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Rostampour N, Dalili S, Moravej H, Afshar Z, Yazdani N, Mousavi ST, Rostami P, Zamanfar D, Yahay M, Nikravesh A, Beyzaei Z, Davoodi MA, Sedaghat A, Hakemzadeh T, Talea A. Comprehensive Iranian guidelines for the diagnosis and management of maple syrup urine disease: an evidence- and consensus- based approach. Orphanet J Rare Dis 2025; 20:8. [PMID: 39773751 PMCID: PMC11707931 DOI: 10.1186/s13023-025-03533-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 12/27/2024] [Indexed: 01/11/2025] Open
Abstract
Maple Syrup Urine Disease (MSUD) disease is a defect in the function of the Branched-chain 2-ketoacid dehydrogenase complex (BCKDH). It is caused by pathogenic biallelic variants in BCKDHA, BCKA decarboxylase, or dihydrolipoamide dehydrogenase. The brain is the major organ involved in MSUD. MSUD happens in about 1 in 86,800 to 185,000 live births. According to some diversity in the management of Iranian patients with MSUD, the development of a national guideline is essential. This guideline is provided through a literature search on articles in PubMed, Scopus, Web of Sciences, Cochrane, and Embase databases from 2001 to 2022 accompanied by a consensus of physicians of different centers in Iran who are experts in the diagnosis and management of this disease. This article considers pathogenesis, epidemiology, clinical manifestations, diagnosis, treatment, and monitoring of MSUD patients with limited recourse.
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Affiliation(s)
- Noushin Rostampour
- Liver Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Setila Dalili
- Pediatric Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Hossein Moravej
- Neonatal Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Zhila Afshar
- Department of Pediatrics Endocrinology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negar Yazdani
- Community Based Psychiatric Care Research Center, School of Nursing and Midwifery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyedeh Tahereh Mousavi
- Assisstant Professor of Pediatrics Endocrinology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Parastoo Rostami
- Division of Endocrinology and Metabolism, Department of Pediatrics, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Daniel Zamanfar
- Diabetic Research Center, Mazandaran University of Medical Sciences, Mazandaran, Iran
| | - Maryam Yahay
- Department of Clinical Nutrition Food Sciences & Technology, School of Nutrition & Food Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abdolhossein Nikravesh
- Department of Pediatric Endocrinology & Metabolism, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Zahra Beyzaei
- Shiraz Transplant Research Center (STRC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Ahangar Davoodi
- Department of Pediatric Endocrinology & Metabolism, Arak University of Medical Sciences, Clinical Research Development Center of Amirkabir Hospital, Arak, Iran
| | - Atefeh Sedaghat
- Department of Pediatrics Endocrinology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Tahora Hakemzadeh
- Pediatric Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Ali Talea
- Pediatric Endocrinologist, Metabolic Disorders Research Center, Molecular-cellular Endocrinology & Metabolism Research Institute, Tehran University of medical Sciences, Tehran, Iran
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Ruiz-Pozo VA, Guevara-Ramírez P, Paz-Cruz E, Tamayo-Trujillo R, Cadena-Ullauri S, Frias-Toral E, Simancas-Racines D, Altuna-Roshkova Y, Reytor-González C, Zambrano AK. The role of the Mediterranean diet in prediabetes management and prevention: a review of molecular mechanisms and clinical outcomes. FOOD AGR IMMUNOL 2024; 35. [DOI: 10.1080/09540105.2024.2398042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/23/2024] [Indexed: 01/04/2025] Open
Affiliation(s)
- Viviana A. Ruiz-Pozo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Elius Paz-Cruz
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rafael Tamayo-Trujillo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Santiago Cadena-Ullauri
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | | | - Daniel Simancas-Racines
- Centro de Investigación de Salud Pública y Epidemiología Clínica (CISPEC), Universidad UTE, Quito, Ecuador
| | - Yekaterina Altuna-Roshkova
- Centro de Investigación de Salud Pública y Epidemiología Clínica (CISPEC), Universidad UTE, Quito, Ecuador
| | - Claudia Reytor-González
- Centro de Investigación de Salud Pública y Epidemiología Clínica (CISPEC), Universidad UTE, Quito, Ecuador
| | - Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
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3
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Yue JR, Liu YJ, Yuan SH, Sun H, Lou HY, Li YM, Guo HY, Liu ZH, Zhang FT, Zhai N, Zhang SQ, Bai JF, Zhang LP. Uncovering seed vigor responsive miRNA in hybrid wheat and its parents by deep sequencing. BMC Genomics 2024; 25:991. [PMID: 39438825 PMCID: PMC11515737 DOI: 10.1186/s12864-024-10878-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 10/08/2024] [Indexed: 10/25/2024] Open
Abstract
BACKGROUND Two-line hybrid wheat technology system is one way to harness wheat heterosis both domestically and internationally. Seed vigor is a crucial parameter for assessing seed quality, as enhanced seed vigor can lead to yield increments of over 20% to a certain extent. MicroRNAs (miRNAs) were known to participate in the development and vigor of seed in plants, but its impact on seed vigor in two-line hybrid wheat remains poorly elucidated. RESULTS The hybrid (BS1453/11GF5135) wheat exhibited superiority in seed vigor and anti-aging capacity, compared to its male parent (11GF5135, MP) and female parent (BS1453, FP). We identified four miRNAs associated with seed vigor, all of which are novel miRNAs. The majority of targets of miRNAs were related to ubiquitin ligases, kinases, sucrose synthases and hydrolases, involving in starch and sucrose metabolism, hydrolysis, catalysis, plant hormone signal transduction, and other pathways, which played crucial roles in seed development. Additionally, we also found miR531 was differentially expressed in both male parent and hybrid, and its target gene was a component of the E1 subunit of α-ketoate dehydrogenase complex, which interacted with dihydrolipoamide acetyltransferase (E2) and dihydrolipoyl dehydrogenase (E3). Finally, We established a presumptive interaction model to speculate the relationship of miR531 and seed vigor. CONCLUSIONS This study analyzed the seed vigor of two-line hybrid wheat, and screened seed vigor-related miRNAs. Meanwhile speculated the genetic relationship of hybrid and parents, in terms of miRNAs. Consequently, the present study provides new insights into the miRNA-mediated gene and protein interaction network that regulates seed vigor. These findings hold significance for enhancing the yield and quality of two-line hybrid wheat, facilitating its future applications.
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Affiliation(s)
- Jie-Ru Yue
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yong-Jie Liu
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shao-Hua Yuan
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hui Sun
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hong-Yao Lou
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yan-Mei Li
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hao-Yu Guo
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Zi-Han Liu
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Feng-Ting Zhang
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Nuo Zhai
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Sheng-Quan Zhang
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Jian-Fang Bai
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Li-Ping Zhang
- Institute of Hybrid Wheat, Beijing Key Laboratory of Molecular Genetics in Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Fries BD, Hummon AB. FAS Inhibited Proteomics and Phosphoproteomics Profiling of Colorectal Cancer Spheroids Shows Activation of Ferroptotic Death Mechanism. J Proteome Res 2024; 23:3904-3916. [PMID: 39079039 DOI: 10.1021/acs.jproteome.4c00252] [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] [Indexed: 09/07/2024]
Abstract
Colorectal cancer (CRC) is projected to become the third most diagnosed and third most fatal cancer in the United States by 2024, with early onset CRC on the rise. Research is constantly underway to discover novel therapeutics for the treatment of various cancers to improve patient outcomes and survival. Fatty acid synthase (FAS) has become a druggable target of interest for the treatment of many different cancers. One such inhibitor, TVB-2640, has gained popularity for its high specificity for FAS and has entered a phase 1 clinical trial for the treatment of solid tumors. However, the distinct molecular differences that occur upon inhibition of FAS have yet to be understood. Here, we conduct proteomics and phosphoproteomics analyses on HCT 116 and HT-29 CRC spheroids inhibited with either a generation 1 (cerulenin) or generation 2 (TVB-2640) FAS inhibitor. Proteins involved in lipid metabolism and cellular respiration were altered in abundance. It was also observed that proteins involved in ferroptosis─an iron mediated form of cell death─were altered. These results show that HT-29 spheroids exposed to cerulenin or TVB-2640 are undergoing a ferroptotic death mechanism. The data were deposited to the ProteomeXchange Consortium via the PRIDE repository with the identifier PXD050987.
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Affiliation(s)
- Brian D Fries
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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5
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Tresbach RH, Sperb-Ludwig F, Ligabue-Braun R, Bitencourt FHD, Tonon T, Souza CFMD, Poswar FDO, Leite MEDQ, Amorim T, Porta G, Seda Neto J, Miura IK, Steiner CE, Martins AM, Pessoa ALS, Ribeiro EM, Schwartz IVD. Maple syrup urine disease diagnosis in Brazilian patients by massive parallel sequencing. Mol Genet Metab 2024; 143:108569. [PMID: 39270351 DOI: 10.1016/j.ymgme.2024.108569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024]
Abstract
Biallelic pathogenic variants cause maple syrup urine disease (MSUD) in one of the branched-chain α-keto acid dehydrogenase (BCKDH) complex genes (BCKDHA, BCKDHB, DBT, DLD, and PPM1K) leading to the accumulation of leucine, isoleucine, and valine. This study aimed to perform a molecular diagnosis of Brazilian patients with MSUD using gene panels and massive parallel sequencing. Eighteen Brazilian patients with a biochemical diagnosis of MSUD were analyzed by massive parallel sequencing in the Ion PGM Torrent Server using a gene panel with the BCKDHA, BCKDHB, and DBT genes. The American College of Medical Genetics and Genomics guidelines were used to determine variant pathogenicity. Thirteen patients had both variants found by massive parallel sequencing, whereas 3 patients had only one variant found. In 2 patients, the variants were not found by this analysis. These 5 patients required additional Sanger sequencing to confirm their genotype. Twenty-five pathogenic variants were identified in the 3 MSUD-related genes (BCKDHA, BCKDHB, and DBT). Most variants were present in the BCKDHB gene, and no common variants were found. Nine novel variants were observed: c.922 A > G, c.964C > A, and c.1237 T > C in the BCKDHA gene; and c.80_90dup, c.384delA, c.478 A > T, c.528C > G, c.977 T > C, and c.1039-2 A > G in the BCKDHB gene. All novel variants were classified as pathogenic. Molecular modeling of the novel variants indicated that the binding of monomers was affected in the BCKDH complex tetramer, which could lead to a change in the stability and activity of the enzyme. Massive parallel sequencing with targeted gene panels seems to be a cost-effective method that can provide a molecular diagnosis of MSUD.
