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Zaganas I, Vorgia P, Spilioti M, Mathioudakis L, Raissaki M, Ilia S, Giorgi M, Skoula I, Chinitrakis G, Michaelidou K, Paraskevoulakos E, Grafakou O, Kariniotaki C, Psyllou T, Zafeiris S, Tzardi M, Briassoulis G, Dinopoulos A, Mitsias P, Evangeliou A. Genetic cause of epilepsy in a Greek cohort of children and young adults with heterogeneous epilepsy syndromes. Epilepsy Behav Rep 2021; 16:100477. [PMID: 34568804 PMCID: PMC8449081 DOI: 10.1016/j.ebr.2021.100477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 12/01/2022] Open
Abstract
We describe a cohort of 10 unrelated Greek patients (4 females, 6 males; median age 6.5 years, range 2-18 years) with heterogeneous epilepsy syndromes with a genetic basis. In these patients, causative genetic variants, including two novel ones, were identified in 9 known epilepsy-related genes through whole exome sequencing. A patient with glycine encephalopathy was a compound heterozygote for the p.Arg222Cys and the p.Ser77Leu AMT variant. A patient affected with Lafora disease carried the homozygous p.Arg171His EPM2A variant. A de novo heterozygous variant in the GABRG2 gene (p.Pro282Thr) was found in one patient and a pathogenic variant in the GRIN2B gene (p.Gly820Val) in another patient. Infantile-onset lactic acidosis with seizures was associated with the p.Arg446Ter PDHX gene variant in one patient. In two additional epilepsy patients, the p.Ala1662Val and the novel non-sense p.Phe1330Ter SCN1A gene variants were found. Finally, in 3 patients we observed a novel heterozygous missense variant in SCN2A (p.Ala1874Thr), a heterozygous splice site variant in SLC2A1 (c.517-2A>G), as a cause of Glut1 deficiency syndrome, and a pathogenic variant in STXBP1 (p.Arg292Leu), respectively. In half of our cases (patients with variants in the GRIN2B, SCN1A, SCN2A and SLC2A1 genes), a genetic cause with potential management implications was identified.
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Affiliation(s)
- Ioannis Zaganas
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
- Neurology Department, University Hospital of Heraklion, Crete, Greece
| | - Pelagia Vorgia
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Martha Spilioti
- AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Lambros Mathioudakis
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Maria Raissaki
- Department of Radiology, University Hospital of Heraklion, Crete, Greece
| | - Stavroula Ilia
- Pediatric Intensive Care Unit, University Hospital of Heraklion, Crete, Greece
| | | | - Irene Skoula
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | | | - Kleita Michaelidou
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | | | - Olga Grafakou
- Pediatric Department, Venizelion General Hospital, Heraklio, Crete, Greece
| | - Chariklia Kariniotaki
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Thekla Psyllou
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Spiros Zafeiris
- Neurology Department, University Hospital of Heraklion, Crete, Greece
| | - Maria Tzardi
- Pathology Department, Medical School, University of Crete, Greece
| | - George Briassoulis
- Pediatric Intensive Care Unit, University Hospital of Heraklion, Crete, Greece
| | | | - Panayiotis Mitsias
- Neurology Department, University Hospital of Heraklion, Crete, Greece
- Department of Neurology, Henry Ford Hospital/Wayne State University, Detroit, MI, USA
| | - Athanasios Evangeliou
- Papageorgiou General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Liu N, Qin L, Mazhar M, Miao S. Integrative transcriptomic-proteomic analysis revealed the flavor formation mechanism and antioxidant activity in rice-acid inoculated with Lactobacillus paracasei and Kluyveromyces marxianus. J Proteomics 2021; 238:104158. [PMID: 33631365 DOI: 10.1016/j.jprot.2021.104158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/18/2022]
Abstract
In the study on fermented acid rice soup (rice-acid) inoculated with L. paracasei H4-11 and K. marxianus L1-1, the concentrations of main flavor components on the third day of fermentation were significantly higher than those on the first day. Transcriptome analysis and proteome analysis based on RNA sequencing and 4D label-free proteomic techniques were combined to provide new insights into the molecular mechanisms of flavor characteristics and antioxidant activity of the two strains during the development of rice-acid. The key up-regulated genes and proteins in L. paracasei and K. marxianus L1-1, which were involved in flavor formation and antioxidant activity in rice-acid development, were different. The KEGG pathways involving the up-regulated genes and proteins in L. paracasei included starch and sucrose metabolism, pyruvate metabolism, amino sugar, and nucleotide sugar metabolism, and glycolysis/guconeogenesis. The KEGG pathways involving the up-regulated genes and proteins in K. marxianus L1-1 mainly included glycolysis/gluconeogenesis, TCA cycle, pyruvate metabolism, and other pathways related to antioxidant capacity. We successfully identified key genes and proteins associated with the metabolism and accumulation of flavor components and antioxidant activity. These findings provide new insights into the molecular mechanisms of flavor formation in co-cultivation with L. paracasei and K. marxianus. SIGNIFICANCE: It is anticipated that this study would provide us an insight into the mechanisms of flavor components accumulation and antioxidant activity of acid rice soup in China's minority areas. Importantly, this research provides the foundation of biological and chemical analysis for the application of the co-culture of L. paracasei H4-11 and K. marxianus in non-dairy products.
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Affiliation(s)
- Na Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Likang Qin
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China.
| | - Muhammad Mazhar
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
| | - Song Miao
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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3
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Ceccatelli Berti C, di Punzio G, Dallabona C, Baruffini E, Goffrini P, Lodi T, Donnini C. The Power of Yeast in Modelling Human Nuclear Mutations Associated with Mitochondrial Diseases. Genes (Basel) 2021; 12:300. [PMID: 33672627 PMCID: PMC7924180 DOI: 10.3390/genes12020300] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
The increasing application of next generation sequencing approaches to the analysis of human exome and whole genome data has enabled the identification of novel variants and new genes involved in mitochondrial diseases. The ability of surviving in the absence of oxidative phosphorylation (OXPHOS) and mitochondrial genome makes the yeast Saccharomyces cerevisiae an excellent model system for investigating the role of these new variants in mitochondrial-related conditions and dissecting the molecular mechanisms associated with these diseases. The aim of this review was to highlight the main advantages offered by this model for the study of mitochondrial diseases, from the validation and characterisation of novel mutations to the dissection of the role played by genes in mitochondrial functionality and the discovery of potential therapeutic molecules. The review also provides a summary of the main contributions to the understanding of mitochondrial diseases emerged from the study of this simple eukaryotic organism.
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Affiliation(s)
| | | | | | | | | | | | - Claudia Donnini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy; (C.C.B.); (G.d.P.); (C.D.); (E.B.); (P.G.); (T.L.)
