adulthood. The heterogeneous group of platyspondylic lethal skeletal dysplasias (PLSD) originally included thanatophoric dysplasias (TD1/2: MIM 187600, 187100) as the most common forms of this condition, as well as TD variants San Diego type (PLSD-SD: MIM 270230) and Torrance-Luton type (PLSD-TL: MIM 151210). Fibroblast growth factor receptor 3 ( FGFR3) gene mutations have been detected in TD1/2 and PLSD-SD. Molecular studies in one of our two families with the Torrance-Luton type did not disclose mutations in the FGFR3 coding region, suggesting that this type of platyspondylic chondrodysplasia is not a thanatophoric dysplasia variant. In contrast to TD1/2 and PLD-SD, the Torrance-Luton type platyspondylic dysplasia is compatible with survival to adulthood.

Adult↗
PubMed2002

Genomic studies of the spleen protein tyrosine kinase locus reveal a complex promoter structure and several genetic variants.

Here we show that the gene of the cytoplasmic tyrosine kinase SYK spans a region of 90kb with 13 coding exons, an alternative exon 14 and at least two 5' untranslated regions exons 1a and 1b. 5' RACE (Rapid amplification of cDNA ends) of human Syk cDNAs demonstrated a complex promoter usage and splicing pattern. We identified three common single nucleotide polymorphisms in the exon la promoter region of the Syk gene as well as a variant Syk cDNA haplotype. This haplotype was characterized by a constellation of 5 silent mutations in the Syk cDNA: 1065(C-T), 1302(G-C), 1338(G-A), 1521(C-T) and 1545(T-C). A hypervariable CATATA(n) repeat polymorphism was also localized to the intron between exons 11 and 12. These novel insights into the genomic organization, promoter structure and genetic variability of Syk will serve as a foundation for detailed molecular epidemiological investigation of its potential role in human cancer biology.

5' Untranslated Regions↗
PubMed1995

Salmonella typhimurium DT 193: differentiation of an epidemic phage type by antibiogram, plasmid profile, plasmid fingerprint and salmonella plasmid virulence (spv) gene probe.

Of over 2000 isolates of Salmonella typhimurium DT 193 from humans examined in the 2 year period 1991-92, 93% were antibiotic-resistant with the most common R-types being ASSuT (38%) and T (29%). Fourteen plasmid profiles were identified in DT 193 R-type ASSuT with the majority of isolates being characterized by a single plasmid of 80 MDa (pDEP 34) which in addition to coding for ASSuT, also hybridized with a spv gene probe prepared from the 50 MDa Salm. dublin serovar-specific plasmid. On the basis of restriction fragment length polymorphisms, two variant lines of pDEP 34-like plasmids were identified and a third line which had lost the genes coding for resistance to ampicillin, streptomycin and sulphonamides, was recognized. Although 18 plasmid profile types were identified in DT 193 R-type T, all isolates carried a high mol. wt plasmid which coded for tetracycline resistance only. Further discrimination was achieved on the basis of hybridization of tetracycline resistance plasmids with the spv gene probe and restriction enzyme fingerprinting. These results demonstrate that Salm. typhimurium DT 193 can be rapidly subdivided by antibiogram and that further subdivision can be achieved on the basis of plasmid profile, plasmid fingerprint and hybridization with a spv gene probe.

Animals↗
PubMed1996

Molecular characterization of replication-competent variants of adenovirus vectors and genome modifications to prevent their occurrence.