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Affiliation(s)
- Rafael Hencke Tresbach
- BRAIN Laboratory (Basic Research and Advanced Investigations in Neurosciences), Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fernanda Sperb-Ludwig
- BRAIN Laboratory (Basic Research and Advanced Investigations in Neurosciences), Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Graduate Program in Biological Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Fernanda Hendges de Bitencourt
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Clinical Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Tássia Tonon
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Clinical Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Carolina Fischinger Moura de Souza
- Clinical Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Fabiano de Oliveira Poswar
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Maria Efigênia de Queiroz Leite
- Newborn Screening Reference Center - Association of Parents and Friends of People with Disabilities (APAE), Salvador, BA, Brazil
| | - Tatiana Amorim
- Newborn Screening Reference Center - Association of Parents and Friends of People with Disabilities (APAE), Salvador, BA, Brazil
| | - Gilda Porta
- Pedro de Alcântara Children's Institute - Hospital das Clínicas, Medical School, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - João Seda Neto
- Department of Hepatology and Liver Transplantation, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Irene Kazumi Miura
- Department of Hepatology and Liver Transplantation, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Carlos Eduardo Steiner
- Department of Translational Medicine, School of Medical Sciences, Universidade Estadual de Campinas (Unicamp), Campinas, SP, Brazil
| | - Ana Maria Martins
- Reference Center for Inborn Errors of Metabolism, Universidade Federal de São Paulo (Unifesp), São Paulo, SP, Brazil
| | - André Luiz Santos Pessoa
- Hospital Infantil Albert Sabin, Fortaleza, CE, Brazil; Department of Pediatrics, Universidade Estadual do Ceará (UECE), Fortaleza, CE, Brazil
| | | | - Ida Vanessa Doederlein Schwartz
- BRAIN Laboratory (Basic Research and Advanced Investigations in Neurosciences), Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Clinical Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; InRaras, National Institute of Rare Diseases, Brazil
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6
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Mailloux RJ. The emerging importance of the α-keto acid dehydrogenase complexes in serving as intracellular and intercellular signaling platforms for the regulation of metabolism. Redox Biol 2024; 72:103155. [PMID: 38615490 PMCID: PMC11021975 DOI: 10.1016/j.redox.2024.103155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024] Open
Abstract
The α-keto acid dehydrogenase complex (KDHc) class of mitochondrial enzymes is composed of four members: pyruvate dehydrogenase (PDHc), α-ketoglutarate dehydrogenase (KGDHc), branched-chain keto acid dehydrogenase (BCKDHc), and 2-oxoadipate dehydrogenase (OADHc). These enzyme complexes occupy critical metabolic intersections that connect monosaccharide, amino acid, and fatty acid metabolism to Krebs cycle flux and oxidative phosphorylation (OxPhos). This feature also imbues KDHc enzymes with the heightened capacity to serve as platforms for propagation of intracellular and intercellular signaling. KDHc enzymes serve as a source and sink for mitochondrial hydrogen peroxide (mtH2O2), a vital second messenger used to trigger oxidative eustress pathways. Notably, deactivation of KDHc enzymes through reversible oxidation by mtH2O2 and other electrophiles modulates the availability of several Krebs cycle intermediates and related metabolites which serve as powerful intracellular and intercellular messengers. The KDHc enzymes also play important roles in the modulation of mitochondrial metabolism and epigenetic programming in the nucleus through the provision of various acyl-CoAs, which are used to acylate proteinaceous lysine residues. Intriguingly, nucleosomal control by acylation is also achieved through PDHc and KGDHc localization to the nuclear lumen. In this review, I discuss emerging concepts in the signaling roles fulfilled by the KDHc complexes. I highlight their vital function in serving as mitochondrial redox sensors and how this function can be used by cells to regulate the availability of critical metabolites required in cell signaling. Coupled with this, I describe in detail how defects in KDHc function can cause disease states through the disruption of cell redox homeodynamics and the deregulation of metabolic signaling. Finally, I propose that the intracellular and intercellular signaling functions of the KDHc enzymes are controlled through the reversible redox modification of the vicinal lipoic acid thiols in the E2 subunit of the complexes.
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Affiliation(s)
- Ryan J Mailloux
- School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.
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7
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Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [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] [Indexed: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
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Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
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8
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Bunik V. The Therapeutic Potential of Vitamins B1, B3 and B6 in Charcot-Marie-Tooth Disease with the Compromised Status of Vitamin-Dependent Processes. BIOLOGY 2023; 12:897. [PMID: 37508330 PMCID: PMC10376249 DOI: 10.3390/biology12070897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023]
Abstract
Understanding the molecular mechanisms of neurological disorders is necessary for the development of personalized medicine. When the diagnosis considers not only the disease symptoms, but also their molecular basis, treatments tailored to individual patients may be suggested. Vitamin-responsive neurological disorders are induced by deficiencies in vitamin-dependent processes. These deficiencies may occur due to genetic impairments of proteins whose functions are involved with the vitamins. This review considers the enzymes encoded by the DHTKD1, PDK3 and PDXK genes, whose mutations are observed in patients with Charcot-Marie-Tooth (CMT) disease. The enzymes bind or produce the coenzyme forms of vitamins B1 (thiamine diphosphate, ThDP) and B6 (pyridoxal-5'-phosphate, PLP). Alleviation of such disorders through administration of the lacking vitamin or its derivative calls for a better introduction of mechanistic knowledge to medical diagnostics and therapies. Recent data on lower levels of the vitamin B3 derivative, NAD+, in the blood of patients with CMT disease vs. control subjects are also considered in view of the NAD-dependent mechanisms of pathological axonal degeneration, suggesting the therapeutic potential of vitamin B3 in these patients. Thus, improved diagnostics of the underlying causes of CMT disease may allow patients with vitamin-responsive disease forms to benefit from the administration of the vitamins B1, B3, B6, their natural derivatives, or their pharmacological forms.
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Affiliation(s)
- Victoria Bunik
- Belozersky Institute of Physicochemical Biology, Department of Biokinetics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
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9
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Blair MC, Neinast MD, Jang C, Chu Q, Jung JW, Axsom J, Bornstein MR, Thorsheim C, Li K, Hoshino A, Yang S, Roth Flach RJ, Zhang BB, Rabinowitz JD, Arany Z. Branched-chain amino acid catabolism in muscle affects systemic BCAA levels but not insulin resistance. Nat Metab 2023; 5:589-606. [PMID: 37100997 PMCID: PMC10278155 DOI: 10.1038/s42255-023-00794-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/29/2023] [Indexed: 04/28/2023]
Abstract
Elevated levels of plasma branched-chain amino acids (BCAAs) have been associated with insulin resistance and type 2 diabetes since the 1960s. Pharmacological activation of branched-chain α-ketoacid dehydrogenase (BCKDH), the rate-limiting enzyme of BCAA oxidation, lowers plasma BCAAs and improves insulin sensitivity. Here we show that modulation of BCKDH in skeletal muscle, but not liver, affects fasting plasma BCAAs in male mice. However, despite lowering BCAAs, increased BCAA oxidation in skeletal muscle does not improve insulin sensitivity. Our data indicate that skeletal muscle controls plasma BCAAs, that lowering fasting plasma BCAAs is insufficient to improve insulin sensitivity and that neither skeletal muscle nor liver account for the improved insulin sensitivity seen with pharmacological activation of BCKDH. These findings suggest potential concerted contributions of multiple tissues in the modulation of BCAA metabolism to alter insulin sensitivity.
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Affiliation(s)
- Megan C Blair
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael D Neinast
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Qingwei Chu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jae Woo Jung
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessie Axsom
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marc R Bornstein
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chelsea Thorsheim
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Steven Yang
- Washington University School of Medicine, St Louis, MO, USA
| | | | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Zoltan Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Branched chain amino acids catabolism as a source of new drug targets in pathogenic protists. Exp Parasitol 2023; 249:108499. [PMID: 36898495 DOI: 10.1016/j.exppara.2023.108499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/11/2023]
Abstract
Leucine, isoleucine, and valine, collectively termed Branched Chain Amino Acids (BCAA), are hydrophobic amino acids (AAs) and are essential for most eukaryotes since in these organisms they cannot be biosynthesized and must be supplied by the diet. These AAs are structurally relevant for muscle cells and, of course, important for the protein synthesis process. The metabolism of BCAA and its participation in different biological processes in mammals have been relatively well described. However, for other organisms as pathogenic parasites, the literature is really scarce. Here we review the BCAA catabolism, compile evidence on their relevance for pathogenic eukaryotes with special emphasis on kinetoplastids and highlight unique aspects of this underrated pathway.
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Liu S, Kormos BL, Knafels JD, Sahasrabudhe PV, Rosado A, Sommese RF, Reyes AR, Ward J, Roth Flach RJ, Wang X, Buzon LM, Reese MR, Bhattacharya SK, Omoto K, Filipski KJ. Structural studies identify angiotensin II receptor blocker-like compounds as branched-chain ketoacid dehydrogenase kinase inhibitors. J Biol Chem 2023; 299:102959. [PMID: 36717078 PMCID: PMC9976451 DOI: 10.1016/j.jbc.2023.102959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/30/2023] Open
Abstract
The mammalian mitochondrial branched-chain ketoacid dehydrogenase (BCKD) complex is a multienzyme complex involved in the catabolism of branched-chain amino acids. BCKD is regulated by the BCKD kinase, or BCKDK, which binds to the E2 subunit of BCKD, phosphorylates its E1 subunit, and inhibits enzymatic activity. Inhibition of the BCKD complex results in increased levels of branched-chain amino acids and branched-chain ketoacids, and this buildup has been associated with heart failure, type 2 diabetes mellitus, and nonalcoholic fatty liver disease. To find BCKDK inhibitors for potential treatment of these diseases, we performed both NMR and virtual fragment screening and identified tetrazole-bearing fragments that bind BCKDK at multiple sites. Through structure-based virtual screening expanding from these fragments, the angiotensin receptor blocker class antihypertension drugs and angiotensin receptor blocker-like compounds were discovered to be potent BCKDK inhibitors, suggesting potential new avenues for heart failure treatment combining BCKDK inhibition and antihypertension.
