Human Phenylalanine Hydroxylase Gene Research Articles

The Missense p.S231F Phenylalanine Hydroxylase Gene Mutation Causes Complete Loss of Enzymatic Activity In Vitro

Phenylketonuria (PKU), the most frequent disorder of amino acid metabolism, is caused by mutations in human phenylalanine hydroxylase gene (PAH), leading to deficient enzyme activity. Previously reported but uncharacterized PAH gene mutation, p.S231F (c.692C > T), was detected in Serbian patients with classical PKU. We analyzed p.S231F PAH protein in prokaryotic (Escherichia coli) and eukaryotic expression system (hepatoma cells). In both systems the mutant enzyme was unstable. Residual enzyme activity in vitro was approximately 1%. Mutation p.S231F PAH was not activated by pre-incubation with phenylalanine substrate. We found no GroEL/GroES chaperone effect and slightly positive effect of the (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)) on the stabilization of the protein structure. Our findings were in accordance with severe patients' phenotypes. In conclusion, p.S231F should be classified as a functionally null PAH gene mutation as it drastically reduces stability and activity of the PAH enzyme in vitro.

Independent origin of rare Y168H mutation of human phenylalanine hydroxylase gene in Russia

Mutation Y168H of the human phenylalanine hydroxylase (PAH) gene determining phenylketonuria was described only twice: in a patient from Catalonia (Spain) and by us in a patient from Western Siberia (Russia). The association of Y168H in these families with allelic variants of STR and VNTR repeats and a number of neutral point polymorphisms of the PHA gene (IVS3nt-22C > T, Q232Q, V245V, L385L) was studied in this work. The Y186H mutation in these families was found to be associated with different haplotypes. Strong linkage of the selected markers and the mutation region excludes recombination as a possible cause of association of Y168H with different haplotypes. It was concluded that Y168H occurred independently in different populations.

Characterization of phenylalanine hydroxylase from Caenorhabditis elegans. Insights into the evolution of human activity and regulation

Phenylalanine hydroxylase (PAH) is an iron dependent enzyme that catalyzes the L-Phe to L-Tyr hydroxylation using tetrahydrobiopterin (BH4) as natural cofactor and O2 as cosubstrate. Mutations in the human PAH (hPAH) gene are associated to phenylketonuria. hPAH activity is tightly regulated by different mechanisms, including activation by L-Phe and phosphorylation, and inhibition by BH4. These regulatory effects are mediated by ligand induced changes in intra- and inter-subunit interactions in the tetramer. PAH enzymes from lower organisms have also been studied in some detail, but their catalytic and regulatory properties are unknown. We report the expression, purification and molecular characterization of a tetrameric PAH from C. elegans (cePAH). Our data show that cePAH and hPAH display similar specific activity, apparent affinities for L-Phe, BH4 and O2, secondary structure and thermal stability, but substantially diverges in its regulatory properties. Thus, cePAH did not require incubation with L-Phe to display maximal activity and also lacked positive cooperativity for the substrate. These results appear to be related to structural differences between both enzymes. Our results also provide further insights into the physiological role of PAH in lower organisms and the changes in PAH architecture, activity and regulation along evolution. This research was supported by the Research Council of Norway

Structural and functional analyses of mutations of the human phenylalanine hydroxylase gene

Background Phenylketonuria (PKU) is an inborn error of metabolism that results from a deficiency of phenylalanine hydroxylase (PAH). We demonstrated PAH mutational spectrum from patients with PKU, including 10 novel and 3 tetrahydrobiopterin (BH 4)-responsive mutations. In this study, 11 PAH missense mutations, including 6 novel mutations (P69S, G103S, L293M, G332V, S391I, A447P) found in our previous study, 2 mutations common in east Asian patients with PKU (R243Q, R413P), and 3 tetrahydrobiopterin (BH 4)-responsive mutations (R53H, R241C, R408Q) have been functionally and structurally analyzed. Methods A transient protein overexpression system and an in vitro BH 4-responsiveness study were used. The effects of PAH missense mutations on the PAH protein structure were also analyzed. To determine the conservation of 12 mutated residues, PAH was aligned using BLAST against full genomic sequences of 221 different species. Model structures of PAH protein and the composite tetramer were constructed using the software program, SHEBA. Results No PAH activity was detected for some mutants. However, the residual activities associated with other mutants ranged over a wide spectrum. The missense mutations responsive to BH 4 were not highly conserved throughout the 43 species in the multiple sequence alignment that encode PAH. The composite model structure of PAH revealed that dimer stability was reduced in the BH 4-responsive mutants, whereas tetramer stability remained normal. Conclusion This expression study analyzed PAH mutations and model structures of mutant PAH proteins are proposed. Correlation between the proposed mutant PAH structures and functions are suggested.

