1
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Favilli L, Griffith CM, Schymanski EL, Linster CL. High-throughput Saccharomyces cerevisiae cultivation method for credentialing-based untargeted metabolomics. Anal Bioanal Chem 2023:10.1007/s00216-023-04724-5. [PMID: 37212869 DOI: 10.1007/s00216-023-04724-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/23/2023]
Abstract
Identifying metabolites in model organisms is critical for many areas of biology, including unravelling disease aetiology or elucidating functions of putative enzymes. Even now, hundreds of predicted metabolic genes in Saccharomyces cerevisiae remain uncharacterized, indicating that our understanding of metabolism is far from complete even in well-characterized organisms. While untargeted high-resolution mass spectrometry (HRMS) enables the detection of thousands of features per analysis, many of these have a non-biological origin. Stable isotope labelling (SIL) approaches can serve as credentialing strategies to distinguish biologically relevant features from background signals, but implementing these experiments at large scale remains challenging. Here, we developed a SIL-based approach for high-throughput untargeted metabolomics in S. cerevisiae, including deep-48 well format-based cultivation and metabolite extraction, building on the peak annotation and verification engine (PAVE) tool. Aqueous and nonpolar extracts were analysed using HILIC and RP liquid chromatography, respectively, coupled to Orbitrap Q Exactive HF mass spectrometry. Of the approximately 37,000 total detected features, only 3-7% of the features were credentialed and used for data analysis with open-source software such as MS-DIAL, MetFrag, Shinyscreen, SIRIUS CSI:FingerID, and MetaboAnalyst, leading to the successful annotation of 198 metabolites using MS2 database matching. Comparable metabolic profiles were observed for wild-type and sdh1Δ yeast strains grown in deep-48 well plates versus the classical shake flask format, including the expected increase in intracellular succinate concentration in the sdh1Δ strain. The described approach enables high-throughput yeast cultivation and credentialing-based untargeted metabolomics, providing a means to efficiently perform molecular phenotypic screens and help complete metabolic networks.
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Affiliation(s)
- Lorenzo Favilli
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg.
| | - Corey M Griffith
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
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2
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Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023; 64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.
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Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian Li
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
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3
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Human cytosolic transaminases: side activities and patterns of discrimination towards physiologically available alternative substrates. Cell Mol Life Sci 2022; 79:421. [PMID: 35834009 PMCID: PMC9283133 DOI: 10.1007/s00018-022-04439-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/03/2022]
Abstract
Transaminases play key roles in central metabolism, transferring the amino group from a donor substrate to an acceptor. These enzymes can often act, with low efficiency, on compounds different from the preferred substrates. To understand what might have shaped the substrate specificity of this class of enzymes, we examined the reactivity of six human cytosolic transaminases towards amino acids whose main degradative pathways do not include any transamination. We also tested whether sugars and sugar phosphates could serve as alternative amino group acceptors for these cytosolic enzymes. Each of the six aminotransferases reacted appreciably with at least three of the alternative amino acid substrates in vitro, albeit at usually feeble rates. Reactions with L-Thr, L-Arg, L-Lys and L-Asn were consistently very slow-a bias explained in part by the structural differences between these amino acids and the preferred substrates of the transaminases. On the other hand, L-His and L-Trp reacted more efficiently, particularly with GTK (glutamine transaminase K; also known as KYAT1). This points towards a role of GTK in the salvage of L-Trp (in cooperation with ω-amidase and possibly with the cytosolic malate dehydrogenase, MDH1, which efficiently reduced the product of L-Trp transamination). Finally, the transaminases were extremely ineffective at utilizing sugars and sugar derivatives, with the exception of the glycolytic intermediate dihydroxyacetone phosphate, which was slowly but appreciably transaminated by some of the enzymes to yield serinol phosphate. Evidence for the formation of this compound in a human cell line was also obtained. We discuss the biological and evolutionary implications of our results.
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Abstract
Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal.
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5
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Salar U, Atia-Tul-Wahab, Choudhary MI. Functional and ligand binding studies of NAD(P)H hydrate dehydratase enzyme from vancomycin-resistant Staphylococcus aureus by NMR spectroscopic approach, including saturation transfer difference (STD-NMR) spectroscopy. Biochimie 2022; 201:148-156. [PMID: 35716900 DOI: 10.1016/j.biochi.2022.06.004] [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: 10/11/2021] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
NADH and NADPH are labile coenzymes that undergo hydration by enzymatic reaction or by heat at 5,6 double bond, and convert into non-functional hydrates, NADHX and NADPHX, respectively. The NAD(P)H hydrate dehydratase enzyme catalyzes the dehydration of S-NADHX/S-NADPHX at the expense of ATP, and thus contributes in the nicotinamide nucleotide repair process. This enzyme is also known as "metabolite-proofreading enzyme". Herein, we report the molecular cloning and expression of this highly conserved enzyme of vancomycin-resistant Staphylococcus aureus (VRSA). Its functional and inhibition studies were performed for the first time by NMR spectroscopy. NMR studies showed the dehydration of S epimer of NADHX, in the presence of R-NADHX and cyc-NADHX, by NAD(P)H hydrate dehydratase. In addition, by employing the STD-NMR approach, a library of drugs and natural products (total 79) were evaluated for their binding interactions with the NAD(P)H hydrate dehydratase enzyme. Among them, seven compounds showed ligand-like interactions with the enzyme, and thus functional activity of the enzyme was again checked in the presence of each ligand. Compound 2 (Thiamine HCl) was found to fully inhibit the enzyme's function, and recognized as a potential inhibitor. Current study demonstrates that this enzyme deserves further studies as a potential drug target, as its inhibition can disrupt the normal metabolism of pathogenic VRSA.
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Affiliation(s)
- Uzma Salar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Atia-Tul-Wahab
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan; H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21412, Saudi Arabia
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6
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Tserga A, Pouloudi D, Saulnier-Blache JS, Stroggilos R, Theochari I, Gakiopoulou H, Mischak H, Zoidakis J, Schanstra JP, Vlahou A, Makridakis M. Proteomic Analysis of Mouse Kidney Tissue Associates Peroxisomal Dysfunction with Early Diabetic Kidney Disease. Biomedicines 2022; 10:biomedicines10020216. [PMID: 35203426 PMCID: PMC8869654 DOI: 10.3390/biomedicines10020216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/01/2023] Open
Abstract
Background: The absence of efficient inhibitors for diabetic kidney disease (DKD) progression reflects the gaps in our understanding of DKD molecular pathogenesis. Methods: A comprehensive proteomic analysis was performed on the glomeruli and kidney cortex of diabetic mice with the subsequent validation of findings in human biopsies and omics datasets, aiming to better understand the underlying molecular biology of early DKD development and progression. Results: LC–MS/MS was employed to analyze the kidney proteome of 2 DKD models: Ins2Akita (early and late DKD) and db/db mice (late DKD). The abundance of detected proteins was defined. Pathway analysis of differentially expressed proteins in the early and late DKD versus the respective controls predicted dysregulation in DKD hallmarks (peroxisomal lipid metabolism and β-oxidation), supporting the functional relevance of the findings. Comparing the observed protein changes in early and late DKD, the consistent upregulation of 21 and downregulation of 18 proteins was detected. Among these were downregulated peroxisomal and upregulated mitochondrial proteins. Tissue sections from 16 DKD patients were analyzed by IHC confirming our results. Conclusion: Our study shows an extensive differential expression of peroxisomal proteins in the early stages of DKD that persists regardless of the disease severity, providing new perspectives and potential markers of diabetic kidney dysfunction.
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Affiliation(s)
- Aggeliki Tserga
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (R.S.); (J.Z.)
| | - Despoina Pouloudi
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (D.P.); (I.T.); (H.G.)
| | - Jean Sébastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France;
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Rafael Stroggilos
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (R.S.); (J.Z.)
| | - Irene Theochari
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (D.P.); (I.T.); (H.G.)
| | - Harikleia Gakiopoulou
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (D.P.); (I.T.); (H.G.)
| | | | - Jerome Zoidakis
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (R.S.); (J.Z.)
| | - Joost Peter Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France;
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
- Correspondence: (J.P.S.); (A.V.); (M.M.); Tel.: +33-5-31224078 (J.P.S.); +30-210-6597506 (A.V.); +30-210-6597485 (M.M.)
| | - Antonia Vlahou
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (R.S.); (J.Z.)
- Correspondence: (J.P.S.); (A.V.); (M.M.); Tel.: +33-5-31224078 (J.P.S.); +30-210-6597506 (A.V.); +30-210-6597485 (M.M.)
| | - Manousos Makridakis
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (R.S.); (J.Z.)
- Correspondence: (J.P.S.); (A.V.); (M.M.); Tel.: +33-5-31224078 (J.P.S.); +30-210-6597506 (A.V.); +30-210-6597485 (M.M.)
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7
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Griffith CM, Walvekar AS, Linster CL. Approaches for completing metabolic networks through metabolite damage and repair discovery. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:None. [PMID: 34957344 PMCID: PMC8669784 DOI: 10.1016/j.coisb.2021.100379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Metabolites are prone to damage, either via enzymatic side reactions, which collectively form the underground metabolism, or via spontaneous chemical reactions. The resulting non-canonical metabolites that can be toxic, are mended by dedicated "metabolite repair enzymes." Deficiencies in the latter can cause severe disease in humans, whereas inclusion of repair enzymes in metabolically engineered systems can improve the production yield of value-added chemicals. The metabolite damage and repair loops are typically not yet included in metabolic reconstructions and it is likely that many remain to be discovered. Here, we review strategies and associated challenges for unveiling non-canonical metabolites and metabolite repair enzymes, including systematic approaches based on high-resolution mass spectrometry, metabolome-wide side-activity prediction, as well as high-throughput substrate and phenotypic screens.
