New Polymorphic Sites in the Human Phenylalanine Hydroxylase Gene

A previously unknown sequence of the human phelylalanine hydroxylase (PAH) gene intron 7 (GeneBank AN AF204239) has been reported. Screening of the group of phenylketonuria patients from Nobosibirsk region for polymorphic sites within intron 7 revealed single nucleotide substitutions at intron positions 332, 451, 574 and 791. Polymorphic site at intron position 791 corresponds to one of the eight restriction sites (MspI) utilized for haplotype construction. Analysis of the MspI allele frequencies in 29 phenylketonuria patients showed that the frequency of the MspI+ allele in this group was 79.4%. Polymorphic sites at nucleotide position +97 from the beginning of intron 10, and at nucleotide position –54 from the end of intron 5, were also described. The polymorphic sites revealed can be used as markers for identification of the PAH alleles in population genetic studies, and also serve for diagnostics of phenylketonuria (PKU). The presence of numerous nucleotide substitutions within the intronic sequences confirms highly polymorphic structure of the PAH gene.     

Characterization of Mutations at the Mouse Phenylalanine Hydroxylase Locus

Two genetic mouse models for human phenylketonuria have been characterized by DNA sequence analysis. For each, a distinct mutation was identified within the protein coding sequence of the phenylalanine hydroxylase gene. This establishes that the mutated locus is the same as that causing human phenylketonuria and allows a comparison between these mouse phenylketonuria models and the human disease. A genotype/phenotype relationship that is strikingly similar to the human disease emerges, underscoring the similarity of phenylketonuria in mouse and man. InPAH^ENU1,the phenotype is mild. ThePah^enu1mutation predicts a conservative valine to alanine amino acid substitution and is located in exon 3, a gene region where serious mutations are rare in humans. InPAH^ENU2,the phenotype is severe. ThePah^enu2mutation predicts a radical phenylalanine to serine substitution and is located in exon 7, a gene region where serious mutations are common in humans. InPAH^ENU2,the sequence information was used to devise a direct genotyping system based on the creation of a newAlw26I restriction endonuclease site.     

Dynamic Regulation of Phenylalanine Hydroxylase by Simulated Redox Manipulation

Recent clinical studies revealed increased phenylalanine levels and phenylalanine to tyrosine ratios in patients suffering from infection, inflammation and general immune activity. These data implicated down-regulation of activity of phenylalanine hydroxylase by oxidative stress upon in vivo immune activation. Though the structural damage of oxidative stress is expected to be comparably small, a structural rationale for this experimental finding was lacking. Hence, we investigated the impact of side chain oxidation at two vicinal cysteine residues on local conformational flexibility in the protein by comparative molecular dynamics simulations. Analysis of backbone dynamics revealed a highly flexible loop region (Tyr138-loop) in proximity to the active center of phenylalanine hydroxylase. We observed elevated loop dynamics in connection with a loop movement towards the active site in the oxidized state, thereby partially blocking access for the substrate phenylalanine. These findings were confirmed by extensive replica exchange molecular dynamics simulations and serve as a first structural explanation for decreased enzyme turnover in situations of oxidative stress.     

中国人21-羟化酶缺乏症基因型和临床表型特点研究

利用快速可靠的基因突变检测方法研究中国人21-羟化酶缺乏症(21-hydroxylase deficiency ,21-OHD)基因突变特点及基因型和临床表型的关系.用8例非经典型患者、35例经典型患者及34例正常对照者基因组DNA作模板,用特定引物特异性扩增CYP21的两个片段,片段1从Exon1→Exon3,片段2从Exon3→Exon10.用片段1和片段2为模板进行第二轮PCR,用特定限制性内切酶消化后经琼脂糖凝胶电泳鉴定9种突变,包括Del、Exon3 Del8 bp、Q318X、 R356W、Exon6Cluster、i2g、I172N、P30L和 V281L.结果表明,43例患者的86个等位基因中的79个(91.9%)检测出突变,最常见的是I172N(36.0%),其次为i2g(20.9%)、Del(8.6%)、P30L(7.0%)、Q318X(7.0%)、V281L(4.7%)、R356W(2.3%)、E6Cluster(2.3%)和Exon3 Del8 bp(1.2%).失盐型、单纯男性化型和非经典型21-羟化酶缺乏症各临床分型中最常见的突变分别是 Del(44.4%)、I172N(44.2%)和 P30L(37.5%).另外根据对21-羟化酶活性影响程度将基因型分为轻、中、重3组,3组间初诊年龄、17-羟孕酮(17-OHP)、该病亚型构成均存在显著差异(P<0.05),提示基因型决定临床表型.研究结果表明,中国人21-OHD最常见的突变为I172N、i2g和Del,中国人21-OHD基因型和临床表型密切相关.     

