Human erythrocyte carbonic anhydrase polymorphism in Kenya

Summary In this study, 1736 Western Kenyans were examined for red cell carbonic anhydrase (CA) variants. No CA I variants were detected, but the CA II₂ isozyme was found with a calculated gene frequency of 0.054.     

Prevalence of genetic variants associated with cardiovascular disease risk and drug response in the Southern Indian population of Kerala

BACKGROUND AND AIM:

This study reports the prevalence of five clinically significant variants associated with increased risk of cardiovascular disorders, and variable responses of individuals to commonly prescribed cardiovascular drugs in a South Indian population from the state of Kerala.

MATERIALS AND METHODS:

Genomic DNA isolated from 100 out-patient samples from Kerala were sequenced to examine the frequency of clinically relevant polymorphisms in the genes MYBPC3 (cardiomyopathy), SLCO1B1 (statin-induced myopathy), CYP2C9, VKORC1 (response to warfarin) and CYP2C19 (response to clopidogrel).

RESULTS:

Our analyses revealed the frequency of a 25 bp deletion variant of MYBPC3 associated with risk of cardiomyopathy was 7%, and the SLCO1B1 “C” allele associated with risk for statin-induced myopathy was 15% in this sample group. Among the other variants associated with dose-induced toxicity of warfarin, VKORC1 (c.1639G>A), was detected at 22%, while CYP2C9*3 and CYP2C9*2 alleles were present at a frequency of 15% and 3% respectively. Significantly, the tested sample population showed high prevalence (66%) of CYP2C19*2 variant, which determines response to clopidogrel therapy.

CONCLUSIONS:

We have identified that certain variants associated with cardiovascular disease and related drug response in the five genes, especially those in VKORC1, CYP2C19 and MYBPC3, are highly prevalent in the Kerala population, with almost 2 times higher prevalence of CYP2C19*2 variant compared with other regions in the country. Since the variants chosen in this study have relevance in disease phenotype and/or drug response, and are detected at a higher frequency, this study is likely to encourage clinicians to perform genetic testing before prescribing therapy.     

Genetic polymorphisms of blood proteins in the troops of Japanese macaques,Macaca fuscata: III. Erythrocyte carbonic anhydrase polymorphism inMacaca fuscata

In order to clarify the genetic relationships between troops of Japanese macaques, the authors have been looking for the genetic variation of blood proteins by electrophoretical technique. In this work the genetic variants of erythrocyte carbonic anhydrase isozymes of 1273 blood samples from 34 troops of this species were examined. The genetic polymorphisms were observed in several troops. The variable troops of CA I were Fukushima, Takasakiyama, Kohchi, Shimane, Shodoshima I, K, and T, Kashima, Kawara, Takasakiyama A, B, and C, and Tomogashima. The variant allele found in these troops is onlyd ₂ allele, which was probably identical with that reported byTashian et al. (1971). The frequencies ofd ₂ allele in the Shodoshima and Kashima troops were very high, and this phenomenon was interpreted as being a result of the founder effect and the random fluctuation of gene frequencies in these troops.     

Further Characterization of Glycolaldehyde Dehydrogenase Isozymes from Escherichia coli B Involvement in Vitamin B6 Biosynthesis

Kinetic study of glycolaldehyde dehydrogenase was performed with isozymes of Escherichia coli B. The reaction equilibrium of isozyme A was estimated to lie in glycolate formation, while those of isozymes B and C were in glycolaldehyde formation. Isozyme A was released from cells with osmotic shock, while the others were not. Isozymes B and C were found in cytoplasmic fraction. Some reversal mutants derived from WG3 strain (one of vitamin B₆ auxotrophs) acquired ability to produce isozyme C. Based on these results, the non-involvement of isozyme A in vitamin B₆ biosynthesis was discussed.     