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Affiliation(s)
- Shenping Liu
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA.
| | | | | | | | - Amy Rosado
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA
| | | | - Allan R Reyes
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Jessica Ward
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, Massachusetts, USA
| | | | - Xiaochun Wang
- Medicine Design, Pfizer Inc, Groton, Connecticut, USA
| | | | | | | | - Kiyoyuki Omoto
- Medicine Design, Pfizer Inc, Cambridge, Massachusetts, USA
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12
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Turberville A, Semple H, Davies G, Ivanov D, Holdgate GA. A perspective on the discovery of enzyme activators. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:419-427. [PMID: 36089246 DOI: 10.1016/j.slasd.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022]
Abstract
Enzyme activation remains a largely under-represented and poorly exploited area of drug discovery despite some key literature examples of the successful application of enzyme activators by various mechanisms and their importance in a wide range of therapeutic interventions. Here we describe the background nomenclature, present the current position of this field of drug discovery and discuss the challenges of hit identification for enzyme activation, as well as our perspectives on the approaches needed to overcome these challenges in early drug discovery.
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Affiliation(s)
- Antonia Turberville
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Hannah Semple
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Gareth Davies
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Delyan Ivanov
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Geoffrey A Holdgate
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom.
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13
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Liu S, Xia X, Zhen J, Li Z, Zhou ZH. Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney. Cell Discov 2022; 8:126. [PMID: 36414632 PMCID: PMC9681731 DOI: 10.1038/s41421-022-00487-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/20/2022] [Indexed: 11/23/2022] Open
Abstract
The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.
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Affiliation(s)
- Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Xian Xia
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - James Zhen
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Zihang Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
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14
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Gokcan H, Bedoyan JK, Isayev O. Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function. J Chem Inf Model 2022; 62:3463-3475. [PMID: 35797142 DOI: 10.1021/acs.jcim.2c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyruvate dehydrogenase complex (PDC) deficiency is a major cause of primary lactic acidemia resulting in high morbidity and mortality, with limited therapeutic options. The E1 component of the mitochondrial multienzyme PDC (PDC-E1) is a symmetric dimer of heterodimers (αβ/α'β') encoded by the PDHA1 and PDHB genes, with two symmetric active sites each consisting of highly conserved phosphorylation loops A and B. PDHA1 mutations are responsible for 82-88% of cases. Greater than 85% of E1α residues with disease-causing missense mutations (DMMs) are solvent-inaccessible, with ∼30% among those involved in subunit-subunit interface contact (SSIC). We performed molecular dynamics simulations of wild-type (WT) PDC-E1 and E1 variants with E1α DMMs at R349 and W185 (residues involved in SSIC), to investigate their impact on human PDC-E1 structure. We evaluated the change in E1 structure and dynamics and examined their implications on E1 function with the specific DMMs. We found that the dynamics of phosphorylation Loop A, which is crucial for E1 biological activity, changes with DMMs that are at least about 15 Å away. Because communication is essential for PDC-E1 activity (with alternating active sites), we also investigated the possible communication network within WT PDC-E1 via centrality analysis. We observed that DMMs altered/disrupted the communication network of PDC-E1. Collectively, these results indicate allosteric effect in PDC-E1, with implications for the development of novel small-molecule therapeutics for specific recurrent E1α DMMs such as replacements of R349 responsible for ∼10% of PDC deficiency due to E1α DMMs.
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Affiliation(s)
- Hatice Gokcan
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jirair K Bedoyan
- Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224, United States.,Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, United States
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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15
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Palmieri F, Monné M, Fiermonte G, Palmieri L. Mitochondrial transport and metabolism of the vitamin B-derived cofactors thiamine pyrophosphate, coenzyme A, FAD and NAD + , and related diseases: A review. IUBMB Life 2022; 74:592-617. [PMID: 35304818 PMCID: PMC9311062 DOI: 10.1002/iub.2612] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 01/19/2023]
Abstract
Multiple mitochondrial matrix enzymes playing key roles in metabolism require cofactors for their action. Due to the high impermeability of the mitochondrial inner membrane, these cofactors need to be synthesized within the mitochondria or be imported, themselves or one of their precursors, into the organelles. Transporters belonging to the protein family of mitochondrial carriers have been identified to transport the coenzymes: thiamine pyrophosphate, coenzyme A, FAD and NAD+ , which are all structurally similar to nucleotides and derived from different B-vitamins. These mitochondrial cofactors bind more or less tightly to their enzymes and, after having been involved in a specific reaction step, are regenerated, spontaneously or by other enzymes, to return to their active form, ready for the next catalysis round. Disease-causing mutations in the mitochondrial cofactor carrier genes compromise not only the transport reaction but also the activity of all mitochondrial enzymes using that particular cofactor and the metabolic pathways in which the cofactor-dependent enzymes are involved. The mitochondrial transport, metabolism and diseases of the cofactors thiamine pyrophosphate, coenzyme A, FAD and NAD+ are the focus of this review.
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Affiliation(s)
- Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- Department of SciencesUniversity of BasilicataPotenzaItaly
| | - Giuseppe Fiermonte
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
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16
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Duarte IF, Caio J, Moedas MF, Rodrigues LA, Leandro AP, Rivera IA, Silva MFB. Dihydrolipoamide dehydrogenase, pyruvate oxidation, and acetylation-dependent mechanisms intersecting drug iatrogenesis. Cell Mol Life Sci 2021; 78:7451-7468. [PMID: 34718827 PMCID: PMC11072406 DOI: 10.1007/s00018-021-03996-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 10/19/2022]
Abstract
In human metabolism, pyruvate dehydrogenase complex (PDC) is one of the most intricate and large multimeric protein systems representing a central hub for cellular homeostasis. The worldwide used antiepileptic drug valproic acid (VPA) may potentially induce teratogenicity or a mild to severe hepatic toxicity, where the underlying mechanisms are not completely understood. This work aims to clarify the mechanisms that intersect VPA-related iatrogenic effects to PDC-associated dihydrolipoamide dehydrogenase (DLD; E3) activity. DLD is also a key enzyme of α-ketoglutarate dehydrogenase, branched-chain α-keto acid dehydrogenase, α-ketoadipate dehydrogenase, and the glycine decarboxylase complexes. The molecular effects of VPA will be reviewed underlining the data that sustain a potential interaction with DLD. The drug-associated effects on lipoic acid-related complexes activity may induce alterations on the flux of metabolites through tricarboxylic acid cycle, branched-chain amino acid oxidation, glycine metabolism and other cellular acetyl-CoA-connected reactions. The biotransformation of VPA involves its complete β-oxidation in mitochondria causing an imbalance on energy homeostasis. The drug consequences as histone deacetylase inhibitor and thus gene expression modulator have also been recognized. The mitochondrial localization of PDC is unequivocal, but its presence and function in the nucleus were also demonstrated, generating acetyl-CoA, crucial for histone acetylation. Bridging metabolism and epigenetics, this review gathers the evidence of VPA-induced interference with DLD or PDC functions, mainly in animal and cellular models, and highlights the uncharted in human. The consequences of this interaction may have significant impact either in mitochondrial or in nuclear acetyl-CoA-dependent processes.
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Affiliation(s)
- I F Duarte
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - J Caio
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - M F Moedas
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - L A Rodrigues
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - A P Leandro
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - I A Rivera
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - M F B Silva
- The Research Institute for Medicines (iMed.ULisboa), Metabolism and Genetics Group, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.
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17
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Cui J, Tcherkez G. Potassium dependency of enzymes in plant primary metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:522-530. [PMID: 34174657 DOI: 10.1016/j.plaphy.2021.06.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Potassium is a macroelement essential to many aspects of plant life, such as photosynthesis, phloem transport or cellular electrochemistry. Many enzymes in animals or microbes are known to be stimulated or activated by potassium (K+ ions). Several plant enzymes are also strictly K+-dependent, and this can be critical when plants are under K deficiency and thus intracellular K+ concentration is low. Although metabolic effects of low K conditions have been documented, there is presently no review focusing on roles of K+ for enzyme catalysis or activation in plants. In this mini-review, we compile the current knowledge on K+-requirement of plant enzymes and take advantage of structural data to present biochemical roles of K+. This information is instrumental to explain direct effects of low K+ content on metabolism and this is illustrated with recent metabolomics data.
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Affiliation(s)
- Jing Cui
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, 2601, Canberra, Australia; Institut de Recherche en Horticulture et Semences, INRAe Angers, Université d'Angers, 42 rue Georges Morel, 49070, Beaucouzé, France.
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18
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Thiel CS, Vahlensieck C, Bradley T, Tauber S, Lehmann M, Ullrich O. Metabolic Dynamics in Short- and Long-Term Microgravity in Human Primary Macrophages. Int J Mol Sci 2021; 22:ijms22136752. [PMID: 34201720 PMCID: PMC8269311 DOI: 10.3390/ijms22136752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/24/2022] Open
Abstract
Microgravity acts on cellular systems on several levels. Cells of the immune system especially react rapidly to changes in gravity. In this study, we performed a correlative metabolomics analysis on short-term and long-term microgravity effects on primary human macrophages. We could detect an increased amino acid concentration after five minutes of altered gravity, that was inverted after 11 days of microgravity. The amino acids that reacted the most to changes in gravity were tightly clustered. The observed effects indicated protein degradation processes in microgravity. Further, glucogenic and ketogenic amino acids were further degraded to Glucose and Ketoleucine. The latter is robustly accumulated in short-term and long-term microgravity but not in hypergravity. We detected highly dynamic and also robust adaptative metabolic changes in altered gravity. Metabolomic studies could contribute significantly to the understanding of gravity-induced integrative effects in human cells.
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Affiliation(s)
- Cora S. Thiel
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
- Correspondence: (C.S.T.); (O.U.)
| | - Christian Vahlensieck
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
| | - Timothy Bradley
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
| | - Svantje Tauber
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
| | - Martin Lehmann
- Biocenter LMU Muenchen, Department of Biology I–Botany, Großhaderner Strasse 2–4, 82152 Planegg-Martinsried, Germany;
| | - Oliver Ullrich
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
- Space Biotechnology, Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
- Space Medicine, Ernst-Abbe-Hochschule (EAH) Jena, Department of Industrial Engineering, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center (KSC), 505 Odyssey Way, Exploration Park, FL 32953, USA
- Correspondence: (C.S.T.); (O.U.)