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Wang W, Liang K, Chang Y, Ran M, Zhang Y, Ali MA, Dai D, Qazi IH, Zhang M, Zhou G, Yang J, Angel C, Zeng C. miR-26a is Involved in Glycometabolism and Affects Boar Sperm Viability by Targeting PDHX. Cells 2020; 9:E146. [PMID: 31936222 PMCID: PMC7016825 DOI: 10.3390/cells9010146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/26/2019] [Accepted: 12/27/2019] [Indexed: 02/06/2023] Open
Abstract
miR-26a is associated with sperm metabolism and can affect sperm motility and apoptosis. However, how miR-26a affects sperm motility remains largely unknown. Our previous study indicated that the PDHX gene is predicted to be a potential target of miR-26a, which is responsible for pyruvate oxidative decarboxylation which is considered as a key step for connecting glycolysis with oxidative phosphorylation. In this study, we first reported a potential relationship between miR-26a and PDHX and their expressions in fresh, frozen-thawed, and epididymal boar sperm. Then, sperm viability and survival were determined after transfection of miR-26a. mRNA and protein expression level of PDHX in the liquid-preserved boar sperm after transfection were also determined by RT-qPCR and Western Blot (WB). Our results showed that expression level of PDHX was significantly increased during sperm transit from epididymal caput to corpus and cauda. Similarly, expression of PDHX was significantly higher (P < 0.05) in fresh sperm as compared to epididymal cauda and frozen-thawed sperm. However, the expression of miR-26a in epididymal corpus sperm was significantly higher (P < 0.05) than that of caput and cauda sperm. Furthermore, after transfection of boar sperm with miR-26a mimic and inhibitor under liquid storage, the lowest and highest sperm viability was observed in miR-26a mimic and inhibitor treatment (P < 0.05), respectively. The protein levels of PDHX, after 24 and 48 h of transfection of miR-26a mimics and inhibitor, were notably decreased and increased (P < 0.05), respectively, as compared to negative control (NC) group. In conclusion, the novel and enticing findings of our study provide a reasonable evidence that miR-26a via PDHX, a link between glycolysis and oxidative phosphorylation, could regulate the glycometabolic pathway which eventually affect boar sperm viability and survival.
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Affiliation(s)
- Wencan Wang
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Kai Liang
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Yu Chang
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Mingxia Ran
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Yan Zhang
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Malik Ahsan Ali
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
- Department of Theriogenology, Riphah College of Veterinary Sciences, Lahore 54000, Pakistan
| | - Dinghui Dai
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Izhar Hyder Qazi
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
- Department of Veterinary Anatomy & Histology, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand 67210, Pakistan
| | - Ming Zhang
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Guangbin Zhou
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Jiandong Yang
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
| | - Christiana Angel
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China;
- Department of Veterinary Parasitology, Faculty of Veterinary Sciences, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand 67210, Pakistan
| | - Changjun Zeng
- College of Animal Sciences and Technology, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.W.); (K.L.); (Y.C.); (M.R.); (Y.Z.); (M.A.A.); (D.D.); (I.H.Q.); (M.Z.); (G.Z.); (J.Y.)
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5
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Oyarzabal A, Marin-Valencia I. Synaptic energy metabolism and neuronal excitability, in sickness and health. J Inherit Metab Dis 2019; 42:220-236. [PMID: 30734319 DOI: 10.1002/jimd.12071] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 01/06/2019] [Accepted: 01/30/2019] [Indexed: 12/11/2022]
Abstract
Most of the energy produced in the brain is dedicated to supporting synaptic transmission. Glucose is the main fuel, providing energy and carbon skeletons to the cells that execute and support synaptic function: neurons and astrocytes, respectively. It is unclear, however, how glucose is provided to and used by these cells under different levels of synaptic activity. It is even more unclear how diseases that impair glucose uptake and oxidation in the brain alter metabolism in neurons and astrocytes, disrupt synaptic activity, and cause neurological dysfunction, of which seizures are one of the most common clinical manifestations. Poor mechanistic understanding of diseases involving synaptic energy metabolism has prevented the expansion of therapeutic options, which, in most cases, are limited to symptomatic treatments. To shed light on the intersections between metabolism, synaptic transmission, and neuronal excitability, we briefly review current knowledge of compartmentalized metabolism in neurons and astrocytes, the biochemical pathways that fuel synaptic transmission at resting and active states, and the mechanisms by which disorders of brain glucose metabolism disrupt neuronal excitability and synaptic function and cause neurological disease in the form of epilepsy.
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Affiliation(s)
- Alfonso Oyarzabal
- Synaptic Metabolism Laboratory, Department of Neurology, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Isaac Marin-Valencia
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, New York
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6
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Rossi M, Anheim M, Durr A, Klein C, Koenig M, Synofzik M, Marras C, van de Warrenburg BP. The genetic nomenclature of recessive cerebellar ataxias. Mov Disord 2018; 33:1056-1076. [PMID: 29756227 DOI: 10.1002/mds.27415] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/15/2018] [Accepted: 03/25/2018] [Indexed: 12/17/2022] Open
Abstract
The recessive cerebellar ataxias are a large group of degenerative and metabolic disorders, the diagnostic management of which is difficult because of the enormous clinical and genetic heterogeneity. Because of several limitations, the current classification systems provide insufficient guidance for clinicians and researchers. Here, we propose a new nomenclature for the genetically confirmed recessive cerebellar ataxias according to the principles and criteria laid down by the International Parkinson and Movement Disorder Society Task Force on Classification and Nomenclature of Genetic Movement Disorders. We apply stringent criteria for considering an association between gene and phenotype to be established. The newly proposed list of recessively inherited cerebellar ataxias includes 62 disorders that were assigned an ATX prefix, followed by the gene name, because these typically present with ataxia as a predominant and/or consistent feature. An additional 30 disorders that often combine ataxia with a predominant or consistent other movement disorder received a double prefix (e.g., ATX/HSP). We also identified a group of 89 entities that usually present with complex nonataxia phenotypes, but may occasionally present with cerebellar ataxia. These are listed separately without the ATX prefix. This new, transparent and adaptable nomenclature of the recessive cerebellar ataxias will facilitate the clinical recognition of recessive ataxias, guide diagnostic testing in ataxia patients, and help in interpreting genetic findings. © 2018 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Malco Rossi
- Movement Disorders Section, Neuroscience Department, Raul Carrea Institute for Neurological Research, Buenos Aires, Argentina
| | - Mathieu Anheim
- Département de Neurologie, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch, France.,Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, Strasbourg, France
| | - Alexandra Durr
- Brain and Spine Institute, Sorbonne Université, Inserm U1127, CNRS UMR 7225, Pitié-Salpêtrière University Hospital, Paris, France.,Department of Genetics, AP-HP, Pitié-Salpêtrière University Hospital, 7501, Paris, France
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, Luebeck, Germany.,Department of Neurology, University Hospital Schleswig-Holstein, Campus Lübeck, Germany
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares, EA7402, Institut Universitaire de Recherche Clinique, Université de Montpellier, CHU Montpellier, Montpellier, France
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Connie Marras
- Toronto Western Hospital Morton, Gloria Shulman Movement Disorders Centre, and the Edmond J. Safra Program in Parkinson's Disease, University of Toronto, Toronto, Canada
| | - Bart P van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition & Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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7
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Debashree B, Kumar M, Keshava Prasad TS, Natarajan A, Christopher R, Nalini A, Bindu PS, Gayathri N, Srinivas Bharath MM. Mitochondrial dysfunction in human skeletal muscle biopsies of lipid storage disorder. J Neurochem 2018; 145:323-341. [PMID: 29424033 DOI: 10.1111/jnc.14318] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/28/2018] [Accepted: 01/30/2018] [Indexed: 02/06/2023]
Abstract
Mitochondria regulate the balance between lipid metabolism and storage in the skeletal muscle. Altered lipid transport, metabolism and storage influence the bioenergetics, redox status and insulin signalling, contributing to cardiac and neurological diseases. Lipid storage disorders (LSDs) are neurological disorders which entail intramuscular lipid accumulation and impaired mitochondrial bioenergetics in the skeletal muscle causing progressive myopathy with muscle weakness. However, the mitochondrial changes including molecular events associated with impaired lipid storage have not been completely understood in the human skeletal muscle. We carried out morphological and biochemical analysis of mitochondrial function in muscle biopsies of human subjects with LSDs (n = 7), compared to controls (n = 10). Routine histology, enzyme histochemistry and ultrastructural analysis indicated altered muscle cell morphology and mitochondrial structure. Protein profiling of the muscle mitochondria from LSD samples (n = 5) (vs. control, n = 5) by high-throughput mass spectrometric analysis revealed that impaired metabolic processes could contribute to mitochondrial dysfunction and ensuing myopathy in LSDs. We propose that impaired fatty acid and respiratory metabolism along with increased membrane permeability, elevated lipolysis and altered cristae entail mitochondrial dysfunction in LSDs. Some of these mechanisms were unique to LSD apart from others that were common to dystrophic and inflammatory muscle pathologies. Many differentially regulated mitochondrial proteins in LSD are linked with other human diseases, indicating that mitochondrial protection via targeted drugs could be a treatment modality in LSD and related metabolic diseases. Cover Image for this Issue: doi: 10.1111/jnc.14177.