The Primary Structure of Water Buffalo αs1- and β-Casein: Identification of Phosphorylation Sites and Characterization of a Novel β-Casein Variant

The primary structure of water buffalo α_s1-casein and of β-casein A and B variants has been determined using a combination of mass spectrometry and Edman degradation procedures. The phosphorylated residues were localized on the tryptic phosphopeptides after performing a β-elimination/thiol derivatization. Water buffalo α_s1-casein, resolved in three discrete bands by isoelectric focusing, was found to consist of a single protein containing eight, seven, or six phosphate groups. Compared to bovine α_s1-casein C variant, the water buffalo α_s1-casein presented ten amino acid substitutions, seven of which involved charged amino acid residues. With respect to bovine βA₂-casein variant, the two water buffalo β-casein variants A and B presented four and five amino acid substitutions, respectively. In addition to the phosphoserines, a phosphothreonine residue was identified in variant A. From the phylogenetic point of view, both water buffalo β-casein variants seem to be homologous to bovine βA₂-casein.     

Hepatitis C Virus Variants with Decreased Sensitivity to Direct-Acting Antivirals (DAAs) Were Rarely Observed in DAA-Naive Patients prior to Treatment

The prevalence of naturally occurring hepatitis C virus (HCV) variants that are less sensitive to direct-acting antiviral (DAA) inhibitors has not been fully characterized. We used population sequence analysis to assess the frequency of such variants in plasma samples from 3,447 DAA-naive patients with genotype 1 HCV. In general, HCV variants with lower-level resistance (3- to 25-fold increased 50% inhibitor concentration [IC₅₀]) to telaprevir were observed as the dominant species in 0 to 3% of patients, depending on the specific variant, whereas higher-level resistant variants (>25-fold-increased IC₅₀) were not observed. Specific variants resistant to NS5A inhibitors were predominant in up to 6% of patients. Most variants resistant to nucleo(s/t)ide active-site NS5B polymerase inhibitors were not observed, whereas variants resistant to non-nucleoside allosteric inhibitors were observed in up to 18% of patients. The presence of DAA-resistant variants in NS5A, NS5B, or NS3 (including telaprevir-resistant variants), in baseline samples of treatment-naive patients receiving a telaprevir-based regimen in phase 3 studies did not affect the sustained viral response (SVR). Treatment-naive patients with viral populations containing the telaprevir-resistant variants NS3 V36M, T54S, or R155K at baseline achieved a 74% SVR rate, whereas patients with no resistant variants detected prior to treatment achieved a 76% SVR rate. The effect of specific resistant variant frequency on response to various DAA treatments in different patient populations, including interferon nonresponders, should be further studied.     

Electrophoretic pattern of cytosolic pyruvate kinase fractions A and B (type L and M2) from normal rat liver and Morris hepatoma 7777

Cytosolic pyruvate kinase fractions A and B obtained by salting out procedure from normal rat liver and Morris hepatoma 7777, purified by affinity chromatography on Blue Sepharose CL-6B, have shown similar electrophoretic patterns in polyacrylamide gel at pH 8.3, to previously studied pyruvate kinase extracts from chromatin of cell nuclei. Three variants (α₁, β₁, γ₁) from normal liver pyruvate kinase fraction A (type L) had the greatest electrophoretic mobility, showed sigmoidal kinetics in relation to 2-phosphoenolpyruvate (PEP), and sensitivity to ATP and fructose 1,6-diphosphate (FDP). The fraction A dominated over normal liver fraction B (type M₂), which in electrophoresis showed a slower y2 variant, similar to the fraction A of hepatoma. All variants from fractions B of normal liver and A of hepatoma had linear kinetics and were sensitive to ATP but not to FDP. The greatest differences showed pyruvate kinase fraction B from Morris hepatoma. Its all variants α₂, β₂, γ₃ were more cathodic and had linear kinetics in relation to PEP. They all were insensitive to normal signal molecules (ATP and FDP). The γ₃ alkaline variant acquired sensitivity to inhibition by l-cysteine. Showing several-fold higher activity, much greater affinity to the main substrate, and a lack of sensitivity to feed-back inhibition by ATP, it was responsible for a high rate of aerobic glycolysis and diminution of the Pasteur effect in metabolic studies. It was probably encoded during oncogene activation and plays a special role in different metabolic strategies of tumour cells.     