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19
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Nagy B, Polak M, Ozohanics O, Zambo Z, Szabo E, Hubert A, Jordan F, Novaček J, Adam-Vizi V, Ambrus A. Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure. Biochim Biophys Acta Gen Subj 2021; 1865:129889. [PMID: 33684457 DOI: 10.1016/j.bbagen.2021.129889] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/05/2021] [Accepted: 03/02/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND The human mitochondrial alpha-ketoglutarate dehydrogenase complex (hKGDHc) converts KG to succinyl-CoA and NADH. Malfunction of and reactive oxygen species generation by the hKGDHc as well as its E1-E2 subcomplex are implicated in neurodegenerative disorders, ischemia-reperfusion injury, E3-deficiency and cancers. METHODS We performed cryo-EM, cross-linking mass spectrometry (CL-MS) and molecular modeling analyses to determine the structure of the E2 component of the hKGDHc (hE2k); hE2k transfers a succinyl group to CoA and forms the structural core of hKGDHc. We also assessed the overall structure of the hKGDHc by negative-stain EM and modeling. RESULTS We report the 2.9 Å resolution cryo-EM structure of the hE2k component. The cryo-EM map comprises density for hE2k residues 151-386 - the entire (inner) core catalytic domain plus a few additional residues -, while residues 1-150 are not observed due to the inherent flexibility of the N-terminal region. The structure of the latter segment was also determined by CL-MS and homology modeling. Negative-stain EM on in vitro assembled hKGDHc and previous data were used to build a putative overall structural model of the hKGDHc. CONCLUSIONS The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 × 3 type) assembly. Each lipoyl domain is oriented towards the core domain of an adjacent chain in the hE2k homotrimer. hE1k and hE3 are most likely tethered at the edges and faces, respectively, of the cubic hE2k assembly. GENERAL SIGNIFICANCE The revealed structural information will support the future pharmacologically targeting of the hKGDHc.
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Affiliation(s)
- Balint Nagy
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Martin Polak
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Oliver Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsofia Zambo
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Eszter Szabo
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Agnes Hubert
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Jiří Novaček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vera Adam-Vizi
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary.
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20
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Whole-body metabolic fate of branched-chain amino acids. Biochem J 2021; 478:765-776. [PMID: 33626142 DOI: 10.1042/bcj20200686] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
Oxidation of branched-chain amino acids (BCAAs) is tightly regulated in mammals. We review here the distribution and regulation of whole-body BCAA oxidation. Phosphorylation and dephosphorylation of the rate-limiting enzyme, branched-chain α-ketoacid dehydrogenase complex directly regulates BCAA oxidation, and various other indirect mechanisms of regulation also exist. Most tissues throughout the body are capable of BCAA oxidation, and the flux of oxidative BCAA disposal in each tissue is influenced by three key factors: 1. tissue-specific preference for BCAA oxidation relative to other fuels, 2. the overall oxidative activity of mitochondria within a tissue, and 3. total tissue mass. Perturbations in BCAA oxidation have been implicated in many disease contexts, underscoring the importance of BCAA homeostasis in overall health.
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21
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Ježek P, Holendová B, Jabůrek M, Tauber J, Dlasková A, Plecitá-Hlavatá L. The Pancreatic β-Cell: The Perfect Redox System. Antioxidants (Basel) 2021; 10:antiox10020197. [PMID: 33572903 PMCID: PMC7912581 DOI: 10.3390/antiox10020197] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic β-cell insulin secretion, which responds to various secretagogues and hormonal regulations, is reviewed here, emphasizing the fundamental redox signaling by NADPH oxidase 4- (NOX4-) mediated H2O2 production for glucose-stimulated insulin secretion (GSIS). There is a logical summation that integrates both metabolic plus redox homeostasis because the ATP-sensitive K+ channel (KATP) can only be closed when both ATP and H2O2 are elevated. Otherwise ATP would block KATP, while H2O2 would activate any of the redox-sensitive nonspecific calcium channels (NSCCs), such as TRPM2. Notably, a 100%-closed KATP ensemble is insufficient to reach the -50 mV threshold plasma membrane depolarization required for the activation of voltage-dependent Ca2+ channels. Open synergic NSCCs or Cl- channels have to act simultaneously to reach this threshold. The resulting intermittent cytosolic Ca2+-increases lead to the pulsatile exocytosis of insulin granule vesicles (IGVs). The incretin (e.g., GLP-1) amplification of GSIS stems from receptor signaling leading to activating the phosphorylation of TRPM channels and effects on other channels to intensify integral Ca2+-influx (fortified by endoplasmic reticulum Ca2+). ATP plus H2O2 are also required for branched-chain ketoacids (BCKAs); and partly for fatty acids (FAs) to secrete insulin, while BCKA or FA β-oxidation provide redox signaling from mitochondria, which proceeds by H2O2 diffusion or hypothetical SH relay via peroxiredoxin "redox kiss" to target proteins.
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22
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Marcet-Palacios M, Reyes-Serratos E, Gonshor A, Buck R, Lacy P, Befus AD. Structural and posttranslational analysis of human calcium-binding protein, spermatid-associated 1. J Cell Biochem 2020; 121:4945-4958. [PMID: 32692864 DOI: 10.1002/jcb.29824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 06/23/2020] [Indexed: 12/31/2022]
Abstract
Recently, we detected a novel biomarker in human saliva called calcium-binding protein, spermatid-associated 1 (CABS1). CABS1 protein had previously been described only in testis, and little was known of its characteristics other than it was considered a structurally disordered protein. Levels of human CABS1 (hCABS1) in saliva correlate with stress, whereas smaller sized forms of hCABS1 in saliva are associated with resilience to stress. Interestingly, hCABS1 also has an anti-inflammatory peptide sequence near its carboxyl terminus, similar to that of a rat prohormone, submandibular rat 1. We performed phylogenetic and sequence analysis of hCABS1. We found that from 72 CABS1 sequences currently annotated in the National Center for Biotechnology Information protein database, only 14 contain the anti-inflammatory domain "TxIFELL," all of which are primates. We performed structural unfoldability analysis using PONDER and FoldIndex and discovered three domains that are highly disordered. Predictions of three-dimensional structure of hCABS1 using RaptorX, IonCom, and I-TASSER software agreed with these findings. Predicted neutrophil elastase cleavage density also correlated with hCABS1 regions of high structural disorder. Ligand binding prediction identified Ca2+ , Mg2+ , Zn2+ , leucine, and thiamine pyrophosphate, a pattern observed in enzymes associated with energy metabolism and mitochondrial localization. These new observations on hCABS1 raise intriguing questions about the interconnection between the autonomic nervous system, stress, and the immune system. However, the precise molecular mechanisms involved in the complex biology of hCABS1 remain unclear. We provide a detailed in silico analysis of relevant aspects of the structure and function of hCABS1 and postulate extracellular and intracellular roles.
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Affiliation(s)
- Marcelo Marcet-Palacios
- Department of Medicine, Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
- Northern Alberta Institute of Technology, Biological Sciences, Edmonton, Alberta, Canada
| | - Eduardo Reyes-Serratos
- Department of Medicine, Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
| | | | - Robert Buck
- Fluids iQ Inc., Ottawa, Ontario, Canada
- GB Diagnostics, Kingman, Arizona
| | - Paige Lacy
- Department of Medicine, Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
| | - A D Befus
- Department of Medicine, Alberta Respiratory Centre, University of Alberta, Edmonton, Alberta, Canada
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23
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Amer M, Toogood H, Scrutton NS. Engineering nature for gaseous hydrocarbon production. Microb Cell Fact 2020; 19:209. [PMID: 33187524 PMCID: PMC7661322 DOI: 10.1186/s12934-020-01470-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
The development of sustainable routes to the bio-manufacture of gaseous hydrocarbons will contribute widely to future energy needs. Their realisation would contribute towards minimising over-reliance on fossil fuels, improving air quality, reducing carbon footprints and enhancing overall energy security. Alkane gases (propane, butane and isobutane) are efficient and clean-burning fuels. They are established globally within the transportation industry and are used for domestic heating and cooking, non-greenhouse gas refrigerants and as aerosol propellants. As no natural biosynthetic routes to short chain alkanes have been discovered, de novo pathways have been engineered. These pathways incorporate one of two enzymes, either aldehyde deformylating oxygenase or fatty acid photodecarboxylase, to catalyse the final step that leads to gas formation. These new pathways are derived from established routes of fatty acid biosynthesis, reverse β-oxidation for butanol production, valine biosynthesis and amino acid degradation. Single-step production of alkane gases in vivo is also possible, where one recombinant biocatalyst can catalyse gas formation from exogenously supplied short-chain fatty acid precursors. This review explores current progress in bio-alkane gas production, and highlights the potential for implementation of scalable and sustainable commercial bioproduction hubs.
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Affiliation(s)
- Mohamed Amer
- EPSRC/BBSRC Future Biomanufacturing Research Hub, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, BBSRC/EPSRC, The University of Manchester, Manchester, M1 7DN, UK
| | - Helen Toogood
- EPSRC/BBSRC Future Biomanufacturing Research Hub, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, BBSRC/EPSRC, The University of Manchester, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, BBSRC/EPSRC, The University of Manchester, Manchester, M1 7DN, UK.
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24
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Leandro J, Khamrui S, Wang H, Suebsuwong C, Nemeria NS, Huynh K, Moustakim M, Secor C, Wang M, Dodatko T, Stauffer B, Wilson CG, Yu C, Arkin MR, Jordan F, Sanchez R, DeVita RJ, Lazarus MB, Houten SM. Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex. ACS Chem Biol 2020; 15:2041-2047. [PMID: 32633484 DOI: 10.1021/acschembio.0c00114] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DHTKD1 is the E1 component of the 2-oxoadipate dehydrogenase complex, which is an enzyme involved in the catabolism of (hydroxy-)lysine and tryptophan. Mutations in DHTKD1 have been associated with 2-aminoadipic and 2-oxoadipic aciduria, Charcot-Marie-Tooth disease type 2Q and eosinophilic esophagitis, but the pathophysiology of these clinically distinct disorders remains elusive. Here, we report the identification of adipoylphosphonic acid and tenatoprazole as DHTKD1 inhibitors using targeted and high throughput screening, respectively. We furthermore elucidate the DHTKD1 crystal structure with thiamin diphosphate bound at 2.25 Å. We also report the impact of 10 disease-associated missense mutations on DHTKD1. Whereas the majority of the DHTKD1 variants displayed impaired folding or reduced thermal stability in combination with absent or reduced enzyme activity, three variants showed no abnormalities. Our work provides chemical and structural tools for further understanding of the function of DHTKD1 and its role in several human pathologies.