Probing Cofactor Specificity in Phenylalanine Hydroxylase by Molecular Dynamics Simulations

Abstract

Phenylalanine hydroxylase (PAH) is a tetrahydrobiopterin-dependent enzyme that catalyzes the hydroxylation of L-phenylalanine (L-Phe) to L-tyrosine using dioxygen as an additional substrate. The requirement of PAH for a cofactor is absolute, but several cofactor analogs are able to substitute the natural cofactor in catalysis. However, it is only the natural cofactor 6R-tetrahydrobiopterin (6R-BH₄) that induces a negative regulatory effect on the enzyme. In order to get further insights on the molecular basis for this specificity, we studied the structure of the cofactor-enzyme complex and the conformational changes induced by cofactor binding by molecular dynamics simulations. Simulations were carried out on the enzyme alone and complexed with 6R-BH₄ and with two cofactor analogs, 6S-BH₄ and 6-methyl-tetrahydropterin (6M-PH₄). In the resting unbound enzyme Tyr377 in the catalytic domain is hydrogen bonded to both Ser23 and Glu21 of the autoregulatory N-terminal sequence. This hydrogen bonding network is disturbed by the binding of BH₄, which interacts with Ser23. By doing so, 6R-BH₄ facilitates an interaction between Glu21 and the active site iron, further pulling the N-terminal into the active site of PAH and blocking the L-Phe binding site. Thus, in the 6R-BH₄ complexed enzyme, the N-terminal functions as an intrinsic amino acid regulatory sequence (IARS). Neither 6M-PH₄ nor 6S-BH₄ can interact favorably with Ser23, and do not induce an inhibitory effect on PAH. These simulations thus explain the previous findings that the two hydroxyl groups in the side chain of the 6R epimer of BH₄ are essential for the inhibitory regulatory effect on PAH.     

Structural Features of the Regulatory ACT Domain of Phenylalanine Hydroxylase

Phenylalanine hydroxylase (PAH) catalyzes the conversion of L-Phe to L-Tyr. Defects in PAH activity, caused by mutations in the human gene, result in the autosomal recessively inherited disease hyperphenylalaninemia. PAH activity is regulated by multiple factors, including phosphorylation and ligand binding. In particular, PAH displays positive cooperativity for L-Phe, which is proposed to bind the enzyme on an allosteric site in the N-terminal regulatory domain (RD), also classified as an ACT domain. This domain is found in several proteins and is able to bind amino acids. We used molecular dynamics simulations to obtain dynamical and structural insights into the isolated RD of PAH. Here we show that the principal motions involve conformational changes leading from an initial open to a final closed domain structure. The global intrinsic motions of the RD are correlated with exposure to solvent of a hydrophobic surface, which corresponds to the ligand binding-site of the ACT domain. Our results strongly suggest a relationship between the Phe-binding function and the overall dynamic behaviour of the enzyme. This relationship may be affected by structure-disturbing mutations. To elucidate the functional implications of the mutations, we investigated the structural effects on the dynamics of the human RD PAH induced by six missense hyperphenylalaninemia-causing mutations, namely p.G46S, p.F39C, p.F39L, p.I65S, p.I65T and p.I65V. These studies showed that the alterations in RD hydrophobic interactions induced by missense mutations could affect the functionality of the whole enzyme.     

中国北方人苯丙氨酸羟化酶基因外显子7内新突变的鉴定

应用ＰＣＲ－单链构象多态性分析及ＤＮＡ直接测序,对４５例中国北方苯丙酮尿症（ＰＫＵ）患者苯丙氨酸羟化酶（ＰＡＨ）基因外显子７内突变进行了鉴定。共检出６种错义突变及一种静止突变：Ｒ２４３Ｑ．Ｒ４１Ｈ,Ｇ２４７Ｖ．Ｌ２４９Ｈ．Ｐ２５４Ｉ．Ｇ２５７Ｖ和Ｖ２４５Ｖ。经与国际ＰＡＨ基因突变数据库比较,确认Ｇ２５７Ｖ．Ｐ２５４Ｉ和Ｌ２４９Ｈ为国际上首次发现的突变。结果揭示,中国人与其他种族及中国北方与南方人群ＰＡＨ突变特点不同。明确了中国北方人群中ＰＡＨ基因外显子７基因突变分布,有助于提高ＰＫＵ的基因诊断率,对基因的起源、进化研究有参考价值     