Extensive regions of homology in front of the two hsp70 heat shock variant genes in Drosophila melanogaster

The major heat shock protein of 70,000 M_r in Drosophila melanogaster is encoded by two variant gene types located, respectively, at the chromosomal sites 87A7 and 87C1. We present the DNA sequence of a complete hsp70² gene of the 87A7 type and of the adjacent regions from both variants, extending to 1·2 × 10³ bases upstream from the start of the messenger coding region. We find an untranslated region of 250 nucleotides at the 5′ end of the messenger coding sequence in both variants. There is only one open reading frame which allows coding of a 70,000 M_r protein within the 87A7 variant, as found for an 87C1 variant (Ingolia et al., 1980). We observe 4·2% nucleotide divergence between these two variants with complete conservation of the reading frame. There is a conserved sequence of 355 nucleotides in front of each hsp70 gene, which is 85% homologous between the two variants. The presence of the same sequence element in γ, in front of the αβ heat shock genes (R. W. Hackett & J. T. Lis, personal communication) suggests that this element contains the regulatory signals for the coordinate expression of both the hsp70 and the αβ heat shock genes. Finally we find a very A + T-rich sequence of 150 basepairs which is highly conserved (91·8%) 0·6 × 10³ bases upstream from two hps70 gene variants.     

New genetic polymorphisms within ovine β- and αS2-caseins

Casein genes in ruminants are organized in a cluster including α_S1-casein (CSN1S1), β-casein (CSN2), α_S2-casein (CSN1S2), and κ-casein (CSN3). Considering the results obtained in cattle and goat species concerning the influence of genetic polymorphisms on milk composition, quality, and technological properties, research on the polymorphisms of ewe's milk has known a new impulse in the last decade. A total of 54 samples belonging to the Massese dairy breed, to the double pourpose (milk and meat) Garfagnina population and to the Pomarancina and Zerasca meat populations, reared in the Centre of Italy, were analysed by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). New PCR-SSCP patterns were found in both CSN2 and CSN1S2 genes. Sequencing of the samples carrying the new patterns revealed 2 new variants at CSN2 gene. Frequencies of the 2 variants in the samples analysed were 0.18 and 0.02. The less common variant is characterized by a silent mutation in the triplet coding for Gln₁₉₂, whereas in the more frequent one a C to A transversion is responsible for the aminoacid exchange Leu₁₉₆ → Ile₁₉₆. At the CSN1S2 gene only a new variant was found with a frequency of 0.02. The variant is characterized by two linked mutations: a C to G transversion, responsible for the aminoacid change Asn₂₀₀ → Lys₂₀₀ already described at the protein level, and a T to A transversion at the 14th nucleotide of the 16th intron. The ovine caseins deserve a bigger attention that has to be directed to a complete characterization of the described variants and to the understanding of their functional meaning.     

A thiabendazole sulfonamide shows potent inhibitory activity against mammalian and nematode α-carbonic anhydrases

A sulfonamide derivative of the antihelmintic drug thiabendazole was prepared and investigated for inhibition of the zinc enzyme carbonic anhydrase CA (EC 4.2.1.1). Mammalian isoforms CA I–XIV and the nematode enzyme of Caenorhabditis elegans CAH-4b were included in this study. Thiabendazole-5-sulfonamide was a very effective inhibitor of CAH-4b and CA IX (K_Is of 6.4–9.5 nm) and also inhibited effectively isozymes CA I, II, IV–VII, and XII, with K_Is in the range of 17.8–73.2 nM. The high resolution X-ray crystal structure of its adduct with isozyme II evidenced the structural elements responsible for this potent inhibitory activity.     

Genetics and ontogeny of aldehyde dehydrogenase isozymes in the mouse: Localization of Ahd-1 encoding the mitochondrial isozyme on chromosome 4

Electrophoretic variants for the mitochondrial isozyme of aldehyde dehydrogenase (AHD) have been observed in inbred strains and in Harwell linkage testing stocks of Mus musculus. F₁ (LVC×C57BL/Go) mice showed a codominant allele three-banded phenotype, which suggests a dimeric subunit structure (designated AHD-A₂). The anodal-migrating supernatant isozyme of AHD was electrophoretically invariant among the 23 inbred strains and stocks examined. The genetic locus encoding AHD-A₂ (suggested name Ahd-1) is localized on chromosome 4 and was mapped close to je (jerker) and Gpd-1 (encoding the liver and kidney isozyme of glucose-6-phosphate dehydrogenase). Ontogenetic analyses demonstrated that both AHD isozymes exhibited low activity in late fetal and early neonatal liver and kidney extracts, and reached adult levels within 3 weeks of birth.     