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Affiliation(s)
- João Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Susmita Khamrui
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Hui Wang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Chalada Suebsuwong
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Natalia S. Nemeria
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, New Jersey 07102, United States
| | - Khoi Huynh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Moses Moustakim
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Cody Secor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - May Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Brandon Stauffer
- Mount Sinai Genomics, Inc, Stamford, Connecticut 06902, United States
| | - Christopher G. Wilson
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Chunli Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Mount Sinai Genomics, Inc, Stamford, Connecticut 06902, United States
| | - Michelle R. Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, New Jersey 07102, United States
| | - Roberto Sanchez
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Robert J. DeVita
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Michael B. Lazarus
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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Metal-dependent Ser/Thr protein phosphatase PPM family: Evolution, structures, diseases and inhibitors. Pharmacol Ther 2020; 215:107622. [PMID: 32650009 DOI: 10.1016/j.pharmthera.2020.107622] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
Protein phosphatases and kinases control multiple cellular events including proliferation, differentiation, and stress responses through regulating reversible protein phosphorylation, the most important post-translational modification. Members of metal-dependent protein phosphatase (PPM) family, also known as PP2C phosphatases, are Ser/Thr phosphatases that bind manganese/magnesium ions (Mn2+/Mg2+) in their active center and function as single subunit enzymes. In mammals, there are 20 isoforms of PPM phosphatases: PPM1A, PPM1B, PPM1D, PPM1E, PPM1F, PPM1G, PPM1H, PPM1J, PPM1K, PPM1L, PPM1M, PPM1N, ILKAP, PDP1, PDP2, PHLPP1, PHLPP2, PP2D1, PPTC7, and TAB1, whereas there are only 8 in yeast. Phylogenetic analysis of the DNA sequences of vertebrate PPM isoforms revealed that they can be divided into 12 different classes: PPM1A/PPM1B/PPM1N, PPM1D, PPM1E/PPM1F, PPM1G, PPM1H/PPM1J/PPM1M, PPM1K, PPM1L, ILKAP, PDP1/PDP2, PP2D1/PHLPP1/PHLPP2, TAB1, and PPTC7. PPM-family members have a conserved catalytic core region, which contains the metal-chelating residues. The different isoforms also have isoform specific regions within their catalytic core domain and terminal domains, and these regions may be involved in substrate recognition and/or functional regulation of the phosphatases. The twenty mammalian PPM phosphatases are involved in regulating diverse cellular functions, such as cell cycle control, cell differentiation, immune responses, and cell metabolism. Mutation, overexpression, or deletion of the PPM phosphatase gene results in abnormal cellular responses, which lead to various human diseases. This review focuses on the structures and biological functions of the PPM-phosphatase family and their associated diseases. The development of specific inhibitors against the PPM phosphatase family as a therapeutic strategy will also be discussed.
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Bezerra GA, Foster WR, Bailey HJ, Hicks KG, Sauer SW, Dimitrov B, McCorvie TJ, Okun JG, Rutter J, Kölker S, Yue WW. Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism. IUCRJ 2020; 7:693-706. [PMID: 32695416 PMCID: PMC7340257 DOI: 10.1107/s205225252000696x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/22/2020] [Indexed: 05/05/2023]
Abstract
DHTKD1 is a lesser-studied E1 enzyme among the family of 2-oxoacid de-hydrogenases. In complex with E2 (di-hydro-lipo-amide succinyltransferase, DLST) and E3 (dihydrolipo-amide de-hydrogenase, DLD) components, DHTKD1 is involved in lysine and tryptophan catabolism by catalysing the oxidative de-carboxyl-ation of 2-oxoadipate (2OA) in mitochondria. Here, the 1.9 Å resolution crystal structure of human DHTKD1 is solved in complex with the thi-amine diphosphate co-factor. The structure reveals how the DHTKD1 active site is modelled upon the well characterized homologue 2-oxoglutarate (2OG) de-hydrogenase but engineered specifically to accommodate its preference for the longer substrate of 2OA over 2OG. A 4.7 Å resolution reconstruction of the human DLST catalytic core is also generated by single-particle electron microscopy, revealing a 24-mer cubic scaffold for assembling DHTKD1 and DLD protomers into a megacomplex. It is further demonstrated that missense DHTKD1 variants causing the inborn error of 2-amino-adipic and 2-oxoadipic aciduria impact on the complex formation, either directly by disrupting the interaction with DLST, or indirectly through destabilizing the DHTKD1 protein. This study provides the starting framework for developing DHTKD1 modulators to probe the intricate mitochondrial energy metabolism.
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Affiliation(s)
- Gustavo A. Bezerra
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - William R. Foster
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Henry J. Bailey
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Kevin G. Hicks
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Sven W. Sauer
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Bianca Dimitrov
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Thomas J. McCorvie
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Jürgen G. Okun
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Stefan Kölker
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Wyatt W. Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
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27
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Nguyen TTN, Vu CD, Nguyen NL, Nguyen TTH, Nguyen NK, Nguyen HH. Identification of novel mutations in BCKDHB and DBT genes in Vietnamese patients with maple sirup urine disease. Mol Genet Genomic Med 2020; 8:e1337. [PMID: 32515140 PMCID: PMC7434729 DOI: 10.1002/mgg3.1337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 01/10/2023] Open
Abstract
Background Maple sirup urine disease (MSUD) is an autosomal recessive inherited metabolic disorder. The disease‐causing mutations can affect the BCKDHA, BCKDHB, and DBT genes encoding for the E1α, E1β, and E2 subunits of the multienzyme branched‐chain α‐keto acid dehydrogenase (BCKDH) complex. In the present study, novel pathogenic variants in BCKDHB and DBT genes were identified in three Vietnamese families with MSUD. Methods Three newborn patients from three unrelated Vietnamese families were diagnosed with MSUD at the Metabolic Clinic, National Hospital of Pediatrics. Blood samples of 11 relatives from two generations of the three families diagnosed with MSUD were analyzed using exome and Sanger sequencing analyses. Results Novel pathogenic variants in BCKDHB (c.1103C>T, c.989A>G, and c.704G>A), and DBT (c.263_265delAAG) genes were identified in three pediatric patients with MSUD. Conclusions We have identified novel pathogenic variants in the MSUD‐related genes in the pedigree of the three patient's families. Our findings expand the mutational spectrum of MSUD and provide the scientific basis for genetic counseling for the patient's families.
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Affiliation(s)
- Thi T N Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Chi D Vu
- National Hospital of Pediatrics, Hanoi, Vietnam
| | - Ngoc L Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi T H Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | | | - Huy H Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
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28
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Ma C, Mu Q, Wang L, Shi Y, Zhu L, Zhang S, Xue Y, Tao Y, Ma Y, Yu B. Bio-production of high-purity propionate by engineering l-threonine degradation pathway in Pseudomonas putida. Appl Microbiol Biotechnol 2020; 104:5303-5313. [DOI: 10.1007/s00253-020-10619-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/30/2020] [Accepted: 04/09/2020] [Indexed: 01/08/2023]
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Amer M, Hoeven R, Kelly P, Faulkner M, Smith MH, Toogood HS, Scrutton NS. Renewable and tuneable bio-LPG blends derived from amino acids. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:125. [PMID: 32684978 PMCID: PMC7362463 DOI: 10.1186/s13068-020-01766-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/08/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Microbial biorefinery approaches are beginning to define renewable and sustainable routes to clean-burning and non-fossil fuel-derived gaseous alkanes (known as 'bio-LPG'). The most promising strategies have used a terminal fatty acid photodecarboxylase, enabling light-driven propane production from externally fed waste butyric acid. Use of Halomonas (a robust extremophile microbial chassis) with these pathways has enabled bio-LPG production under non-sterile conditions and using waste biomass as the carbon source. Here, we describe new engineering approaches to produce next-generation pathways that use amino acids as fuel precursors for bio-LPG production (propane, butane and isobutane blends). RESULTS Multiple pathways from the amino acids valine, leucine and isoleucine were designed in E. coli for the production of propane, isobutane and butane, respectively. A branched-chain keto acid decarboxylase-dependent pathway utilising fatty acid photodecarboxylase was the most effective route, generating higher alkane gas titres over alternative routes requiring coenzyme A and/or aldehyde deformylating oxygenase. Isobutane was the major gas produced in standard (mixed amino acid) medium, however valine supplementation led to primarily propane production. Transitioning pathways into Halomonas strain TQ10 enabled fermentative production of mixed alkane gases under non-sterile conditions on simple carbon sources. Chromosomal integration of inducible (~ 180 mg/g cells/day) and constitutive (~ 30 mg/g cells/day) pathways into Halomonas generated production strains shown to be stable for up to 7 days. CONCLUSIONS This study highlights new microbial pathways for the production of clean-burning bio-LPG fuels from amino acids. The use of stable Halomonas production strains could lead to gas production in the field under non-sterile conditions following process optimisation.