Identification of Mutations in Phenylalanine Hydroxylase Gene Using an Automated Genetic Analyzer

Mutations were studied in phenylalanine hydroxylase gene of phenylketonuria patients from Kemerovo oblast and Altaiskii krai (15 and 2 families, respectively). The following mutations were identified in exons of this gene: R408W, R261Q, R243Q, R158Q, Y414C, Y386C, P281L, Y168H, R68S (lead to amino acid substitutions), R243X (leads to stop codon formation), and three splice site mutations (IVS12nt1g a, IVS2nt-13t g, IVS7nt 1g a).     

Activation of Phenylalanine Hydroxylase Induces Positive Cooperativity toward the Natural Cofactor

Protein misfolding with loss-of-function of the enzyme phenylalanine hydroxylase (PAH) is the molecular basis of phenylketonuria in many individuals carrying missense mutations in the PAH gene. PAH is complexly regulated by its substrate l-Phenylalanine and its natural cofactor 6R-l-erythro-5,6,7,8-tetrahydrobiopterin (BH₄). Sapropterin dihydrochloride, the synthetic form of BH₄, was recently approved as the first pharmacological chaperone to correct the loss-of-function phenotype. However, current knowledge about enzyme function and regulation in the therapeutic setting is scarce. This illustrates the need for comprehensive analyses of steady state kinetics and allostery beyond single residual enzyme activity determinations to retrace the structural impact of missense mutations on the phenylalanine hydroxylating system. Current standard PAH activity assays are either indirect (NADH) or discontinuous due to substrate and product separation before detection. We developed an automated fluorescence-based continuous real-time PAH activity assay that proved to be faster and more efficient but as precise and accurate as standard methods. Wild-type PAH kinetic analyses using the new assay revealed cooperativity of activated PAH toward BH₄, a previously unknown finding. Analyses of structurally preactivated variants substantiated BH₄-dependent cooperativity of the activated enzyme that does not rely on the presence of l-Phenylalanine but is determined by activating conformational rearrangements. These findings may have implications for an individualized therapy, as they support the hypothesis that the patient''s metabolic state has a more significant effect on the interplay of the drug and the conformation and function of the target protein than currently appreciated.     

中国人苯丙氨酸羟化酶基因的一个新的切接位点突变的鉴定

本文鉴定了苯丙氨酸羟化酶基因355位密码子上的一个新的错义突变Q355 H, 此突变异致谷氨酰胺变成了组氨酸。此突变位点恰位于外显子10和内含子11的交界处, 因此将引起mRNA形成过程中的剪接错误而产生异常的mR NA。Q355H的鉴定为一例苯丙酮尿症胎儿的产前诊断提供了理论依据。 Abstract:A novel missense mutation at code 355 of phenylalanine hydroxlase gene was identified,this mutation caused the substitution of Gln 355 for His 355.The mutant site was at the boundary of exon 10 and intro 11 and might cause splicing errors during RNA processing,Which could result in abnormal mRNA.Identification of Q355H provided a theortic evidence for prenatal diagnosis of a fetus with PKU.     

The Progeroid Phenotype of Ku80 Deficiency Is Dominant over DNA-PKCS Deficiency

Ku80 and DNA-PK_CS are both involved in the repair of double strand DNA breaks via the nonhomologous end joining (NHEJ) pathway. While ku80^−/− mice exhibit a severely reduced lifespan and size, this phenotype is less pronounced in dna-pk_cs^−/− mice. However, these observations are based on independent studies with varying genetic backgrounds. Here, we generated ku80^−/−, dna-pk_cs^−/− and double knock out mice in a C57Bl6/J*FVB F1 hybrid background and compared their lifespan, end of life pathology and mutation frequency in liver and spleen using a lacZ reporter. Our data confirm that inactivation of Ku80 and DNA-PK_CS causes reduced lifespan and bodyweights, which is most severe in ku80^−/− mice. All mutant mice exhibited a strong increase in lymphoma incidence as well as other aging-related pathology (skin epidermal and adnexal atrophy, trabacular bone reduction, kidney tubular anisokaryosis, and cortical and medullar atrophy) and severe lymphoid depletion. LacZ mutation frequency analysis did not show strong differences in mutation frequencies between knock out and wild type mice. The ku80^−/− mice had the most severe phenotype and the Ku80-mutation was dominant over the DNA-PK_CS-mutation. Presumably, the more severe degenerative effect of Ku80 inactivation on lifespan compared to DNA-PK_CS inactivation is caused by additional functions of Ku80 or activity of free Ku70 since both Ku80 and DNA-PK_CS are essential for NHEJ.     