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Affiliation(s)
- Bandopadhyay Debashree
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Manish Kumar
- Institute of Bioinformatics, Bangalore, Karnataka, India.,Manipal University, Manipal, Karnataka, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, Bangalore, Karnataka, India.,Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, Karnataka, India
| | - Archana Natarajan
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Parayil Sankaran Bindu
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Narayanappa Gayathri
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
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Abstract
The family of 2-oxoacid dehydrogenase complexes (2-OADC), typified by the pyruvate dehydrogenase multi-enzyme complex (PDC) as its most prominent member, are massive molecular machines (Mr, 4-10 million) controlling key steps in glucose homeostasis (PDC), citric acid cycle flux (OGDC, 2-oxoglutarate dehydrogenase) and the metabolism of the branched-chain amino acids, leucine, isoleucine and valine (BCOADC, branched-chain 2-OADC). These highly organised mitochondrial arrays, composed of multiple copies of three separate enzymes, have been widely studied as paradigms for the analysis of enzyme cooperativity, substrate channelling, protein-protein interactions and the regulation of activity by phosphorylation . This chapter will highlight recent advances in our understanding of the structure-function relationships, the overall organisation and the transport and assembly of PDC in particular, focussing on both native and recombinant forms of the complex and their individual components or constituent domains. Biophysical approaches, including X-ray crystallography (MX), nuclear magnetic resonance spectroscopy (NMR), cryo-EM imaging, analytical ultracentrifugation (AUC) and small angle X-ray and neutron scattering (SAXS and SANS), have all contributed significant new information on PDC subunit organisation, stoichiometry, regulatory mechanisms and mode of assembly. Moreover, the recognition of specific genetic defects linked to PDC deficiency, in combination with the ability to analyse recombinant PDCs housing both novel naturally-occurring and engineered mutations, have all stimulated renewed interest in these classical metabolic assemblies. In addition, the role played by PDC, and its constituent proteins, in certain disease states will be briefly reviewed, focussing on the development of new and exciting areas of medical and immunological research.
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Affiliation(s)
- Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - John Gordon Lindsay
- Institute of Molecular, Cell and Systems Biology, Davidson Building, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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Sperl W, Fleuren L, Freisinger P, Haack TB, Ribes A, Feichtinger RG, Rodenburg RJ, Zimmermann FA, Koch J, Rivera I, Prokisch H, Smeitink JA, Mayr JA. The spectrum of pyruvate oxidation defects in the diagnosis of mitochondrial disorders. J Inherit Metab Dis 2015; 38:391-403. [PMID: 25526709 DOI: 10.1007/s10545-014-9787-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 10/20/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
Abstract
Pyruvate oxidation defects (PODs) are among the most frequent causes of deficiencies in the mitochondrial energy metabolism and represent a substantial subset of classical mitochondrial diseases. PODs are not only caused by deficiency of subunits of the pyruvate dehydrogenase complex (PDHC) but also by various disorders recently described in the whole pyruvate oxidation route including cofactors, regulation of PDHC and the mitochondrial pyruvate carrier. Our own patients from 2000 to July 2014 and patients identified by a systematic survey of the literature from 1970 to July 2014 with a pyruvate oxidation disorder and a genetically proven defect were included in the study (n=628). Of these defects 74.2% (n=466) belong to PDHC subunits, 24.5% (n=154) to cofactors, 0.5% (n=3) to PDHC regulation and 0.8% (n=5) to mitochondrial pyruvate import. PODs are underestimated in the field of mitochondrial diseases because not all diagnostic centres include biochemical investigations of PDHC in their routine analysis. Cofactor and transport defects can be missed, if pyruvate oxidation is not measured in intact mitochondria routinely. Furthermore deficiency of the X-chromosomal PDHA1 can be biochemically missed depending on the X-inactivation pattern. This is reflected by an increasing number of patients diagnosed recently by genetic high throughput screening approaches. PDHC deficiency including regulation and import affect mainly the glucose dependent central and peripheral nervous system and skeletal muscle. PODs with combined enzyme defects affect also other organs like heart, lung and liver. The spectrum of clinical presentation of PODs is still expanding. PODs are a therapeutically interesting group of mitochondrial diseases since some can be bypassed by ketogenic diet or treated by cofactor supplementation. PDHC kinase inhibition, chaperone therapy and PGC1α stimulation is still a matter of further investigations.
