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Sarodaya N, Tyagi A, Kim HJ, Colaco JC, Kang JS, Kim WJ, Kim KS, Ramakrishna S. Deubiquitinase USP19 enhances phenylalanine hydroxylase protein stability and its enzymatic activity. Cell Biol Toxicol 2023; 39:2295-2310. [PMID: 35449354 DOI: 10.1007/s10565-022-09719-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Phenylalanine hydroxylase (PAH) is the key enzyme in phenylalanine metabolism, deficiency of which is associated with the most common metabolic phenotype of phenylketonuria (PKU) and hyperphenylalaninemia (HPA). A bulk of PKU disease-associated missense mutations in the PAH gene have been studied, and the consequence of each PAH variant vary immensely. Prior research established that PKU-associated variants possess defects in protein folding with reduced cellular stability leading to rapid degradation. However, recent evidence revealed that PAH tetramers exist as a mixture of resting state and activated state whose transition depends upon the phenylalanine concentration and certain PAH variants that fail to modulate the structural equilibrium are associated with PKU disease. Collectively, these findings framed our understanding of the complex genotype-phenotype correlation in PKU. In the current study, we substantiate a link between PAH protein stability and its degradation by the ubiquitin-mediated proteasomal degradation system. Here, we provide an evidence that PAH protein undergoes ubiquitination and proteasomal degradation, which can be reversed by deubiquitinating enzymes (DUBs). We identified USP19 as a novel DUB that regulates PAH protein stability. We found that ectopic expression of USP19 increased PAH protein level, whereas depletion of USP19 promoted PAH protein degradation. Our study indicates that USP19 interacts with PAH and prevents polyubiquitination of PAH subsequently extending the half-life of PAH protein. Finally, the increase in the level of PAH protein by the deubiquitinating activity of USP19 resulted in enhanced metabolic function of PAH. In summary, our study identifies the role of USP19 in regulating PAH protein stability and promotes its metabolic activity. Graphical highlights 1. E3 ligase Cdh1 promotes PAH protein degradation leading to insufficient cellular amount of PAH causing PKU. 2. A balance between E3 ligase and DUB is important to regulate the proteostasis of PAH. 3. USP19 deubiquitinates and stabilizes PAH further protecting it from rapid degradation. 4. USP19 increases the enzymatic activity of PAH, thus maintaining normal Phe levels.
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Affiliation(s)
- Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Hyun-Jin Kim
- Department of Pharmacology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Jencia Carminha Colaco
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Ju-Seop Kang
- Department of Pharmacology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.
- College of Medicine, Hanyang University, Seoul, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea.
- College of Medicine, Hanyang University, Seoul, South Korea.
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Rovelli V, Cefalo G, Ercoli V, Zuvadelli J, Olivia T, Graziani D, Luisella A, Bassi D, Re Dionigi A, Selmi R, Paci S, Salvatici E, Banderali G. Hyperphenylalaninemias genotyping: Results of over 60 years of history in Lombardy, Italy. Endocrinol Diabetes Metab 2023; 6:e396. [PMID: 36537053 PMCID: PMC10000623 DOI: 10.1002/edm2.396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Hyperphenylalaninemias (HPA) are due to several gene mutations, of which the PAH gene is the most frequently involved. Prevalence and incidence of disease vary between populations, with genotype/phenotype correlations not always capable to correctly predict disease severity. The aim of this study was to give an overview of PAH mutations among one of the largest cohort of patients among Europe, born in Lombardy (Italy) starting from late 1970 s and including over a 60 years of activity; furthermore, to evaluate and discuss identified genotype/phenotype correlations and related reliability. PATIENTS/METHODS Eight hundred and twenty-six HPA patients in current follow-up at the San Paolo Hospital in Milan (Italy) were retrospectively reviewed, including molecular results and allelic phenotype and genotype values (attributed on the basis of the APV/GPV system) to verify genotype-phenotype correlations. RESULTS A total of 166 different PAH variants were reviewed; of those, seven variants were identified as not previously described in literature. Most frequently reported variant was p.Ala403Val, followed by p.Arg261Gln, p.Val245Ala, IVS10-11 g>a, p.Tyr414Cys and p.Leu48Ser. Phenotype prediction, based on APV/GPV, matched the actual phenotype in most cases, but not always. CONCLUSION/DISCUSSION The cohort of patients included in this study constitute a representative sample of the HPA population worldwide. Studies on this sample may allow to improve clinical and genetic evaluation performances for affected patients, consequently to develop personalized medicine interventions and provide more precise indications on the correct treatment approach based on the accumulated evidence, also in light of a prognostically reliable but not always conclusive APV/GPV system.