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Affiliation(s)
| | | | - Carole L. Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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8
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Toward sustainable, cell-free biomanufacturing. Curr Opin Biotechnol 2021; 69:136-144. [PMID: 33453438 DOI: 10.1016/j.copbio.2020.12.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Industrial biotechnology is an attractive approach to address the need for low-cost fuels and products from sustainable resources. Unfortunately, cells impose inherent limitations on the effective synthesis and release of target products. One key constraint is that cellular survival objectives often work against the production objectives of biochemical engineers. Additionally, industrial strains release CO2 and struggle to utilize sustainable, potentially profitable feedstocks. Cell-free biotechnology, which uses biological machinery harvested from cells, can address these challenges with advantages including: (i) shorter development times, (ii) higher volumetric production rates, and (iii) tolerance to otherwise toxic molecules. In this review, we highlight recent advances in cell-free technologies toward the production of non-protein products beyond lab-scale demonstrations and describe guiding principles for designing cell-free systems. Specifically, we discuss carbon and energy sources, reaction homeostasis, and scale-up. Expanding the scope of cell-free biomanufacturing practice could enable innovative approaches for the industrial production of green chemicals.
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Dimitrov B, Molema F, Williams M, Schmiesing J, Mühlhausen C, Baumgartner MR, Schumann A, Kölker S. Organic acidurias: Major gaps, new challenges, and a yet unfulfilled promise. J Inherit Metab Dis 2021; 44:9-21. [PMID: 32412122 DOI: 10.1002/jimd.12254] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/29/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Organic acidurias (OADs) comprise a biochemically defined group of inherited metabolic diseases. Increasing awareness, reliable diagnostic work-up, newborn screening programs for some OADs, optimized neonatal and intensive care, and the development of evidence-based recommendations have improved neonatal survival and short-term outcome of affected individuals. However, chronic progression of organ dysfunction in an aging patient population cannot be reliably prevented with traditional therapeutic measures. Evidence is increasing that disease progression might be best explained by mitochondrial dysfunction. Previous studies have demonstrated that some toxic metabolites target mitochondrial proteins inducing synergistic bioenergetic impairment. Although these potentially reversible mechanisms help to understand the development of acute metabolic decompensations during catabolic state, they currently cannot completely explain disease progression with age. Recent studies identified unbalanced autophagy as a novel mechanism in the renal pathology of methylmalonic aciduria, resulting in impaired quality control of organelles, mitochondrial aging and, subsequently, progressive organ dysfunction. In addition, the discovery of post-translational short-chain lysine acylation of histones and mitochondrial enzymes helps to understand how intracellular key metabolites modulate gene expression and enzyme function. While acylation is considered an important mechanism for metabolic adaptation, the chronic accumulation of potential substrates of short-chain lysine acylation in inherited metabolic diseases might exert the opposite effect, in the long run. Recently, changed glutarylation patterns of mitochondrial proteins have been demonstrated in glutaric aciduria type 1. These new insights might bridge the gap between natural history and pathophysiology in OADs, and their exploitation for the development of targeted therapies seems promising.
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Affiliation(s)
- Bianca Dimitrov
- Division of Child Neurology and Metabolic Medicine, Centre for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Femke Molema
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Monique Williams
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Jessica Schmiesing
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Chris Mühlhausen
- Department of Pediatrics and Adolescent Medicine, University Medical Centre Göttingen, Göttingen, Germany
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Anke Schumann
- Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, University Hospital of Freiburg, Freiburg, Germany
| | - Stefan Kölker
- Division of Child Neurology and Metabolic Medicine, Centre for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
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10
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Van Bergen NJ, Linster CL, Christodoulou J. Reply: NAD(P)HX dehydratase protein-truncating mutations are associated with neurodevelopmental disorder exacerbated by acute illness. Brain 2020; 143:e55. [PMID: 32462208 DOI: 10.1093/brain/awaa131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Kids Research, The Children's Hospital at Westmead, and Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
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11
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Borna NN, Kishita Y, Abe J, Furukawa T, Ogawa-Tominaga M, Fushimi T, Imai-Okazaki A, Takeda A, Ohtake A, Murayama K, Okazaki Y. NAD(P)HX dehydratase protein-truncating mutations are associated with neurodevelopmental disorder exacerbated by acute illness. Brain 2020; 143:e54. [PMID: 32462209 DOI: 10.1093/brain/awaa130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Nurun Nahar Borna
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Jiro Abe
- Department of Paediatrics, Graduate School of Medicine, Hokkaido University, Kita-Ku, Sapporo 060-8638, Japan
| | - Takuro Furukawa
- Department of Paediatrics, Asahikawa City Hospital, Asahikawa, Sapporo 078-8510, Japan
| | - Minako Ogawa-Tominaga
- Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba 266-0007, Japan
| | - Takuya Fushimi
- Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba 266-0007, Japan
| | - Atsuko Imai-Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan.,Medical Genomics Center: National Center for Global Health and Medicine, Shinjuku City, Tokyo 162-8655, Japan
| | - Atsuhito Takeda
- Department of Paediatrics, Graduate School of Medicine, Hokkaido University, Kita-Ku, Sapporo 060-8648, Japan
| | - Akira Ohtake
- Department of Paediatrics and Clinical Genomics, Faculty of Medicine, Saitama Medical University, Moroyama, Saitama 350-0495, Japan.,Center for Intractable Diseases, Saitama Medical University Hospital, Moroyama, Saitama 350-0495, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba 266-0007, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo 113-8421, Japan.,Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
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12
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Dienel GA. Hypothesis: A Novel Neuroprotective Role for Glucose-6-phosphatase (G6PC3) in Brain-To Maintain Energy-Dependent Functions Including Cognitive Processes. Neurochem Res 2020; 45:2529-2552. [PMID: 32815045 DOI: 10.1007/s11064-020-03113-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022]
Abstract
The isoform of glucose-6-phosphatase in liver, G6PC1, has a major role in whole-body glucose homeostasis, whereas G6PC3 is widely distributed among organs but has poorly-understood functions. A recent, elegant analysis of neutrophil dysfunction in G6PC3-deficient patients revealed G6PC3 is a neutrophil metabolite repair enzyme that hydrolyzes 1,5-anhydroglucitol-6-phosphate, a toxic metabolite derived from a glucose analog present in food. These patients exhibit a spectrum of phenotypic characteristics and some have learning disabilities, revealing a potential linkage between cognitive processes and G6PC3 activity. Previously-debated and discounted functions for brain G6PC3 include causing an ATP-consuming futile cycle that interferes with metabolic brain imaging assays and a nutritional role involving astrocyte-neuron glucose-lactate trafficking. Detailed analysis of the anhydroglucitol literature reveals that it competes with glucose for transport into brain, is present in human cerebrospinal fluid, and is phosphorylated by hexokinase. Anhydroglucitol-6-phosphate is present in rodent brain and other organs where its accumulation can inhibit hexokinase by competition with ATP. Calculated hexokinase inhibition indicates that energetics of brain and erythrocytes would be more adversely affected by anhydroglucitol-6-phosphate accumulation than heart. These findings strongly support the paradigm-shifting hypothesis that brain G6PC3 removes a toxic metabolite, thereby maintaining brain glucose metabolism- and ATP-dependent functions, including cognitive processes.
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Affiliation(s)
- Gerald A Dienel
- Department of Neurology, University of Arkansas for Medical Sciences, 4301 W. Markham St., Mail Slot 500, Little Rock, AR, 72205, USA.
- Department of Cell Biology and Physiology, University of New Mexico School of Medicine, Albuquerque, NM, 87131, USA.
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13
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Lucas N, Dückers G, Speckmann C, Ehl S, Utz N, Cheng B, Fang M, Niehues T, Lee-Kirsch MA. NAXD Deficiency Associated with Perinatal Autoinflammation, Pancytopenia, Dermatitis, Colitis, and Cystic Encephalomalacia. JOURNAL OF PEDIATRIC NEUROLOGY 2020. [DOI: 10.1055/s-0040-1713682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractNAD(P)HX dehydratase (NAXD) catalyzes the recovery of toxic derivatives of nicotinamide adenine dinucleotides which play an essential role in mitochondrial metabolism. Mutations in NAXD were recently shown to cause early-onset neurodegeneration exacerbated by febrile illness. Here, we report a novel homozygous stop-gain variant in NAXD in an infant who presented with a fulminant course of autoinflammation, dermatitis, colitis, and cystic encephalomalacia beginning at 3 weeks of age. Our findings support the central role of NAXD-mediated metabolite repair for normal tissue function and implicate innate immune processes in the pathogenesis of NAXD deficiency.