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Affiliation(s)
- Wolfgang Sperl
- Department of Paediatrics, Paracelsus Medical University, SALK Salzburg, Salzburg, 5020, Austria,
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Völgyi K, Gulyássy P, Háden K, Kis V, Badics K, Kékesi KA, Simor A, Györffy B, Tóth EA, Lubec G, Juhász G, Dobolyi A. Synaptic mitochondria: a brain mitochondria cluster with a specific proteome. J Proteomics 2015; 120:142-57. [PMID: 25782751 DOI: 10.1016/j.jprot.2015.03.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/16/2015] [Accepted: 03/04/2015] [Indexed: 01/15/2023]
Abstract
UNLABELLED The synapse is a particularly important compartment of neurons. To reveal its molecular characteristics we isolated whole brain synaptic (sMito) and non-synaptic mitochondria (nsMito) from the mouse brain with purity validated by electron microscopy and fluorescence activated cell analysis and sorting. Two-dimensional differential gel electrophoresis and mass spectrometry based proteomics revealed 22 proteins with significantly higher and 34 proteins with significantly lower levels in sMito compared to nsMito. Expression differences in some oxidative stress related proteins, such as superoxide dismutase [Mn] (Sod2) and complement component 1Q subcomponent-binding protein (C1qbp), as well as some tricarboxylic acid cycle proteins, including isocitrate dehydrogenase subunit alpha (Idh3a) and ATP-forming β subunit of succinyl-CoA ligase (SuclA2), were verified by Western blot, the latter two also by immunohistochemistry. The data suggest altered tricarboxylic acid metabolism in energy supply of synapse while the marked differences in Sod2 and C1qbp support high sensitivity of synapses to oxidative stress. Further functional clustering demonstrated that proteins with higher synaptic levels are involved in synaptic transmission, lactate and glutathione metabolism. In contrast, mitochondrial proteins associated with glucose, lipid, ketone metabolism, signal transduction, morphogenesis, protein synthesis and transcription were enriched in nsMito. Altogether, the results suggest a specifically tuned composition of synaptic mitochondria. BIOLOGICAL SIGNIFICANCE Neurons communicate with each other through synapse, a compartment metabolically isolated from the cell body. Mitochondria are concentrated in presynaptic terminals by active transport to provide energy supply for information transfer. Mitochondrial composition in the synapse may be different than in the cell body as some examples have demonstrated altered mitochondrial composition with cell type and cellular function in the muscle, heart and liver. Therefore, we posed the question whether protein composition of synaptic mitochondria reflects its specific functions. The determined protein difference pattern was in accordance with known functional specialties of high demand synaptic mitochondria. The data also suggest specifically tuned metabolic fluxes for energy production by means of interaction with glial cells surrounding the synapse. These findings provide possible mechanisms for dynamically adapting synaptic mitochondrial output to actual demand. In turn, an increased vulnerability of synaptic mitochondria to oxidative stress is implied by the data. This is important from theoretical but potentially also from therapeutic aspects. Mitochondria are known to be affected in some neurodegenerative and psychiatric disorders, and proteins with elevated level in synaptic mitochondria, e.g. C1qbp represent targets for future drug development, by which synaptic and non-synaptic mitochondria can be differentially affected.
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Affiliation(s)
- Katalin Völgyi
- MTA-ELTE NAP Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest H-1117, Hungary; Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Péter Gulyássy
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary; MTA-TTK NAP MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Krisztina Háden
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Viktor Kis
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Kata Badics
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Katalin Adrienna Kékesi
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary; Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Attila Simor
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Balázs Györffy
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Eszter Angéla Tóth
- Department of Immunology, Eötvös Loránd University, Budapest H-1117, Hungary; Faculty of Science Research and Instrument Core Facility (ELTE FS-RICF), Eötvös Loránd University, Budapest H-1117, Hungary
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Vienna A-1090, Austria
| | - Gábor Juhász
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary; MTA-TTK NAP MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Arpád Dobolyi
- MTA-ELTE NAP Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and Eötvös Loránd University, Budapest H-1117, Hungary.
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11
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Abstract
Pyruvate dehydrogenase and pyruvate carboxylase deficiency are the most common disorders in pyruvate metabolism. Diagnosis is made by enzymatic and DNA analysis after basic biochemical tests in plasma, urine, and CSF. Pyruvate dehydrogenase has three main subunits, an additional E3-binding protein and two complex regulatory enzymes. Most frequent are deficiencies in PDH-E1α. There is a spectrum of clinical presentations in E1α deficiency, ranging in boys from severe neonatal lactic acidosis, Leigh encephalopathy, to later onset of neurological disease such as intermittent ataxia or dystonia. Females tend to have a more uniform presentation resembling nonprogressive cerebral palsy. Neuroradiological abnormalities such as corpus callosum agenesis are seen more frequently in girls, basal ganglia and midbrain disturbances in boys. Deficiencies in the other subunits have also been described, but in a smaller number of patients. Pyruvate carboxylase deficiency has three clinical phenotypes. The infantile type is characterized mainly by severe developmental delay, failure to thrive, and seizures. The second type is characterized by neonatal onset of severe lactic acidosis with rigidity and hypokinesia. A third form is rarer with intermittent episodes of lactic acidosis and ketoacidosis. Neuroradiological findings such as cystic periventricular leukomalacia have been described.
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12
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Pyruvate dehydrogenase deficiency caused by a new mutation of PDHX gene in two Moroccan patients. Eur J Med Genet 2012; 55:535-40. [PMID: 22766002 DOI: 10.1016/j.ejmg.2012.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 06/12/2012] [Indexed: 11/21/2022]
Abstract
Pyruvate dehydrogenase deficiency is one of the genetic defects of mitochondrial energy metabolism. Clinical features are heterogeneous, ranging from fatal lactic acidosis in the newborn period to chronic neurodegenerative abnormalities. Most cases have mutations in the gene for the E1alpha subunit of the pyruvate dehydrogenase complex. Primary defects of the E3 binding protein component of the pyruvate dehydrogenase complex are rarier. We describe two unrelated Moroccan patients with the same new mutation c.1182 + 2T > C in the E3 binding protein gene PDHX and different clinical forms.
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13
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Patel KP, O’Brien TW, Subramony SH, Shuster J, Stacpoole PW. The spectrum of pyruvate dehydrogenase complex deficiency: clinical, biochemical and genetic features in 371 patients. Mol Genet Metab 2012; 106:385-94. [PMID: 22896851 PMCID: PMC4003492 DOI: 10.1016/j.ymgme.2012.03.017] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CONTEXT Pyruvate dehydrogenase complex (PDC) deficiency is a genetic mitochondrial disorder commonly associated with lactic acidosis, progressive neurological and neuromuscular degeneration and, usually, death during childhood. There has been no recent comprehensive analysis of the natural history and clinical course of this disease. OBJECTIVE We reviewed 371 cases of PDC deficiency, published between 1970 and 2010, that involved defects in subunits E1α and E1β and components E1, E2, E3 and the E3 binding protein of the complex. DATA SOURCES AND EXTRACTION English language peer-reviewed publications were identified, primarily by using PubMed and Google Scholar search engines. RESULTS Neurodevelopmental delay and hypotonia were the commonest clinical signs of PDC deficiency. Structural brain abnormalities frequently included ventriculomegaly, dysgenesis of the corpus callosum and neuroimaging findings typical of Leigh syndrome. Neither gender nor any clinical or neuroimaging feature differentiated the various biochemical etiologies of the disease. Patients who died were younger, presented clinically earlier and had higher blood lactate levels and lower residual enzyme activities than subjects who were still alive at the time of reporting. Survival bore no relationship to the underlying biochemical or genetic abnormality or to gender. CONCLUSIONS Although the clinical spectrum of PDC deficiency is broad, the dominant clinical phenotype includes presentation during the first year of life; neurological and neuromuscular degeneration; structural lesions revealed by neuroimaging; lactic acidosis and a blood lactate:pyruvate ratio ≤ 20.