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Affiliation(s)
- Valentina Rovelli
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Graziella Cefalo
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Vittoria Ercoli
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Juri Zuvadelli
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Turri Olivia
- Department of Laboratory Diagnostic TechnologiesSan Paolo Hospital, ASST Santi Paolo e CarloMilanItaly
| | - Daniela Graziani
- Department of Laboratory Diagnostic TechnologiesSan Paolo Hospital, ASST Santi Paolo e CarloMilanItaly
| | - Alberti Luisella
- Regional Laboratory of Newborn Screening, Department of Women, Mothers and Neonatal Care, Children's Hospital “V. Buzzi”ASST Fatebenefratelli SaccoMilanItaly
| | - Davide Bassi
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Alice Re Dionigi
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Raed Selmi
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Sabrina Paci
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Elisabetta Salvatici
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
| | - Giuseppe Banderali
- Clinical Department of Pediatrics, Inborn Errors of Metabolism Unit, San Paolo Hospital, ASST Santi Paolo e CarloUniversity of MilanMilanItaly
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3
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Deubiquitinase USP19 extends the residual enzymatic activity of phenylalanine hydroxylase variants. Sci Rep 2022; 12:14243. [PMID: 35987969 PMCID: PMC9392723 DOI: 10.1038/s41598-022-18656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) is a key enzyme in mammals that maintains the phenylalanine (Phe) concentration at an appropriate physiological level. Some genetic mutations in the PAH gene lead to destabilization of the PAH enzyme, leading to phenylketonuria (PKU). Destabilized PAH variants can have a certain amount of residual enzymatic activity that is sufficient for metabolism of Phe. However, accelerated degradation of those variants can lead to insufficient amounts of cellular PAH protein. The optimal protein level of PAH in cells is regulated by a balancing act between E3 ligases and deubiquitinating enzymes (DUBs). In this work, we analyzed the protein expression and stability of two PKU-linked PAH protein variants, R241C and R243Q, prevalent in the Asian population. We found that the tested PAH variants were highly ubiquitinated and thus targeted for rapid protein degradation. We demonstrated that USP19, a DUB that interacts with both PAH variants, plays a regulatory role by extending their half-lives. The deubiquitinating activity of USP19 prevents protein degradation and increases the abundance of both PAH protein variants. Thus, our study reveals a novel mechanism by which deubiquitinating activity of USP19 extends the residual enzymatic activity of PAH variants.
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Perez-Garcia CG, Diaz-Trelles R, Vega JB, Bao Y, Sablad M, Limphong P, Chikamatsu S, Yu H, Taylor W, Karmali PP, Tachikawa K, Chivukula P. Development of an mRNA replacement therapy for phenylketonuria. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:87-98. [PMID: 35356682 PMCID: PMC8933640 DOI: 10.1016/j.omtn.2022.02.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/25/2022] [Indexed: 12/19/2022]
Abstract
Phenylketonuria (PKU) is an inborn error caused by deficiencies in phenylalanine (Phe) metabolism. Mutations in the phenylalanine hydroxylase (PAH) gene are the main cause of the disease whose signature hallmarks of toxically elevated levels of Phe accumulation in plasma and organs such as the brain, result in irreversible intellectual disability. Here, we present a unique approach to treating PKU deficiency by using an mRNA replacement therapy. A full-length mRNA encoding human PAH (hPAH) is encapsulated in our proprietary lipid nanoparticle LUNAR and delivered to a Pahenu2 mouse model that carries a missense mutation in the mouse PAH gene. Animals carrying this missense mutation develop hyperphenylalanemia and hypotyrosinemia in plasma, two clinical features commonly observed in the clinical presentation of PKU. We show that intravenous infusion of LUNAR-hPAH mRNA can generate high levels of hPAH protein in hepatocytes and restore the Phe metabolism in the Pahenu2 mouse model. Together, these data establish a proof of principle of a novel mRNA replacement therapy to treat PKU.
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Affiliation(s)
- Carlos G Perez-Garcia
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Ramon Diaz-Trelles
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Jerel Boyd Vega
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Yanjie Bao
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Marciano Sablad
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Patty Limphong
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Simon Chikamatsu
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Hailong Yu
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Wendy Taylor
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Priya P Karmali
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Kiyoshi Tachikawa
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
| | - Padmanabh Chivukula
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, Suite 250, San Diego, CA 92121, USA
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5
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Diaz-Trelles R, Perez-Garcia CG. Present and future of lipid nanoparticle-mRNA technology in phenylketonuria disease treatment. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 372:159-174. [PMID: 36064263 DOI: 10.1016/bs.ircmb.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Phenylketonuria (PKU) is a metabolic rare disease characterized by a failure of the body to clear out the high levels of Phenylalanine (Phe), leading to devastating neurological defects and growth retardation. PKU was discovered in 1934 by AsbjrØrn FØlling, and even though there have been continuous efforts from the scientific community to find therapeutic approaches to modulate the high levels of phenylalanine found in the body of the PKU patients, an efficient therapy still needs to be developed. Current standard of care includes low phenylalanine diets, but the strict restrictions for patients and families makes it very difficult to adequately being implemented. FDA has approved two drugs to help reduce Phe levels in PKU patients: an enzyme substitution therapy, Palynziq® (PEGylated recombinant phenylalanine ammonia lyase), and Kuvan®, a supplemental tetrahydrobiopterin (BH4) cofactor that enhances residual enzyme activity. Both treatments are restricted to certain PKU patients' population, and, therefore, there are still high unmet needs for most of the patients. The present review will focus on current advancements in lipid nanoparticles (LNP)-mRNA technologies and their potential in treating the root cause of PKU, a therapeutic approach that will be analyzed in the context of other promising therapeutic approaches that are been developed for PKU.