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Affiliation(s)
- Mohamed Amer
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Robin Hoeven
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Paul Kelly
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Matthew Faulkner
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Michael H. Smith
- C3 Biotechnologies Ltd, The Railway Goods Yard, Middleton-in-Lonsdale, Lancashire, LA6 2NF UK
| | - Helen S. Toogood
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Nigel S. Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC, Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
- C3 Biotechnologies Ltd, The Railway Goods Yard, Middleton-in-Lonsdale, Lancashire, LA6 2NF UK
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Abiri M, Saei H, Eghbali M, Karamzadeh R, Shirzadeh T, Sharifi Z, Zeinali S. Maple syrup urine disease mutation spectrum in a cohort of 40 consanguineous patients and insilico analysis of novel mutations. Metab Brain Dis 2019; 34:1145-1156. [PMID: 31119508 DOI: 10.1007/s11011-019-00435-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/13/2019] [Indexed: 01/12/2023]
Abstract
Maple syrup urine disease is the primary aminoacidopathy affecting branched-chain amino acid (BCAA) metabolism. The disease is mainly caused by the deficiency of an enzyme named branched-chained α-keto acid dehydrogenase (BCKD), which consist of four subunits (E1α, E1β, E2, and E3), and encoded by BCKDHA, BCKDHB, DBT, and DLD gene respectively. BCKD is the main enzyme in the catabolism pathway of BCAAs. Hight rate of autosomal recessive disorders is expected from consanguineous populations like Iran. In this study, we selected two sets of STR markers linked to the four genes, that mutation in which can result in MSUD disease. The patients who had a homozygous haplotype for selected markers of the genes were sequenced. In current survey, we summarized our recent molecular genetic findings to illustrate the mutation spectrum of MSUD in our country. Ten novel mutations including c.484 A > G, c.834_836dup CAC, c.357del T, and c. (343 + 1_344-1) _ (742 + 1_743-1)del in BCKDHB, c.355-356 ins 7 nt ACAAGGA, and c.703del T in BCKDHA, and c.363delCT/c.1238 T > C, c. (433 + 1_434-1) _ (939 + 1_940-1)del, c.1174 A > C, and c.85_86ins AACG have been found in DBT gene. Additionally, structural models of MSUD mutations have been performed to predict the pathogenicity of the newly identified variants.
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Affiliation(s)
- Maryam Abiri
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Science, Tehran, 14494-14539, Iran.
| | - Hassan Saei
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Science, Tehran, 14494-14539, Iran
- Student Research Committee, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Eghbali
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Razieh Karamzadeh
- Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Tina Shirzadeh
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, No. 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zohreh Sharifi
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, No. 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sirous Zeinali
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, No. 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran.
- Department of Molecular Medicine, Biotech Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Liu YD, Chu X, Liu RH, Sun Y, Kong QX, Li QB. Paroxysmal spasticity of lower extremities as the initial symptom in two siblings with maple syrup urine disease. Mol Med Rep 2019; 19:4872-4880. [PMID: 30957186 PMCID: PMC6522870 DOI: 10.3892/mmr.2019.10133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/01/2019] [Indexed: 12/28/2022] Open
Abstract
Maple syrup urine disease (MSUD) is a rare autosomal recessive metabolic disorder caused by mutations in genes that encode subunits of the branched‑chain α‑ketoacid dehydrogenase (BCKD) complex. Impairment of the BCKD complex results in an abnormal accumulation of branched‑chain amino acids and their corresponding branched‑chain keto acids in the blood and cerebrospinal fluid, which are neurovirulent and may become life‑threatening. An 11‑day‑old boy was admitted to the hospital with paroxysmal spasticity of lower extremities. Of note, his 10‑year‑old sister presented similar symptoms during the neonatal period, and her condition was diagnosed as MSUD when she was 1.5 years old. Genetic screening was performed, and the boy and his sister exhibited two novel compound heterozygous mutations in the branched chain keto acid dehydrogenase E1 subunit β (BCKDHB) gene: A substitution from guanine to adenine in the coding region at position 1,076 (c.1,076G>A) in exon 10 and a deletion of a thymine at position 705 (c.705delT) in exon 6. The missense mutation c.1076G>A results in an amino acid substitution from arginine to lysine at position 359 (p.Arg359Lys), whereas the mutation c.705delT results in the replacement of a cysteine at position 235 with a stop codon (p.Cys235Ter). Neither of the BCKDHB alleles in the compound heterozygote patients is able to generate normal E1β subunits, resulting in a possible impairment of the activity of the BCKD complex. In the present study, it was hypothesized that the two novel heterozygous mutations in the BCKDHB gene found in the Chinese family may be responsible for the phenotype of the two siblings with MSUD.
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Affiliation(s)
- Yi-Dan Liu
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Xu Chu
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Rui-Hua Liu
- Department of Pediatrics, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Ying Sun
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Qing-Xia Kong
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Qiu-Bo Li
- Department of Pediatrics, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
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Ali EZ, Ngu LH. Fourteen new mutations of BCKDHA, BCKDHB and DBT genes associated with maple syrup urine disease (MSUD) in Malaysian population. Mol Genet Metab Rep 2018; 17:22-30. [PMID: 30228974 PMCID: PMC6140420 DOI: 10.1016/j.ymgmr.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022] Open
Abstract
Maple syrup urine disease (MSUD) is a rare autosomal recessive metabolic disorder. This disorder is usually caused by mutations in any one of the genes; BCKDHA, BCKDHB and DBT, which represent E1α, E1β and E2 subunits of the branched-chain α-keto acid dehydrogenase (BCKDH) complex, respectively. This study presents the molecular characterization of 31 MSUD patients. Twenty one mutations including 14 new mutations were identified. The BCKDHB gene was the most commonly affected (45.2%) compared to BCKDHA gene (16.1%) and DBT gene (38.7%). In silico webservers predicted all mutations were disease-causing. In addition, structural evaluation disclosed that all new missenses in BCKDHA, BCKDHB and DBT genes affected stability and formation of E1 and E2 subunits. Majority of the patients had neonatal onset MSUD (26 of 31). Meanwhile, the new mutation; c.1196C > G (p.S399C) in DBT gene was noted to be recurrent and found in 9 patients. Conclusion: Our findings have expanded the mutational spectrum of the MSUD and revealed the genetic heterogeneity among Malaysian MSUD patients. We also discovered the p.S399C from DBT gene was noted as a recurrent mutation in Malay community and it suggested the existence of common and unique mutation in Malay population.
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Affiliation(s)
- Ernie Zuraida Ali
- Molecular Diagnostics and Protein Unit, Specialized Diagnostics Centre, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Lock-Hock Ngu
- Medical Genetics Department, Kuala Lumpur Hospital, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
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Zhang ZY, Monleon D, Verhamme P, Staessen JA. Branched-Chain Amino Acids as Critical Switches in Health and Disease. Hypertension 2018; 72:1012-1022. [DOI: 10.1161/hypertensionaha.118.10919] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhen-Yu Zhang
- From the KU Leuven Department of Cardiovascular Sciences, Research Unit Hypertension and Cardiovascular Epidemiology (Z.-Y.Z., J.A.S.), University of Leuven, Belgium
- Department of Cardiovascular Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China (Z.-Y.Z.)
| | - Daniel Monleon
- Metabolomic and Molecular Image Laboratory, Fundación Investigatión Clínico de Valencia, Spain (D.M.)
| | - Peter Verhamme
- KU Leuven Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology (P.V.), University of Leuven, Belgium
| | - Jan A. Staessen
- From the KU Leuven Department of Cardiovascular Sciences, Research Unit Hypertension and Cardiovascular Epidemiology (Z.-Y.Z., J.A.S.), University of Leuven, Belgium
- Cardiovascular Research Institute, Maastricht University, the Netherlands (J.A.S.)
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Li W, Meng X, Wang W, Lv J, Sun Y, Lv Y, Wang C, Wang H, Wang M, Song D. Silico analysis of a novel mutation c.550delT in a Chinese patient with maple syrup urine disease. Clin Case Rep 2018; 6:1989-1993. [PMID: 30349713 PMCID: PMC6186878 DOI: 10.1002/ccr3.1774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/19/2018] [Accepted: 07/29/2018] [Indexed: 01/25/2023] Open
Abstract
Twelve days after birth, the child was admitted to hospital because of "poor response, lethargy, and poor appetite for 6 days" and developed into coma immediately. The ventilator is required. The urine had significant maple syrup odor. After different diagnosis, she was diagnosed with classical maple syrup urine disease.
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Affiliation(s)
- Wenjie Li
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
| | - Xianze Meng
- People's Liberation Army No 401 HospitalQingdaoShandongChina
| | - Weiqing Wang
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
| | - Jinfeng Lv
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
| | - Yingmei Sun
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
| | - Yanan Lv
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
| | - Caijuan Wang
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
| | - Hongqin Wang
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
| | - Mei Wang
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
| | - Dongpo Song
- Neonatal Screening LabQingdao Women and Children HospitalQingdaoShandongChina
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Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa. Sci Rep 2018; 8:11334. [PMID: 30054521 PMCID: PMC6063907 DOI: 10.1038/s41598-018-29535-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/12/2018] [Indexed: 01/30/2023] Open
Abstract
S-adenosyl-l-homocysteine hydrolase from Pseudomonas aeruginosa (PaSAHase) coordinates one K+ ion and one Zn2+ ion in the substrate binding area. The cations affect the enzymatic activity and substrate binding but the molecular mechanisms of their action are unknown. Enzymatic and isothermal titration calorimetry studies demonstrated that the K+ ions stimulate the highest activity and strongest ligand binding in comparison to other alkali cations, while the Zn2+ ions inhibit the enzyme activity. PaSAHase was crystallized in the presence of adenine nucleosides and K+ or Rb+ ions. The crystal structures show that the alkali ion is coordinated in close proximity of the purine ring and a 23Na NMR study showed that the monovalent cation coordination site is formed upon ligand binding. The cation, bound in the area of a molecular hinge, orders and accurately positions the amide group of Q65 residue to allow its interaction with the ligand. Moreover, binding of potassium is required to enable unique dynamic properties of the enzyme that ensure its maximum catalytic activity. The Zn2+ ion is bound in the area of a molecular gate that regulates access to the active site. Zn2+ coordination switches the gate to a shut state and arrests the enzyme in its closed, inactive conformation.