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Affiliation(s)
- Kavi P. Patel
- Department of Medicine (Division of Endocrinology, Metabolism and
Diabetes), College of Medicine, University of Florida, Gainesville, FL 32611,
USA
| | - Thomas W. O’Brien
- Department of Biochemistry and Molecular Biology, College of
Medicine, University of Florida, Gainesville, FL 32611, USA
| | | | - Jonathan Shuster
- Department of Epidemiology and Health Policy Research, College of
Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Peter W. Stacpoole
- Department of Medicine (Division of Endocrinology, Metabolism and
Diabetes), College of Medicine, University of Florida, Gainesville, FL 32611,
USA
- Department of Biochemistry and Molecular Biology, College of
Medicine, University of Florida, Gainesville, FL 32611, USA
- Corresponding author at: UF College of Medicine, 1600 SW
Archer Road M2-238, P.O. Box 100226, Gainesville, FL 32610, USA. Fax: +1
352 273 9013. (P.W. Stacpoole)
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14
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Stobbe MD, Houten SM, Kampen AHC, Wanders RJA, Moerland PD. Improving the description of metabolic networks: the TCA cycle as example. FASEB J 2012; 26:3625-36. [DOI: 10.1096/fj.11-203091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Miranda D. Stobbe
- Bioinformatics LaboratoryUniversity of AmsterdamAmsterdamThe Netherlands
- Netherlands Bioinformatics CentreNijmegenThe Netherlands
| | - Sander M. Houten
- Laboratory Genetic Metabolic DiseasesAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Antoine H. C. Kampen
- Bioinformatics LaboratoryUniversity of AmsterdamAmsterdamThe Netherlands
- Biosystems Data AnalysisSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
- Netherlands Consortium for Systems BiologyUniversity of AmsterdamAmsterdamThe Netherlands
- Netherlands Bioinformatics CentreNijmegenThe Netherlands
| | - Ronald J. A. Wanders
- Laboratory Genetic Metabolic DiseasesAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Perry D. Moerland
- Bioinformatics LaboratoryUniversity of AmsterdamAmsterdamThe Netherlands
- Netherlands Bioinformatics CentreNijmegenThe Netherlands
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15
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Patel KP, O'Brien TW, Subramony SH, Shuster J, Stacpoole PW. The spectrum of pyruvate dehydrogenase complex deficiency: clinical, biochemical and genetic features in 371 patients. Mol Genet Metab 2012; 105:34-43. [PMID: 22079328 PMCID: PMC3754811 DOI: 10.1016/j.ymgme.2011.09.032] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 09/27/2011] [Accepted: 09/27/2011] [Indexed: 01/01/2023]
Abstract
CONTEXT Pyruvate dehydrogenase complex (PDC) deficiency is a genetic mitochondrial disorder commonly associated with lactic acidosis, progressive neurological and neuromuscular degeneration and, usually, death during childhood. There has been no recent comprehensive analysis of the natural history and clinical course of this disease. OBJECTIVE We reviewed 371 cases of PDC deficiency, published between 1970 and 2010, that involved defects in subunits E1α and E1β and components E1, E2, E3 and the E3 binding protein of the complex. DATA SOURCES AND EXTRACTION English language peer-reviewed publications were identified, primarily by using PubMed and Google Scholar search engines. RESULTS Neurodevelopmental delay and hypotonia were the commonest clinical signs of PDC deficiency. Structural brain abnormalities frequently included ventriculomegaly, dysgenesis of the corpus callosum and neuroimaging findings typical of Leigh syndrome. Neither gender nor any clinical or neuroimaging feature differentiated the various biochemical etiologies of the disease. Patients who died were younger, presented clinically earlier and had higher blood lactate levels and lower residual enzyme activities than subjects who were still alive at the time of reporting. Survival bore no relationship to the underlying biochemical or genetic abnormality or to gender. CONCLUSIONS Although the clinical spectrum of PDC deficiency is broad, the dominant clinical phenotype includes presentation during the first year of life; neurological and neuromuscular degeneration; structural lesions revealed by neuroimaging; lactic acidosis and a blood lactate:pyruvate ratio ≤20.
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Affiliation(s)
- Kavi P. Patel
- Department of Medicine (Division of Endocrinology and Metabolism), College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Thomas W. O'Brien
- Department of Biochemistry and Molecular Biology College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | | | - Jonathan Shuster
- Epidemiology and Health Policy Research College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Peter W. Stacpoole
- Department of Medicine (Division of Endocrinology and Metabolism), College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Biochemistry and Molecular Biology College of Medicine, University of Florida, Gainesville, FL, 32611, USA
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16
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Ahmed SS, Santosh W, Kumar S, Christlet HTT. Metabolic profiling of Parkinson's disease: evidence of biomarker from gene expression analysis and rapid neural network detection. J Biomed Sci 2009; 16:63. [PMID: 19594911 PMCID: PMC2720938 DOI: 10.1186/1423-0127-16-63] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 07/13/2009] [Indexed: 01/09/2023] Open
Abstract
Background Parkinson's disease (PD) is a neurodegenerative disorder. The diagnosis of Parkinsonism is challenging because currently none of the clinical tests have been proven to help in diagnosis. PD may produce characteristic perturbations in the metabolome and such variations can be used as the marker for detection of disease. To test this hypothesis, we used proton NMR and multivariate analysis followed by neural network pattern detection. Methods & Results 1H nuclear magnetic resonance spectroscopy analysis was carried out on plasma samples of 37 healthy controls and 43 drug-naive patients with PD. Focus on 22 targeted metabolites, 17 were decreased and 5 were elevated in PD patients (p < 0.05). Partial least squares discriminant analysis (PLS-DA) showed that pyruvate is the key metabolite, which contributes to the separation of PD from control samples. Furthermore, gene expression analysis shows significant (p < 0.05) change in expression of PDHB and NPFF genes leading to increased pyruvate concentration in blood plasma. Moreover, the implementation of 1H- NMR spectral pattern in neural network algorithm shows 97.14% accuracy in the detection of disease progression. Conclusion The results increase the prospect of a robust molecular definition in detection of PD through the early symptomatic phase of the disease. This is an ultimate opening for therapeutic intervention. If validated in a genuinely prospective fashion in larger samples, the biomarker trajectories described here will go a long way to facilitate the development of useful therapies. Moreover, implementation of neural network will be a breakthrough in clinical screening and rapid detection of PD.
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Affiliation(s)
- Shiek Ssj Ahmed
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur, Tamil Nadu, 603 203, India.
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17
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Miné M, Chen JM, Brivet M, Desguerre I, Marchant D, de Lonlay P, Bernard A, Férec C, Abitbol M, Ricquier D, Marsac C. A large genomic deletion in the PDHX gene caused by the retrotranspositional insertion of a full-length LINE-1 element. Hum Mutat 2007; 28:137-42. [PMID: 17152059 DOI: 10.1002/humu.20449] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The long interspersed element-1 (LINE-1 or L1) retrotransposition has altered the human genome in many ways. In particular, recent in vitro studies have demonstrated that the retrotranspositional insertion of L1 elements has resulted in significant genomic deletions. Here we provide evidence for its operation in the human genome by identifying a approximately 46-kb pathological genomic deletion in the PDHX gene directly linked to the insertion of a full-length L1 element, in a patient with pyruvate dehydrogenase complex (PDHc) deficiency. Both the deduced bottom and top strand cleavage sites in the PDHX gene coincide with the consensus L1 endonuclease (EN) target sequence 5'-TTTT/A-3', while the full-length L1 element is followed by a 67-bp poly(A) tail. Interestingly, two hairpin structures, potentially formed by the inverted repeats present immediately 5' to the top strand nick site and 3' to the bottom strand nick site, may have facilitated the accessibility of L1 EN to the target sequences and also brought the two otherwise distantly located sequences into close proximity. Since the L1 element inserted in the PDHX gene is full-length, we favor the model of the template jumping as opposed to that of the microhomology-mediated end-joining for linking the 5' end of the nascent L1 copy to its genomic target. Our finding not only serves as an important complement to the in vitro approaches to studying L1 retrotransposition, but also reveals a novel mechanism causing human genetic disease.