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6
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Lin C, Li Y, Zhang E, Feillet F, Zhang S, Blau N. Importance of the long non-coding RNA (lncRNA) transcript HULC for the regulation of phenylalanine hydroxylase and treatment of phenylketonuria. Mol Genet Metab 2022; 135:171-178. [PMID: 35101330 DOI: 10.1016/j.ymgme.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
More than 1280 variants in the phenylalanine hydroxylase (PAH) gene are responsible for a broad spectrum of phenylketonuria (PKU) phenotypes. While the genotype-phenotype correlation is reaching 88%, for some inconsistent phenotypes with the same genotype additional factors like tetrahydrobiopterin (BH4), the PAH co-chaperone DNAJC12, phosphorylation of the PAH residues or epigenetic factors may play an important role. Very recently an additional player, the long non-coding RNA (lncRNA) transcript HULC, was described to regulate PAH activity and enhance residual enzyme activity of some PAH variants (e.g., the most common p.R408W) by using HULC mimics. In this review we present an overview of the lncRNA function and in particular the interplay of the HUCL transcript with the PAH and discuss potential applications for the future treatment of some PKU patients.
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Affiliation(s)
- Chunru Lin
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Yajuan Li
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Eric Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - François Feillet
- INSERM, U1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy, France; Pediatric Department Reference Center for Inborn Errors of Metabolism Children University Hospital Nancy, Nancy, France
| | - Shuxing Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital Zürich, Zurich, Switzerland.
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7
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Li Y, Tan Z, Zhang Y, Zhang Z, Hu Q, Liang K, Jun Y, Ye Y, Li YC, Li C, Liao L, Xu J, Xing Z, Pan Y, Chatterjee SS, Nguyen TK, Hsiao H, Egranov SD, Putluri N, Coarfa C, Hawke DH, Gunaratne PH, Tsai KL, Han L, Hung MC, Calin GA, Namour F, Guéant JL, Muntau AC, Blau N, Sutton VR, Schiff M, Feillet F, Zhang S, Lin C, Yang L. A noncoding RNA modulator potentiates phenylalanine metabolism in mice. Science 2021; 373:662-673. [PMID: 34353949 PMCID: PMC9714245 DOI: 10.1126/science.aba4991] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 08/31/2020] [Accepted: 06/25/2021] [Indexed: 12/13/2022]
Abstract
The functional role of long noncoding RNAs (lncRNAs) in inherited metabolic disorders, including phenylketonuria (PKU), is unknown. Here, we demonstrate that the mouse lncRNA Pair and human HULC associate with phenylalanine hydroxylase (PAH). Pair-knockout mice exhibited excessive blood phenylalanine (Phe), musty odor, hypopigmentation, growth retardation, and progressive neurological symptoms including seizures, which faithfully models human PKU. HULC depletion led to reduced PAH enzymatic activities in human induced pluripotent stem cell-differentiated hepatocytes. Mechanistically, HULC modulated the enzymatic activities of PAH by facilitating PAH-substrate and PAH-cofactor interactions. To develop a therapeutic strategy for restoring liver lncRNAs, we designed GalNAc-tagged lncRNA mimics that exhibit liver enrichment. Treatment with GalNAc-HULC mimics reduced excessive Phe in Pair -/- and Pah R408W/R408W mice and improved the Phe tolerance of these mice.
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Affiliation(s)
- Yajuan Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhi Tan
- Intelligent Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Yaohua Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Qingsong Hu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ke Liang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yao Jun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Yi-Chuan Li
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Chunlai Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lan Liao
- Genetically Engineered Mouse Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianming Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhen Xing
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yinghong Pan
- Department of Biochemistry and Biology, University of Houston, Houston, TX 77030, USA
| | - Sujash S Chatterjee
- Department of Biochemistry and Biology, University of Houston, Houston, TX 77030, USA
| | - Tina K Nguyen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Heidi Hsiao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sergey D Egranov
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - David H Hawke
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Preethi H Gunaratne
- Department of Biochemistry and Biology, University of Houston, Houston, TX 77030, USA
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
- Department of Biotechnology, Asia University, Taichung 413, Taiwan
| | - George A Calin
- Department of Translational Molecular Pathology, Division of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fares Namour
- Department of Molecular Medicine and Reference Center for Inborn Errors of Metabolism, University Hospital of Nancy, Nancy F-54000, France
- INSERM, U1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Jean-Louis Guéant
- Department of Molecular Medicine and Reference Center for Inborn Errors of Metabolism, University Hospital of Nancy, Nancy F-54000, France
- INSERM, U1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Ania C Muntau
- University Children's Hospital, University Medical Center Hamburg Eppendorf, Hamburg 20246, Germany
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital Zurich, CH-8032 Zurich, Switzerland
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Manuel Schiff
- Necker Hospital, APHP, Reference Center for Inborn Error of Metabolism and Filière G2M, Pediatrics Department, University of Paris, Paris 75007, France
- Inserm UMR_S1163, Institut Imagine, Paris 75015, France
| | - François Feillet
- INSERM, U1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France.