Adenovirus (Ad) vectors for gene therapy are made replication defective by deletion of E1 region genes. For isolation, propagation, and large-scale production of such vectors, E1 functions are supplied in trans from a stable cell line. Virtually all Ad vectors used for clinical studies are produced in the 293 cell, a human embryonic kidney cell line expressing E1 functions from an integrated segment of the left end of the Ad type 5 (Ad5) genome. Replication-competent vector variants that have regained E1 sequences have been observed within populations of Ad vectors grown on 293 cells. These replication-competent variants presumably result from recombination between vector and 293 cell Ad5 sequences. We have developed Ad2-based vectors and have characterized at the molecular level examples of replication-competent variants. All such variants analyzed are Ad2-Ad5 chimeras in which the 293 cell Ad5 E1 sequences have become incorporated into the viral genome by legitimate recombination events. A map of Ad5 sequences within the 293 cell genome developed in parallel is consistent with the proposed recombination events. To provide a convenient vector production system that circumvents the generation of replication-competent variants, we have modified the Ad2 vector backbone by deleting or rearranging the protein IX coding region normally present downstream from the E1 region such that the frequency of recombination between vector and 293 cell Ad5 sequences is greatly reduced. Twelve serial passages of an Ad2 vector lacking the protein IX gene were carried out without generating replication-competent variants. In the course of producing and testing more than 30 large-scale preparations of vectors lacking the protein IX gene or having a rearranged protein IX gene, only three examples of replication-competent variants were observed. Use of these genome modifications allows use of conventional 293 cells for production of large-scale preparations of Ad-based vectors lacking replication-competent variants.

Adenovirus E1 Proteins↗
PubMed2005

Purified recombinant hypothetical protein coded by open reading frame Rv1885c of Mycobacterium tuberculosis exhibits a monofunctional AroQ class of periplasmic chorismate mutase activity.

Naturally occurring variants of the enzyme chorismate mutase are known to exist that exhibit diversity in enzyme structure, regulatory properties, and association with other proteins. Chorismate mutase was not annotated in the initial genome sequence of Mycobacterium tuberculosis (Mtb) because of low sequence similarity between known chorismate mutases. Recombinant protein coded by open reading frame Rv1885c of Mtb exhibited chorismate mutase activity in vitro. Biochemical and biophysical characterization of the recombinant protein suggests its resemblance to the AroQ class of chorismate mutases, prototype examples of which include the Escherichia coli and yeast chorismate mutases. We also demonstrate that unlike the corresponding proteins of E. coli, Mtb chorismate mutase does not have any associated prephenate dehydratase or dehydrogenase activity, indicating its monofunctional nature. The Rv1885c-encoded chorismate mutase showed allosteric regulation by pathway-specific as well as cross-pathway-specific ligands, as evident from proteolytic cleavage protection and enzyme assays. The predicted N-terminal signal sequence of Mtb chorismate mutase was capable of functioning as one in E. coli, suggesting that Mtb chorismate mutase belongs to the AroQ class of chorismate mutases. It was evident that Rv1885c may not be the only enzyme with chorismate mutase enzyme function within Mtb, based on our observation of the presence of chorismate mutase activity displayed by another hypothetical protein coded by open reading frame Rv0948c, a novel instance of the existence of two monofunctional chorismate mutases ever reported in any pathogenic bacterium.

Allosteric Regulation↗
PubMed1999

Sulfonamide resistance in clinical isolates of Campylobacter jejuni: mutational changes in the chromosomal dihydropteroate synthase.

The characterization of the genetic basis of sulfonamide resistance in Campylobacter jejuni was attempted. The resistance determinant from a sulfonamide-resistant strain of C. jejuni was cloned and was found to show 42% identity with the folP gene (which codes for dihydropteroate synthase, the target of sulfonamides) of the related bacterium Helicobacter pylori. The sequences of the areas surrounding the folP gene in C. jejuni showed similarity to those of the areas surrounding the corresponding gene in H. pylori. The folP gene of C. jejuni, which mediates the resistance, was observed to show particular features when it was compared to other known folP genes. One of these features is the presence of two pairs of direct repeats (15 and 27 bp) within the coding sequence of the gene. Comparison of the C. jejuni folP genes that mediate susceptibility and resistance revealed the occurrence of mutations that changed four amino acid residues. Resistance of C. jejuni to sulfonamides could be associated with one or several of these four mutational substitutions, which all occurred in the five different resistant isolates studied. The codon for one of these changed amino acids was found to be located in the second direct repeat within the coding sequence of the gene. The change made the repeat perfect. The transformation of both the resistance and the susceptibility variants of the gene into an Escherichia coli folP knockout mutant was found to complement the dihydropteroate synthase deficiency, confirming that the characterized sulfonamide resistance determinant codes for the C. jejuni dihydropteroate synthase enzyme. Kinetic measurements established different affinities of sulfonamide for the dihydropteroate synthase enzyme isolated from the resistant and susceptible strains. In conclusion, sulfonamide resistance in C. jejuni was shown to be associated with mutational changes in the chromosomally located gene for dihydropteroate synthase, the target of sulfonamides.