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Affiliation(s)
- Manuèle Miné
- Centre de Recherches Thérapeutiques en Ophtalmologie, Faculté de Médecine Necker, Paris, France
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18
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Reisch AS, Elpeleg O. Biochemical assays for mitochondrial activity: assays of TCA cycle enzymes and PDHc. Methods Cell Biol 2007; 80:199-222. [PMID: 17445696 DOI: 10.1016/s0091-679x(06)80010-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ann Saada Reisch
- The Metabolic Disease Unit, Hadassah-Hebrew University Medical Centre, Jerusalem 91120, Israel
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19
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Smolle M, Prior AE, Brown AE, Cooper A, Byron O, Lindsay JG. A new level of architectural complexity in the human pyruvate dehydrogenase complex. J Biol Chem 2006; 281:19772-80. [PMID: 16679318 PMCID: PMC3954457 DOI: 10.1074/jbc.m601140200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian pyruvate dehydrogenase multienzyme complex (PDC) is a key metabolic assembly comprising a 60-meric pentagonal dodecahedral E2 (dihydrolipoamide acetyltransferase) core attached to which are 30 pyruvate decarboxylase E1 heterotetramers and 6 dihydrolipoamide dehydrogenase E3 homodimers at maximal occupancy. Stable E3 integration is mediated by an accessory E3-binding protein (E3BP) located on each of the 12 E2 icosahedral faces. Here, we present evidence for a novel subunit organization in which E3 and E3BP form subcomplexes with a 1:2 stoichiometry implying the existence of a network of E3 "cross-bridges" linking pairs of E3BPs across the surface of the E2 core assembly. We have also determined a low resolution structure for a truncated E3BP/E3 subcomplex using small angle x-ray scattering showing one of the E3BP lipoyl domains docked into the E3 active site. This new level of architectural complexity in mammalian PDC contrasts with the recently published crystal structure of human E3 complexed with its cognate subunit binding domain and provides important new insights into subunit organization, its catalytic mechanism and regulation by the intrinsic PDC kinase.
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Affiliation(s)
- Michaela Smolle
- Division of Biochemistry & Molecular Biology, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- Division of Infection & Immunity, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Alison Elizabeth Prior
- Division of Biochemistry & Molecular Biology, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Audrey Elaine Brown
- Division of Biochemistry & Molecular Biology, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Alan Cooper
- Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Olwyn Byron
- Division of Infection & Immunity, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - John Gordon Lindsay
- Division of Biochemistry & Molecular Biology, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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20
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Schiff M, Miné M, Brivet M, Marsac C, Elmaleh-Bergés M, Evrard P, Ogier de Baulny H. Leigh's disease due to a new mutation in the PDHX gene. Ann Neurol 2006; 59:709-14. [PMID: 16566017 DOI: 10.1002/ana.20818] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
OBJECTIVE To describe the clinical course, neuroradiological presentation, biochemical and molecular studies of a new patient with pyruvate dehydrogenase complex (PDHc) deficiency. To compare this case with the data on other published cases. METHODS Brain magnetic resonance imaging (MRI), basal metabolic investigations with lactate measurements in body fluids, PDHc activity assay on cultured skin fibroblasts, immunoblot analysis and molecular studies (polymerase chain reaction [PCR] and sequencing procedures). RESULTS Our patient accused an unspecific encephalopathy for years and presented at 13 years of age an acute deterioration with basal ganglia necrosis and subcortical white matter involvement. PDHc deficiency was secondary to a large deletion (3913 bp) in the PDHX gene, which encodes E3 binding protein (E3BP) subunit. INTERPRETATION These data provide an additional case of E3BP deficiency with a unique and previously unreported deletion in the PDHX gene.
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Affiliation(s)
- Manuel Schiff
- Service de Neuropédiatrie et Maladies métaboliques, Hôpital Robert Debré, Paris, France.
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21
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Ueki I, Koga Y, Povalko N, Akita Y, Nishioka J, Yatsuga S, Fukiyama R, Matsuishi T. Mitochondrial tRNA gene mutations in patients having mitochondrial disease with lactic acidosis. Mitochondrion 2006; 6:29-36. [PMID: 16337222 DOI: 10.1016/j.mito.2005.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2005] [Revised: 10/17/2005] [Accepted: 10/19/2005] [Indexed: 11/25/2022]
Abstract
Lactic acidosis has been associated with a variety of clinical conditions and can be due to mutation in nuclear or mitochondrial genes. We performed mutations screening of all mitochondrial tRNA genes in 44 patients who referred as hyperlactic acidosis. Patients showed heterogeneous phenotypes including Leigh disease in four, MELAS in six, unclassified mitochondrial myopathy in 10, cardiomyopathy in five, MERRF in one, pure lactic acidosis in six, and others in 12 including facio-scaplo-femoral muscular dystrophy (FSFD), familial cerebellar ataxia, recurrent Reye syndrome, cerebral palsy with mental retardation. We measured enzymatic activities of pyruvate dehydrogenase complex, and respiratory chain enzymes. All mitochondrial tRNA genes and known mutation of ATPase 6 were studied by single strand conformation polymorphism (SSCP), automated DNA sequence and PCR-RFLP methods. We have found one patient with PDHC deficiency and six patients with Complex I+IV deficiency, though the most of the patients showed subnormal to deficient state of respiratory chain enzyme activities. We have identified one of the nucleotide changes in 29 patients. Single nucleotide changes in mitochondrial tRNA genes are found in 27 patients and one in ATPase 6 gene in two patients. One of four pathogenic point mutations (A3243G, C3303T, A8348G, and T8993G) was identified in 12 patients who showed the phenotype of Leigh syndrome, MELAS, cardimyopathy and cerebral palsy with epilepsy. Seventeen patients have one of the normal polymorphisms in the mitochondrial tRNA gene reported before. SSCP and PCR-RFLP could detect the heteroplasmic condition when the percentage of mutant up to 5, however, it cannot be observed by direct sequencing method. It is important to screen the mtDNA mutation not only by direct sequence but also by PCR-RFLP and the other sensitive methods to detect the heroplasmy when lactic acidosis has been documented in the patients who are not fulfilled the criteria of mitochondrial disorders.