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Affiliation(s)
- Nadja Lucas
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Carsten Speckmann
- Center for Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Institute for Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Center for Chronic Immunodeficiency, Institute for Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Norbert Utz
- Helios Children's Hospital, Krefeld, Germany
| | - Bochen Cheng
- BGI-Shenzhen and China National GeneBank, Shenzhen, China
| | - Mingyan Fang
- BGI-Shenzhen and China National GeneBank, Shenzhen, China
| | - Tim Niehues
- Helios Children's Hospital, Krefeld, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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14
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Zhou J, Li J, Stenton SL, Ren X, Gong S, Fang F, Prokisch H. NAD(P)HX dehydratase (NAXD) deficiency: a novel neurodegenerative disorder exacerbated by febrile illnesses. Brain 2020; 143:e8. [PMID: 31755961 DOI: 10.1093/brain/awz375] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Ji Zhou
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Jiuwei Li
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Sarah L Stenton
- Institute of Human Genetics, Technische Universität München, München, Germany
| | - Xiaotun Ren
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Shuai Gong
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, München, Germany
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15
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The Metabolite Repair Enzyme Phosphoglycolate Phosphatase Regulates Central Carbon Metabolism and Fosmidomycin Sensitivity in Plasmodium falciparum. mBio 2019; 10:mBio.02060-19. [PMID: 31822583 PMCID: PMC6904873 DOI: 10.1128/mbio.02060-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The malaria parasite has a voracious appetite, requiring large amounts of glucose and nutrients for its rapid growth and proliferation inside human red blood cells. The host cell is resource rich, but this is a double-edged sword; nutrient excess can lead to undesirable metabolic reactions and harmful by-products. Here, we demonstrate that the parasite possesses a metabolite repair enzyme (PGP) that suppresses harmful metabolic by-products (via substrate dephosphorylation) and allows the parasite to maintain central carbon metabolism. Loss of PGP leads to the accumulation of two damaged metabolites and causes a domino effect of metabolic dysregulation. Accumulation of one damaged metabolite inhibits an essential enzyme in the pentose phosphate pathway, leading to substrate accumulation and secondary inhibition of glycolysis. This work highlights how the parasite coordinates metabolic flux by eliminating harmful metabolic by-products to ensure rapid proliferation in its resource-rich niche. Members of the haloacid dehalogenase (HAD) family of metabolite phosphatases play an important role in regulating multiple pathways in Plasmodium falciparum central carbon metabolism. We show that the P. falciparum HAD protein, phosphoglycolate phosphatase (PGP), regulates glycolysis and pentose pathway flux in asexual blood stages via detoxifying the damaged metabolite 4-phosphoerythronate (4-PE). Disruption of the P. falciparumpgp gene caused accumulation of two previously uncharacterized metabolites, 2-phospholactate and 4-PE. 4-PE is a putative side product of the glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase, and its accumulation inhibits the pentose phosphate pathway enzyme, 6-phosphogluconate dehydrogenase (6-PGD). Inhibition of 6-PGD by 4-PE leads to an unexpected feedback response that includes increased flux into the pentose phosphate pathway as a result of partial inhibition of upper glycolysis, with concomitant increased sensitivity to antimalarials that target pathways downstream of glycolysis. These results highlight the role of metabolite detoxification in regulating central carbon metabolism and drug sensitivity of the malaria parasite.
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16
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Metabolite Repair Enzymes Control Metabolic Damage in Glycolysis. Trends Biochem Sci 2019; 45:228-243. [PMID: 31473074 DOI: 10.1016/j.tibs.2019.07.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/19/2019] [Accepted: 07/31/2019] [Indexed: 12/29/2022]
Abstract
Hundreds of metabolic enzymes work together smoothly in a cell. These enzymes are highly specific. Nevertheless, under physiological conditions, many perform side-reactions at low rates, producing potentially toxic side-products. An increasing number of metabolite repair enzymes are being discovered that serve to eliminate these noncanonical metabolites. Some of these enzymes are extraordinarily conserved, and their deficiency can lead to diseases in humans or embryonic lethality in mice, indicating their central role in cellular metabolism. We discuss how metabolite repair enzymes eliminate glycolytic side-products and prevent negative interference within and beyond this core metabolic pathway. Extrapolating from the number of metabolite repair enzymes involved in glycolysis, hundreds more likely remain to be discovered that protect a wide range of metabolic pathways.
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17
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Van Bergen NJ, Guo Y, Rankin J, Paczia N, Becker-Kettern J, Kremer LS, Pyle A, Conrotte JF, Ellaway C, Procopis P, Prelog K, Homfray T, Baptista J, Baple E, Wakeling M, Massey S, Kay DP, Shukla A, Girisha KM, Lewis LES, Santra S, Power R, Daubeney P, Montoya J, Ruiz-Pesini E, Kovacs-Nagy R, Pritsch M, Ahting U, Thorburn DR, Prokisch H, Taylor RW, Christodoulou J, Linster CL, Ellard S, Hakonarson H. NAD(P)HX dehydratase (NAXD) deficiency: a novel neurodegenerative disorder exacerbated by febrile illnesses. Brain 2019; 142:50-58. [PMID: 30576410 DOI: 10.1093/brain/awy310] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023] Open
Abstract
Physical stress, including high temperatures, may damage the central metabolic nicotinamide nucleotide cofactors [NAD(P)H], generating toxic derivatives [NAD(P)HX]. The highly conserved enzyme NAD(P)HX dehydratase (NAXD) is essential for intracellular repair of NAD(P)HX. Here we present a series of infants and children who suffered episodes of febrile illness-induced neurodegeneration or cardiac failure and early death. Whole-exome or whole-genome sequencing identified recessive NAXD variants in each case. Variants were predicted to be potentially deleterious through in silico analysis. Reverse-transcription PCR confirmed altered splicing in one case. Subject fibroblasts showed highly elevated concentrations of the damaged cofactors S-NADHX, R-NADHX and cyclic NADHX. NADHX accumulation was abrogated by lentiviral transduction of subject cells with wild-type NAXD. Subject fibroblasts and muscle biopsies showed impaired mitochondrial function, higher sensitivity to metabolic stress in media containing galactose and azide, but not glucose, and decreased mitochondrial reactive oxygen species production. Recombinant NAXD protein harbouring two missense variants leading to the amino acid changes p.(Gly63Ser) and p.(Arg608Cys) were thermolabile and showed a decrease in Vmax and increase in KM for the ATP-dependent NADHX dehydratase activity. This is the first study to identify pathogenic variants in NAXD and to link deficient NADHX repair with mitochondrial dysfunction. The results show that NAXD deficiency can be classified as a metabolite repair disorder in which accumulation of damaged metabolites likely triggers devastating effects in tissues such as the brain and the heart, eventually leading to early childhood death.
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Affiliation(s)
- Nicole J Van Bergen
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Melbourne, Australia
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - Julia Rankin
- University of Exeter Medical School, Exeter, UK.,Royal Devon Exeter NHS Foundation Trust, Exeter, UK
| | - Nicole Paczia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Julia Becker-Kettern
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Laura S Kremer
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jean-François Conrotte
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carolyn Ellaway
- Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Discipline of Genetic Medicine, University of Sydney, Sydney, Australia.,Neurology Department, Children's Hospital at Westmead, Sydney, Australia
| | - Peter Procopis
- Neurology Department, Children's Hospital at Westmead, Sydney, Australia.,Discipline of Child and Adolescent Health, University of Sydney, Australia
| | - Kristina Prelog
- Medical Imaging Department, Children's Hospital at Westmead, Sydney, Australia
| | - Tessa Homfray
- Royal Brompton and St George's University Hospital, London, UK
| | - Júlia Baptista
- University of Exeter Medical School, Exeter, UK.,Royal Devon Exeter NHS Foundation Trust, Exeter, UK
| | - Emma Baple
- University of Exeter Medical School, Exeter, UK.,Royal Devon Exeter NHS Foundation Trust, Exeter, UK
| | | | - Sean Massey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Melbourne, Australia
| | - Daniel P Kay
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College and Hospital, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College and Hospital, Manipal Academy of Higher Education, Manipal, India
| | - Leslie E S Lewis
- Department of Paediatrics, Kasturba Medical College and Hospital, Manipal Academy of Higher Education, Manipal, India
| | | | | | - Piers Daubeney
- Royal Brompton Hospital, London, UK.,National Heart and Lung Institute, Imperial College, London, UK
| | - Julio Montoya
- Departamento de Bioquimica y Biologia Molecular y Celular- CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IISAragon), Universidad Zaragoza, Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquimica y Biologia Molecular y Celular- CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IISAragon), Universidad Zaragoza, Zaragoza, Spain
| | - Reka Kovacs-Nagy
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Martin Pritsch
- Department of Pediatric Neurology, DRK-Childrens-Hospital, Siegen, Germany
| | - Uwe Ahting
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Melbourne, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - John Christodoulou
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Melbourne, Australia.,Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Discipline of Genetic Medicine, University of Sydney, Sydney, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Australia
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Sian Ellard
- University of Exeter Medical School, Exeter, UK.,Royal Devon Exeter NHS Foundation Trust, Exeter, UK
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA USA
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18
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Wang S, Alseekh S, Fernie AR, Luo J. The Structure and Function of Major Plant Metabolite Modifications. MOLECULAR PLANT 2019; 12:899-919. [PMID: 31200079 DOI: 10.1016/j.molp.2019.06.001] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.
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Affiliation(s)
- Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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19
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Kempaiah Nagappa L, Satha P, Govindaraju T, Balaram H. Phosphoglycolate phosphatase is a metabolic proofreading enzyme essential for cellular function in Plasmodium berghei. J Biol Chem 2019; 294:4997-5007. [PMID: 30700551 PMCID: PMC6442027 DOI: 10.1074/jbc.ac118.007143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/28/2019] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum (Pf) 4-nitrophenylphosphatase has been shown previously to be involved in vitamin B1 metabolism. Here, conducting a BLASTp search, we found that 4-nitrophenylphosphatase from Pf has significant homology with phosphoglycolate phosphatase (PGP) from mouse, human, and yeast, prompting us to reinvestigate the biochemical properties of the Plasmodium enzyme. Because the recombinant PfPGP enzyme is insoluble, we performed an extended substrate screen and extensive biochemical characterization of the recombinantly expressed and purified homolog from Plasmodium berghei (Pb), leading to the identification of 2-phosphoglycolate and 2-phospho-L-lactate as the relevant physiological substrates of PbPGP. 2-Phosphoglycolate is generated during repair of damaged DNA ends, 2-phospho-L-lactate is a product of pyruvate kinase side reaction, and both potently inhibit two key glycolytic enzymes, triosephosphate isomerase and phosphofructokinase. Hence, PGP-mediated clearance of these toxic metabolites is vital for cell survival and functioning. Our results differ significantly from those in a previous study, wherein the PfPGP enzyme has been inferred to act on 2-phospho-D-lactate and not on the L isomer. Apart from resolving the substrate specificity conflict through direct in vitro enzyme assays, we conducted PGP gene knockout studies in P. berghei, confirming that this conserved metabolic proofreading enzyme is essential in Plasmodium In summary, our findings establish PbPGP as an essential enzyme for normal physiological function in P. berghei and suggest that drugs that specifically inhibit Plasmodium PGP may hold promise for use in anti-malarial therapies.