- Pediatric Department Reference Center for Inborn Errors of Metabolism Children University Hospital Nancy, Nancy F-54000, France
| | - Shuxing Zhang
- Intelligent Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
- The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Berestova TV, Gizatov RR, Galimov MN, Mustafin AG. Influence of the absolute configuration of the ligand's chiral center on the structure of planar-square phenyl-containing bis-(N,O)copper(II) chelates. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Arturo EC, Merkel GW, Hansen MR, Lisowski S, Almeida D, Gupta K, Jaffe EK. Manipulation of a cation-π sandwich reveals conformational flexibility in phenylalanine hydroxylase. Biochimie 2021; 183:63-77. [PMID: 33221376 PMCID: PMC9856217 DOI: 10.1016/j.biochi.2020.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 01/24/2023]
Abstract
Phenylalanine hydroxylase (PAH) is an allosteric enzyme that maintains phenylalanine (Phe) below neurotoxic levels; its failure results in phenylketonuria, an inborn error of amino acid metabolism. Wild type (WT) PAH equilibrates among resting-state (RS-PAH) and activated (A-PAH) conformations, whose equilibrium position depends upon allosteric Phe binding. The RS-PAH conformation of WT rat PAH (rPAH) contains a cation-π sandwich involving Phe80 that cannot exist in the A-PAH conformation. Phe80 variants F80A, F80D, F80L, and F80R were prepared and evaluated using native PAGE, size exclusion chromatography, ion exchange behavior, intrinsic protein fluorescence, enzyme kinetics, and limited proteolysis, each as a function of [Phe]. Like WT rPAH, F80A and F80D show allosteric activation by Phe while F80L and F80R are constitutively active. Maximal activity of all variants suggests relief of a rate-determining conformational change. Limited proteolysis of WT rPAH (minus Phe) reveals facile cleavage within a 4-helix bundle that is buried in the RS-PAH tetramer interface, reflecting dynamic dissociation of that tetramer. This cleavage is not seen for the Phe80 variants, which all show proteolytic hypersensitivity in a linker that repositions during the RS-PAH to A-PAH interchange. Hypersensitivity is corrected by addition of Phe such that all variants become like WT rPAH and achieve the A-PAH conformation. Thus, manipulation of Phe80 perturbs the conformational space sampled by PAH, increasing sampling of on-pathway intermediates in the RS-PAH and A-PAH interchange. The behavior of the Phe80 variants mimics that of disease-associated R68S and suggests a molecular basis for proteolytic susceptibility in PKU-associated human PAH variants.
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Affiliation(s)
- Emilia C. Arturo
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111,Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - George W. Merkel
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111
| | - Michael R. Hansen
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111
| | - Sophia Lisowski
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111
| | - Deeanne Almeida
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111
| | - Kushol Gupta
- Department pf Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Eileen K. Jaffe
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 10111,To whom correspondence should be addressed: Eileen K. Jaffe: Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111; ; Tel.(215) 728-3695; Fax. (215) 728-2412
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10
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Lopes RR, Tomé CS, Russo R, Paterna R, Leandro J, Candeias NR, Gonçalves LMD, Teixeira M, Sousa PMF, Guedes RC, Vicente JB, Gois PMP, Leandro P. Modulation of Human Phenylalanine Hydroxylase by 3-Hydroxyquinolin-2(1H)-One Derivatives. Biomolecules 2021; 11:biom11030462. [PMID: 33808760 PMCID: PMC8003416 DOI: 10.3390/biom11030462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/08/2021] [Accepted: 03/13/2021] [Indexed: 01/14/2023] Open
Abstract
Phenylketonuria (PKU) is a genetic disease caused by deficient activity of human phenylalanine hydroxylase (hPAH) that, when untreated, can lead to severe psychomotor impairment. Protein misfolding is recognized as the main underlying pathogenic mechanism of PKU. Therefore, the use of stabilizers of protein structure and/or activity is an attractive therapeutic strategy for this condition. Here, we report that 3-hydroxyquinolin-2(1H)-one derivatives can act as protectors of hPAH enzyme activity. Electron paramagnetic resonance spectroscopy demonstrated that the 3-hydroxyquinolin-2(1H)-one compounds affect the coordination of the non-heme ferric center at the enzyme active-site. Moreover, surface plasmon resonance studies showed that these stabilizing compounds can be outcompeted by the natural substrate l-phenylalanine. Two of the designed compounds functionally stabilized hPAH by maintaining protein activity. This effect was observed on the recombinant purified protein and in a cellular model. Besides interacting with the catalytic iron, one of the compounds also binds to the N-terminal regulatory domain, although to a different location from the allosteric l-Phe binding site, as supported by the solution structures obtained by small-angle X-ray scattering.