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Affiliation(s)
- Isao Ueki
- Department of Pediatrics and Child Health, Kurume University School of Medicine, 67 Asahi-Machi, Kurume 830-0011, Japan
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22
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Brautigam CA, Wynn RM, Chuang JL, Machius M, Tomchick DR, Chuang DT. Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex. Structure 2006; 14:611-21. [PMID: 16442803 PMCID: PMC2879633 DOI: 10.1016/j.str.2006.01.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 01/04/2006] [Accepted: 01/06/2006] [Indexed: 11/17/2022]
Abstract
The 9.5 MDa human pyruvate dehydrogenase complex (PDC) utilizes the specific dihydrolipoamide dehydrogenase (E3) binding protein (E3BP) to tether the essential E3 component to the 60-meric core of the complex. Here, we report crystal structures of the binding domain (E3BD) of human E3BP alone and in complex with human E3 at 1.6 angstroms and 2.2 angstroms, respectively. The latter structure shows that residues from E3BD contact E3 across its 2-fold axis, resulting in one E3BD binding site on the E3 homodimer. Negligible conformational changes occur in E3BD upon its high-affinity binding to E3. Modifications of E3BD residues at the center of the E3BD/E3 interface impede E3 binding far more severely than those of residues on the periphery, validating the "hot spot" paradigm for protein interactions. A cluster of disease-causing E3 mutations located near the center of the E3BD/E3 interface prevents the efficient recruitment of these E3 variants by E3BP into the PDC, leading to the dysfunction of the PDC catalytic machine.
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Affiliation(s)
- Chad A. Brautigam
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
- Corresponding authors: ,
| | - R. Max Wynn
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
- Department of Internal Medicine, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Jacinta L. Chuang
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Mischa Machius
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Diana R. Tomchick
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - David T. Chuang
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
- Department of Internal Medicine, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
- Corresponding authors: ,
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23
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Brown RM, Head RA, Boubriak II, Leonard JV, Thomas NH, Brown GK. Mutations in the gene for the E1beta subunit: a novel cause of pyruvate dehydrogenase deficiency. Hum Genet 2004; 115:123-7. [PMID: 15138885 DOI: 10.1007/s00439-004-1124-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Accepted: 03/24/2004] [Indexed: 11/29/2022]
Abstract
We describe two unrelated patients with pyruvate dehydrogenase (PDH) deficiency attributable to mutations in the gene encoding the E1beta subunit of the complex. This is a previously unrecognised form of PDH deficiency, which most commonly results from mutations in the X-linked gene for the E1alpha subunit. Both patients had reduced immunoreactive E1beta protein and both had missense mutations in the E1beta gene. Activity of the PDH complex was restored in cultured fibroblasts from both patients by transfection and expression of the normal E1beta coding sequence.
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Affiliation(s)
- Ruth M Brown
- Genetics Unit, Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
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Ramadan DG, Head RA, Al-Tawari A, Habeeb Y, Zaki M, Al-Ruqum F, Besley GTN, Wraith JE, Brown RM, Brown GK. Lactic acidosis and developmental delay due to deficiency of E3 binding protein (protein X) of the pyruvate dehydrogenase complex. J Inherit Metab Dis 2004; 27:477-85. [PMID: 15303005 DOI: 10.1023/b:boli.0000037336.91549.44] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Pyruvate dehydrogenase deficiency is an important cause of primary lactic acidosis. Most cases occur as a result of mutations in the gene for the E1 alpha subunit of the complex, with a small number resulting from mutations in genes for other components, most commonly the E3 and E3-binding protein subunits. We describe pyruvate dehydrogenase E3-binding protein deficiency in two siblings in each of two unrelated families from Kuwait. The index patient in each family had reduced pyruvate dehydrogenase activity in cultured fibroblasts and no detectable immunoreactive E3-binding protein. Both were homozygous for nonsense mutations in the E3-binding protein gene, one involving the codon for glutamine 266, the other the codon for tryptophan 5.
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Affiliation(s)
- D G Ramadan
- Metabolic Clinic, Endocrine Unit, Paediatric Department, Sabah Hospital, Kuwait
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25
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Dey R, Mine M, Desguerre I, Slama A, Van Den Berghe L, Brivet M, Aral B, Marsac C. A new case of pyruvate dehydrogenase deficiency due to a novel mutation in the PDX1 gene. Ann Neurol 2003; 53:273-7. [PMID: 12557299 DOI: 10.1002/ana.10478] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report a case of neonatal congenital lactic acidosis associated with pyruvate dehydrogenase E3-binding protein deficiency in a newborn girl. She had a severe encephalopathy, and magnetic resonance imaging of the brain showed large subependymal cysts and no basal ganglia lesions. She died 35 days after birth. We detected a novel homozygous deletion (620delC) in the PDX1 gene, which encodes for the E3BP subunit of the pyruvate dehydrogenase complex.
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Affiliation(s)
- Runu Dey
- Laboratoire CERTO, CNRS UPR 1524, Faculté de Médecine Necker, Paris, France
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26
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Dey R, Aral B, Abitbol M, Marsac C. Pyruvate dehydrogenase deficiency as a result of splice-site mutations in the PDX1 gene. Mol Genet Metab 2002; 76:344-7. [PMID: 12208141 DOI: 10.1016/s1096-7192(02)00104-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations in the E3-binding protein component of pyruvate dehydrogenase complex have been demonstrated in a few cases of Leigh syndrome. We report that two mutations previously detected in the E3-binding protein cDNA are the consequence of splice-site mutations. Both involved a single base substitution in the conserved dinucleotides of splice junctions, one leading to skipping of an exon and the other, to activation of a cryptic site. Our findings add to the understanding of molecular basis of E3-binding protein deficiency and indicate yet again the high frequency of splicing mutations in this gene.
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Affiliation(s)
- Runu Dey
- Laboratoire CERTO, Faculté de Medécine Necker, 156 rue de Vaugirard, Paris, France
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27
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Perham RN. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu Rev Biochem 2001; 69:961-1004. [PMID: 10966480 DOI: 10.1146/annurev.biochem.69.1.961] [Citation(s) in RCA: 489] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multistep chemical reactions are increasingly seen as important in a growing number of complex biotransformations. Covalently attached prosthetic groups or swinging arms, and their associated protein domains, are essential to the mechanisms of active-site coupling and substrate channeling in a number of the multifunctional enzyme systems responsible. The protein domains, for which the posttranslational machinery in the cell is highly specific, are crucially important, contributing to the processes of molecular recognition that define and protect the substrates and the catalytic intermediates. The domains have novel folds and move by virtue of conformationally flexible linker regions that tether them to other components of their respective multienzyme complexes. Structural and mechanistic imperatives are becoming apparent as the assembly pathways and the coupling of multistep reactions catalyzed by these dauntingly complex molecular machines are unraveled.
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Affiliation(s)
- R N Perham
- Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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28
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Seyda A, Robinson BH. Expression and functional characterization of human protein X variants in SV40-immortalized protein X-deficient and E2-deficient human skin fibroblasts. Arch Biochem Biophys 2000; 382:219-23. [PMID: 11068872 DOI: 10.1006/abbi.2000.2026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To gain further insight into the nature and function of the domains of the human protein X (a pyruvate dehydrogenase complex component also known as the E3-binding protein), we expressed the wild-type as well as two artificially created variants, K37E and S422H, in SV40-immortalized protein X-deficient and E2-deficient human skin fibroblasts. The former mutant does not carry the lipoic acid moiety, the latter mutant was designed to investigate the possibility that protein X could exhibit an intrinsic acetyltransferase activity and use either its own catalytic center or the catalytic center of E2. Similar experiments have been performed in the past using the Saccharomyces cerevisiae expression system. However, lack of sequence similarity between the mammalian and the yeast protein X homologues suggests they are not biochemically equivalent. Mutant cells transfected with the wild-type gene for protein X produced a PDH complex that exhibited about 50% overall activity of the control cells. None of the expressed protein X variants had an effect on the specific activity of the PDH complex, suggesting that the human protein X plays a purely structural role in the functioning of the pyruvate dehydrogenase complex.