Amino Acid Sequence↗
PubMed2001

Expression of Ca(2+)-activated K(+) channel subunits and splice variants in the rat cochlea.

The recently manifested important role of the Ca(2+)-activated K(+) channels, especially of the Slo gene-coded channels, for the cochlea function of the chicken raised the question of homolog expression in mammalian inner ear tissue. Molecular biological methods were used to demonstrate the expression of Ca(2+)-activated K(+) channel subunits and splice variants of the Slo gene in the rat organ of Corti. RT-PCR experiments for the detection of rat Slo alpha subunit mRNA revealed the presence of several already known splice variants including variants which appeared to be typical for the organ of Corti (+58 aa) and for the brain (+61 aa). To detect the accessory beta subunit we used Southern blot hybridization. Our data support the hypothesis that Ca(2+)-activated K(+) channel subunits (i.e. Slo variants) are also involved in the hearing of mammals in the organ of Corti.

Amino Acid Sequence↗
PubMed2001

Frequency of single nucleotide polymorphisms in the P-glycoprotein drug transporter MDR1 gene in white subjects.

BACKGROUND: P-glycoprotein, the gene product of MDR1, confers multidrug resistance against antineoplastic agents but also plays an important role in the bioavailability of common drugs in medical treatment. Various polymorphisms in the MDR1 gene were recently identified. A silent mutation in exon 26 (C3435T) was correlated with intestinal P-glycoprotein expression and oral bioavailability of digoxin. OBJECTIVE: We wanted to establish easy-to-use and cost-effective genotyping assays for the major known MDR1 single nucleotide polymorphisms and study the allelic frequency distribution of the single nucleotide polymorphisms in a large sample of volunteers. METHODS: In this study, the distribution of the major MDR1 alleles was determined in 461 white volunteers with the use of polymerase chain reaction and restriction fragment length polymorphism. RESULTS: Five amino acid exchanges were found with allelic frequencies of 11.2% for Asn21Asp and 5.5% for Ser400Asn. Strikingly, in exon 21 three variants were discovered at the same locus: 2677G (56.4%), 2677T (41.6%), and 2677A (1.9%), coding for 893Ala, Ser, or Thr. A novel missense Gln1107Pro mutation was found in two cases (0.2%). The highest frequencies were observed for intronic and silent polymorphisms; C3435T occurred in 53.9% of the subjects heterozygously, and 28.6% of individuals were homozygous carriers of 3435T/T with functionally restrained P-glycoprotein. CONCLUSION: This study provides the first analysis of MDR1 variant genotype distribution in a large sample of white subjects. It gives a basis for large-scale clinical investigations on the functional role of MDR1 allelic variants for bioavailability of a substantial number of drugs.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2002

Melanocortin-3 receptor gene variants in a Maori kindred with obesity and early onset type 2 diabetes.

Genetic studies suggest a diabetes susceptibility locus on human chromosome 20, near the melanocortin receptor-3 (MC3-R) gene. We examined the MC3-R as a candidate gene for type 2 diabetes in 12 members of a large Maori kindred with multiple affected members. The coding region of the MC3-R gene was sequenced for both diabetic and non-diabetic individuals. Two separate single base pair substitutions were found in the MC3-R coding sequence and these resulted in amino acid changes, Lysine6Threonine and Isoleucine81Valine. Neither of these MC3-R variants tracked with the presence of diabetes. Furthermore, the variant and wild type MC3-R showed similar functional coupling to adenylyl cyclase. A polymorphic marker (D20S32e) close to the human MC3-R (hMC3-R) coding sequence was investigated in a 60-member pedigree for association with diabetes and other metabolic parameters. There was an association between D20S32e genotype and fasting insulin (P=0.0085) and the insulin resistance index, HOMA-R (P=0.0042). An association was also found between genotype and HDL levels during oral glucose tolerance testing (P=0.0037). These associations were independent of BMI, age, gender and diabetes. Our data do not support a role for variations in the coding region of the hMC3-R in the development of type 2 diabetes in this Maori kindred, but suggest that a locus on chromosome 20 q, close to D20S32e, may contribute to both insulin secretion and action in the Maori kindred.