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Affiliation(s)
| | - Pardhasaradhi Satha
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
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20
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Abstract
Glucose is the long-established, obligatory fuel for brain that fulfills many critical functions, including ATP production, oxidative stress management, and synthesis of neurotransmitters, neuromodulators, and structural components. Neuronal glucose oxidation exceeds that in astrocytes, but both rates increase in direct proportion to excitatory neurotransmission; signaling and metabolism are closely coupled at the local level. Exact details of neuron-astrocyte glutamate-glutamine cycling remain to be established, and the specific roles of glucose and lactate in the cellular energetics of these processes are debated. Glycolysis is preferentially upregulated during brain activation even though oxygen availability is sufficient (aerobic glycolysis). Three major pathways, glycolysis, pentose phosphate shunt, and glycogen turnover, contribute to utilization of glucose in excess of oxygen, and adrenergic regulation of aerobic glycolysis draws attention to astrocytic metabolism, particularly glycogen turnover, which has a high impact on the oxygen-carbohydrate mismatch. Aerobic glycolysis is proposed to be predominant in young children and specific brain regions, but re-evaluation of data is necessary. Shuttling of glucose- and glycogen-derived lactate from astrocytes to neurons during activation, neurotransmission, and memory consolidation are controversial topics for which alternative mechanisms are proposed. Nutritional therapy and vagus nerve stimulation are translational bridges from metabolism to clinical treatment of diverse brain disorders.
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Affiliation(s)
- Gerald A Dienel
- Department of Neurology, University of Arkansas for Medical Sciences , Little Rock, Arkansas ; and Department of Cell Biology and Physiology, University of New Mexico , Albuquerque, New Mexico
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21
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Failure to eliminate a phosphorylated glucose analog leads to neutropenia in patients with G6PT and G6PC3 deficiency. Proc Natl Acad Sci U S A 2019; 116:1241-1250. [PMID: 30626647 PMCID: PMC6347702 DOI: 10.1073/pnas.1816143116] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Neutropenia presents an important clinical problem in patients with G6PC3 or G6PT deficiency, yet why neutropenia occurs is unclear. We discovered that G6PC3 and G6PT collaborate to dephosphorylate a noncanonical metabolite (1,5-anhydroglucitol-6-phosphate; 1,5AG6P) which is produced when glucose-phosphorylating enzymes erroneously act on 1,5-anhydroglucitol, a food-derived polyol present in blood. In patients or mice with G6PC3 or G6PT deficiency, 1,5AG6P accumulates and inhibits the first step of glycolysis. This is particularly detrimental in neutrophils, since their energy metabolism depends almost entirely on glycolysis. Consistent with our findings, we observed that treatment with a 1,5-anhydroglucitol-lowering drug treats neutropenia in G6PC3-deficient mice. Our findings highlight that the elimination of noncanonical side products by metabolite-repair enzymes makes an important contribution to mammalian physiology. Neutropenia represents an important problem in patients with genetic deficiency in either the glucose-6-phosphate transporter of the endoplasmic reticulum (G6PT/SLC37A4) or G6PC3, an endoplasmic reticulum phosphatase homologous to glucose-6-phosphatase. While affected granulocytes show reduced glucose utilization, the underlying mechanism is unknown and causal therapies are lacking. Using a combination of enzymological, cell-culture, and in vivo approaches, we demonstrate that G6PT and G6PC3 collaborate to destroy 1,5-anhydroglucitol-6-phosphate (1,5AG6P), a close structural analog of glucose-6-phosphate and an inhibitor of low-KM hexokinases, which catalyze the first step in glycolysis in most tissues. We show that 1,5AG6P is made by phosphorylation of 1,5-anhydroglucitol, a compound normally present in human plasma, by side activities of ADP-glucokinase and low-KM hexokinases. Granulocytes from patients deficient in G6PC3 or G6PT accumulate 1,5AG6P to concentrations (∼3 mM) that strongly inhibit hexokinase activity. In a model of G6PC3-deficient mouse neutrophils, physiological concentrations of 1,5-anhydroglucitol caused massive accumulation of 1,5AG6P, a decrease in glucose utilization, and cell death. Treating G6PC3-deficient mice with an inhibitor of the kidney glucose transporter SGLT2 to lower their blood level of 1,5-anhydroglucitol restored a normal neutrophil count, while administration of 1,5-anhydroglucitol had the opposite effect. In conclusion, we show that the neutropenia in patients with G6PC3 or G6PT mutations is a metabolite-repair deficiency, caused by a failure to eliminate the nonclassical metabolite 1,5AG6P.
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22
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Bowman CE, Wolfgang MJ. Role of the malonyl-CoA synthetase ACSF3 in mitochondrial metabolism. Adv Biol Regul 2019; 71:34-40. [PMID: 30201289 PMCID: PMC6347522 DOI: 10.1016/j.jbior.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 12/26/2022]
Abstract
Malonyl-CoA is a central metabolite in fatty acid biochemistry. It is the rate-determining intermediate in fatty acid synthesis but is also an allosteric inhibitor of the rate-setting step in mitochondrial long-chain fatty acid oxidation. While these canonical cytoplasmic roles of malonyl-CoA have been well described, malonyl-CoA can also be generated within the mitochondrial matrix by an alternative pathway: the ATP-dependent ligation of malonate to Coenzyme A by the malonyl-CoA synthetase ACSF3. Malonate, a competitive inhibitor of succinate dehydrogenase of the TCA cycle, is a potent inhibitor of mitochondrial respiration. A major role for ACSF3 is to provide a metabolic pathway for the clearance of malonate by the generation of malonyl-CoA, which can then be decarboxylated to acetyl-CoA by malonyl-CoA decarboxylase. Additionally, ACSF3-derived malonyl-CoA can be used to malonylate lysine residues on proteins within the matrix of mitochondria, possibly adding another regulatory layer to post-translational control of mitochondrial metabolism. The discovery of ACSF3-mediated generation of malonyl-CoA defines a new mitochondrial metabolic pathway and raises new questions about how the metabolic fates of this multifunctional metabolite intersect with mitochondrial metabolism.
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Affiliation(s)
- Caitlyn E Bowman
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michael J Wolfgang
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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23
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Peracchi A. The Limits of Enzyme Specificity and the Evolution of Metabolism. Trends Biochem Sci 2018; 43:984-996. [DOI: 10.1016/j.tibs.2018.09.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 12/23/2022]
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24
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de Crécy-Lagard V, Haas D, Hanson AD. Newly-discovered enzymes that function in metabolite damage-control. Curr Opin Chem Biol 2018; 47:101-108. [PMID: 30268903 DOI: 10.1016/j.cbpa.2018.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/19/2018] [Accepted: 09/11/2018] [Indexed: 01/26/2023]
Abstract
Enzymes of unknown function are estimated to make up around 25% of the sequenced proteome. In the past decade, over 20 conserved families have been shown to function in the metabolism of 'damaged' or abnormal metabolites that are wasteful and often toxic. These newly discovered damage-control enzymes either repair or inactivate the offending metabolites, or pre-empt their formation in the first place. Comparative genomics has been of prime importance in predicting the functions of damage-control enzymes and in guiding the biochemical and genetic tests required to validate these functions.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA; Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Drago Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
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25
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Becker-Kettern J, Paczia N, Conrotte JF, Zhu C, Fiehn O, Jung PP, Steinmetz LM, Linster CL. NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells. FEBS J 2018; 285:3376-3401. [PMID: 30098110 DOI: 10.1111/febs.14631] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/20/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
NADHX and NADPHX are hydrated and redox inactive forms of the NADH and NADPH cofactors, known to inhibit several dehydrogenases in vitro. A metabolite repair system that is conserved in all domains of life and that comprises the two enzymes NAD(P)HX dehydratase and NAD(P)HX epimerase, allows reconversion of both the S- and R-epimers of NADHX and NADPHX to the normal cofactors. An inherited deficiency in this system has recently been shown to cause severe neurometabolic disease in children. Although evidence for the presence of NAD(P)HX has been obtained in plant and human cells, little is known about the mechanism of formation of these derivatives in vivo and their potential effects on cell metabolism. Here, we show that NAD(P)HX dehydratase deficiency in yeast leads to an important, temperature-dependent NADHX accumulation in quiescent cells with a concomitant depletion of intracellular NAD+ and serine pools. We demonstrate that NADHX potently inhibits the first step of the serine synthesis pathway in yeast. Human cells deficient in the NAD(P)HX dehydratase also accumulated NADHX and showed decreased viability. In addition, those cells consumed more glucose and produced more lactate, potentially indicating impaired mitochondrial function. Our results provide first insights into how NADHX accumulation affects cellular functions and pave the way for a better understanding of the mechanism(s) underlying the rapid and severe neurodegeneration leading to early death in NADHX repair-deficient children.