Reversal of gene expression profile in the phenylketonuria mouse model after adeno-associated virus vector-mediated gene therapy

Phenylketonuria (PKU) is an autosomal recessive metabolic disorder caused by phenylalanine hydroxylase (PAH) deficiency. Accumulation of phenylalanine leads to severe mental and psychomotor retardation, and hypopigmentation of skin and hair. We have demonstrated the cognitive outcome of biochemical and phenotypic reversal by the adeno-associated virus vector-mediated gene delivery of a human PAH transgene. In this study, we identified the expression of genes related to pathologic abnormalities of the PKU-affected brain, in which the symptoms of PKU are mainly manifest, and transcriptional changes in effective gene therapy treatment using oligonucleotide array. Therapeutic effectiveness was verified by change in enzyme activity (15 ± 5.84%), phenylalanine plasma level (261 ± 108 μM), and coat color. Our data indicated that 12 genes were significantly up-regulated in PKU. Four are involved in defense and inflammatory responses of neutrophils (NE, MPO, NGP, and CRAMP), three other overexpressed genes are related to extracellular matrix organization and degradation (COL1A1, COL1A2, and MMP13); the remainder were a nociceptor in sensory neurons ( MrgA1), a structural gene of P lysozyme (Lzp-s), an immunoglobulin α heavy chain constant region gene (Igh-2), an osteocalcin-related protein precursor (Bglap-rs1), and a membrane-spanning 4 domain, subfamily A, member 3 (Ms4a3). Data demonstrated that elevated genes in the PKU-affected brain could be normalized by human PAH gene delivery. Although we could not precisely link transcript level changes and neurologic pathogenesis, this study provides a more comprehensive understanding of the PKU-affected brain at the molecular level, possibly resulting in better therapeutic approaches.

Universal method for SNP identification

A new approach to the identification of point mutations by allele-specific PCR was proposed. The mutation R408W of the human phenylalanine hydroxylase gene was used as a model. A high specificity of the approach was achieved by the use of primers partially complementary to the genomic DNA. Polyethylene glycol covalently attached to one of the allele-specific primers provides for the differential identification of the PCR products due to a change in electrophoretic mobility.

Tetrahydrobiopterin protects phenylalanine hydroxylase activity in vivo: Implications for tetrahydrobiopterin-responsive hyperphenylalaninemia

The natural cofactor of phenylalanine hydroxylase (PAH), tetrahydrobiopterin (BH 4), regulates the enzyme activity as well as being essential in catalysis. BH 4-responsive PAH deficiency is a variant of hyperphenylalaninemia or phenylketonuria (PKU) caused by mutations in the human PAH gene that respond to oral BH 4 loading by stimulating enzyme activity and therefore lowering serum phenylalanine. Here, we showed in a coupled transcription–translation in vitro assay that upon expression in the presence of BH 4, wild-type PAH enzyme activity was enhanced. We then investigated the effect of BH 4 on PAH activity in transgenic mice that had a complete or partial deficiency in the endogenous cofactor biosynthesis. The rate of hepatic PAH enzyme activity increased significantly with BH 4 content without affecting gene expression or Pah-mRNA stability. These results indicate that BH 4 has a chaperon-like effect on PAH synthesis and/or is a protecting cofactor against enzyme auto-inactivation and degradation also in vivo. Our findings thus contribute to the understanding of the regulation of PAH by its cofactor BH 4 on an additional level and provide a molecular explanation for cofactor-responsive PKU.

Long-term enzymatic and phenotypic correction in the phenylketonuria mouse model by adeno-associated virus vector-mediated gene transfer.

Phenylketonuria (PKU) is an autosomal recessive metabolic disorder caused by a deficiency of phenylalanine hydroxylase (PAH). The accumulation of phenylalanine leads to severe mental and psychomotor retardation, and hypopigmentation of skin and hair. Low-phenylalanine diet therapy can prevent irreversible damage if instituted from birth. However, poor compliance with the strict lifelong dietary therapy leads to various neurologic and behavioral problems. To develop a safe and promising gene therapy method for PKU, we investigated whether a recombinant adeno-associated virus could be used as a PAH gene transfer vector to reduce the excessive phenylalanine level in the PKU mouse model. A recombinant adeno-associated virus vector encoding the human PAH gene (rAAV-hPAH), driven by EF1-alpha promoter, was infused into PAH-deficient mice, Pah(enu2), via the hepatic portal vein. Two weeks after injection, the plasma phenylalanine level dramatically decreased to 360 microM in male PKU mice, accompanied by the coat color changing to black. The mean plasma phenylalanine level of untreated PKU mice was 1800 microM. The PAH enzyme activities of treated mice increased to 10-17% of wild-type mice. No signs of liver toxicity were observed after gene transfer. The biochemical and phenotypic corrections were sustained for up to 25 wk (25-wk detection period). In contrast, the treatment was less effective in female PKU mice. These results indicate that recombinant adeno-associated virus vector-mediated gene therapy can be a useful therapeutic candidate for patients with PKU. Further studies are needed to clarify the differences in PKU pathogenesis in males and females, and to explore alternative administration routes besides hepatic portal vein injection.