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Affiliation(s)
- Raquel R. Lopes
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - Catarina S. Tomé
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal;
- Instituto de Biologia Experimental e Tecnológica, Quinta do Marquês, 2780-155 Oeiras, Portugal;
| | - Roberto Russo
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - Roberta Paterna
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - João Leandro
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - Nuno R. Candeias
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33101 Tampere, Finland;
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Lídia M. D. Gonçalves
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal;
| | - Pedro M. F. Sousa
- Instituto de Biologia Experimental e Tecnológica, Quinta do Marquês, 2780-155 Oeiras, Portugal;
| | - Rita C. Guedes
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - João B. Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal;
- Correspondence: (J.B.V.); (P.M.P.G.); (P.L.); Tel.: +351-217946400 (P.L.)
| | - Pedro M. P. Gois
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
- Correspondence: (J.B.V.); (P.M.P.G.); (P.L.); Tel.: +351-217946400 (P.L.)
| | - Paula Leandro
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
- Correspondence: (J.B.V.); (P.M.P.G.); (P.L.); Tel.: +351-217946400 (P.L.)
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11
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Jaffe EK. Wrangling Shape-Shifting Morpheeins to Tackle Disease and Approach Drug Discovery. Front Mol Biosci 2020; 7:582966. [PMID: 33330623 PMCID: PMC7729013 DOI: 10.3389/fmolb.2020.582966] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Homo-multimeric proteins that can come apart, change shape, and reassemble differently with functional consequences have been called morpheeins and/or transformers; these provide a largely unexplored context for understanding disease and developing allosteric therapeutics. This article describes such proteins within the context of protein structure dynamics, provides one detailed example related to an inborn error of metabolism and potential herbicide development, and describes the context for applying these ideas for understanding disease and designing bioactive molecules, such as therapeutics.
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Affiliation(s)
- Eileen K Jaffe
- Fox Chase Cancer Center, Philadelphia, PA, United States
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12
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Enzyme dysfunction at atomic resolution: Disease-associated variants of human phosphoglucomutase-1. Biochimie 2020; 183:44-48. [PMID: 32898648 DOI: 10.1016/j.biochi.2020.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/26/2020] [Accepted: 08/30/2020] [Indexed: 11/20/2022]
Abstract
Once experimentally prohibitive, structural studies of individual missense variants in proteins are increasingly feasible, and can provide a new level of insight into human genetic disease. One example of this is the recently identified inborn error of metabolism known as phosphoglucomutase-1 (PGM1) deficiency. Just as different variants of a protein can produce different patient phenotypes, they may also produce distinct biochemical phenotypes, affecting properties such as catalytic activity, protein stability, or 3D structure/dynamics. Experimental studies of missense variants, and particularly structural characterization, can reveal details of the underlying biochemical pathomechanisms of missense variants. Here, we review four examples of enzyme dysfunction observed in disease-related variants of PGM1. These studies are based on 11 crystal structures of wild-type (WT) and mutant enzymes, and multiple biochemical assays. Lessons learned include the value of comparing mutant and WT structures, synergy between structural and biochemical studies, and the rich understanding of molecular pathomechanism provided by experimental characterization relative to the use of predictive algorithms. We further note functional insights into the WT enzyme that can be gained from the study of pathogenic variants.
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13
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Sarodaya N, Suresh B, Kim KS, Ramakrishna S. Protein Degradation and the Pathologic Basis of Phenylketonuria and Hereditary Tyrosinemia. Int J Mol Sci 2020; 21:ijms21144996. [PMID: 32679806 PMCID: PMC7404301 DOI: 10.3390/ijms21144996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
A delicate intracellular balance among protein synthesis, folding, and degradation is essential to maintaining protein homeostasis or proteostasis, and it is challenged by genetic and environmental factors. Molecular chaperones and the ubiquitin proteasome system (UPS) play a vital role in proteostasis for normal cellular function. As part of protein quality control, molecular chaperones recognize misfolded proteins and assist in their refolding. Proteins that are beyond repair or refolding undergo degradation, which is largely mediated by the UPS. The importance of protein quality control is becoming ever clearer, but it can also be a disease-causing mechanism. Diseases such as phenylketonuria (PKU) and hereditary tyrosinemia-I (HT1) are caused due to mutations in PAH and FAH gene, resulting in reduced protein stability, misfolding, accelerated degradation, and deficiency in functional proteins. Misfolded or partially unfolded proteins do not necessarily lose their functional activity completely. Thus, partially functional proteins can be rescued from degradation by molecular chaperones and deubiquitinating enzymes (DUBs). Deubiquitination is an important mechanism of the UPS that can reverse the degradation of a substrate protein by covalently removing its attached ubiquitin molecule. In this review, we discuss the importance of molecular chaperones and DUBs in reducing the severity of PKU and HT1 by stabilizing and rescuing mutant proteins.
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Affiliation(s)
- Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
| | - Bharathi Suresh
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.-S.K.); or (S.R.)