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Affiliation(s)
- Julia Becker-Kettern
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Nicole Paczia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Jean-François Conrotte
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Chenchen Zhu
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, CA, USA
| | - Paul P Jung
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, CA, USA
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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26
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Jeffryes JG, Seaver SMD, Faria JP, Henry CS. A pathway for every product? Tools to discover and design plant metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:61-70. [PMID: 29907310 DOI: 10.1016/j.plantsci.2018.03.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
The vast diversity of plant natural products is a powerful indication of the biosynthetic capacity of plant metabolism. Synthetic biology seeks to capitalize on this ability by understanding and reconfiguring the biosynthetic pathways that generate this diversity to produce novel products with improved efficiency. Here we review the algorithms and databases that presently support the design and manipulation of metabolic pathways in plants, starting from metabolic models of native biosynthetic pathways, progressing to novel combinations of known reactions, and finally proposing new reactions that may be carried out by existing enzymes. We show how these tools are useful for proposing new pathways as well as identifying side reactions that may affect engineering goals.
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Affiliation(s)
- James G Jeffryes
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - Samuel M D Seaver
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - José P Faria
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - Christopher S Henry
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States.
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27
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Buege MJ, DiPippo AJ, DiNardo CD. Evolving Treatment Strategies for Elderly Leukemia Patients with IDH Mutations. Cancers (Basel) 2018; 10:E187. [PMID: 29882807 PMCID: PMC6025071 DOI: 10.3390/cancers10060187] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/23/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is a debilitating and life-threatening condition, especially for elderly patients who account for over 50% of diagnoses. For over four decades, standard induction therapy with intensive cytotoxic chemotherapy for AML had remained unchanged. However, for most patients, standard therapy continues to have its shortcomings, especially for elderly patients who may not be able to tolerate the complications from intensive cytotoxic chemotherapy. New research into the development of targeted and alternative therapies has led to a new era in AML therapy. For the nearly 20% of diagnoses harboring a mutation in isocitrate dehydrogenase 1 or 2 (IDH1/2), potential treatment options have undergone a paradigm shift away from intensive cytotoxic chemotherapy and towards targeted therapy alone or in combination with lower intensity chemotherapy. The first FDA approved IDH2 inhibitor was enasidenib in 2017. In addition, IDH1 inhibitors are in ongoing clinical studies, and the oral BCL-2 inhibitor venetoclax shows preliminary efficacy in this subset of patients. These new tools aim to improve outcomes and change the treatment paradigm for elderly patients with IDH mutant AML. However, the challenge of how to best incorporate these agents into standard practice remains.
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Affiliation(s)
- Michael J Buege
- Pharmacy Clinical Programs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Adam J DiPippo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Courtney D DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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28
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Ellens KW, Christian N, Singh C, Satagopam VP, May P, Linster CL. Confronting the catalytic dark matter encoded by sequenced genomes. Nucleic Acids Res 2017; 45:11495-11514. [PMID: 29059321 PMCID: PMC5714238 DOI: 10.1093/nar/gkx937] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 10/03/2017] [Indexed: 01/02/2023] Open
Abstract
The post-genomic era has provided researchers with a deluge of protein sequences. However, a significant fraction of the proteins encoded by sequenced genomes remains without an identified function. Here, we aim at determining how many enzymes of uncertain or unknown function are still present in the Saccharomyces cerevisiae and human proteomes. Using information available in the Swiss-Prot, BRENDA and KEGG databases in combination with a Hidden Markov Model-based method, we estimate that >600 yeast and 2000 human proteins (>30% of their proteins of unknown function) are enzymes whose precise function(s) remain(s) to be determined. This illustrates the impressive scale of the ‘unknown enzyme problem’. We extensively review classical biochemical as well as more recent systematic experimental and computational approaches that can be used to support enzyme function discovery research. Finally, we discuss the possible roles of the elusive catalysts in light of recent developments in the fields of enzymology and metabolism as well as the significance of the unknown enzyme problem in the context of metabolic modeling, metabolic engineering and rare disease research.
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Affiliation(s)
- Kenneth W Ellens
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Nils Christian
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Charandeep Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Venkata P Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
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29
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Asai S, Miura N, Sawada Y, Noda T, Kikugawa T, Tanji N, Saika T. Silencing of ECHDC1 inhibits growth of gemcitabine-resistant bladder cancer cells. Oncol Lett 2017; 15:522-527. [PMID: 29391886 DOI: 10.3892/ol.2017.7269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
Combined gemcitabine and cisplatin (GC) treatment is a first line chemotherapy for bladder cancer. However, acquired resistance to GC has been a major problem. To address the mechanism of gemcitabine resistance, and to identify potential biomarkers or target proteins for its therapy, we aimed to identify candidate proteins associated with gemcitabine resistance using proteomic analysis. We established gemcitabine-resistant human bladder cancer cell lines (UMUC3GR and HT1376GR) from gemcitabine-sensitive human bladder cancer cell lines (UMUC3 and HT1376). We compared the protein expression of parental and gemcitabine-resistant cell lines using isobaric tags for relative and absolute quantification (iTRAQ) and liquid chromatography tandem mass spectrometry. Among the identified proteins, ethylmalonyl-CoA decarboxylase (ECHDC1) expression was significantly increased in both of the gemcitabine-resistant cell lines compared to the respective parental cell lines. Silencing of ECHDC1 reduced ECHDC1 expression and significantly inhibited the proliferation of UMUC3GR cells. Furthermore, silencing of ECHDC1 induced upregulation of p27, which is critical for cell cycle arrest in the G1 phase, and induced G1 arrest. In conclusion, ECHDC1 expression is increased in gemcitabine-resistant bladder cancer cells, and is involved in their cell growth. ECHDC1, which is a metabolite proofreading enzyme, may be a novel potential target for gemcitabine-resistant bladder cancer therapy.
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Affiliation(s)
- Seiji Asai
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Noriyoshi Miura
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Yuichiro Sawada
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Terutaka Noda
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Tadahiko Kikugawa
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Nozomu Tanji
- Department of Urology, Houshasen-Daiichi Hospital, Imabari, Ehime 794-0054, Japan
| | - Takashi Saika
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
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30
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Pertusi DA, Moura ME, Jeffryes JG, Prabhu S, Walters Biggs B, Tyo KEJ. Predicting novel substrates for enzymes with minimal experimental effort with active learning. Metab Eng 2017; 44:171-181. [PMID: 29030274 DOI: 10.1016/j.ymben.2017.09.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/20/2017] [Accepted: 09/18/2017] [Indexed: 01/26/2023]
Abstract
Enzymatic substrate promiscuity is more ubiquitous than previously thought, with significant consequences for understanding metabolism and its application to biocatalysis. This realization has given rise to the need for efficient characterization of enzyme promiscuity. Enzyme promiscuity is currently characterized with a limited number of human-selected compounds that may not be representative of the enzyme's versatility. While testing large numbers of compounds may be impractical, computational approaches can exploit existing data to determine the most informative substrates to test next, thereby more thoroughly exploring an enzyme's versatility. To demonstrate this, we used existing studies and tested compounds for four different enzymes, developed support vector machine (SVM) models using these datasets, and selected additional compounds for experiments using an active learning approach. SVMs trained on a chemically diverse set of compounds were discovered to achieve maximum accuracies of ~80% using ~33% fewer compounds than datasets based on all compounds tested in existing studies. Active learning-selected compounds for testing resolved apparent conflicts in the existing training data, while adding diversity to the dataset. The application of these algorithms to wide arrays of metabolic enzymes would result in a library of SVMs that can predict high-probability promiscuous enzymatic reactions and could prove a valuable resource for the design of novel metabolic pathways.
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Affiliation(s)
- Dante A Pertusi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Matthew E Moura
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - James G Jeffryes
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, United States
| | - Siddhant Prabhu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Bradley Walters Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States.
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31
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Sun J, Jeffryes JG, Henry CS, Bruner SD, Hanson AD. Metabolite damage and repair in metabolic engineering design. Metab Eng 2017; 44:150-159. [PMID: 29030275 DOI: 10.1016/j.ymben.2017.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 01/05/2023]
Abstract
The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it. Metabolite damage and repair are highly relevant to engineered pathway design: metabolite damage reactions can reduce flux rates and product yields, and repair enzymes can provide robust, host-independent solutions. Herein, after introducing the core principles of metabolite damage and repair, we use case histories to document how damage and repair processes affect efficient operation of engineered pathways - particularly those that are heterologous, non-natural, or cell-free. We then review how metabolite damage reactions can be predicted, how repair reactions can be prospected, and how metabolite damage and repair can be built into genome-scale metabolic models. Lastly, we propose a versatile 'plug and play' set of well-characterized metabolite repair enzymes to solve metabolite damage problems known or likely to occur in metabolic engineering and synthetic biology projects.
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Affiliation(s)
- Jiayi Sun
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - James G Jeffryes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA; Computation Institute, The University of Chicago, Chicago, IL, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
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Coupling between d-3-phosphoglycerate dehydrogenase and d-2-hydroxyglutarate dehydrogenase drives bacterial l-serine synthesis. Proc Natl Acad Sci U S A 2017; 114:E7574-E7582. [PMID: 28827360 DOI: 10.1073/pnas.1619034114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
l-Serine biosynthesis, a crucial metabolic process in most domains of life, is initiated by d-3-phosphoglycerate (d-3-PG) dehydrogenation, a thermodynamically unfavorable reaction catalyzed by d-3-PG dehydrogenase (SerA). d-2-Hydroxyglutarate (d-2-HG) is traditionally viewed as an abnormal metabolite associated with cancer and neurometabolic disorders. Here, we reveal that bacterial anabolism and catabolism of d-2-HG are involved in l-serine biosynthesis in Pseudomonas stutzeri A1501 and Pseudomonas aeruginosa PAO1. SerA catalyzes the stereospecific reduction of 2-ketoglutarate (2-KG) to d-2-HG, responsible for the major production of d-2-HG in vivo. SerA combines the energetically favorable reaction of d-2-HG production to overcome the thermodynamic barrier of d-3-PG dehydrogenation. We identified a bacterial d-2-HG dehydrogenase (D2HGDH), a flavin adenine dinucleotide (FAD)-dependent enzyme, that converts d-2-HG back to 2-KG. Electron transfer flavoprotein (ETF) and ETF-ubiquinone oxidoreductase (ETFQO) are also essential in d-2-HG metabolism through their capacity to transfer electrons from D2HGDH. Furthermore, while the mutant with D2HGDH deletion displayed decreased growth, the defect was rescued by adding l-serine, suggesting that the D2HGDH is functionally tied to l-serine synthesis. Substantial flux flows through d-2-HG, being produced by SerA and removed by D2HGDH, ETF, and ETFQO, maintaining d-2-HG homeostasis. Overall, our results uncover that d-2-HG-mediated coupling between SerA and D2HGDH drives bacterial l-serine synthesis.