Age of Onset↗
PubMed1984

Expression of several amplified genes in an adenylate-deaminase overproducing variant of Chinese hamster fibroblasts.

Unstable variants with increasing amounts of adenylate-deaminase (AMPD) have been stepwise recovered from Chinese hamster fibroblasts plated in selective medium containing increasing coformycin concentrations; several polypeptides accumulate in the variants in parallel to AMPD: they are no longer detectable in cells which reverted to the wild-type enzyme level. We report here the molecular cloning of cDNA sequences complementary to mRNAs coding for four such polypeptides. The plasmidic probes have been exploited to characterize their complementary mRNAs and to quantify the copies of these cognate genes in a variant and in two revertant clones. The results show that different mRNAs code for the four polypeptides; their accumulation is accounted for by amplification of their specific genes; these observations suggest that cells overproducing AMPD are characterized by the presence of amplification units comprising several expressed genes.

AMP Deaminase↗
PubMed1989

Hybridization of Escherichia coli producing Shiga-like toxin I, Shiga-like toxin II, and a variant of Shiga-like toxin II with synthetic oligonucleotide probes.

Synthetic oligonucleotides, constructed from the nucleotide sequences of genes coding for the A subunit of Shiga-like toxin (SLT) I and the B subunit of SLT-II, were used as probes at different degrees of stringency to identify Escherichia coli producing different types of SLTs. At 45 degrees C, the A-I oligonucleotide probe hybridized with E. coli producing SLT-I, SLT-II, and variant of SLT-II (SLT-IIv). At 53 degrees C, only SLT-I-producing E. coli hybridized with this probe. At 45 degrees C, the B-II oligonucleotide probe hybridized with SLT-II- and SLT-IIv-producing E. coli. At 53 degrees C, this probe hybridized with only SLT-II-producing E. coli. The A-I and B-II oligonucleotide probes were subsequently tested for hybridization with 73 SLT-producing E. coli and 49 non-SLT-producing E. coli isolated in Asia and Canada. At 45 degrees C, the A-I oligomer had a sensitivity of 97% and a specificity of 100% in identifying SLT-producing E. coli. At 53 degrees C, the A-I oligonucleotide probe had a sensitivity of 92% and a specificity of 91% in identifying E. coli containing genes encoding SLT-I. At 45 degrees C, the B-II oligonucleotide had a 100% sensitivity and 97% specificity in identifying E. coli that hybridized with the SLT-II probe. Of 17 E. coli that hybridized only with the SLT-II probe, 10 did not hybridize with the B-II oligonucleotide at 53 degrees C. All 10 isolates were cytotoxic to Vero cells but not to HeLa cells, confirming that the B-II oligonucleotide probe used at 53 degrees C will differentiate isolates producing SLT-II and SLT-IIv.

Adult↗
PubMed2005

Polymorphisms in the goat beta-lactoglobulin gene.

Beta-lactoglobulin polymorphisms have been reported in the milk of different goat breeds, although no genetic variants affecting the protein have been characterized. In the present study, we amplified and sequenced the proximal promoter and the first six exons containing the entire coding region for the beta-lactoglobulin gene in eleven goat breeds from Spain, France, Italy, Switzerland, Senegal and Asia to identify genetic variants. Fifteen polymorphisms were detected, nine in the promoter region and six in the exons of the beta-lactoglobulin gene. All polymorphisms were single nucleotide substitutions with the exception of one deletion/insertion in the promoter region. The polymorphisms in the coding region did not produce any amino acid change. In addition, pyrosequencing technology was used to genotype four polymorphisms in the promoter region in 200 goats belonging to eleven breeds. Differences in allelic frequencies for these polymorphisms between breeds are described and a specific polymorphism for the Italian populations was identified. Finally, the analysis of association between these four promoter point mutations was investigated resulting in five haplotypes, GCGC being the most frequent haplotype in all breeds analysed.