Inherited Interleukin-12 Deficiency: IL12B Genotype and Clinical Phenotype of 13 Patients from Six Kindreds

Interleukin-12 (IL12) is a cytokine that is secreted by activated phagocytes and dendritic cells and that induces interferon-gamma production by natural-killer and T lymphocytes. It consists of two subunits, p35 and p40, which are encoded by IL12A and IL12B, respectively. The first reported patient with a genetic cytokine disorder was a Pakistani child, who was homozygous for a large loss-of-function deletion (g.482+82_856-854del) in IL12B. This IL12-deficient child suffered from infections caused by bacille Calmette-Guérin (BCG) and Salmonella enteritidis. We herein report 12 additional patients from five other kindreds. In one kindred from India, the same large deletion that was described elsewhere (g.482+82_856-854del) was identified. In four kindreds from Saudi Arabia, a recessive loss-of-function frameshift insertion (g.315_316insA) was found. A conserved haplotype encompassing the IL12B gene suggested that a founder effect accounted for the recurrence of each mutation. The two founder mutational events-g.482+82_856-854del and g.315_316insA-were estimated to have occurred approximately 700 and approximately 1,100 years ago, respectively. Among a total of 13 patients with IL12 deficiency, 1 child had salmonellosis only and 12 suffered from clinical disease due to BCG or environmental nontuberculous mycobacteria. One patient also had clinical disease caused by virulent Mycobacterium tuberculosis, five patients had clinical disease caused by Salmonella serotypes, and one patient had clinical disease caused by Nocardia asteroides. The clinical outcome varies from case to case, since five patients (aged 2-11 years) died of overwhelming infection, whereas eight patients (aged 3-12 years) are still in good health and are not currently taking antibiotics. In conclusion, IL12 deficiency is not limited to a single kindred, shows significant variability of outcome, and should be considered in the genetic diagnosis of patients with mycobacteriosis and/or salmonellosis. To date, two founder IL12B mutations have been identified, accounting for the recurrence of a large deletion and a small insertion within populations from the Indian subcontinent and from the Arabian Peninsula, respectively.     

Recurrence of the R408W Mutation in the Phenylalanine Hydroxylase Locus in Europeans

The relative frequency of the common phenylalanine hydroxylase (PAH) mutation R408W and its associations with polymorphic RFLP, VNTR, and short-tandem-repeat (STR) sites in the PAH gene were examined in many European populations and one representative North American population of defined European descent. This mutation was found to cluster in two regions: in northwest Europe among Irish and Scottish peoples, and in eastern Europe, including the Commonwealth of Independent States. This allele was significantly less frequent in intervening populations. In eastern European populations, the R408W mutation is strongly associated with RFLP haplotype 2, the three-copy VNTR allele (VNTR 3), and the 240-bp STR allele. In northwestern European populations, it is strongly associated with RFLP haplotype 1, the VNTR allele containing eight repeats (VNTR 8), and the 244-bp STR allele. An examination of the linkage between the R408W mutation and highly polymorphic RFLP, VNTR, and STR haplotypes suggests that recurrence is the most likely mechanism to account for the two different major haplotype associations of R408W in Europe.     

Human Phenylalanine Hydroxylase Mutations and Hyperphenylalaninemia Phenotypes: A Metanalysis of Genotype-Phenotype Correlations