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.-S.K.); or (S.R.)
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14
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Tran ML, Génisson Y, Ballereau S, Dehoux C. Second-Generation Pharmacological Chaperones: Beyond Inhibitors. Molecules 2020; 25:molecules25143145. [PMID: 32660097 PMCID: PMC7397201 DOI: 10.3390/molecules25143145] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 02/06/2023] Open
Abstract
Protein misfolding induced by missense mutations is the source of hundreds of conformational diseases. The cell quality control may eliminate nascent misfolded proteins, such as enzymes, and a pathological loss-of-function may result from their early degradation. Since the proof of concept in the 2000s, the bioinspired pharmacological chaperone therapy became a relevant low-molecular-weight compound strategy against conformational diseases. The first-generation pharmacological chaperones were competitive inhibitors of mutant enzymes. Counterintuitively, in binding to the active site, these inhibitors stabilize the proper folding of the mutated protein and partially rescue its cellular function. The main limitation of the first-generation pharmacological chaperones lies in the balance between enzyme activity enhancement and inhibition. Recent research efforts were directed towards the development of promising second-generation pharmacological chaperones. These non-inhibitory ligands, targeting previously unknown binding pockets, limit the risk of adverse enzymatic inhibition. Their pharmacophore identification is however challenging and likely requires a massive screening-based approach. This review focuses on second-generation chaperones designed to restore the cellular activity of misfolded enzymes. It intends to highlight, for a selected set of rare inherited metabolic disorders, the strategies implemented to identify and develop these pharmacologically relevant small organic molecules as potential drug candidates.
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Affiliation(s)
| | | | | | - Cécile Dehoux
- Correspondence: (S.B.); (C.D.); Tel.: +33-5-6155-6127 (C.D.)
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15
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Tomé CS, Lopes RR, Sousa PMF, Amaro MP, Leandro J, Mertens HDT, Leandro P, Vicente JB. Structure of full-length wild-type human phenylalanine hydroxylase by small angle X-ray scattering reveals substrate-induced conformational stability. Sci Rep 2019; 9:13615. [PMID: 31541188 PMCID: PMC6754429 DOI: 10.1038/s41598-019-49944-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/03/2019] [Indexed: 01/30/2023] Open
Abstract
Human phenylalanine hydroxylase (hPAH) hydroxylates L-phenylalanine (L-Phe) to L-tyrosine, a precursor for neurotransmitter biosynthesis. Phenylketonuria (PKU), caused by mutations in PAH that impair PAH function, leads to neurological impairment when untreated. Understanding the hPAH structural and regulatory properties is essential to outline PKU pathophysiological mechanisms. Each hPAH monomer comprises an N-terminal regulatory, a central catalytic and a C-terminal oligomerisation domain. To maintain physiological L-Phe levels, hPAH employs complex regulatory mechanisms. Resting PAH adopts an auto-inhibited conformation where regulatory domains block access to the active site. L-Phe-mediated allosteric activation induces a repositioning of the regulatory domains. Since a structure of activated wild-type hPAH is lacking, we addressed hPAH L-Phe-mediated conformational changes and report the first solution structure of the allosterically activated state. Our solution structures obtained by small-angle X-ray scattering support a tetramer with distorted P222 symmetry, where catalytic and oligomerisation domains form a core from which regulatory domains protrude, positioning themselves close to the active site entrance in the absence of L-Phe. Binding of L-Phe induces a large movement and dimerisation of regulatory domains, exposing the active site. Activated hPAH is more resistant to proteolytic cleavage and thermal denaturation, suggesting that the association of regulatory domains stabilises hPAH.
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Affiliation(s)
- Catarina S Tomé
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Raquel R Lopes
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro M F Sousa
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Mariana P Amaro
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - João Leandro
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Paula Leandro
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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16
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Arturo EC, Gupta K, Hansen MR, Borne E, Jaffe EK. Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium. J Biol Chem 2019; 294:10131-10145. [PMID: 31076506 PMCID: PMC6664189 DOI: 10.1074/jbc.ra119.008294] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/09/2019] [Indexed: 11/06/2022] Open
Abstract
Dysfunction of human phenylalanine hydroxylase (hPAH, EC 1.14.16.1) is the primary cause of phenylketonuria, the most common inborn error of amino acid metabolism. The dynamic domain rearrangements of this multimeric protein have thwarted structural study of the full-length form for decades, until now. In this study, a tractable C29S variant of hPAH (C29S) yielded a 3.06 Å resolution crystal structure of the tetrameric resting-state conformation. We used size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) to analyze the full-length hPAH solution structure both in the presence and absence of Phe, which serves as both substrate and allosteric activators. Allosteric Phe binding favors accumulation of an activated PAH tetramer conformation, which is biophysically distinct in solution. Protein characterization with enzyme kinetics and intrinsic fluorescence revealed that the C29S variant and hPAH are otherwise equivalent in their response to Phe, further supported by their behavior on various chromatography resins and by analytical ultracentrifugation. Modeling of resting-state and activated forms of C29S against SAXS data with available structural data created and evaluated several new models for the transition between the architecturally distinct conformations of PAH and highlighted unique intra- and inter-subunit interactions. Three best-fitting alternative models all placed the allosteric Phe-binding module 8-10 Å farther from the tetramer center than do all previous models. The structural insights into allosteric activation of hPAH reported here may help inform ongoing efforts to treat phenylketonuria with novel therapeutic approaches.