Alleles↗
PubMed2006

Contribution of melanocortin-1 receptor gene variants to sporadic cutaneous melanoma risk in a population in central Italy: a case-control study.

The melanocortin-1 receptor (MC1R) gene is a key determinant of the physiological variation in human skin pigmentation. It is highly polymorphic, and specific MC1R allelic variants have been shown to be low-penetrance melanoma susceptibility alleles. We investigated the contribution of the MC1R genotype to the risk of sporadic cutaneous melanoma in a population in central Italy. One hundred patients with sporadic cutaneous melanoma of any stage and 100 unrelated control individuals were consecutively recruited between 1 September 2000 and 31 December 2001. Information on ethnic background and residential history, phenotypic risk factors for melanoma and ultraviolet exposure habits was collected through a standardized questionnaire and total skin examination. Sequence analysis of the entire coding region of the MC1R gene was performed. A total of 26 MC1R variants, including a novel 123_124insT allele, was identified in our population, with the most frequent allele being V60L. Carriers of high-penetrance 'R' MC1R alleles, that define MC1R variants strongly associated with the red hair colour phenotype, showed a statistically significant increase in melanoma risk [odds ratio (OR), 2.55; 95% confidence interval (CI), 1.19-5.55]. No significant association with melanoma risk was observed for carriers of 'r' variants (OR, 0.90; 95% CI, 0.45-1.82). Amongst individual MC1R variants, the R151C allele was significantly associated with melanoma, with an OR of 2.94 (95% CI, 1.04-8.31). After stratification for clinical and ultraviolet exposure risk factors, the melanoma risk associated with high-penetrance 'R' variants appeared to increase significantly, mainly in the presence of clinically atypical naevi, more than 50 melanocytic naevi, high recreational sun exposure and occupational sun exposure. These results support the contribution of high-penetrance MC1R variant alleles to genetic predisposition to sporadic cutaneous melanoma in a population in central Italy.

Adolescent↗
PubMed1997

Complete coding regions of two novel HLA-B alleles detected by phototyping (PCR-SSP) in the British caucasoid population: B*5108 and B*5002.

Two previously reported PCR-SSP variants of the HLA-B locus, B51GAC and B45v, were investigated by RT-PCR cloning and nucleotide sequence analysis of their complete coding regions. They have been shown to correspond to the new alleles B*5108 and B*5002, both of which differ from the common B*5101 and B*5001 subtypes, respectively, by amino acid replacements at their alpha-2 domain alpha-helices. The primary structure of B*5002, intermediate between those of B*4501 and B*5001, raises further concern about the current classification of B*45 as a B12 rather than as a B*50 subtype.

Alleles↗
PubMed1998

Cloning and characterization of ZNF189, a novel human Krüppel-like zinc finger gene localized to chromosome 9q22-q31.

A 3-kb-long cDNA encoding a Krüppel-like human zinc finger protein was isolated and mapped to chromosome 9q22-q31. The ZNF189 gene encodes a protein with 16 zinc fingers at its C-terminus and belongs to the Krüppel-associated box (KRAB)-containing group of zinc finger proteins. Four differently spliced cDNA transcripts, differing at the 5' coding region where a KRAB A repressor domain is encoded, were isolated. In addition, Northern blot analysis indicates the presence of two additional unidentified splice variants. Comparison of cDNA and genomic sequences shows that the ZNF189 gene spans approximately 11 kb and is organized into at least four exons, the large 3'-end exon coding for the complete zinc finger domain and the 3' untranslated region. ZNF189 is expressed in all tissues and cell types currently investigated, at varying levels, but with a tissue- or cell-type-restricted expression pattern for the different splice variants. ZNF189 is conserved in the genome of several mammalian species. Direct sequencing of the ZNF189 gene in microdissected tumor biopsies of sporadic basal cell carcinoma and squamous cell carcinoma reveals no mutations in the coding sequence or at exon/intron boundaries.

Amino Acid Sequence↗