Identification and characterization of a novel liver-specific enhancer of the human phenylalanine hydroxylase gene.

The liver-specific phenylalanine hydroxylase catalyzes the conversion of phenylalanine to tyrosine. Genetic defects in the gene result in the autosomal recessive disorder phenylketonuria. We have identified a phenylalanine hydroxylase mutation, designated as -4173_-407del, in a hyperphenylalaninemic patient with a 3.7-kb deletion in the 5'-flanking region of the phenylalanine hydroxylase gene. Characterization of the deleted sequence has led to the identification of a novel liver-specific DNase I hypersensitive site located 3.3 kb upstream of the RNA initiation site of the phenylalanine hydroxylase gene. We show that this site comprises a liver-specific enhancer with cAMP responsiveness. We further show by mutational analysis that the enhancer carries a major hepatocyte nuclear factor-1-binding site important for the enhancer function but not for cAMP responsiveness. In transient transfection assays with a reporter gene, we demonstrate that a phenylalanine hydroxylase plasmid construct carrying the -4173_-407del mutation is severely impaired in phenylalanine hydroxylase transcriptional activity. Our data indicate that the 3.7-kb deletion uncovered in the genomic DNA of the phenylketonuria proband is linked to the observed phenylketonuria phenotype as a result of a deletion of the newly identified liver-specific enhancer. Our systematic approach to the analysis and subsequent discovery of the novel deletion mutation may be applicable to the search for other mutations in the 5' regulatory region of phenylalanine hydroxylase and other genes.

Prokaryotic expression analysis of I269L and R270K mutations of the phenylalanine hydroxylase gene

The I269L (c.805A→C) and R270K (c.809G→A) mutations in exon 7 of the human phenylalanine hydroxylase (PAH) gene were identified in the Portuguese phenylketonuric (PKU) population with a frequency of 0.4 % and 6.2 %, respectively. To confirm that these changes at the DNA level are responsible for the PKU phenotype presented by those patients, and to establish a correlation between the genotype and the presented phenotype, these two mutations were produced in a prokaryotic expression system and characterized. In the present study we show that, using the pTrcHis system, the R270K mutation results in a severe loss of PAH enzyme activity and that mutation I269L only causes a moderate reduction in the specific activity of the enzyme. The obtained results are compatible with the clinical/metabolic phenotype of the affected patients.

A silent mutation induces exon skipping in the phenylalanine hydroxylase gene in phenylketonuria.

An A-->T substitution in cDNA nucleotide 1197 (c.1197A/T) of the human phenylalanine hydroxylase (PAH) gene has been regarded as a silent mutation, because both the wild-type (GUA) and the mutant (GUU) alleles encode a valine residue at codon 399 (V399 V). The nucleotide c.1197 is located at the 3'-end of exon 11at position -3 of the exon-intron junction. To explore whether the substitution exerts any effects on the processing of the PAH mRNA, illegitimate PAH transcripts from lymphoblast cultures of a phenylketonuria (PKU) patient heterozygous for c.1197A/T were analyzed by the polymerase chain reaction following reverse-transcription (RT-PCR). mRNAs with an exon 11 deletion were revealed. Furthermore, by using an R408 W mutation in the paternal allele as a marker, sequence analysis of the RT-PCR products indicates that virtually all PAH transcripts from the maternal allele with the c. 1197A/T substitution do not contain exon 11. To address whether this substitution is the main determinant for exon skipping, PAH minigenes with or without the substitution were constructed and transfected to a human hepatoma cell line. Analysis of the transcription products by S1 nuclease mapping clearly indicated that such exon 11 skipping was directly associated with the c.1197A/T substitution. Thus, this study demonstrates that the c.1197A/T substitution in the PAH gene is not just a neutral polymorphism but a mutation that induces post-transcriptional skipping of exon 11 leading to a PKU phenotype.

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.