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Affiliation(s)
- Emilia C Arturo
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
- the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, and
| | - Kushol Gupta
- the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michael R Hansen
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
| | - Elias Borne
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
| | - Eileen K Jaffe
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111,
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17
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Flydal MI, Alcorlo-Pagés M, Johannessen FG, Martínez-Caballero S, Skjærven L, Fernandez-Leiro R, Martinez A, Hermoso JA. Structure of full-length human phenylalanine hydroxylase in complex with tetrahydrobiopterin. Proc Natl Acad Sci U S A 2019; 116:11229-11234. [PMID: 31118288 PMCID: PMC6561269 DOI: 10.1073/pnas.1902639116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) is a key enzyme in the catabolism of phenylalanine, and mutations in this enzyme cause phenylketonuria (PKU), a genetic disorder that leads to brain damage and mental retardation if untreated. Some patients benefit from supplementation with a synthetic formulation of the cofactor tetrahydrobiopterin (BH4) that partly acts as a pharmacological chaperone. Here we present structures of full-length human PAH (hPAH) both unbound and complexed with BH4 in the precatalytic state. Crystal structures, solved at 3.18-Å resolution, show the interactions between the cofactor and PAH, explaining the negative regulation exerted by BH4 BH4 forms several H-bonds with the N-terminal autoregulatory tail but is far from the catalytic FeII Upon BH4 binding a polar and salt-bridge interaction network links the three PAH domains, explaining the stability conferred by BH4 Importantly, BH4 binding modulates the interaction between subunits, providing information about PAH allostery. Moreover, we also show that the cryo-EM structure of hPAH in absence of BH4 reveals a highly dynamic conformation for the tetramers. Structural analyses of the hPAH:BH4 subunits revealed that the substrate-induced movement of Tyr138 into the active site could be coupled to the displacement of BH4 from the precatalytic toward the active conformation, a molecular mechanism that was supported by site-directed mutagenesis and targeted molecular dynamics simulations. Finally, comparison of the rat and human PAH structures show that hPAH is more dynamic, which is related to amino acid substitutions that enhance the flexibility of hPAH and may increase the susceptibility to PKU-associated mutations.
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Affiliation(s)
| | - Martín Alcorlo-Pagés
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | | | | | - Lars Skjærven
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Rafael Fernandez-Leiro
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway;
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain;
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18
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Scheller R, Stein A, Nielsen SV, Marin FI, Gerdes AM, Di Marco M, Papaleo E, Lindorff-Larsen K, Hartmann-Petersen R. Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations. Hum Mutat 2019; 40:444-457. [PMID: 30648773 DOI: 10.1002/humu.23707] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/18/2018] [Accepted: 01/13/2019] [Indexed: 01/22/2023]
Abstract
Phenylketonuria (PKU) is a genetic disorder caused by variants in the gene encoding phenylalanine hydroxylase (PAH), resulting in accumulation of phenylalanine to neurotoxic levels. Here, we analyzed the cellular stability, localization, and interaction with wild-type PAH of 20 selected PKU-linked PAH protein missense variants. Several were present at reduced levels in human cells, and the levels increased in the presence of a proteasome inhibitor, indicating that proteins are proteasome targets. We found that all the tested PAH variants retained their ability to associate with wild-type PAH, and none formed aggregates, suggesting that they are only mildly destabilized in structure. In all cases, PAH variants were stabilized by the cofactor tetrahydrobiopterin (BH4 ), a molecule known to alleviate symptoms in certain PKU patients. Biophysical calculations on all possible single-site missense variants using the full-length structure of PAH revealed a strong correlation between the predicted protein stability and the observed stability in cells. This observation rationalizes previously observed correlations between predicted loss of protein destabilization and disease severity, a correlation that we also observed using new calculations. We thus propose that many disease-linked PAH variants are structurally destabilized, which in turn leads to proteasomal degradation and insufficient amounts of cellular PAH protein.