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Liu G, Ma D, Hu P, Wang W, Luo C, Wang Y, Sun Y, Zhang J, Jiang T, Xu Z. A Novel Whole Gene Deletion of BCKDHB by Alu-Mediated Non-allelic Recombination in a Chinese Patient With Maple Syrup Urine Disease. Front Genet 2018; 9:145. [PMID: 29740478 PMCID: PMC5928131 DOI: 10.3389/fgene.2018.00145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Abstract
Maple syrup urine disease (MSUD) is an autosomal recessive inherited metabolic disorder caused by mutations in the BCKDHA, BCKDHB, DBT, and DLD genes. Among the wide range of disease-causing mutations in BCKDHB, only one large deletion has been associated with MSUD. Compound heterozygous mutations in BCKDHB were identified in a Chinese patient with typical MSUD using next-generation sequencing, quantitative PCR, and array comparative genomic hybridization. One allele presented a missense mutation (c.391G > A), while the other allele had a large deletion; both were inherited from the patient’s unaffected parents. The deletion breakpoints were characterized using long-range PCR and sequencing. A novel 383,556 bp deletion (chr6: g.80811266_81194921del) was determined, which encompassed the entire BCKDHB gene. The junction site of the deletion was localized within a homologous sequence in two AluYa5 elements. Hence, Alu-mediated non-allelic homologous recombination is speculated as the mutational event underlying the large deletion. In summary, this study reports a recombination mechanism in the BCKDHB gene causing a whole gene deletion in a newborn with MSUD.
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Affiliation(s)
- Gang Liu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Dingyuan Ma
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Wen Wang
- Reproductive Genetic Center, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Chunyu Luo
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan Wang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yun Sun
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jingjing Zhang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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Fernández-Lainez C, Aláez-Verson C, Ibarra-González I, Enríquez-Flores S, Carrillo-Sanchez K, Flores-Lagunes L, Guillén-López S, Belmont-Martínez L, Vela-Amieva M. In silico prediction of the pathogenic effect of a novel variant of BCKDHA leading to classical maple syrup urine disease identified using clinical exome sequencing. Clin Chim Acta 2018; 483:33-38. [PMID: 29673582 DOI: 10.1016/j.cca.2018.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
Abstract
Maple syrup urine disease (MSUD) is a metabolic disorder caused by mutations in three of the branched-chain α-keto acid dehydrogenase complex (BCKDC) genes. Classical MSUD symptom can be observed immediately after birth and include ketoacidosis, irritability, lethargy, and coma, which can lead to death or irreversible neurodevelopmental delay in survivors. The molecular diagnosis of MSUD can be time-consuming and difficult to establish using conventional Sanger sequencing because it could be due to pathogenic variants of any of the BCKDC genes. Next-generation sequencing-based methodologies have revolutionized the molecular diagnosis of inborn errors in metabolism and offer a superior approach for genotyping these patients. Here, we report an MSUD case whose molecular diagnosis was performed by clinical exome sequencing (CES), and the possible structural pathogenic effect of a novel E1α subunit pathogenic variant was analyzed using in silico analysis of α and β subunit crystallographic structure. Molecular analysis revealed a new homozygous non-sense c.1267C>T or p.Gln423Ter variant of BCKDHA. The novel BCKDHA variant is considered pathogenic because it caused a premature stop codon that probably led to the loss of the last 22 amino acid residues of the E1α subunit C-terminal end. In silico analysis of this region showed that it is in contact with several residues of the E1β subunit mainly through polar contacts, hydrogen bonds, and hydrophobic interactions. CES strategy could benefit the patients and families by offering precise and prompt diagnosis and better genetic counseling.
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Affiliation(s)
- Cynthia Fernández-Lainez
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Av. Imán #1 piso 9, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Ciudad de México C.P. 04530, Mexico
| | - Carmen Aláez-Verson
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Periférico Sur # 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de México C.P. 14610, Mexico.
| | - Isabel Ibarra-González
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, UNAM-Instituto Nacional de Pediatría, Av. Imán #1 piso 9, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Ciudad de México CP 04530, Mexico.
| | - Sergio Enríquez-Flores
- Subdirección de Medicina Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Av. Imán #1, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Ciudad de México CP 04530, Mexico.
| | - Karol Carrillo-Sanchez
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Periférico Sur # 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de México C.P. 14610, Mexico.
| | - Leonardo Flores-Lagunes
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Periférico Sur # 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de México C.P. 14610, Mexico.
| | - Sara Guillén-López
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Av. Imán #1 piso 9, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Ciudad de México C.P. 04530, Mexico
| | - Leticia Belmont-Martínez
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Av. Imán #1 piso 9, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Ciudad de México C.P. 04530, Mexico
| | - Marcela Vela-Amieva
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Av. Imán #1 piso 9, Col. Insurgentes Cuicuilco, Delegación Coyoacán, Ciudad de México C.P. 04530, Mexico.
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38
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Mucke HA. Patent highlights October-November 2017. Pharm Pat Anal 2018; 7:73-81. [PMID: 29417883 DOI: 10.4155/ppa-2017-0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 01/02/2017] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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Zeynalzadeh M, Tafazoli A, Aarabi A, Moghaddassian M, Ashrafzadeh F, Houshmand M, Taghehchian N, Abbaszadegan MR. Four novel mutations of the BCKDHA, BCKDHB and DBT genes in Iranian patients with maple syrup urine disease. J Pediatr Endocrinol Metab 2018; 31:205-212. [PMID: 29306928 DOI: 10.1515/jpem-2017-0305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/04/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND Maple syrup urine disease (MSUD) is a rare metabolic autosomal recessive disorder caused by dysfunction of the branched-chain α-ketoacid dehydrogenase (BCKDH) complex. Mutations in the BCKDHA, BCKDHB and DBT genes are responsible for MSUD. The current study analyzed seven Iranian MSUD patients genetically and explored probable correlations between their genotype and phenotype. METHODS The panel of genes, including BCKDHA, BCKDHB and DBT, was evaluated, using routine the polymerase chain reaction (PCR)-sequencing method. In addition, protein modeling (homology and threading modeling) of the deduced novel mutations was performed. The resulting structures were then analyzed, using state-of-the-art bioinformatics tools to better understand the structural and functional effects caused by mutations. RESULTS Seven mutations were detected in seven patients, including four novel pathogenic mutations in BCKDHA (c.1198delA, c.629C>T), BCKDHB (c.652C>T) and DBT (c.1150A>G) genes. Molecular modeling of the novel mutations revealed clear changes in the molecular energy levels and stereochemical traits of the modeled proteins, which may be indicative of strong correlations with the functional modifications of the genes. Structural deficiencies were compatible with the observed phenotypes. CONCLUSIONS Any type of MSUD can show heterogeneous clinical manifestations in different ethnic groups. Comprehensive molecular investigations would be necessary for differential diagnosis.
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Affiliation(s)
- Monica Zeynalzadeh
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Alireza Tafazoli
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Azadeh Aarabi
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Morteza Moghaddassian
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, Faculty of Applied Science and Engineering, University of Toronto, Ontario, Canada
| | - Farah Ashrafzadeh
- Department of Pediatric Neurology, Qaem Medical Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Negin Taghehchian
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center and Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad 9196773117, Iran
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Rowland EA, Snowden CK, Cristea IM. Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease. Curr Opin Chem Biol 2017; 42:76-85. [PMID: 29169048 DOI: 10.1016/j.cbpa.2017.11.003] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 02/07/2023]
Abstract
Lipoylation is a rare, but highly conserved lysine posttranslational modification. To date, it is known to occur on only four multimeric metabolic enzymes in mammals, yet these proteins are staples in the core metabolic landscape. The dysregulation of these mitochondrial proteins is linked to a range of human metabolic disorders. Perhaps most striking is that lipoylation itself, the proteins that add or remove the modification, as well as the proteins it decorates are all evolutionarily conserved from bacteria to humans, highlighting the importance of this essential cofactor. Here, we discuss the biological significance of protein lipoylation, the importance of understanding its regulation in health and disease states, and the advances in mass spectrometry-based proteomic technologies that can aid these studies.
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Affiliation(s)
- Elizabeth A Rowland
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States
| | - Caroline K Snowden
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States.
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Avermectin biosynthesis: stable functional expression of branched chain α-keto acid dehydrogenase complex from Streptomyces avermitilis in Escherichia coli by selectively regulating individual subunit gene expression. Biotechnol Lett 2017; 39:1567-1574. [DOI: 10.1007/s10529-017-2389-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 06/10/2017] [Indexed: 12/28/2022]
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Krishnan B, Massilamany C, Basavalingappa RH, Gangaplara A, Kang G, Li Q, Uzal FA, Strande JL, Delhon GA, Riethoven JJ, Steffen D, Reddy J. Branched chain α-ketoacid dehydrogenase kinase 111-130, a T cell epitope that induces both autoimmune myocarditis and hepatitis in A/J mice. IMMUNITY INFLAMMATION AND DISEASE 2017; 5:421-434. [PMID: 28597552 PMCID: PMC5691315 DOI: 10.1002/iid3.177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/14/2017] [Accepted: 05/18/2017] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Organ-specific autoimmune diseases are believed to result from immune responses generated against self-antigens specific to each organ. However, when such responses target antigens expressed promiscuously in multiple tissues, then the immune-mediated damage may be wide spread. METHODS In this report, we describe a mitochondrial protein, branched chain α-ketoacid dehydrogenase kinase (BCKDk ) that can act as a target autoantigen in the development of autoimmune inflammatory reactions in both heart and liver. RESULTS We demonstrate that BCKDk protein contains at least nine immunodominant epitopes, three of which, BCKDk 71-90, BCKDk 111-130 and BCKDk 141-160, were found to induce varying degrees of myocarditis in immunized mice. One of these, BCKDk 111-130, could also induce hepatitis without affecting lungs, kidneys, skeletal muscles, and brain. In immunogenicity testing, all three peptides induced antigen-specific T cell responses, as verified by proliferation assay and/or major histocompatibility complex class II/IAk dextramer staining. Finally, the disease-inducing abilities of BCKDk peptides were correlated with the production of interferon-γ, and the activated T cells could transfer disease to naive recipients. CONCLUSIONS The disease induced by BCKDk peptides could serve as a useful model to study the autoimmune events of inflammatory heart and liver diseases.