PAHdb: a locus-specific knowledgebase.

PAHdb is an online relational locus-specific "mutation database" (http://www.mcgill.ca/pahdb) for the human phenylalanine hydroxylase gene (symbol PAH) and its associated phenotypes (protein, metabolic, clinical). When combined with associated information (population distribution of allele, haplotype association, etc.) PAHdb functions as a knowledgebase. From the outset, and in the absence of raw data (e.g., sequence gels), PAHdb has instead been an annotated repository of information about mutations maintained by a team of curators. It is also disease-oriented, being focused on a variant phenotype (hyperphenylalaninemia (HPA) and its most important form of disease, phenylketonuria (PKU)) resulting from primary dysfunction of the PAH enzyme (EC 1.14.16.1); it is "patient friendly" in that it contains information for those personally involved with HPA/PKU (MIM# 261600). PAHdb also serves its community through direct interaction.

The Structural Basis of Phenylketonuria

The human phenylalanine hydroxylase gene (PAH) (locus on human chromosome 12q24.1) contains the expressed nucleotide sequence which encodes the hepatic enzyme phenylalanine hydroxylase (PheOH). The PheOH enzyme hydroxylates the essential amino acid l-phenylalanine resulting in another amino acid, tyrosine. This is the major pathway for catabolizing dietary l-phenylalanine and accounts for approximately 75% of the disposal of this amino acid. The autosomal recessive disease phenylketonuria (PKU) is the result of a deficiency of PheOH enzymatic activity due to mutations in the PAH gene. Of the mutant alleles that cause hyperphenylalaninemia or PKU 99% map to the PAH gene. The remaining 1% maps to several genes that encode enzymes involved in the biosynthesis or regeneration of the cofactor ((6R)-l-erythro-5,6,7,8-tetrahydrobiopterin) regenerating the cofactor (tetrahydrobiopterin) necessary for the hydroxylation reaction. The recently solved crystal structures of human phenylalanine hydroxylase provide a structural scaffold for explaining the effects of some of the mutations in the PAH gene and suggest future biochemical studies that may increase our understanding of the PKU mutations.

Diverse PAH transcripts in lymphocytes of PKU patients with putative nonsense (G272X, Y356X) and missense (P281L, R408Q) mutations

The majority of mutations in the human phenylalanine hydroxylase (PAH) gene that lead to the recessive disease phenylketonuria (PKU) are believed to affect the activity or stability of the PAH enzyme. In this study we have performed in vivo analyses of lymphocyte PAH mRNA from PKU patients homozygous for the PKU missense mutations P281L and R408Q as well as the nonsense mutations G272X and Y356X. The mutations G272X, P281L and R408Q, which are located outside the consensus splice site sequence, result in transcripts with one or more exons skipped in addition to full-length transcripts. The mutation Y356X results in transcripts with one or more exons skipped, but no full-length transcripts. Our findings question the value of functional and structural predictions of mutations at the protein level without analyses of the corresponding transcript.

Human Phenylalanine Hydroxylase Gene Expression in Kidney and Other Nonhepatic Tissues

Phenylalanine hydroxylase (PAH) is the key enzyme in phenylalanine metabolism. PAH deficiency results in hyperphenylalaninemia, leading to severe mental retardation in the classical form of the disease, phenylketonuria (PKU). Previously the expression of PAH could only unambiguously be demonstrated in human liver, whereas in rodents PAH expression has been established in kidney and liver. Reports concerning PAH activity in other human or rodent tissues were severely questioned by subsequent investigations such that they did not gain general recognition. Conducting Northern blot analyses, we detected the PAH transcript in RNA isolated from human liver, kidney, pancreas, and brain. PAH gene expression in human kidney was subsequently investigated by RNase protection assay analyses, RNA in situ hybridization, immunohistochemistry, enzyme assay, and cDNA isolation. These experiments allowed the conclusive verification of a functional PAH enzyme in human kidney. The primary structure of the kidney transcript corresponded to the structure of the liver transcript. Human kidney PAH may play a significant role in phenylalanine homeostasis of the organism, as impaired phenylalanine hydroxylation has been observed in renal failure and differences in the regulation of the kidney versus the liver enzyme have been indicated. These results provide new aspects to research into the basis for the heterogeneity of hyperphenylalaninemia phenotypes and establish that the expression of the human PAH gene is not limited to the liver.

Partial characterization and three-dimensional-structural localization of eight mutations in exon 7 of the human phenylalanine hydroxylase gene associated with phenylketonuria.