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33
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A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis. Biochem J 2017; 474:2887-2895. [DOI: 10.1042/bcj20170437] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 01/26/2023]
Abstract
The canonical kinase (ThiD) that converts the thiamin biosynthesis intermediate hydroxymethylpyrimidine (HMP) monophosphate into the diphosphate can also very efficiently convert free HMP into the monophosphate in prokaryotes, plants, and fungi. This HMP kinase activity enables salvage of HMP, but it is not substrate-specific and so allows toxic HMP analogs and damage products to infiltrate the thiamin biosynthesis pathway. Comparative analysis of bacterial genomes uncovered a gene, thiD2, that is often fused to the thiamin synthesis gene thiE and could potentially encode a replacement for ThiD. Standalone ThiD2 proteins and ThiD2 fusion domains are small (∼130 residues) and do not belong to any previously known protein family. Genetic and biochemical analyses showed that representative standalone and fused ThiD2 proteins catalyze phosphorylation of HMP monophosphate, but not of HMP or its toxic analogs and damage products such as bacimethrin and 5-(hydroxymethyl)-2-methylpyrimidin-4-ol. As strictly monofunctional HMP monophosphate kinases, ThiD2 proteins eliminate a potentially fatal vulnerability of canonical ThiD, at the cost of the ability to reclaim HMP formed by thiamin turnover.
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34
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A molecular rheostat maintains ATP levels to drive a synthetic biochemistry system. Nat Chem Biol 2017; 13:938-942. [PMID: 28671683 DOI: 10.1038/nchembio.2418] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/11/2017] [Indexed: 11/08/2022]
Abstract
Synthetic biochemistry seeks to engineer complex metabolic pathways for chemical conversions outside the constraints of the cell. Establishment of effective and flexible cell-free systems requires the development of simple systems to replace the intricate regulatory mechanisms that exist in cells for maintaining high-energy cofactor balance. Here we describe a simple rheostat that regulates ATP levels by controlling the flow down either an ATP-generating or non-ATP-generating pathway according to the free-phosphate concentration. We implemented this concept for the production of isobutanol from glucose. The rheostat maintains adequate ATP concentrations even in the presence of ATPase contamination. The final system including the rheostat produced 24.1 ± 1.8 g/L of isobutanol from glucose in 91% theoretical yield with an initial productivity of 1.3 g/L/h. The molecular rheostat concept can be used in the design of continuously operating, self-sustaining synthetic biochemistry systems.
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35
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The Mammalian Malonyl-CoA Synthetase ACSF3 Is Required for Mitochondrial Protein Malonylation and Metabolic Efficiency. Cell Chem Biol 2017; 24:673-684.e4. [PMID: 28479296 DOI: 10.1016/j.chembiol.2017.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/08/2017] [Accepted: 04/07/2017] [Indexed: 12/13/2022]
Abstract
Malonyl-coenzyme A (malonyl-CoA) is a central metabolite in mammalian fatty acid biochemistry generated and utilized in the cytoplasm; however, little is known about noncanonical organelle-specific malonyl-CoA metabolism. Intramitochondrial malonyl-CoA is generated by a malonyl-CoA synthetase, ACSF3, which produces malonyl-CoA from malonate, an endogenous competitive inhibitor of succinate dehydrogenase. To determine the metabolic requirement for mitochondrial malonyl-CoA, ACSF3 knockout (KO) cells were generated by CRISPR/Cas-mediated genome editing. ACSF3 KO cells exhibited elevated malonate and impaired mitochondrial metabolism. Unbiased and targeted metabolomics analysis of KO and control cells in the presence or absence of exogenous malonate revealed metabolic changes dependent on either malonate or malonyl-CoA. While ACSF3 was required for the metabolism and therefore detoxification of malonate, ACSF3-derived malonyl-CoA was specifically required for lysine malonylation of mitochondrial proteins. Together, these data describe an essential role for ACSF3 in dictating the metabolic fate of mitochondrial malonate and malonyl-CoA in mammalian metabolism.
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36
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Cairns RA, Mak TW. Fire and water: Tumor cell adaptation to metabolic conditions. Exp Cell Res 2017; 356:204-208. [PMID: 28457987 DOI: 10.1016/j.yexcr.2017.04.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 12/23/2022]
Abstract
Lorenz Poellinger was a leader in understanding the effects of altered microenvironmental conditions in tumor biology and in normal physiology. His work examining the effects of hypoxia and the HIF transcription factors has expanded our understanding of the role of the microenvironment in affecting the behaviour of both normal and malignant cells. Furthermore, his work provides a model for understanding the adaptive responses to other metabolic stress conditions. By investigating the molecular mechanisms responsible for the adaptive responses to metabolic stress in normal physiological situations, across pathological conditions, and in different model organisms, his work shows the power of combining data from different model systems and physiological contexts. In cancers, it has become clear that in order to evolve to become an aggressive malignant disease, tumor cells must acquire the capacity to tolerate a host of abnormal and stressful metabolic conditions. This metabolic stress can be thought of as a fire that tumor cells must douse with enough water to survive, and may offer opportunities to exploit smoldering vulnerabilities in order to eradicate malignant cells.
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Affiliation(s)
- Rob A Cairns
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada M5G 2C1.
| | - Tak W Mak
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada M5G 2C1
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37
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Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proc Natl Acad Sci U S A 2017; 114:E3233-E3242. [PMID: 28373563 DOI: 10.1073/pnas.1613736114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The mammalian gene Nit1 (nitrilase-like protein 1) encodes a protein that is highly conserved in eukaryotes and is thought to act as a tumor suppressor. Despite being ∼35% sequence identical to ω-amidase (Nit2), the Nit1 protein does not hydrolyze efficiently α-ketoglutaramate (a known physiological substrate of Nit2), and its actual enzymatic function has so far remained a puzzle. In the present study, we demonstrate that both the mammalian Nit1 and its yeast ortholog are amidases highly active toward deaminated glutathione (dGSH; i.e., a form of glutathione in which the free amino group has been replaced by a carbonyl group). We further show that Nit1-KO mutants of both human and yeast cells accumulate dGSH and the same compound is excreted in large amounts in the urine of Nit1-KO mice. Finally, we show that several mammalian aminotransferases (transaminases), both cytosolic and mitochondrial, can form dGSH via a common (if slow) side-reaction and provide indirect evidence that transaminases are mainly responsible for dGSH formation in cultured mammalian cells. Altogether, these findings delineate a typical instance of metabolite repair, whereby the promiscuous activity of some abundant enzymes of primary metabolism leads to the formation of a useless and potentially harmful compound, which needs a suitable "repair enzyme" to be destroyed or reconverted into a useful metabolite. The need for a dGSH repair reaction does not appear to be limited to eukaryotes: We demonstrate that Nit1 homologs acting as excellent dGSH amidases also occur in Escherichia coli and other glutathione-producing bacteria.
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38
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Hariharan VA, Denton TT, Paraszcszak S, McEvoy K, Jeitner TM, Krasnikov BF, Cooper AJL. The Enzymology of 2-Hydroxyglutarate, 2-Hydroxyglutaramate and 2-Hydroxysuccinamate and Their Relationship to Oncometabolites. BIOLOGY 2017; 6:biology6020024. [PMID: 28358347 PMCID: PMC5485471 DOI: 10.3390/biology6020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/10/2017] [Accepted: 03/13/2017] [Indexed: 12/17/2022]
Abstract
Many enzymes make "mistakes". Consequently, repair enzymes have evolved to correct these mistakes. For example, lactate dehydrogenase (LDH) and mitochondrial malate dehydrogenase (mMDH) slowly catalyze the reduction of 2-oxoglutarate (2-OG) to the oncometabolite l-2-hydroxyglutarate (l-2-HG). l-2-HG dehydrogenase corrects this error by converting l-2-HG to 2-OG. LDH also catalyzes the reduction of the oxo group of 2-oxoglutaramate (2-OGM; transamination product of l-glutamine). We show here that human glutamine synthetase (GS) catalyzes the amidation of the terminal carboxyl of both the l- and d- isomers of 2-HG. The reaction of 2-OGM with LDH and the reaction of l-2-HG with GS generate l-2-hydroxyglutaramate (l-2-HGM). We also show that l-2-HGM is a substrate of human ω-amidase. The product (l-2-HG) can then be converted to 2-OG by l-2-HG dehydrogenase. Previous work showed that 2-oxosuccinamate (2-OSM; transamination product of l-asparagine) is an excellent substrate of LDH. Finally, we also show that human ω-amidase converts the product of this reaction (i.e., l-2-hydroxysuccinamate; l-2-HSM) to l-malate. Thus, ω-amidase may act together with hydroxyglutarate dehydrogenases to repair certain "mistakes" of GS and LDH. The present findings suggest that non-productive pathways for nitrogen metabolism occur in mammalian tissues in vivo. Perturbations of these pathways may contribute to symptoms associated with hydroxyglutaric acidurias and to tumor progression. Finally, methods for the synthesis of l-2-HGM and l-2-HSM are described that should be useful in determining the roles of ω-amidase/4- and 5-C compounds in photorespiration in plants.