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Affiliation(s)
- Bharathi Krishnan
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Chandirasegaran Massilamany
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Rakesh H Basavalingappa
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Arunakumar Gangaplara
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Guobin Kang
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Francisco A Uzal
- School of Veterinary Medicine, University of California, Davis, California, USA
| | - Jennifer L Strande
- Department of Medicine, Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gustavo A Delhon
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jean-Jack Riethoven
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - David Steffen
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Gong W, Jia J, Zhang B, Mi S, Zhang L, Xie X, Guo H, Shi J, Tu C. Serum Metabolomic Profiling of Piglets Infected with Virulent Classical Swine Fever Virus. Front Microbiol 2017; 8:731. [PMID: 28496435 PMCID: PMC5406397 DOI: 10.3389/fmicb.2017.00731] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/07/2017] [Indexed: 12/14/2022] Open
Abstract
Classical swine fever (CSF) is a highly contagious swine infectious disease and causes significant economic losses for the pig industry worldwide. The objective of this study was to determine whether small molecule metabolites contribute to the pathogenesis of CSF. Birefly, serum metabolomics of CSFV Shimen strain-infected piglets were analyzed by ultraperformance liquid chromatography/electrospray ionization time-of-flight mass spectrometry (UPLC/ESI-Q-TOF/MS) in combination with multivariate statistical analysis. In CSFV-infected piglets at days 3 and 7 post-infection changes were found in metabolites associated with several key metabolic pathways, including tryptophan catabolism and the kynurenine pathway, phenylalanine metabolism, fatty acid and lipid metabolism, the tricarboxylic acid and urea cycles, branched-chain amino acid metabolism, and nucleotide metabolism. Several pathways involved in energy metabolism including fatty acid biosynthesis and β-oxidation, branched-chain amino acid metabolism, and the tricarboxylic acid cycle were significantly inhibited. Changes were also observed in several metabolites exclusively associated with gut microbiota. The metabolomic profiles indicate that CSFV-host gut microbiome interactions play a role in the development of CSF.
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Affiliation(s)
- Wenjie Gong
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China.,Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State UniversityManhattan, KS, USA
| | - Junjie Jia
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Bikai Zhang
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Shijiang Mi
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Li Zhang
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Xiaoming Xie
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Huancheng Guo
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State UniversityManhattan, KS, USA
| | - Changchun Tu
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
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Abiri M, Karamzadeh R, Mojbafan M, Alaei MR, Jodaki A, Safi M, Kianfar S, Bandehi Sarhaddi A, Noori-Daloii MR, Karimipoor M, Zeinali S. In silico analysis of novel mutations in maple syrup urine disease patients from Iran. Metab Brain Dis 2017; 32:105-113. [PMID: 27507644 DOI: 10.1007/s11011-016-9867-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/28/2016] [Indexed: 11/26/2022]
Abstract
Maple Syrup Urine Disease (MSUD) is a rare autosomal recessive disorder of branched-chain amino acid (BCAA) metabolism. The disease is mainly caused by mutations either in the BCKDHA, BCKDHB, DBT or DLD genes encoding components of the E1α, E1β, E2 and E3 subunits of branched-chain α-keto acid dehydrogenase complex (BCKDC), respectively. BCKDC is a mitochondrial enzyme which is responsible for the normal breakdown of BCAA. The rate of consanguineous marriage in Iran is 38.6 %, so the prevalence of autosomal recessive disorders is higher in comparison to other countries. Consanguinity increases the chance of the presence of pathogenic mutations in a homoallelic state. This phenomenon has made homozygosity mapping a powerful tool for finding the probable causative gene in heterogeneous disorders like IEM (Inborn Errors of Metabolism). In this study, two sets of multiplex polymorphic STR (Short Tandem Repeat) markers linked to the above-mentioned genes were selected to identify the probable pathogenic gene in the studied families. The families who showed a homozygous haplotype for the STR markers of the BCKDHB gene were subsequently sequenced. Four novel mutations including c.633 + 1G > A, c.988G > A, c.833_834insCAC, and a homozygous deletion of whole exon 3 c. (274 + 1_275-1) _(343 + 1_344-1), as well as one recently reported (c. 508G > T) mutation have been identified. Interestingly, three families shared a common haplotype structure along with the c. 508G > T mutation. Also, four other families revealed another similar haplotype with c.988G > A mutation. Founder effect can be a suggestive mechanism for the disease. Additionally, structural models of MSUD mutations have been performed to predict the pathogenesis of the newly identified variants.
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Affiliation(s)
- Maryam Abiri
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Pasteur St, Tehran, Iran
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Razieh Karamzadeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Marziyeh Mojbafan
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Pasteur St, Tehran, Iran
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Reza Alaei
- Pediatric Endocrinology and Metabolism, Mofid Children's Hospital, Tehran, Iran
- Pediatric Endocrinology and Metabolism, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atefeh Jodaki
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, No. 41 Majlesi St., Vali Asr St, Tehran, 1595645513, Iran
| | | | - Soodeh Kianfar
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, No. 41 Majlesi St., Vali Asr St, Tehran, 1595645513, Iran
| | - Ameneh Bandehi Sarhaddi
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, No. 41 Majlesi St., Vali Asr St, Tehran, 1595645513, Iran
- Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Reza Noori-Daloii
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Pasteur St, Tehran, Iran
| | - Morteza Karimipoor
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, No. 41 Majlesi St., Vali Asr St, Tehran, 1595645513, Iran.
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Artiukhov AV, Graf AV, Bunik VI. Directed regulation of multienzyme complexes of 2-oxo acid dehydrogenases using phosphonate and phosphinate analogs of 2-oxo acids. BIOCHEMISTRY (MOSCOW) 2016; 81:1498-1521. [DOI: 10.1134/s0006297916120129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Solomon KV, Ovadia E, Yu F, Mizunashi W, O’Malley MA. Mitochondrial targeting increases specific activity of a heterologous valine assimilation pathway in Saccharomyces cerevisiae. Metab Eng Commun 2016; 3:68-75. [PMID: 29468114 PMCID: PMC5779707 DOI: 10.1016/j.meteno.2016.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 03/14/2016] [Indexed: 01/13/2023] Open
Abstract
Bio-based isobutantol is a sustainable 'drop in' substitute for petroleum-based fuels. However, well-studied production routes, such as the Ehrlich pathway, have yet to be commercialized despite more than a century of research. The more versatile bacterial valine catabolism may be a competitive alternate route producing not only an isobutanol precursor but several carboxylic acids with applications as biomonomers, and building blocks for other advanced biofuels. Here, we transfer the first two committed steps of the pathway from pathogenic Pseudomonas aeruginosa PAO1 to yeast to evaluate their activity in a safer model organism. Genes encoding the heteroligomeric branched chain keto-acid dehydrogenase (BCKAD; bkdA1, bkdA2, bkdB, lpdV), and the homooligomeric acyl-CoA dehydrogenase (ACD; acd1) were tagged with fluorescence epitopes and targeted for expression in either the mitochondria or cytoplasm of S. cerevisiae. We verified the localization of our constructs with confocal fluorescence microscopy before measuring the activity of tag-free constructs. Despite reduced heterologous expression of mitochondria-targeted enzymes, their specific activities were significantly improved with total enzyme activities up to 138% greater than those of enzymes expressed in the cytoplasm. In total, our results demonstrate that the choice of protein localization in yeast has significant impact on heterologous activity, and suggests a new path forward for isobutanol production.
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Affiliation(s)
- Kevin V. Solomon
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, United States
| | - Elisa Ovadia
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, United States
| | - Fujio Yu
- Science and Technology Research Center, Inc., Mitsubishi Rayon Group, Yokohama, Kanagawa 227-8502, Japan
| | - Wataru Mizunashi
- Science and Technology Research Center, Inc., Mitsubishi Rayon Group, Yokohama, Kanagawa 227-8502, Japan
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, United States
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Gohara DW, Di Cera E. Molecular Mechanisms of Enzyme Activation by Monovalent Cations. J Biol Chem 2016; 291:20840-20848. [PMID: 27462078 DOI: 10.1074/jbc.r116.737833] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Regulation of enzymes through metal ion complexation is widespread in biology and underscores a physiological need for stability and high catalytic activity that likely predated proteins in the RNA world. In addition to divalent metals such as Ca2+, Mg2+, and Zn2+, monovalent cations often function as efficient and selective promoters of catalysis. Advances in structural biology unravel a rich repertoire of molecular mechanisms for enzyme activation by Na+ and K+ Strategies range from short-range effects mediated by direct participation in substrate binding, to more distributed effects that propagate long-range to catalytic residues. This review addresses general considerations and examples.
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Affiliation(s)
- David W Gohara
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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Abiri M, Karamzadeh R, Karimipoor M, Ghadami S, Alaei MR, Bagheri SD, Bagherian H, Setoodeh A, Noori-Daloii MR, Sirous Zeinali. Identification of six novel mutations in Iranian patients with maple syrup urine disease and their in silico analysis. Mutat Res 2016; 786:34-40. [PMID: 26901124 DOI: 10.1016/j.mrfmmm.2016.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/12/2016] [Accepted: 01/22/2016] [Indexed: 01/09/2023]
Abstract
Maple syrup urine disease (MSUD) is a rare inborn error of branched-chain amino acid metabolism. The disease prevalence is higher in populations with elevated rate of consanguineous marriages such as Iran. Different types of disease causing mutations have been previously reported in BCKDHA, BCKDHB, DBT and DLD genes known to be responsible for MSUD phenotype. In this study, two sets of multiplex polymorphic STR (Short Tandem Repeat) markers linked to the above genes were used to aid in homozygosity mapping in order to find probable pathogenic change(s) in the studied families. The families who showed homozygote haplotype for the BCKDHA gene were subsequently sequenced. Our findings showed that exons 2, 4 and 6 contain most of the mutations which are novel. The changes include two single nucleotide deletion (i.e. c. 143delT and c.702delT), one gross deletion covering the whole exon four c.(375+1_376-1)_(8849+1_885-1), two splice site changes (c.1167+1G>T, c. 288+1G>A), and one point mutation (c.731G>A). Computational approaches were used to analyze these two novel mutations in terms of their impact on protein structure. Computational structural modeling indicated that these mutations might affect structural stability and multimeric assembly of branched-chain α-keto acid dehydrogenase complex (BCKDC).
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Affiliation(s)
- Maryam Abiri
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Razieh Karamzadeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Biophysics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Morteza Karimipoor
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Shirin Ghadami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Reza Alaei
- Pediatric Endocrinology and Metabolism, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Dabagh Bagheri
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Hamideh Bagherian
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Aria Setoodeh
- Department of Pediatrics, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran; Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran.
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Vašák M, Schnabl J. Sodium and Potassium Ions in Proteins and Enzyme Catalysis. Met Ions Life Sci 2016; 16:259-90. [DOI: 10.1007/978-3-319-21756-7_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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