1
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Cui J, Ju KS. Biosynthesis of Bacillus Phosphonoalamides Reveals Highly Specific Amino Acid Ligation. ACS Chem Biol 2024; 19:1506-1514. [PMID: 38885091 PMCID: PMC11259534 DOI: 10.1021/acschembio.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Phosphonate natural products have a history of commercial success across numerous industries due to their potent inhibition of metabolic processes. Over the past decade, genome mining approaches have successfully led to the discovery of numerous bioactive phosphonates. However, continued success is dependent upon a greater understanding of phosphonate metabolism, which will enable the prioritization and prediction of biosynthetic gene clusters for targeted isolation. Here, we report the complete biosynthetic pathway for phosphonoalamides E and F, antimicrobial phosphonopeptides with a conserved C-terminal l-phosphonoalanine (PnAla) residue. These peptides, produced by Bacillus, are the direct result of PnAla biosynthesis and serial ligation by two ATP-grasp ligases. A critical step of this pathway was the reversible transamination of phosphonopyruvate to PnAla by a dedicated transaminase with preference for the forward reaction. The dipeptide ligase PnfA was shown to ligate alanine to PnAla to afford phosphonoalamide E, which was subsequently ligated to alanine by PnfB to form phosphonoalamide F. Specificity profiling of both ligases found each to be highly specific, although the limited acceptance of noncanonical substrates by PnfA allowed for in vitro formation of products incorporating alternative pharmacophores. Our findings further establish the transaminative branch of phosphonate metabolism, unveil insights into the specificity of ATP-grasp ligation, and highlight the biocatalytic potential of biosynthetic enzymes.
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Affiliation(s)
- Jerry Cui
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Fan Z, Hao Y, Huo Y, Cao F, Li L, Xu J, Song Y, Yang K. Modulators for palmitoylation of proteins and small molecules. Eur J Med Chem 2024; 271:116408. [PMID: 38621327 DOI: 10.1016/j.ejmech.2024.116408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
As an essential form of lipid modification for maintaining vital cellular functions, palmitoylation plays an important role in in the regulation of various physiological processes, serving as a promising therapeutic target for diseases like cancer and neurological disorders. Ongoing research has revealed that palmitoylation can be categorized into three distinct types: N-palmitoylation, O-palmitoylation and S-palmitoylation. Herein this paper provides an overview of the regulatory enzymes involved in palmitoylation, including palmitoyltransferases and depalmitoylases, and discusses the currently available broad-spectrum and selective inhibitors for these enzymes.
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Affiliation(s)
- Zeshuai Fan
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China
| | - Yuchen Hao
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China
| | - Yidan Huo
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China
| | - Fei Cao
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, Hebei, 071002, China
| | - Longfei Li
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, Hebei, 071002, China
| | - Jianmei Xu
- Department of hematopathology, Affiliated Hospital of Hebei University, Hebei University, Baoding, 071002, China
| | - Yali Song
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, Hebei, 071002, China
| | - Kan Yang
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, Hebei, 071002, China.
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3
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Zhang DK, Song KY, Yan YQ, Zheng JT, Xu J, Da LT, Xu MJ. Structural and mechanistic investigations on CC bond forming α-oxoamine synthase allowing L-glutamate as substrate. Int J Biol Macromol 2024; 268:131696. [PMID: 38642679 DOI: 10.1016/j.ijbiomac.2024.131696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/23/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Carbon‑carbon (C-C) bonds serve as the fundamental structural backbone of organic molecules. As a critical CC bond forming enzyme, α-oxoamine synthase is responsible for the synthesis of α-amino ketones by performing the condensation reaction between amino acids and acyl-CoAs. We previously identified an α-oxoamine synthase (AOS), named as Alb29, involved in albogrisin biosynthesis in Streptomyces albogriseolus MGR072. This enzyme belongs to the α-oxoamine synthase family, a subfamily under the pyridoxal 5'-phosphate (PLP) dependent enzyme superfamily. In this study, we report the crystal structures of Alb29 bound to PLP and L-Glu, which provide the atomic-level structural insights into the substrate recognition by Alb29. We discover that Alb29 can catalyze the amino transformation from L-Gln to L-Glu, besides the condensation of L-Glu with β-methylcrotonyl coenzyme A. Subsequent structural analysis has revealed that one flexible loop in Alb29 plays an important role in both amino transformation and condensation. Based on the crystal structure of the S87G mutant in the loop region, we capture two distinct conformations of the flexible loop in the active site, compared with the wild-type Alb29. Our study offers valuable insights into the catalytic mechanism underlying substrate recognition of Alb29.
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Affiliation(s)
- Dai-Ke Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Kai-Yuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ya-Qian Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jian-Ting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
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4
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Tahia F, Basu SK, Prislovsky A, Mondal K, Ma D, Kochat H, Brown K, Stephenson DJ, Chalfant CE, Mandal N. Sphingolipid biosynthetic inhibitor L-Cycloserine prevents oxidative-stress-mediated death in an in vitro model of photoreceptor-derived 661W cells. Exp Eye Res 2024; 242:109852. [PMID: 38460719 PMCID: PMC11089890 DOI: 10.1016/j.exer.2024.109852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/11/2024]
Abstract
Oxidative stress plays a pivotal role in the pathogenesis of several neurodegenerative diseases. Retinal degeneration causes irreversible death of photoreceptor cells, ultimately leading to vision loss. Under oxidative stress, the synthesis of bioactive sphingolipid ceramide increases, triggering apoptosis in photoreceptor cells and leading to their death. This study investigates the effect of L-Cycloserine, a small molecule inhibitor of ceramide biosynthesis, on sphingolipid metabolism and the protection of photoreceptor-derived 661W cells from oxidative stress. The results demonstrate that treatment with L-Cycloserine, an inhibitor of Serine palmitoyl transferase (SPT), markedly decreases bioactive ceramide and associated sphingolipids in 661W cells. A nontoxic dose of L-Cycloserine can provide substantial protection of 661W cells against H2O2-induced oxidative stress by reversing the increase in ceramide level observed under oxidative stress conditions. Analysis of various antioxidant, apoptotic and sphingolipid pathway genes and proteins also confirms the ability of L-Cycloserine to modulate these pathways. Our findings elucidate the generation of sphingolipid mediators of cell death in retinal cells under oxidative stress and the potential of L-Cycloserine as a therapeutic candidate for targeting ceramide-induced degenerative diseases by inhibiting SPT. The promising therapeutic prospect identified in our findings lays the groundwork for further validation in in-vivo and preclinical models of retinal degeneration.