The molecular basis for the metabolic defect in patients with phenylketonuria has been characterized for seven missense point mutations (R252G/Q, L255V/S, A259V/T and R270S) and a termination mutation (G272X) in an evolutionarily conserved motif of exon 7 in the catalytic domain of the human phenylalanine hydroxylase (hPAH) gene. The mutations were expressed in three heterologous in vitro systems. When expressed as fusion proteins with maltose-binding protein in Escherichia coli five of the mutant proteins demonstrated a defect in the normal ability of hPAH to fold and assemble as homotetramer/dimer, and they were mostly recovered as inactive aggregated forms. Only for the R252Q and L255V mutants were catalytically active tetramer and dimer recovered and for R252G some dimer, i.e. 20% (R252Q, tetramer), 44% (L255V, tetramer) and 4.4% (R252G, dimer) of the activity for the respective wild-type (wt) forms. When expressed by a coupled in vitro transcription-translation system, all the mutant enzymes were recovered as a mixture of non-phosphorylated and phosphorylated forms with a low homospecific activity (i.e. maximum 11% of wt-hPAH for the L255V mutant). When transiently expressed in human embryonic kidney (A293) cells a very low level of immunoreactive PAH protein was recovered in spite of normal PAH mRNA levels. All these mutations resulted in variant hPAH proteins which revealed a defect in oligomerization, an increased sensitivity to limited proteolysis in vitro, reduced cellular stability and a variable reduction in their catalytic activity. All these effects seem to result from structural perturbations of the monomer, and based on the crystal structure of the catalytic domain of hPAH, an explanation is provided for the impact of the mutations on the folding and oligomerization of the monomers.

Identification of hepatic nuclear factor 1 binding sites in the 5' flanking region of the human phenylalanine hydroxylase gene: implication of a dual function of phenylalanine hydroxylase stimulator in the phenylalanine hydroxylation system.

Phenylalanine hydroxylase stimulator (PHS) is a component of the phenylalanine hydroxylation system that is involved in the regeneration of the cofactor tetrahydrobiopterin. It is also identical to the dimerization cofactor of hepatocyte nuclear factor 1 (HNF1) (DCoH) that is able to enhance the transcriptional activity of HNF1. Moreover, it has the structural potential for binding macromolecules such as proteins and nucleic acids, consistent with its involvement in gene expression. We investigated whether PHS/DCoH could enhance the expression of phenylalanine hydroxylase (PAH). Cotransfection assays showed that DCoH itself could not transactivate the 9-kb human PAH 5' flanking fragment. However, this 9-kb fragment was transactivated by HNF1 in a dose-dependent manner with a maximum of nearly 8-fold activation; DCoH potentiated this transactivation by another 1.6-fold. The HNF1 binding sites were located at -3.5 kb in a region that is 77.5% identical to the mouse liver-specific hormone-inducible PAH gene enhancer. This study suggests a possible dual function of PHS in vivo in the human phenylalanine hydroxylation system: it is involved in the regeneration of the cofactor tetrahydrobiopterin and can also enhance the expression of the human PAH gene.

Alterations in protein aggregation and degradation due to mild and severe missense mutations (A104D, R157N) in the human phenylalanine hydroxylase gene (PAH)

Alterations in protein aggregation and degradation due to mild and severe missense mutations (A104D, R157N) in the human phenylalanine hydroxylase gene (PAH)

Alterations in protein aggregation and degradation due to mild and severe missense mutations (A104D, R157N) in the human phenylalanine hydroxylase gene (PAH).

Phenylalanine hydroxylase (PAH) catalyzes the conversion of phenylalanine to tyrosine; its activity is the major determinant of phenylalanine disposal. Mutations in the corresponding human gene (PAH), which encodes the human hepatic PAH enzyme, result in hyperphenylalaninemia; the resulting phenotypes can range in severity from mild forms of hyperphenylalaninemia with benign outcome to the severe form, phenylketonuria with impaired cognitive development. This paper describes the detailed characterization of two inherited recessive missense mutations in PAH, c.311C-->A (A104D) and [c.470G-->A;c.471A-->C] (R157N), which are associated, respectively, in the homozygous or functionally hemizygous states, with mild and severe metabolic phenotypes. We used three different in vitro PAH expression systems (in Escherichia coli, cell-free rabbit reticulocyte lysates, and human embryonal kidney cells), as well as a unique assay for phenylalanine oxidation in vivo. In each system, we observed alterations of PAH function and physical properties, compared with wild-type enzyme, and differences in relative severity of effects between these two mutations. Pulse-chase experiments showed increased PAH degradation, probably related to observed aberrations in protein folding and altered oligomerization, as a basic mechanism underlying effects of these missense mutations.