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Affiliation(s)
- A Seyda
- Department of Biochemistry, University of Toronto, Ontario
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29
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Rouillac C, Aral B, Fouque F, Marchant D, Saudubray JM, Dumez Y, Lindsay G, Abitbol M, Dufier JL, Marsac C, Benelli C. First prenatal diagnosis of defects in the HsPDX1 gene encoding protein X, an additional lipoyl-containing subunit of the human pyruvate dehydrogenase complex. Prenat Diagn 1999; 19:1160-4. [PMID: 10590436 DOI: 10.1002/(sici)1097-0223(199912)19:12<1160::aid-pd712>3.0.co;2-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have previously reported a genetic study of a neonatal lactic acidosis linked to a pyruvate dehydrogenase complex deficiency due to the absence of the protein X subunit. This rare autosomal recessive disorder is associated with specific deletions in this polypeptide which is encoded by the HsPDX1 gene, located on chromosome 11p1.3. The pathology of the patient was considered to arise from a large homozygous deletion (78del85) found at the 5' end of the HsPDX1 coding sequence. Her heterozygous mother underwent prenatal diagnosis during a subsequent pregnancy. Chorionic villus samples were used for three independent studies: (1) normal levels of the protein X component of the PDH complex were detected by immunoblotting; (2) RT-PCR analysis showed no deletion at the 5' end of the cDNA but the presence of a distinct heterozygous deletion (965del59) at its 3' end inherited from the father; (3) haplotype analysis revealed the presence of the father's mutated allele and the mother's normal allele. It was concluded that the fetus was heterozygous for this separate 3' deletion, so, it was likely to be not affected. This study permitted us to characterize more precisely the genetic abnormalities of the HsPDX1 cDNA occurring in each family's member.
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Affiliation(s)
- C Rouillac
- Centre de Recherches Thérapeutiques en Ophtalmologie (CERTO), Faculté de Médecine Necker, Paris, France
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30
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Gawin B, Niederführ A, Schumacher N, Hummerich H, Little PF, Gessler M. A 7.5 Mb sequence-ready PAC contig and gene expression map of human chromosome 11p13-p14.1. Genome Res 1999; 9:1074-86. [PMID: 10568747 PMCID: PMC310838 DOI: 10.1101/gr.9.11.1074] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The region p13 of the short arm of human chromosome 11 has been studied intensely during the search for genes involved in the etiology of the Wilms' tumor, aniridia, genitourinary abnormalities, mental retardation (WAGR) syndrome, and related conditions. The gene map for this region is far from being complete, however, strengthening the need for additional gene identification efforts. We describe the extension of an existing contig map with P1-derived artificial chromosomes (PACs) to cover 7.5 Mb of 11p13-14.1. The extended sequence-ready contig was established by end probe walking and fingerprinting and consists of 201 PAC clones. Utilizing bins defined by overlapping PACs, we generated a detailed gene map containing 20 genes as well as 22 anonymous ESTs which have been identified by searching the RH databases. RH maps and our established gene map show global correlation, but the limits of resolution of the current RH panels are evident at this scale. Initial expression studies on the novel genes have been performed by Northern blot analyses. To extend these expression profiles, corresponding mouse cDNA clones were identified by database search and employed for Northern blot analyses and RNA in situ hybridizations to mouse embryo sections. Genomic sequencing of clones along a minimal tiling path through the contig is currently under way and will facilitate these expression studies by in silico gene identification approaches.
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Affiliation(s)
- B Gawin
- Physiologische Chemie I, Biozentrum der Universität Würzburg, Germany
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31
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Santiard-Baron D, Gosset P, Nicole A, Sinet PM, Christen Y, Ceballos-Picot I. Identification of beta-amyloid-responsive genes by RNA differential display: early induction of a DNA damage-inducible gene, gadd45. Exp Neurol 1999; 158:206-13. [PMID: 10448433 DOI: 10.1006/exnr.1999.7076] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease is a neurodegenerative disorder characterized by the extracellular deposition in the brain of amyloid beta-peptide (A beta), presumed to play a pathogenic role. However, the precise molecular mechanisms of its neurotoxicity are not fully understood. Recent studies have suggested that it may exert its toxic effect via activation of transcription factors. We investigated A beta-responsive genes in human preneuron NT2 cells, at early stages of A beta (25-35) exposure, by RNA differential display. A beta induced the expression of (i) the growth arrest and DNA damage-inducible gene (gadd45) implicated in the DNA excision-repair process; (ii) a stress-signaling kinase gene encoding the mitogen-activated protein kinase/Erk kinase kinase-1 (MEKK1); (iii) a new growth factor-inducible immediate-early gene, CYR61, the product of which functions as an extracellular matrix signaling molecule; (iv) other immediate-early genes, such as c-jun and c-fos; (v) the gene encoding the basic fibroblast growth factor (bFGF); (vi) a gene encoding a constituent of the mitochondrial pyruvate dehydrogenase complex, the dihydrolipoamide dehydrogenase-binding protein (E3-BP); and (vii) an unidentified human gene (KIAA0099). A beta not only activates but also respresses genes: (i) the gene encoding "hinge" protein, a subunit of the mitochondrial cytochrome-c reductase and (ii) the SRp55 gene encoding a splicing factor involved in constitutive pre-mRNA splicing and alternative splice site selection. Our results underscored A beta-responsive genes that play key roles in the response (damage/recovery) of neuron cells to A beta exposure. In particular, the strong upregulation of gadd45, indicating DNA damage, was detected early in A beta cytotoxicity. This suggests that DNA strand breaks occurred rapidly in cells exposed to A beta, which may be a critical event in A beta neurotoxicity.
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32
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Terwilliger JD, Weiss KM. Linkage disequilibrium mapping of complex disease: fantasy or reality? Curr Opin Biotechnol 1998; 9:578-94. [PMID: 9889136 DOI: 10.1016/s0958-1669(98)80135-3] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In the past year, data about the level and nature of linkage disequilibrium between alleles of tightly linked SNPs have started to become available. Furthermore, increasing evidence of allelic heterogeneity at the loci predisposing to complex disease has been observed, which has lead to initial attempts to develop methods of linkage disequilibrium detection allowing for this difficulty. It has also become more obvious that we will need to think carefully about the types of populations we need to analyze in an attempt to identify these elusive genes, and it is becoming clear that we need to carefully re-evaluate the prognosis of the current paradigm with regard to its robustness to the types of problems that are likely to exist.
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Affiliation(s)
- J D Terwilliger
- Columbia University Department of Psychiatry Columbia and Genome Center 60, Haven Avenue #15-C New York NY 10032 USA. joseph.
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