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Affiliation(s)
- Faiza Tahia
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, USA; Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Sandip K Basu
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Amanda Prislovsky
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA; Memphis VA Medical Center, Memphis, TN, 38104, USA
| | - Koushik Mondal
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Dejian Ma
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Harry Kochat
- Plough Center for Sterile Drug Delivery Solutions, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Kennard Brown
- Office of Executive Vice Chancellor and Chief Operations Officer, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Daniel J Stephenson
- Departments of Medicine and Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Charles E Chalfant
- Departments of Medicine and Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA; Research Service, Richmond Veterans Administration Medical Center, Richmond VA, 23298, USA
| | - Nawajes Mandal
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, USA; Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA; Memphis VA Medical Center, Memphis, TN, 38104, USA; Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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5
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Jamjoum R, Majumder S, Issleny B, Stiban J. Mysterious sphingolipids: metabolic interrelationships at the center of pathophysiology. Front Physiol 2024; 14:1229108. [PMID: 38235387 PMCID: PMC10791800 DOI: 10.3389/fphys.2023.1229108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
Metabolic pathways are complex and intertwined. Deficiencies in one or more enzymes in a given pathway are directly linked with genetic diseases, most of them having devastating manifestations. The metabolic pathways undertaken by sphingolipids are diverse and elaborate with ceramide species serving as the hubs of sphingolipid intermediary metabolism and function. Sphingolipids are bioactive lipids that serve a multitude of cellular functions. Being pleiotropic in function, deficiency or overproduction of certain sphingolipids is associated with many genetic and chronic diseases. In this up-to-date review article, we strive to gather recent scientific evidence about sphingolipid metabolism, its enzymes, and regulation. We shed light on the importance of sphingolipid metabolism in a variety of genetic diseases and in nervous and immune system ailments. This is a comprehensive review of the state of the field of sphingolipid biochemistry.
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Affiliation(s)
- Rama Jamjoum
- Department of Pharmacy, Birzeit University, West Bank, Palestine
| | - Saurav Majumder
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Rockville, MD, United States
| | - Batoul Issleny
- Department of Pharmacy, Birzeit University, West Bank, Palestine
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
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6
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Mohassel P, Abdullah M, Eichler FS, Dunn TM. Serine Palmitoyltransferase (SPT)-related Neurodegenerative and Neurodevelopmental Disorders. J Neuromuscul Dis 2024; 11:735-747. [PMID: 38788085 DOI: 10.3233/jnd-240014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Motor neuron diseases and peripheral neuropathies are heterogeneous groups of neurodegenerative disorders that manifest with distinct symptoms due to progressive dysfunction or loss of specific neuronal subpopulations during different stages of development. A few monogenic, neurodegenerative diseases associated with primary metabolic disruptions of sphingolipid biosynthesis have been recently discovered. Sphingolipids are a subclass of lipids that form critical building blocks of all cellular and subcellular organelle membranes including the membrane components of the nervous system cells. They are especially abundant within the lipid portion of myelin. In this review, we will focus on our current understanding of disease phenotypes in three monogenic, neuromuscular diseases associated with pathogenic variants in components of serine palmitoyltransferase, the first step in sphingolipid biosynthesis. These include hereditary sensory and autonomic neuropathy type 1 (HSAN1), a sensory predominant peripheral neuropathy, and two neurodegenerative disorders: juvenile amyotrophic lateral sclerosis affecting the upper and lower motor neurons with sparing of sensory neurons, and a complicated form of hereditary spastic paraplegia with selective involvement of the upper motor neurons and more broad CNS neurodegeneration. We will also review our current understanding of disease pathomechanisms, therapeutic approaches, and the unanswered questions to explore in future studies.
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Affiliation(s)
- Payam Mohassel
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Meher Abdullah
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Florian S Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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7
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Radka CD, Miller DJ, Frank MW, Rock CO. Biochemical characterization of the first step in sulfonolipid biosynthesis in Alistipes finegoldii. J Biol Chem 2022; 298:102195. [PMID: 35760102 PMCID: PMC9304779 DOI: 10.1016/j.jbc.2022.102195] [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: 05/10/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/01/2022] Open
Abstract
Sulfonolipids are unusual lipids found in the outer membranes of Gram-negative bacteria in the phylum Bacteroidetes. Sulfonolipid and its deacylated derivative, capnine, are sulfur analogs of ceramide-1-phosphate and sphingosine-1-phosphate, respectively; thus, sulfonolipid biosynthesis is postulated to be similar to the sphingolipid biosynthetic pathway. Here, we identify the first enzyme in sulfonolipid synthesis in Alistipes finegoldii, an anaerobic gut commensal bacterium, as the product of the alfi_1224 gene, cysteate acyl-acyl carrier protein (ACP) transferase (SulA). We show SulA catalyzes the condensation of acyl-ACP and cysteate (3-sulfo-alanine) to form 3-ketocapnine. Acyl-CoA is a poor substrate. We show SulA has a bound pyridoxal phosphate (PLP) cofactor that undergoes a spectral redshift in the presence of cysteate, consistent with the transition of the lysine-aldimine complex to a substrate-aldimine complex. Furthermore, the SulA crystal structure shows the same prototypical fold found in bacterial serine palmitoyltransferases (Spt), enveloping the PLP cofactor bound to Lys251. We observed the SulA and Spt active sites are identical except for Lys281 in SulA, which is an alanine in Spt. Additionally, SulA(K281A) is catalytically inactive, but binds cysteate and forms the external aldimine normally, highlighting the structural role of the Lys281 side chain in walling off the active site from bulk solvent. Finally, the electropositive groove on the protein surface adjacent to the active site entrance provides a landing pad for the electronegative acyl-ACP surface. Taken together, these data identify the substrates, products, and mechanism of SulA, the PLP-dependent condensing enzyme that catalyzes the first step in sulfonolipid synthesis in a gut commensal bacterium.
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Affiliation(s)
- Christopher D Radka
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA.
| | - Darcie J Miller
- Departments of, Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
| | - Matthew W Frank
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
| | - Charles O Rock
- Departments of, Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38015, USA
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8
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Nakamura R, Ogawa S, Takahashi Y, Fujishiro T. Cycloserine enantiomers inhibit PLP‐dependent cysteine desulfurase SufS via distinct mechanisms. FEBS J 2022; 289:5947-5970. [DOI: 10.1111/febs.16455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/20/2022] [Accepted: 04/07/2022] [Indexed: 01/31/2023]
Affiliation(s)
- Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Japan
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9
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Nasir G, Chopra R, Elwood F, Ahmed SS. Krabbe Disease: Prospects of Finding a Cure Using AAV Gene Therapy. Front Med (Lausanne) 2021; 8:760236. [PMID: 34869463 PMCID: PMC8633897 DOI: 10.3389/fmed.2021.760236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Krabbe Disease (KD) is an autosomal metabolic disorder that affects both the central and peripheral nervous systems. It is caused by a functional deficiency of the lysosomal enzyme, galactocerebrosidase (GALC), resulting in an accumulation of the toxic metabolite, psychosine. Psychosine accumulation affects many different cellular pathways, leading to severe demyelination. Although there is currently no effective therapy for Krabbe disease, recent gene therapy-based approaches in animal models have indicated a promising outlook for clinical treatment. This review highlights recent findings in the pathogenesis of Krabbe disease, and evaluates AAV-based gene therapy as a promising strategy for treating this devastating pediatric disease.