Characterization of active site variants of xanthine hydroxylase from Aspergillus nidulans

Xanthine/α-ketoglutarate (αKG) dioxygenase (XanA) is a non-heme mononuclear Fe^II enzyme that decarboxylates αKG to succinate and CO₂ while hydroxylating xanthine to generate uric acid. In the absence of a XanA crystal structure, a homology model was used to target several putative active site residues for mutagenesis. Wild-type XanA and ten enzyme variants were purified from recombinant Escherichia coli cells and characterized. The H149A and D151A variants were inactive and the H340A variant exhibited only 0.17% of the wild-type enzyme activity, consistent with the proposed role of His149, Asp151, and His340 as Fe ligands. The K122A variant led to a 2-fold increase in the K_d of αKG as measured by fluorescence quenching analysis, in agreement with Lys122 acting to stabilize the binding of αKG. The N358A variant exhibited a 23-fold decrease in k_cat/K_m compared to wild-type XanA, pointing to a key role of Asn358 in catalysis. 9-Methylxanthine was exploited as an alternate substrate, and the C357A, E137A, and D138A variants were found to exhibit relatively enhanced activity consistent with Cys357, Glu137, and Asp138 being proximal to N-9 or involved in its proper positioning. 6,8-Dihydroxypurine was identified as a slow-binding competitive inhibitor of XanA, and significant decreases (E137A and D138A) or increases (Q356A and N358A) in of the variants were interpreted in terms of distinct interactions between this compound and the corresponding active site side chains. Further support for Cys357 residing at the active site was obtained using thiol-specific reagents that inactivated wild-type enzyme (with partial protection by substrate), whereas the C357A variant was resistant to these reagents. The Q101A, Q356A, and C357A variants showed elevated ferroxidase activity in the absence of substrates, pointing to the presence of the corresponding side chains at the active site. These results confirm most aspects of the homology model and provide additional insight into the enzyme reactivity.     

Sulfamide derivatives with selective carbonic anhydrase VII inhibitory action

A set of N,N′-disubstituted sulfamides and sodium cyclamate have been tested for their inhibitory action against six isoforms of carbonic anhydrase (CA, EC 4.2.1.1) found in the brain, that is, CA I, CA II, CA VII, CA IX, CA XII and CA XIV, some of which are involved in epileptogenesis. The biological data showed interesting results for CA VII inhibition, the isozyme thought to be a novel antiepileptic target. Strong CA VII inhibitors, with K_i values in the low nanomolar–subnanomolar range were identified. Some of these derivatives showed selectivity for inhibition of CA VII versus the ubiquitous isoform CA II, for which the K_i values were in the micromolar range. Molecular modeling approaches were employed to understand the binding interactions between these compounds and the two CA isoforms, since the mechanism of action of such disubstituted sulfamides was not yet investigated by means of X-ray crystallography.     

Determination of the CCR5∆32 frequency in Emiratis and Tunisians and the screening of the CCR5 gene for novel alleles in Emiratis

Background

The chemokine receptor components play crucial roles in the immune system and some of them serve as co-receptors for the HIV virus. Several studies have documented that variants in chemokine receptors are correlated with susceptibility and resistance to infection with HIV virus. For example, mutations in the chemokine receptor 5 gene (CCR5) resulting in loss-of-function (such as the homozygous CCR5?32) confer high degree of resistance to HIV infection. Heterozygotes for these variants exhibit slow progression to AIDS. The prevalence of CCR5 polymorphisms varies among ethnic and geographical groups. For example, the CCR5?32 variant is present in 10–15% of north Europeans but is rarely encountered among Africans. This study aims to identify the prevalence of some CCR5 variants in two geographically distant Arab populations (namely Emiratis and Tunisians).