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Affiliation(s)
- Vivek A Hariharan
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10590, USA.
| | - Travis T Denton
- Department of Pharmaceutical Sciences, Washington State University, College of Pharmacy, Spokane, WA 99210-1495, USA.
| | - Sarah Paraszcszak
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10590, USA.
| | - Kyle McEvoy
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10590, USA.
| | - Thomas M Jeitner
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10590, USA.
| | - Boris F Krasnikov
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10590, USA.
| | - Arthur J L Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10590, USA.
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Natarajan SK, Muthukrishnan E, Khalimonchuk O, Mott JL, Becker DF. Evidence for Pipecolate Oxidase in Mediating Protection Against Hydrogen Peroxide Stress. J Cell Biochem 2016; 118:1678-1688. [PMID: 27922192 DOI: 10.1002/jcb.25825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/02/2016] [Indexed: 01/16/2023]
Abstract
Pipecolate, an intermediate of the lysine catabolic pathway, is oxidized to Δ1 -piperideine-6-carboxylate (P6C) by the flavoenzyme l-pipecolate oxidase (PIPOX). P6C spontaneously hydrolyzes to generate α-aminoadipate semialdehyde, which is then converted into α-aminoadipate acid by α-aminoadipatesemialdehyde dehydrogenase. l-pipecolate was previously reported to protect mammalian cells against oxidative stress. Here, we examined whether PIPOX is involved in the mechanism of pipecolate stress protection. Knockdown of PIPOX by small interference RNA abolished pipecolate protection against hydrogen peroxide-induced cell death in HEK293 cells suggesting a critical role for PIPOX. Subcellular fractionation analysis showed that PIPOX is localized in the mitochondria of HEK293 cells consistent with its role in lysine catabolism. Signaling pathways potentially involved in pipecolate protection were explored by treating cells with small molecule inhibitors. Inhibition of both mTORC1 and mTORC2 kinase complexes or inhibition of Akt kinase alone blocked pipecolate protection suggesting the involvement of these signaling pathways. Phosphorylation of the Akt downstream target, forkhead transcription factor O3 (FoxO3), was also significantly increased in cells treated with pipecolate, further implicating Akt in the protective mechanism and revealing FoxO3 inhibition as a potentially key step. The results presented here demonstrate that pipecolate metabolism can influence cell signaling during oxidative stress to promote cell survival and suggest that the mechanism of pipecolate protection parallels that of proline, which is also metabolized in the mitochondria. J. Cell. Biochem. 118: 1678-1688, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sathish Kumar Natarajan
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588.,Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, 68583
| | - Ezhumalai Muthukrishnan
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, 68583
| | - Oleh Khalimonchuk
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Justin L Mott
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, 68198
| | - Donald F Becker
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
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40
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Ion BF, Aboelnga MM, Gauld JW. Insights from molecular dynamics on substrate binding and effects of active site mutations in Δ1-pyrroline-5-carboxylate dehydrogenase. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The NAD+-dependent enzyme, Δ1-pyrroline-5-carboxylate dehydrogenase (P5CDH), has an important role in proline and hydroxyproline catabolism for humans. Specifically, this aldehyde dehydrogenase is responsible for the oxidation of both l-glutamate-γ-semialdehyde (GSA) and 4-erythro-hydroxy-l-glutamate-γ-semialdehyde (4-OH-GSA) to their respective l-glutamate product forms. We have performed a detailed molecular dynamics (MD) study of both the reactant and product complex structures of P5CDH to gain insights into ligand binding (i.e., GSA, 4-OH-GSA, NAD+, GLU) in the active site. Moreover, our investigations were further extended to examine the structural impact of S352L, S352A, and E314A mutations on the deficiency in the P5CDH enzymatic activity. Our in silico mutation analysis indicated that the conserved Glu447 has significantly shifted in both the S352L and E314A mutants, causing NAD+ to be displaced from its predictive orientation in the binding site and hence forming a catalytically inactive enzyme. However in the case of S352A, the catalytic site including the oxyanion hole and Cys348 remain virtually unchanged, and the coenzyme maintains its binding position.
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Affiliation(s)
- Bogdan F. Ion
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Mohamed M. Aboelnga
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - James W. Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
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41
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Singh C, Glaab E, Linster CL. Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. J Biol Chem 2016; 292:1005-1028. [PMID: 27909055 DOI: 10.1074/jbc.m116.760744] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
Proteomes of even well characterized organisms still contain a high percentage of proteins with unknown or uncertain molecular and/or biological function. A significant fraction of those proteins is predicted to have catalytic properties. Here we aimed at identifying the function of the Saccharomyces cerevisiae Ydr109c protein and its human homolog FGGY, both of which belong to the broadly conserved FGGY family of carbohydrate kinases. Functionally identified members of this family phosphorylate 3- to 7-carbon sugars or sugar derivatives, but the endogenous substrate of S. cerevisiae Ydr109c and human FGGY has remained unknown. Untargeted metabolomics analysis of an S. cerevisiae deletion mutant of YDR109C revealed ribulose as one of the metabolites with the most significantly changed intracellular concentration as compared with a wild-type strain. In human HEK293 cells, ribulose could only be detected when ribitol was added to the cultivation medium, and under this condition, FGGY silencing led to ribulose accumulation. Biochemical characterization of the recombinant purified Ydr109c and FGGY proteins showed a clear substrate preference of both kinases for d-ribulose over a range of other sugars and sugar derivatives tested, including l-ribulose. Detailed sequence and structural analyses of Ydr109c and FGGY as well as homologs thereof furthermore allowed the definition of a 5-residue d-ribulokinase signature motif (TCSLV). The physiological role of the herein identified eukaryotic d-ribulokinase remains unclear, but we speculate that S. cerevisiae Ydr109c and human FGGY could act as metabolite repair enzymes, serving to re-phosphorylate free d-ribulose generated by promiscuous phosphatases from d-ribulose 5-phosphate. In human cells, FGGY can additionally participate in ribitol metabolism.
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Affiliation(s)
- Charandeep Singh
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
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42
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Sharma M, Sud A, Kaur T, Tandon C, Singla SK. N-acetylcysteine with apocynin prevents hyperoxaluria-induced mitochondrial protein perturbations in nephrolithiasis. Free Radic Res 2016; 50:1032-44. [DOI: 10.1080/10715762.2016.1221507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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43
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A conserved phosphatase destroys toxic glycolytic side products in mammals and yeast. Nat Chem Biol 2016; 12:601-7. [PMID: 27294321 DOI: 10.1038/nchembio.2104] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 03/28/2016] [Indexed: 11/08/2022]
Abstract
Metabolic enzymes are very specific. However, most of them show weak side activities toward compounds that are structurally related to their physiological substrates, thereby producing side products that may be toxic. In some cases, 'metabolite repair enzymes' eliminating side products have been identified. We show that mammalian glyceraldehyde 3-phosphate dehydrogenase and pyruvate kinase, two core glycolytic enzymes, produce 4-phosphoerythronate and 2-phospho-L-lactate, respectively. 4-Phosphoerythronate strongly inhibits an enzyme of the pentose phosphate pathway, whereas 2-phospho-L-lactate inhibits the enzyme producing the glycolytic activator fructose 2,6-bisphosphate. We discovered that a single, widely conserved enzyme, known as phosphoglycolate phosphatase (PGP) in mammals, dephosphorylates both 4-phosphoerythronate and 2-phospho-L-lactate, thereby preventing a block in the pentose phosphate pathway and glycolysis. Its yeast ortholog, Pho13, similarly dephosphorylates 4-phosphoerythronate and 2-phosphoglycolate, a side product of pyruvate kinase. Our work illustrates how metabolite repair enzymes can make up for the limited specificity of metabolic enzymes and permit high flux in central metabolic pathways.
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44
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Hanson AD, Henry CS, Fiehn O, de Crécy-Lagard V. Metabolite Damage and Metabolite Damage Control in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:131-52. [PMID: 26667673 DOI: 10.1146/annurev-arplant-043015-111648] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It is increasingly clear that (a) many metabolites undergo spontaneous or enzyme-catalyzed side reactions in vivo, (b) the damaged metabolites formed by these reactions can be harmful, and (c) organisms have biochemical systems that limit the buildup of damaged metabolites. These damage-control systems either return a damaged molecule to its pristine state (metabolite repair) or convert harmful molecules to harmless ones (damage preemption). Because all organisms share a core set of metabolites that suffer the same chemical and enzymatic damage reactions, certain damage-control systems are widely conserved across the kingdoms of life. Relatively few damage reactions and damage-control systems are well known. Uncovering new damage reactions and identifying the corresponding damaged metabolites, damage-control genes, and enzymes demands a coordinated mix of chemistry, metabolomics, cheminformatics, biochemistry, and comparative genomics. This review illustrates the above points using examples from plants, which are at least as prone to metabolite damage as other organisms.