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Affiliation(s)
- Gibran Nasir
- Department of Neuroscience, Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA, United States
| | - Rajiv Chopra
- AllianThera Biopharma, Boston, MA, United States
| | - Fiona Elwood
- Department of Neuroscience, Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA, United States
| | - Seemin S Ahmed
- Department of Neuroscience, Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA, United States
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10
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Codon optimization of the synthetic 3-ketosphinganine reductase (3KSR) protein for enhancing sphingolipid biosynthetic enzyme expression. Mol Cell Toxicol 2021. [DOI: 10.1007/s13273-021-00153-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Mohassel P, Donkervoort S, Lone MA, Nalls M, Gable K, Gupta SD, Foley AR, Hu Y, Saute JAM, Moreira AL, Kok F, Introna A, Logroscino G, Grunseich C, Nickolls AR, Pourshafie N, Neuhaus SB, Saade D, Gangfuß A, Kölbel H, Piccus Z, Le Pichon CE, Fiorillo C, Ly CV, Töpf A, Brady L, Specht S, Zidell A, Pedro H, Mittelmann E, Thomas FP, Chao KR, Konersman CG, Cho MT, Brandt T, Straub V, Connolly AM, Schara U, Roos A, Tarnopolsky M, Höke A, Brown RH, Lee CH, Hornemann T, Dunn TM, Bönnemann CG. Childhood amyotrophic lateral sclerosis caused by excess sphingolipid synthesis. Nat Med 2021; 27:1197-1204. [PMID: 34059824 PMCID: PMC9309980 DOI: 10.1038/s41591-021-01346-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease of the lower and upper motor neurons with sporadic or hereditary occurrence. Age of onset, pattern of motor neuron degeneration and disease progression vary widely among individuals with ALS. Various cellular processes may drive ALS pathomechanisms, but a monogenic direct metabolic disturbance has not been causally linked to ALS. Here we show SPTLC1 variants that result in unrestrained sphingoid base synthesis cause a monogenic form of ALS. We identified four specific, dominantly acting SPTLC1 variants in seven families manifesting as childhood-onset ALS. These variants disrupt the normal homeostatic regulation of serine palmitoyltransferase (SPT) by ORMDL proteins, resulting in unregulated SPT activity and elevated levels of canonical SPT products. Notably, this is in contrast with SPTLC1 variants that shift SPT amino acid usage from serine to alanine, result in elevated levels of deoxysphingolipids and manifest with the alternate phenotype of hereditary sensory and autonomic neuropathy. We custom designed small interfering RNAs that selectively target the SPTLC1 ALS allele for degradation, leave the normal allele intact and normalize sphingolipid levels in vitro. The role of primary metabolic disturbances in ALS has been elusive; this study defines excess sphingolipid biosynthesis as a fundamental metabolic mechanism for motor neuron disease.
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Affiliation(s)
- Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Museer A Lone
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Matthew Nalls
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jonas Alex Morales Saute
- Medical Genetics division and Neurology division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, and Internal Medicine Department; Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Lucila Moreira
- Neurology Department, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Fernando Kok
- Neurogenetics Outpatient Service, Neurology Department, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil and Mendelics, São Paulo, Brazil
| | - Alessandro Introna
- Neurology Unit, Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari 'Aldo Moro', Bari, Italy
| | - Giancarlo Logroscino
- Neurology Unit, Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari 'Aldo Moro', Bari, Italy
- Department of Clinical Research in Neurology, Center for Neurodegenerative Diseases and the Aging Brain, University of Bari at 'Pia Fondazione Card G. Panico' Hospital Tricase (Le), Bari, Italy
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Alec R Nickolls
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Naemeh Pourshafie
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sarah B Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Dimah Saade
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Andrea Gangfuß
- Department of Paediatric Neurology, Center for Neuromuscular Disorders in Children and Adolescents, University Clinic Essen, University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Heike Kölbel
- Department of Paediatric Neurology, Center for Neuromuscular Disorders in Children and Adolescents, University Clinic Essen, University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Zoe Piccus
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Claire E Le Pichon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chiara Fiorillo
- Paediatric Neurology and Muscular Diseases Unit, G. Gaslini Institute and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health University of Genoa, Genoa, Italy
| | - Cindy V Ly
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Lauren Brady
- Division of Neuromuscular & Neurometabolic Disorders, Department of Paediatrics, McMaster University, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada
| | - Sabine Specht
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Aliza Zidell
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Helio Pedro
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack Meridian School of Medicine, Hackensack, NJ, USA
| | - Eric Mittelmann
- Department of Neurology, Hereditary Neuropathy Foundation Center of Excellence, Neuroscience Institute, Hackensack University Medical Center, Hackensack Meridian School of Medicine, Hackensack, NJ, USA
| | - Florian P Thomas
- Department of Neurology, Hereditary Neuropathy Foundation Center of Excellence, Neuroscience Institute, Hackensack University Medical Center, Hackensack Meridian School of Medicine, Hackensack, NJ, USA
| | - Katherine R Chao
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chamindra G Konersman
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | | | | | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Anne M Connolly
- Department of Paediatrics, Neurology Division, Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Ulrike Schara
- Department of Paediatric Neurology, Center for Neuromuscular Disorders in Children and Adolescents, University Clinic Essen, University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Andreas Roos
- Department of Paediatric Neurology, Center for Neuromuscular Disorders in Children and Adolescents, University Clinic Essen, University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Mark Tarnopolsky
- Division of Neuromuscular & Neurometabolic Disorders, Department of Paediatrics, McMaster University, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada
| | - Ahmet Höke
- Department of Neurology, Neuromuscular Division, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, USA.