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Affiliation(s)
- Rasmus Scheller
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Frederikke I Marin
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Miriam Di Marco
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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19
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Ge Y, Borne E, Stewart S, Hansen MR, Arturo EC, Jaffe EK, Voelz VA. Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding. J Biol Chem 2018; 293:19532-19543. [PMID: 30287685 DOI: 10.1074/jbc.ra118.004909] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/17/2018] [Indexed: 12/20/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) regulates phenylalanine (Phe) levels in mammals to prevent neurotoxicity resulting from high Phe concentrations as observed in genetic disorders leading to hyperphenylalaninemia and phenylketonuria. PAH senses elevated Phe concentrations by transient allosteric Phe binding to a protein-protein interface between ACT domains of different subunits in a PAH tetramer. This interface is present in an activated PAH (A-PAH) tetramer and absent in a resting-state PAH (RS-PAH) tetramer. To investigate this allosteric sensing mechanism, here we used the GROMACS molecular dynamics simulation suite on the Folding@home computing platform to perform extensive molecular simulations and Markov state model (MSM) analysis of Phe binding to ACT domain dimers. These simulations strongly implicated a conformational selection mechanism for Phe association with ACT domain dimers and revealed protein motions that act as a gating mechanism for Phe binding. The MSMs also illuminate a highly mobile hairpin loop, consistent with experimental findings also presented here that the PAH variant L72W does not shift the PAH structural equilibrium toward the activated state. Finally, simulations of ACT domain monomers are presented, in which spontaneous transitions between resting-state and activated conformations are observed, also consistent with a mechanism of conformational selection. These mechanistic details provide detailed insight into the regulation of PAH activation and provide testable hypotheses for the development of new allosteric effectors to correct structural and functional defects in PAH.
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Affiliation(s)
- Yunhui Ge
- From the Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Elias Borne
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and
| | - Shannon Stewart
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and
| | - Michael R Hansen
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and
| | - Emilia C Arturo
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and.,Drexel University College of Medicine, Philadelphia, Pennsylvania 19129
| | - Eileen K Jaffe
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania 19111, and
| | - Vincent A Voelz
- From the Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
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20
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Three novel variants (p.Glu178Lys, p.Val245Met, p.Ser250Phe) of the phenylalanine hydroxylase (PAH) gene impair protein expression and function in vitro. Gene 2018; 668:135-139. [PMID: 29653233 DOI: 10.1016/j.gene.2018.03.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/10/2018] [Accepted: 03/26/2018] [Indexed: 11/21/2022]
Abstract
Phenylketonuria (PKU) is the most common inherited metabolic disease, an autosomal recessive disorder affecting >10,000 newborns each year globally. It can be caused by over 1000 different naturally occurring mutations in the phenylalanine hydroxylase (PAH) gene. We analyzed three novel naturally occurring PAH gene variants: p.Glu178Lys (c.532G>A), p.Val245Met (c.733G>A) and p.Ser250Phe (c.749C>T). The mutant effect on the PAH enzyme structure and function was predicted by bioinformatics software. Vectors expressing the corresponding PAH variants were generated for expression in E. coli and in HEK293T cells. The RNA expression of the three PAH variants was measured by quantitative reverse transcription polymerase chain reaction (RT-qPCR). The mutant PAH protein levels were determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), western blot and enzyme-linked immunosorbent assay (ELISA). All three variants were predicted to be pathogenic by bioinformatics analysis. The transcription of the three PAH variants was similar to the wild type PAH gene in HEK293T cells. In contrast, the levels of mutant PAH proteins decreased significantly compared to the wild type control, in both E. coli and HEK293T cells. Our results indicate that the three novel PAH gene variants (p.Glu178Lys, p.Val245Met, p.Ser250Phe) impair PAH protein expression and function in prokaryotic and eukaryotic cells.
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Blau N, Martinez A, Hoffmann GF, Thöny B. DNAJC12 deficiency: A new strategy in the diagnosis of hyperphenylalaninemias. Mol Genet Metab 2018; 123:1-5. [PMID: 29174366 DOI: 10.1016/j.ymgme.2017.11.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 01/17/2023]
Abstract
Patients with hyperphenylalaninemia (HPA) are detected through newborn screening for phenylketonuria (PKU). HPA is known to be caused by deficiencies of the enzyme phenylalanine hydroxylase (PAH) or its cofactor tetrahydrobiopterin (BH4). Current guidelines for the differential diagnosis of HPA would, however, miss a recently described DNAJC12 deficiency. The co-chaperone DNAJC12 is, together with the 70kDa heat shock protein (HSP70), responsible for the proper folding of PAH. All DNAJC12-deficient patients investigated to date responded to a challenge with BH4 by lowering their blood phenylalanine levels. In addition, the patients presented with low levels of biogenic amine in CSF and responded to supplementation with BH4, L-dopa/carbidopa and 5-hydroxytryptophan. The phenotypic spectrum ranged from mild autistic features or hyperactivity to severe intellectual disability, dystonia and parkinsonism. Late diagnosis result in permanent neurological disability, while early diagnosed and treated patients develop normally. Molecular diagnostics for DNAJC12 variants are thus mandatory in all patients in which deficiencies of PAH and BH4 are genetically excluded.
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Affiliation(s)
- Nenad Blau
- Dietmar-Hopp-Metabolic Center, University Children's Hospital, Heidelberg, Germany.
| | - Aurora Martinez
- Department of Biomedicine and K.G. Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Georg F Hoffmann
- Dietmar-Hopp-Metabolic Center, University Children's Hospital, Heidelberg, Germany
| | - Beat Thöny
- Division of Metabolism, University Children's Hospital Zürich, Zürich, Switzerland
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