Methodology

The prevalence of CCR5 gene variants including CCR5?32, FS299, C101X, A29S and C178R has been determined using PCR and direct DNA sequencing. A total of 403 unrelated healthy individuals (253 Emiratis and 150 Tunisians) were genotyped for the CCR5?32 variant using PCR amplification and gel electrophoresis. In addition, 200 Emiratis have been screened for other SNPs using Sanger DNA sequencing.

Results

Among Emiratis, the allele frequency of the CCR5?32 variant has been found to be 0.002. In addition, two variants L55Q and A159 were found at a frequency of 0.002. Moreover, the prevalence of the CCR5?32 variant in Tunisians was estimated to be 0.013 which is relatively higher than its frequency in Emiratis but lower than Europeans.

Conclusion

We conclude that the allele frequency of the most critical CCR5 polymorphism (?32) is extremely low among Emiratis compared to other Arabs and North Europeans. In addition, very low allele frequencies of other CCR5 polymorphisms have been detected among Emiratis.     

Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis

Genome-wide association studies (GWAS) conducted using commercial single nucleotide polymorphisms (SNP) arrays have proven to be a powerful tool for the detection of common disease susceptibility variants. However, their utility for the detection of lower frequency variants is yet to be practically investigated. Here we describe the application of a rare variant collapsing method to a large genome-wide SNP dataset, the Wellcome Trust Case Control Consortium rheumatoid arthritis (RA) GWAS. We partitioned the data into gene-centric bins and collapsed genotypes of low frequency variants (defined here as MAF ≤0.05) into a single count coupled with univariate analysis. We then prioritised gene regions for further investigation in an independent cohort of 3,355 cases and 2,427 controls based on rare variant signal p value and prior evidence to support involvement in RA. A total of 14,536 gene bins were investigated in the primary analysis and signals mapping to the TNFAIP3 and chr17q24 loci were selected for further investigation. We detected replicating association to low frequency variants in the TNFAIP3 gene (combined p = 6.6 × 10^?6). Even though rare variants are not well-represented and can be difficult to genotype in GWAS, our study supports the application of low frequency variant collapsing methods to genome-wide SNP datasets as a means of exploiting data that are routinely ignored.     

Naturally Occurring Deletion Mutants Are Parasitic Genotypes in a Wild-Type Nucleopolyhedrovirus Population of Spodoptera exigua

A wild-type nucleopolyhedrovirus (NPV) isolate from Spodoptera exigua from Florida (Se-US2) is a variant of the SeMNPV type strain since it has a unique DNA profile but is closely related to other known geographical isolates of SeMNPV. It consists of several genotypic variants, of which seven were identified in a Se-US2 virus stock by a modification of the in vivo cloning method developed by Smith and Crook (Virology 166:240–244, 1988). The US2A variant was the most prevalent genotype, and it was designated the prototype Se-US2 variant, while four of the variants (US2B, US2D, US2F, and US2H) were found at low frequency. US2C and US2E were also very abundant, and their diagnostic bands were easily observed in wild-type isolate restriction endonuclease patterns. The analysis of each variant, compared to the prototype US2A, showed that US2B and US2H presented minor differences, while US2D and US2F contained slightly larger insertions or deletions. Variants US2C and US2E contained major deletions of 21.1 and 14 kb, respectively, mapping at the same genomic region (between 14.5 and 30.2 map units [m.u.] and between 12.8 and 23 m.u., respectively). This is the first report of such deletion mutants in a natural baculovirus population. Variants US2A, US2B, US2D, US2F, and US2H were isolated as pure genotypes, but we failed to clone US2C and US2E in vivo. When these two variants appeared without apparent contamination with any other variant, they lost their pathogenicity for Spodoptera exigua larvae. A further biological characterization showed evidence that these two naturally occurring deletion mutants act as parasitic genotypes in the virus population. Bioassay data also demonstrated that pure US2A is significantly more pathogenic against second-instar S. exigua larvae than the wild-type isolate. The need for precise genotypic characterization of a baculovirus prior to its development as a bioinsecticide is discussed.