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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12
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Shatalin K, Nuthanakanti A, Kaushik A, Shishov D, Peselis A, Shamovsky I, Pani B, Lechpammer M, Vasilyev N, Shatalina E, Rebatchouk D, Mironov A, Fedichev P, Serganov A, Nudler E. Inhibitors of bacterial H 2S biogenesis targeting antibiotic resistance and tolerance. Science 2021; 372:1169-1175. [PMID: 34112687 PMCID: PMC10723041 DOI: 10.1126/science.abd8377] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/09/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Emergent resistance to all clinical antibiotics calls for the next generation of therapeutics. Here we report an effective antimicrobial strategy targeting the bacterial hydrogen sulfide (H2S)-mediated defense system. We identified cystathionine γ-lyase (CSE) as the primary generator of H2S in two major human pathogens, Staphylococcus aureus and Pseudomonas aeruginosa, and discovered small molecules that inhibit bacterial CSE. These inhibitors potentiate bactericidal antibiotics against both pathogens in vitro and in mouse models of infection. CSE inhibitors also suppress bacterial tolerance, disrupting biofilm formation and substantially reducing the number of persister bacteria that survive antibiotic treatment. Our results establish bacterial H2S as a multifunctional defense factor and CSE as a drug target for versatile antibiotic enhancers.
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Affiliation(s)
- Konstantin Shatalin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ashok Nuthanakanti
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Abhishek Kaushik
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Bibhusita Pani
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Mirna Lechpammer
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Elena Shatalina
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Alexander Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119991, Russia
| | | | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
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13
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LeVine SM, Tsau S. Substrate Reduction Therapy for Krabbe Disease: Exploring the Repurposing of the Antibiotic D-Cycloserine. Front Pediatr 2021; 9:807973. [PMID: 35118033 PMCID: PMC8804370 DOI: 10.3389/fped.2021.807973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/24/2021] [Indexed: 01/10/2023] Open
Abstract
Krabbe disease is a lysosomal storage disease that is caused by a deficiency in galactosylceramidase. Infantile onset disease is the most common presentation, which includes progressive neurological deterioration with corresponding demyelination, development of globoid cells, astrocyte gliosis, etc. Hemopoietic stem cell transplantation (HSCT) is a disease modifying therapy, but this intervention is insufficient with many patients still experiencing developmental delays and progressive deterioration. Preclinical studies have used animal models, e.g., twitcher mice, to test different experimental therapies resulting in developments that have led to progressive improvements in the therapeutic impact. Some recent advances have been in the areas of gene therapy and substrate reduction therapy (SRT), as well as using these in combination with HSCT. Unfortunately, new experimental approaches have encountered obstacles which have impeded the translation of novel therapies to human patients. In an effort to identify a safe adjunct therapy, D-cycloserine was tested in preliminary studies in twitcher mice. When administered as a standalone therapy, D-cycloserine was shown to lengthen the lifespan of twitcher mice in a small but significant manner. D-Cycloserine is an FDA approved antibiotic used for drug resistant tuberculosis. It also acts as a partial agonist of the NMDA receptor, which has led to numerous human studies for a range of neuropsychiatric and neurological conditions. In addition, D-cycloserine may inhibit serine palmitoyltransferase (SPT), which catalyzes the rate-limiting step in sphingolipid production. The enantiomer, L-cycloserine, is a much more potent inhibitor of SPT than D-cycloserine. Previously, L-cycloserine was found to act as an effective SRT agent in twitcher mice as both a standalone therapy and as part of combination therapies. L-Cycloserine is not approved for human use, and its potent inhibitory properties may limit its ability to maintain a level of partial inactivation of SPT that is also safe. In theory, D-cycloserine would encompass a much broader dosage range to achieve a safe degree of partial inhibition of SPT, which increases the likelihood it could advance to human studies in patients with Krabbe disease. Furthermore, additional properties of D-cycloserine raise the possibility of other therapeutic mechanisms that could be exploited for the treatment of this disease.
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Affiliation(s)
- Steven M LeVine
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Sheila Tsau
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, United States
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14
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Treatment Outcomes and Adverse Drug Effects of Ethambutol, Cycloserine, and Terizidone for the Treatment of Multidrug-Resistant Tuberculosis in South Africa. Antimicrob Agents Chemother 2020; 65:AAC.00744-20. [PMID: 33046491 DOI: 10.1128/aac.00744-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/30/2020] [Indexed: 11/20/2022] Open
Abstract
Treatment outcomes among multidrug-resistant tuberculosis (MDR-TB) patients receiving ethambutol, cycloserine, or terizidone as part of a standardized regimen were compared, determining occurrence of serious adverse drug events (SADEs). Newly diagnosed adult MDR-TB patients were enrolled between 2000 and 2004, receiving a standardized multidrug regimen for 18 to 24 months, including ethambutol, cycloserine, or terizidone. Cycloserine and terizidone were recorded individually. SADEs and factors associated with culture conversion and unfavorable treatment outcomes (default, death, treatment failure) were determined. Of 858 patients, 435 (51%) received ethambutol, 278 (32%) received cycloserine, and 145 (17%) received terizidone. Demographic and baseline clinical data were comparable. Successful treatment occurred in 56%, significantly more in patients receiving cycloserine (60%) and terizidone (62%) than in those receiving ethambutol (52% [P = 0.03]). Defaults rates were 30% in ethambutol patients versus 15% and 11% for cycloserine and terizidone patients, respectively. Terizidone was associated with fewer unfavorable outcomes (adjusted odds ratio [AOR], 0.4; P = 0.008; 95% confidence interval [CI], 0.2 to 0.8). Patients receiving cycloserine were more likely to achieve culture conversion than those receiving ethambutol or terizidone (AOR, 2.2; P = 0.02; 95% CI, 1.12 to 4.38). Failure to convert increased the odds of unfavorable outcomes (AOR, 23.7; P < 0.001; 95% CI, 13 to 44). SADEs were reported in two patients receiving ethambutol, seven patients receiving cycloserine, and three receiving terizidone (P = 0.05). Ethambutol was associated with high culture conversion and default rates. Cycloserine achieved higher culture conversion rates than terizidone. Fewer patients on terizidone experienced SADEs, with lower default rates. The differences that we observed between cycloserine and terizidone require further elucidation.