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Affiliation(s)
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439;
- Computation Institute, University of Chicago, Chicago, Illinois 60637
| | - Oliver Fiehn
- Genome Center, University of California, Davis, California 95616;
| | - Valérie de Crécy-Lagard
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611; ,
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45
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Becker-Kettern J, Paczia N, Conrotte JF, Kay DP, Guignard C, Jung PP, Linster CL. Saccharomyces cerevisiae Forms D-2-Hydroxyglutarate and Couples Its Degradation to D-Lactate Formation via a Cytosolic Transhydrogenase. J Biol Chem 2016; 291:6036-58. [PMID: 26774271 DOI: 10.1074/jbc.m115.704494] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 12/23/2022] Open
Abstract
The D or L form of 2-hydroxyglutarate (2HG) accumulates in certain rare neurometabolic disorders, and high D-2-hydroxyglutarate (D-2HG) levels are also found in several types of cancer. Although 2HG has been detected in Saccharomyces cerevisiae, its metabolism in yeast has remained largely unexplored. Here, we show that S. cerevisiae actively forms the D enantiomer of 2HG. Accordingly, the S. cerevisiae genome encodes two homologs of the human D-2HG dehydrogenase: Dld2, which, as its human homolog, is a mitochondrial protein, and the cytosolic protein Dld3. Intriguingly, we found that a dld3Δ knock-out strain accumulates millimolar levels of D-2HG, whereas a dld2Δ knock-out strain displayed only very moderate increases in D-2HG. Recombinant Dld2 and Dld3, both currently annotated as D-lactate dehydrogenases, efficiently oxidized D-2HG to α-ketoglutarate. Depletion of D-lactate levels in the dld3Δ, but not in the dld2Δ mutant, led to the discovery of a new type of enzymatic activity, carried by Dld3, to convert D-2HG to α-ketoglutarate, namely an FAD-dependent transhydrogenase activity using pyruvate as a hydrogen acceptor. We also provide evidence that Ser3 and Ser33, which are primarily known for oxidizing 3-phosphoglycerate in the main serine biosynthesis pathway, in addition reduce α-ketoglutarate to D-2HG using NADH and represent major intracellular sources of D-2HG in yeast. Based on our observations, we propose that D-2HG is mainly formed and degraded in the cytosol of S. cerevisiae cells in a process that couples D-2HG metabolism to the shuttling of reducing equivalents from cytosolic NADH to the mitochondrial respiratory chain via the D-lactate dehydrogenase Dld1.
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Affiliation(s)
- Julia Becker-Kettern
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Nicole Paczia
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Jean-François Conrotte
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Daniel P Kay
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Cédric Guignard
- the Luxembourg Institute of Science and Technology, 41 Rue du Brill, L-4422 Belvaux, Luxembourg
| | - Paul P Jung
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Carole L Linster
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
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46
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Gelman SJ, Mahieu NG, Cho K, Llufrio EM, Wencewicz TA, Patti GJ. Evidence that 2-hydroxyglutarate is not readily metabolized in colorectal carcinoma cells. Cancer Metab 2015; 3:13. [PMID: 26629338 PMCID: PMC4665876 DOI: 10.1186/s40170-015-0139-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/09/2015] [Indexed: 12/13/2022] Open
Abstract
Background Two-hydroxyglutarate (2HG) is present at low concentrations in healthy mammalian cells as both an L and D enantiomer. Both the L and D enantiomers have been implicated in regulating cellular physiology by mechanisms that are only partially characterized. In multiple human cancers, the D enantiomer accumulates due to gain-of-function mutations in the enzyme isocitrate dehydrogenase (IDH) and has been hypothesized to drive malignancy through mechanisms that remain incompletely understood. While much attention has been dedicated to identifying the route of 2HG synthesis, the metabolic fate of 2HG has not been studied in detail. Yet the metabolism of 2HG may have important mechanistic consequences influencing cell function and cancer pathogenesis, such as modulating redox potential or producing unknown products with unique modes of action. Results By applying our isotope-based metabolomic platform, we unbiasedly and comprehensively screened for products of L- and D-2HG in HCT116 colorectal carcinoma cells harboring a mutation in IDH1. After incubating HCT116 cells in uniformly 13C-labeled 2HG for 24 h, we used liquid chromatography/mass spectrometry to track the labeled carbons in small molecules. Strikingly, we did not identify any products of 2HG metabolism from the thousands of metabolomic features that we screened. Consistent with these results, we did not detect any significant changes in the labeling patterns of tricarboxylic acid cycle metabolites from wild type or IDH1 mutant cells cultured in 13C-labeled glucose upon the addition of L, D, or racemic mixtures of 2HG. A more sensitive, targeted analysis revealed trace levels of isotopic enrichment (<1 %) in some central carbon metabolites from 13C-labeled 2HG. However, we found that cells do not deplete 2HG from the media at levels above our detection limit over a 48 h time period. Conclusions Taken together, we conclude that 2HG carbon is not readily transformed in the HCT116 cell line. These data indicate that the phenotypic alterations induced by 2HG are not a result of its metabolic products.
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Affiliation(s)
- Susan J Gelman
- Department of Chemistry, Washington University, St. Louis, MO 63130 USA ; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Nathaniel G Mahieu
- Department of Chemistry, Washington University, St. Louis, MO 63130 USA ; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Kevin Cho
- Department of Chemistry, Washington University, St. Louis, MO 63130 USA ; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Elizabeth M Llufrio
- Department of Chemistry, Washington University, St. Louis, MO 63130 USA ; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | | | - Gary J Patti
- Department of Chemistry, Washington University, St. Louis, MO 63130 USA ; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
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Piedrafita G, Keller MA, Ralser M. The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions. Biomolecules 2015; 5:2101-22. [PMID: 26378592 PMCID: PMC4598790 DOI: 10.3390/biom5032101] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/03/2015] [Accepted: 08/31/2015] [Indexed: 11/16/2022] Open
Abstract
Cellular metabolism assembles in a structurally highly conserved, but functionally dynamic system, known as the metabolic network. This network involves highly active, enzyme-catalyzed metabolic pathways that provide the building blocks for cell growth. In parallel, however, chemical reactivity of metabolites and unspecific enzyme function give rise to a number of side products that are not part of canonical metabolic pathways. It is increasingly acknowledged that these molecules are important for the evolution of metabolism, affect metabolic efficiency, and that they play a potential role in human disease—age-related disorders and cancer in particular. In this review we discuss the impact of oxidative and other cellular stressors on the formation of metabolic side products, which originate as a consequence of: (i) chemical reactivity or modification of regular metabolites; (ii) through modifications in substrate specificity of damaged enzymes; and (iii) through altered metabolic flux that protects cells in stress conditions. In particular, oxidative and heat stress conditions are causative of metabolite and enzymatic damage and thus promote the non-canonical metabolic activity of the cells through an increased repertoire of side products. On the basis of selected examples, we discuss the consequences of non-canonical metabolic reactivity on evolution, function and repair of the metabolic network.
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Affiliation(s)
- Gabriel Piedrafita
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK.
| | - Markus A Keller
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK.
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK.
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW1 7AA, UK.
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48
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ω-Amidase: an underappreciated, but important enzyme in l-glutamine and l-asparagine metabolism; relevance to sulfur and nitrogen metabolism, tumor biology and hyperammonemic diseases. Amino Acids 2015; 48:1-20. [DOI: 10.1007/s00726-015-2061-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/24/2015] [Indexed: 12/29/2022]
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49
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Van Schaftingen E, Veiga-da-Cunha M, Linster CL. Enzyme complexity in intermediary metabolism. J Inherit Metab Dis 2015; 38:721-7. [PMID: 25700988 DOI: 10.1007/s10545-015-9821-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 01/30/2015] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
Abstract
A good appraisal of the function of enzymes is essential for the understanding of inborn errors of metabolism. However, it is clear now that the 'one gene, one enzyme, one catalytic function' rule oversimplifies the actual situation. Genes often encode several related proteins, which may differ in their subcellular localisation, regulation or function. Furthermore, enzymes often show several catalytic activities. In some cases, this is because they are multifunctional, possessing two or more different active sites that catalyse different, physiologically related reactions. In enzymes with broad specificity or in multispecificity enzymes, a single type of catalytic site performs the same reaction on different physiological substrates at similar rates. Enzymes that act physiologically in only one reaction often show nonetheless substrate promiscuity: they act at low rates on compounds that resemble their physiological substrate(s), thus forming non-classical metabolites, which are in some cases eliminated by metabolite repair. In addition to their catalytic role, enzymes may have moonlighting functions, i.e. non-catalytic functions that are most often not related with their catalytic activity. Deficiency in such functions may participate in the phenotype of inborn errors of metabolism. Evolution has also made that some enzymes have lost their catalytic activity to become allosteric proteins.
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Affiliation(s)
- Emile Van Schaftingen
- Welbio and de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200, Brussels, Belgium,
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50
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Shim EH, Sudarshan S. Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer. Oncoscience 2015; 2:483-6. [PMID: 26097881 PMCID: PMC4468334 DOI: 10.18632/oncoscience.165] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/06/2015] [Indexed: 12/18/2022] Open
Abstract
Alterations in metabolism are now considered a hallmark of cancer. One of the clearest links between metabolism and malignancy are oncometabolites. To date, several putative oncometabolites with transforming properties have been identified in the context of tumors due to both gain and loss of function mutations in genes encoding enzymes of intermediary metabolism. Through an unbiased metabolomics approach, we identified elevations of the metabolite 2-hydroxyglutarate (2-HG) in the most common histology of kidney cancer that is among the most common malignancies in both men and women. Subsequent analyses demonstrate that the predominant enantiomer of 2-HG elevated in renal cancer is the L(S) form. Notably, elevations of L-2HG are due in part to loss of expression of the L-2HG dehydrogenase (L2HGDH) which normally serves as an enzyme of “metabolite repair” to keep levels of this metabolite from accumulating. Lowering L-2HG levels in RCC through re-expression of L2HGDH mitigates tumor phenotypes and reverses epigenetic alterations known to be targeted by oncometabolites. These data add to the growing body of evidence that metabolites, similarly to oncogenes and oncoproteins, can play a role in tumor development and/or progression. As such, they represent a unique opportunity to utilize these findings in the clinic setting.
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Affiliation(s)
- Eun-Hee Shim
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, United States
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