We analyzed correlations between mutant genotypes at the human phenylalanine hydroxylase locus (gene symbol PAH) and the corresponding hyperphenylalaninemia (HPA) phenotypes (notably, phenylketonuria [OMIM 261600]). We used reports, both published and in the PAH Mutation Analysis Consortium Database, on 365 patients harboring 73 different PAH mutations in 161 different genotypes. HPA phenotypes were classified as phenylketonuria (PKU), variant PKU, and non-PKU HPA. By analysis both of homoallelic mutant genotypes and of "functionally hemizygous" heteroallelic genotypes, we characterized the phenotypic effect of 48 of the 73 different, largely missense mutations. Among those with consistent in vivo expression, 24 caused PKU, 3 caused variant PKU, and 10 caused non-PKU HPA. However, 11 mutations were inconsistent in their effect: 9 appeared in two different phenotype classes, and 2 (I65T and Y414C) appeared in all three classes. Seven mutations were inconsistent in phenotypic effect when in vitro (unit-protein) expression was compared with the corresponding in vivo phenotype (an emergent property). We conclude that the majority of PAH mutations confer a consistent phenotype and that this is concordant with their effects, when known, predicted from in vitro expression analysis. However, significant inconsistencies, both between in vitro and in vivo phenotypes and between different individuals with similar PAH genotypes, reveal that the HPA-phenotype is more complex than that predicted by Mendelian inheritance of alleles at the PAH locus.     

PAH基因内一个A／C多态性位点的分析

在苯丙氨酸羟化酶基因ＩＶＳ３的３‘端－１１位有一个Ａ／Ｃ多态性位点,应用ＳＳＣＰ分析可进行简便检测,Ａ等位基因的频率为０．６５６,Ｃ等位基因的频率为０．３４４,此位点的多态性信息含量（ＰＩＣ）为０．３５１。Ａ／Ｃ位点与同一内含子内的ＳＴＲ位点间没有连锁不平衡性,联合应用这两个多态性位点进行单体型连锁分析,对ＰＫＵ家系进行产前基断诊断率可达７５％。     

Phenotype Refinement Strengthens the Association of AHR and CYP1A1 Genotype with Caffeine Consumption

Two genetic loci, one in the cytochrome P450 1A1 (CYP1A1) and 1A2 (CYP1A2) gene region (rs2472297) and one near the aryl-hydrocarbon receptor (AHR) gene (rs6968865), have been associated with habitual caffeine consumption. We sought to establish whether a more refined and comprehensive assessment of caffeine consumption would provide stronger evidence of association, and whether a combined allelic score comprising these two variants would further strengthen the association. We used data from between 4,460 and 7,520 women in the Avon Longitudinal Study of Parents and Children, a longitudinal birth cohort based in the United Kingdom. Self-report data on coffee, tea and cola consumption (including consumption of decaffeinated drinks) were available at multiple time points. Both genotypes were individually associated with total caffeine consumption, and with coffee and tea consumption. There was no association with cola consumption, possibly due to low levels of consumption in this sample. There was also no association with measures of decaffeinated drink consumption, indicating that the observed association is most likely mediated via caffeine. The association was strengthened when a combined allelic score was used, accounting for up to 1.28% of phenotypic variance. This was not associated with potential confounders of observational association. A combined allelic score accounts for sufficient phenotypic variance in caffeine consumption that this may be useful in Mendelian randomization studies. Future studies may therefore be able to use this combined allelic score to explore causal effects of habitual caffeine consumption on health outcomes.     

Circadian Variations in the Activity of Tyrosine Hydroxylase, Tyrosine Aminotransferase, and Tryptophan Hydroxylase: Relationship to Catecholamine Metabolism

Abstract— Circadian variations in the activity of tyrosine hydroxylase, tyrosine aminotransferase, and tryptophan hydroxylase were observed in the rat brain stem. Tyrosine hydroxylase exhibited a bimodal pattern with peaks occurring during both the light and dark phases of the circadian cycle. Tyrosine aminotransferase had one daily peak of activity occurring late in the light phase, whereas tryptophan hydroxylase activity was maximal late in the dark phase. Circadian fluctuations in tyrosine hydroxylase activity did not correlate well with circadian variations in the turnover rates of norepinephrine or dopamine nor with levels of these catecholamines. This supports the idea that although tyrosine hydroxylase is the rate-limiting enzyme in the synthesis of catecholamines, other factors must also be involved in the in vivo regulation of this process. Administration of α -methyl- p -tyrosine (AMT) methyl ester HC1 (100 mg/kg) had no effect on the activity of tryptophan hydroxylase, but effectively eliminated the peak of tyrosine hydroxylase activity that occurred during the light phase. AMT also lowered levels of tyrosine aminotransferase, but only at times near the daily light to dark transition. These chronotypic effects of AMT emphasize the importance of "time of day" as a factor that must be taken into account in evaluating the biochemical as well as the pharmacological and toxicological effects of drugs.