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15
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Rudden M, Herman R, Rose M, Bawdon D, Cox DS, Dodson E, Holden MTG, Wilkinson AJ, James AG, Thomas GH. The molecular basis of thioalcohol production in human body odour. Sci Rep 2020; 10:12500. [PMID: 32719469 PMCID: PMC7385124 DOI: 10.1038/s41598-020-68860-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022] Open
Abstract
Body odour is a characteristic trait of Homo sapiens, however its role in human behaviour and evolution is poorly understood. Remarkably, body odour is linked to the presence of a few species of commensal microbes. Herein we discover a bacterial enzyme, limited to odour-forming staphylococci that are able to cleave odourless precursors of thioalcohols, the most pungent components of body odour. We demonstrated using phylogenetics, biochemistry and structural biology that this cysteine-thiol lyase (C-T lyase) is a PLP-dependent enzyme that moved horizontally into a unique monophyletic group of odour-forming staphylococci about 60 million years ago, and has subsequently tailored its enzymatic function to human-derived thioalcohol precursors. Significantly, transfer of this enzyme alone to non-odour producing staphylococci confers odour production, demonstrating that this C-T lyase is both necessary and sufficient for thioalcohol formation. The structure of the C-T lyase compared to that of other related enzymes reveals how the adaptation to thioalcohol precursors has evolved through changes in the binding site to create a constrained hydrophobic pocket that is selective for branched aliphatic thioalcohol ligands. The ancestral acquisition of this enzyme, and the subsequent evolution of the specificity for thioalcohol precursors implies that body odour production in humans is an ancient process.
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Affiliation(s)
- Michelle Rudden
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Reyme Herman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Matthew Rose
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Daniel Bawdon
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Diana S Cox
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedford, MK44 1LQ, UK
| | - Eleanor Dodson
- Department of Chemistry, University of York, Wentworth Way, York, YO10 5DD, UK
| | | | - Anthony J Wilkinson
- Department of Chemistry, University of York, Wentworth Way, York, YO10 5DD, UK.
| | - A Gordon James
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedford, MK44 1LQ, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
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16
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Cycloserine enantiomers are reversible inhibitors of human alanine:glyoxylate aminotransferase: implications for Primary Hyperoxaluria type 1. Biochem J 2020; 476:3751-3768. [PMID: 31794008 DOI: 10.1042/bcj20190507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/12/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
Peroxisomal alanine:glyoxylate aminotransferase (AGT) is responsible for glyoxylate detoxification in human liver and utilizes pyridoxal 5'-phosphate (PLP) as coenzyme. The deficit of AGT leads to Primary Hyperoxaluria Type I (PH1), a rare disease characterized by calcium oxalate stones deposition in the urinary tract as a consequence of glyoxylate accumulation. Most missense mutations cause AGT misfolding, as in the case of the G41R, which induces aggregation and proteolytic degradation. We have investigated the interaction of wild-type AGT and the pathogenic G41R variant with d-cycloserine (DCS, commercialized as Seromycin), a natural product used as a second-line treatment of multidrug-resistant tuberculosis, and its synthetic enantiomer l-cycloserine (LCS). In contrast with evidences previously reported on other PLP-enzymes, both ligands are AGT reversible inhibitors showing inhibition constants in the micromolar range. While LCS undergoes half-transamination generating a ketimine intermediate and behaves as a classical competitive inhibitor, DCS displays a time-dependent binding mainly generating an oxime intermediate. Using a mammalian cellular model, we found that DCS, but not LCS, is able to promote the correct folding of the G41R variant, as revealed by its increased specific activity and expression as a soluble protein. This effect also translates into an increased glyoxylate detoxification ability of cells expressing the variant upon treatment with DCS. Overall, our findings establish that DCS could play a role as pharmacological chaperone, thus suggesting a new line of intervention against PH1 based on a drug repositioning approach. To a widest extent, this strategy could be applied to other disease-causing mutations leading to AGT misfolding.
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17
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Palmitic acid damages gut epithelium integrity and initiates inflammatory cytokine production. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158530. [DOI: 10.1016/j.bbalip.2019.158530] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 07/16/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
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18
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Semi-rational approach to expand the Acyl-CoA Chain length tolerance of Sphingomonas paucimobilis serine palmitoyltransferase. Enzyme Microb Technol 2020; 137:109515. [PMID: 32423667 DOI: 10.1016/j.enzmictec.2020.109515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/11/2020] [Accepted: 01/20/2020] [Indexed: 11/21/2022]
Abstract
Serine palmitoyltransferase (SPTase), the first enzyme of the sphingolipid biosynthesis pathway, produces 3-ketodihydrosphingosine by a Claisen-like condensation/decarboxylation reaction of l-Ser and palmitoyl-CoA (n-C16-CoA). Previous structural analysis of Sphingomonas paucimobilis SPTase (SpSPTase) revealed a dynamic active site loop (RPPATP; amino acids 378-383) in which R378 (underlined) forms a salt bridge with the carboxylic acid group of the PLP : l-Ser external aldimine. We hypothesized that this interaction might play a key role in acyl group substrate selectivity and therefore performed site-saturation mutagenesis at position 378 based on semi-rational design to expand tolerance for shorter acyl-CoA's. The resulting library was initially screened for the reaction between l-Ser and dodecanoyl-CoA (n-C12-CoA). The most interesting mutant (R378 K) was then purified and compared to wild-type SpSPTase against a panel of acyl-CoA's. These data showed that the R378 K substitution shifted the acyl group preference to shorter chain lengths, opening the possibility of using this and other engineered variants for biocatalytic C-C bond-forming reactions.
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19
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Fux A, Sieber SA. Biochemical and Proteomic Studies of Human Pyridoxal 5'-Phosphate-Binding Protein (PLPBP). ACS Chem Biol 2020; 15:254-261. [PMID: 31825581 PMCID: PMC9558310 DOI: 10.1021/acschembio.9b00857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The pyridoxal 5′-phosphate-binding protein (PLPBP)
is an
evolutionarily conserved protein linked to pyridoxal 5′-phosphate-binding.
Although mutations in PLPBP were shown to cause vitamin B6-dependent
epilepsy, its cellular role and function remain elusive. We here report
a detailed biochemical investigation of human PLPBP and its epilepsy-causing
mutants by evaluating stability, cofactor binding, and oligomerization.
In this context, chemical cross-linking combined with mass spectrometry
unraveled an unexpected dimeric assembly of PLPBP. Furthermore, the
interaction network of PLPBP was elucidated by chemical cross-linking
paired with co-immunoprecipitation. A mass spectrometric analysis
in a PLPBP knockout cell line resulted in distinct proteomic changes
compared to wild type cells, including upregulation of several cytoskeleton-
and cell division-associated proteins. Finally, transfection experiments
with vitamin B6-dependent epilepsy-causing PLPBP variants indicate
a potential role of PLPBP in cell division as well as proper muscle
function. Taken together, our studies on the structure and cellular
role of human PLPBP enable a better understanding of the physiological
and pathological mechanism of this important protein.
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Affiliation(s)
- Anja Fux
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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20
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Gao S, Liu H, de Crécy-Lagard V, Zhu W, Richards NGJ, Naismith JH. PMP-diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis. Chem Commun (Camb) 2019; 55:14502-14505. [PMID: 31730149 PMCID: PMC6927412 DOI: 10.1039/c9cc06975e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/16/2019] [Indexed: 01/04/2023]
Abstract
ForI is a PLP-dependent enzyme from the biosynthetic pathway of the C-nucleoside antibiotic formycin. Cycloserine is thought to inhibit PLP-dependent enzymes by irreversibly forming a PMP-isoxazole. We now report that ForI forms novel PMP-diketopiperazine derivatives following incubation with both d and l cycloserine. This unexpected result suggests chemical diversity in the chemistry of cycloserine inhibition.
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Affiliation(s)
- Sisi Gao
- Research Complex at Harwell
,
Didcot
, OX11 0FA
, UK
- BSRC
, University of St Andrews
,
St Andrews
, KY16 9ST
, UK
| | - Huanting Liu
- BSRC
, University of St Andrews
,
St Andrews
, KY16 9ST
, UK
| | | | - Wen Zhu
- Department of Chemistry and California
, Institute for Quantitative Biosciences
, University of California
,
Berkeley
, CA 94720
, USA
| | - Nigel G. J. Richards
- School of Chemistry
, Cardiff University
, Park Place
,
Cardiff
, CF10 3AT
, UK
- Foundation for Applied Molecular Evolution
,
Alachua
, FL 32415
, USA
| | - James H. Naismith
- Division of Structural Biology
, University of Oxford
,
Oxford
, OX3 7BN
, UK
.
- The Rosalind Franklin Institute
,
Didcot
, OX11 0FA
, UK
- State Key Laboratory of Biotherapy
, University of Sichuan
,
China
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21
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Fux A, Pfanzelt M, Kirsch VC, Hoegl A, Sieber SA. Customizing Functionalized Cofactor Mimics to Study the Human Pyridoxal 5'-Phosphate-Binding Proteome. Cell Chem Biol 2019; 26:1461-1468.e7. [PMID: 31447350 PMCID: PMC6876276 DOI: 10.1016/j.chembiol.2019.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 01/29/2023]
Abstract
Pyridoxal 5′-phosphate (PLP) is a versatile cofactor that catalyzes a plethora of chemical transformations within a cell. Although many human PLP-dependent enzymes (PLP-DEs) with crucial physiological and pathological roles are known, a global method enabling their cellular profiling is lacking. Here, we demonstrate the utility of a cofactor probe for the identification of human PLP-binding proteins in living cells. Striking selectivity of human pyridoxal kinase led to a customized labeling strategy covering a large fraction of known PLP-binding proteins across various cancer-derived cell lines. Labeling intensities of some PLP-DEs varied depending on the cell type while the overall protein expression levels of these proteins remained constant. In addition, we applied the methodology for in situ screening of PLP-antagonists and unraveled known binders as well as unknown off-targets. Taken together, our proteome-wide method to study PLP-DEs in human cancer-derived cells enables global understanding of the interactome of this important cofactor. Enrichment of human vitamin B6-binding proteins with cofactor-derived probes In situ target screening of vitamin B6 antagonists Comparison of human cell lines suggests cell-type-dependent cofactor loading states
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Affiliation(s)
- Anja Fux
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Martin Pfanzelt
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Volker C Kirsch
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Annabelle Hoegl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany.
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22
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Favrot L, Amorim Franco TM, Blanchard JS. Biochemical Characterization of the Mycobacterium smegmatis Threonine Deaminase. Biochemistry 2018; 57:6003-6012. [PMID: 30226377 DOI: 10.1021/acs.biochem.8b00871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The biosynthesis of branched-chain amino acids or BCAAs (l-isoleucine, l-leucine, and l-valine) is essential in eubacteria, but mammals are branched-chain amino acid auxotrophs, making the enzymes in the pathway excellent targets for antibacterial drug development. The biosynthesis of l-isoleucine, l-leucine, and l-valine is very efficient, requiring only eight enzymes. Threonine dehydratase (TD), a pyridoxal 5'-phosphate (PLP)-dependent enzyme encoded by the ilvA gene, is the enzyme responsible for the conversion of l-threonine (l-Thr) to α-ketobutyrate, ammonia, and water, which is the first step in the biosynthesis of l-isoleucine. We have cloned, expressed, and biochemically characterized the reaction catalyzed by Mycobacterium smegmatis TD (abbreviated as MsIlvA) using steady-state kinetics and kinetic isotope effects. We show here that in addition to l-threonine, l-allo-threonine and l-serine are also used as substrates by TD, and all exhibit sigmoidal, non-Michaelis-Menten kinetics. Curiously, β-chloro-l-alanine was also a substrate rather than an inhibitor as expected. The enzymatic activity of TD is sensitive to the presence of allosteric regulators, including the activator l-valine or the end product feedback inhibitor of the BCAA pathway in which TD is involved, l-isoleucine. Primary deuterium kinetic isotopes are small, suggesting Cα proton abstraction is only partially rate-limiting. Solvent kinetic isotopes were significantly larger, indicating that a proton transfer occurring during the reaction is also partially rate-limiting. Finally, we demonstrate that l-cycloserine, a general inhibitor of PLP-dependent enzymes, is an excellent inhibitor of threonine deaminase.
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Affiliation(s)
- Lorenza Favrot
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Tathyana M Amorim Franco
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - John S Blanchard
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
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23
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Harrison PJ, Dunn T, Campopiano DJ. Sphingolipid biosynthesis in man and microbes. Nat Prod Rep 2018; 35:921-954. [PMID: 29863195 PMCID: PMC6148460 DOI: 10.1039/c8np00019k] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 12/20/2022]
Abstract
A new review covering up to 2018 Sphingolipids are essential molecules that, despite their long history, are still stimulating interest today. The reasons for this are that, as well as playing structural roles within cell membranes, they have also been shown to perform a myriad of cell signalling functions vital to the correct function of eukaryotic and prokaryotic organisms. Indeed, sphingolipid disregulation that alters the tightly-controlled balance of these key lipids has been closely linked to a number of diseases such as diabetes, asthma and various neuropathologies. Sphingolipid biogenesis, metabolism and regulation is mediated by a large number of enzymes, proteins and second messengers. There appears to be a core pathway common to all sphingolipid-producing organisms but recent studies have begun to dissect out important, species-specific differences. Many of these have only recently been discovered and in most cases the molecular and biochemical details are only beginning to emerge. Where there is a direct link from classic biochemistry to clinical symptoms, a number a drug companies have undertaken a medicinal chemistry campaign to try to deliver a therapeutic intervention to alleviate a number of diseases. Where appropriate, we highlight targets where natural products have been exploited as useful tools. Taking all these aspects into account this review covers the structural, mechanistic and regulatory features of sphingolipid biosynthetic and metabolic enzymes.
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Affiliation(s)
- Peter J. Harrison
- School of Chemistry
, University of Edinburgh
,
David Brewster Road
, Edinburgh
, EH9 3FJ
, UK
.
| | - Teresa M. Dunn
- Department of Biochemistry and Molecular Biology
, Uniformed Services University
,
Bethesda
, Maryland
20814
, USA
| | - Dominic J. Campopiano
- School of Chemistry
, University of Edinburgh
,
David Brewster Road
, Edinburgh
, EH9 3FJ
, UK
.
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24
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Sands SA, LeVine SM. Substrate reduction therapy for Krabbe's disease. J Neurosci Res 2017; 94:1261-72. [PMID: 27638608 DOI: 10.1002/jnr.23791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/19/2016] [Accepted: 05/18/2016] [Indexed: 01/30/2023]
Abstract
Krabbe's disease (KD) is a lysosomal storage disorder in which galactosylceramide, a major glycosphingolipid of myelin, and psychosine (galactose-sphingosine) cannot be adequately metabolized because of a deficiency in galactosylceramidase. Substrate reduction therapy (SRT) has been tested in preclinical studies. The premise of SRT is to reduce the synthesis of substrates that are not adequately digested so that the substrate burden is lowered, resulting in less accumulation of unmetabolized material. SRT is used for Gaucher's disease, in which inhibitors of the terminal biosynthetic step are used. Unfortunately, an inhibitor for the final step of galactosylceramide biosynthesis, i.e., UDP glycosyltransferase 8 (a.k.a. UDP-galactose ceramide galactosyltransferase), has not been found. Approaches that inhibit an earlier biosynthetic step or that lessen the substrate burden by other means, such as genetic manipulations, have been tested in the twitcher mouse model of KD. Either as a stand-alone therapy or in combination with other approaches, SRT slowed the disease course, indicating that this approach has potential therapeutic value. For instance, in individuals with adult-onset disease, SRT theoretically could lessen the production of substrates so that residual enzymatic activity could adequately manage the lower substrate burden. In more severe forms of disease, SRT theoretically could be part of a combination therapy. However, SRT has the potential to impair normal function by reducing the synthesis of galactosylceramide to levels that impede myelin function, or SRT could have other deleterious effects. Thus, multiple issues need to be resolved before this approach is ready for testing in humans. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Scott A Sands
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas
| | - Steven M LeVine
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas.
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25
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Amorim Franco TM, Favrot L, Vergnolle O, Blanchard JS. Mechanism-Based Inhibition of the Mycobacterium tuberculosis Branched-Chain Aminotransferase by d- and l-Cycloserine. ACS Chem Biol 2017; 12:1235-1244. [PMID: 28272868 DOI: 10.1021/acschembio.7b00142] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The branched-chain aminotransferase is a pyridoxal 5'-phosphate (PLP)-dependent enzyme responsible for the final step in the biosynthesis of all three branched-chain amino acids, l-leucine, l-isoleucine, and l-valine, in bacteria. We have investigated the mechanism of inactivation of the branched-chain aminotransferase from Mycobacterium tuberculosis (MtIlvE) by d- and l-cycloserine. d-Cycloserine is currently used only in the treatment of multidrug-drug-resistant tuberculosis. Our results show a time- and concentration-dependent inactivation of MtIlvE by both isomers, with l-cycloserine being a 40-fold better inhibitor of the enzyme. Minimum inhibitory concentration (MIC) studies revealed that l-cycloserine is a 10-fold better inhibitor of Mycobacterium tuberculosis growth than d-cycloserine. In addition, we have crystallized the MtIlvE-d-cycloserine inhibited enzyme, determining the structure to 1.7 Å. The structure of the covalent d-cycloserine-PMP adduct bound to MtIlvE reveals that the d-cycloserine ring is planar and aromatic, as previously observed for other enzyme systems. Mass spectrometry reveals that both the d-cycloserine- and l-cycloserine-PMP complexes have the same mass, and are likely to be the same aromatized, isoxazole product. However, the kinetics of formation of the MtIlvE d-cycloserine-PMP and MtIlvE l-cycloserine-PMP adducts are quite different. While the kinetics of the formation of the MtIlvE d-cycloserine-PMP complex can be fit to a single exponential, the formation of the MtIlvE l-cycloserine-PMP complex occurs in two steps. We propose a chemical mechanism for the inactivation of d- and l-cycloserine which suggests a stereochemically determined structural role for the differing kinetics of inactivation. These results demonstrate that the mechanism of action of d-cycloserine's activity against M. tuberculosis may be more complicated than previously thought and that d-cycloserine may compromise the in vivo activity of multiple PLP-dependent enzymes, including MtIlvE.
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Affiliation(s)
- Tathyana Mar Amorim Franco
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Lorenza Favrot
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Olivia Vergnolle
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - John S. Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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26
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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27
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Zhang H, Lu H, Chingin K, Chen H. Stabilization of Proteins and Noncovalent Protein Complexes during Electrospray Ionization by Amino Acid Additives. Anal Chem 2015; 87:7433-8. [DOI: 10.1021/acs.analchem.5b01643] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hua Zhang
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi 330013, P.R. China
| | - Haiyan Lu
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi 330013, P.R. China
| | - Konstantin Chingin
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi 330013, P.R. China
| | - Huanwen Chen
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, Jiangxi 330013, P.R. China
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28
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Clarke DJ, Campopiano DJ. Desalting large protein complexes during native electrospray mass spectrometry by addition of amino acids to the working solution. Analyst 2015; 140:2679-86. [DOI: 10.1039/c4an02334j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A simple method for mitigating the adverse effects of salt adduction during native protein mass spectrometry by addition of amino-acids.
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Affiliation(s)
- David J. Clarke
- School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh
- UK
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29
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Outten FW. Recent advances in the Suf Fe-S cluster biogenesis pathway: Beyond the Proteobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1464-9. [PMID: 25447545 DOI: 10.1016/j.bbamcr.2014.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/21/2023]
Abstract
Fe-S clusters play critical roles in cellular function throughout all three kingdoms of life. Consequently, Fe-S cluster biogenesis systems are present in most organisms. The Suf (sulfur formation) system is the most ancient of the three characterized Fe-S cluster biogenesis pathways, which also include the Isc and Nif systems. Much of the first work on the Suf system took place in Gram-negative Proteobacteria used as model organisms. These early studies led to a wealth of biochemical, genetic, and physiological information on Suf function. From those studies we have learned that SufB functions as an Fe-S scaffold in conjunction with SufC (and in some cases SufD). SufS and SufE together mobilize sulfur for cluster assembly and SufA traffics the complete Fe-S cluster from SufB to target apo-proteins. However, recent progress on the Suf system in other organisms has opened up new avenues of research and new hypotheses about Suf function. This review focuses primarily on the most recent discoveries about the Suf pathway and where those new models may lead the field. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- F Wayne Outten
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC 29208, USA.
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30
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Han WB, Lu YH, Zhang AH, Zhang GF, Mei YN, Jiang N, Lei X, Song YC, Ng SW, Tan RX. Curvulamine, a new antibacterial alkaloid incorporating two undescribed units from a Curvularia species. Org Lett 2014; 16:5366-9. [PMID: 25286294 DOI: 10.1021/ol502572g] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The white croaker (Argyrosomus argentatus) derived Curvularia sp. IFB-Z10 produces curvulamine as a skeletally unprecedented alkaloid incorporating two undescribed extender units. Curvulamine is more selectively antibacterial than tinidazole and biosynthetically unique in the new extenders formed through a decarboxylative condensation between an oligoketide motif and alanine.
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Affiliation(s)
- Wen Bo Han
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, China
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31
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Sulfur mobilization for Fe-S cluster assembly by the essential SUF pathway in the Plasmodium falciparum apicoplast and its inhibition. Antimicrob Agents Chemother 2014; 58:3389-98. [PMID: 24709262 DOI: 10.1128/aac.02711-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plastid of the malaria parasite, the apicoplast, is essential for parasite survival. It houses several pathways of bacterial origin that are considered attractive sites for drug intervention. Among these is the sulfur mobilization (SUF) pathway of Fe-S cluster biogenesis. Although the SUF pathway is essential for apicoplast maintenance and parasite survival, there has been limited biochemical investigation of its components and inhibitors of Plasmodium SUFs have not been identified. We report the characterization of two proteins, Plasmodium falciparum SufS (PfSufS) and PfSufE, that mobilize sulfur in the first step of Fe-S cluster assembly and confirm their exclusive localization to the apicoplast. The cysteine desulfurase activity of PfSufS is greatly enhanced by PfSufE, and the PfSufS-PfSufE complex is detected in vivo. Structural modeling of the complex reveals proximal positioning of conserved cysteine residues of the two proteins that would allow sulfide transfer from the PLP (pyridoxal phosphate) cofactor-bound active site of PfSufS. Sulfide release from the l-cysteine substrate catalyzed by PfSufS is inhibited by the PLP inhibitor d-cycloserine, which forms an adduct with PfSufS-bound PLP. d-Cycloserine is also inimical to parasite growth, with a 50% inhibitory concentration close to that reported for Mycobacterium tuberculosis, against which the drug is in clinical use. Our results establish the function of two proteins that mediate sulfur mobilization, the first step in the apicoplast SUF pathway, and provide a rationale for drug design based on inactivation of the PLP cofactor of PfSufS.
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32
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Preuss J, Hort W, Lang S, Netsch A, Rahlfs S, Lochnit G, Jortzik E, Becker K, Mayser PA. Characterization of tryptophan aminotransferase 1 ofMalassezia furfur, the key enzyme in the production of indolic compounds byM. furfur. Exp Dermatol 2013; 22:736-41. [DOI: 10.1111/exd.12260] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Janina Preuss
- Center for Dermatology, Venerology and Allergology; Justus Liebig University; Giessen Germany
| | - Wiebke Hort
- Center for Dermatology, Venerology and Allergology; Justus Liebig University; Giessen Germany
| | - Sarah Lang
- Institute of Pathology and Cytology; Wetzlar Germany
| | - Anette Netsch
- Center for Dermatology, Venerology and Allergology; Justus Liebig University; Giessen Germany
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology; Justus Liebig University; Giessen Germany
| | - Günter Lochnit
- Institute of Biochemistry; Justus Liebig University; Giessen Germany
| | - Esther Jortzik
- Biochemistry and Molecular Biology; Justus Liebig University; Giessen Germany
| | - Katja Becker
- Biochemistry and Molecular Biology; Justus Liebig University; Giessen Germany
| | - Peter A. Mayser
- Center for Dermatology, Venerology and Allergology; Justus Liebig University; Giessen Germany
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33
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Wadsworth JM, Clarke DJ, McMahon SA, Lowther JP, Beattie AE, Langridge-Smith PRR, Broughton HB, Dunn TM, Naismith JH, Campopiano DJ. The chemical basis of serine palmitoyltransferase inhibition by myriocin. J Am Chem Soc 2013; 135:14276-85. [PMID: 23957439 DOI: 10.1021/ja4059876] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sphingolipids (SLs) are essential components of cellular membranes formed from the condensation of L-serine and a long-chain acyl thioester. This first step is catalyzed by the pyridoxal-5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT) which is a promising therapeutic target. The fungal natural product myriocin is a potent inhibitor of SPT and is widely used to block SL biosynthesis despite a lack of a detailed understanding of its molecular mechanism. By combining spectroscopy, mass spectrometry, X-ray crystallography, and kinetics, we have characterized the molecular details of SPT inhibition by myriocin. Myriocin initially forms an external aldimine with PLP at the active site, and a structure of the resulting co-complex explains its nanomolar affinity for the enzyme. This co-complex then catalytically degrades via an unexpected 'retro-aldol-like' cleavage mechanism to a C18 aldehyde which in turn acts as a suicide inhibitor of SPT by covalent modification of the essential catalytic lysine. This surprising dual mechanism of inhibition rationalizes the extraordinary potency and longevity of myriocin inhibition.
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Affiliation(s)
- John M Wadsworth
- School of Chemistry, The University of Edinburgh , Edinburgh, Scotland, EH9 3JJ, United Kingdom
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34
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Vogel KR, Pearl PL, Theodore WH, McCarter RC, Jakobs C, Gibson KM. Thirty years beyond discovery--clinical trials in succinic semialdehyde dehydrogenase deficiency, a disorder of GABA metabolism. J Inherit Metab Dis 2013; 36:401-10. [PMID: 22739941 PMCID: PMC4349389 DOI: 10.1007/s10545-012-9499-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 05/09/2012] [Accepted: 05/14/2012] [Indexed: 10/28/2022]
Abstract
This review summarizes a presentation made at the retirement Symposium of Prof. Dr. Cornelis Jakobs in November of 2011, highlighting the progress toward clinical trials in succinic semialdehyde dehydrogenase (SSADH) deficiency, a disorder first recognized in 1981. Active and potential clinical interventions, including vigabatrin, L-cycloserine, the GHB receptor antagonist NCS-382, and the ketogenic diet, are discussed. Several biomarkers to gauge clinical efficacy have been identified, including cerebrospinal fluid metabolites, neuropsychiatric testing, MRI, EEG, and measures of GABAergic function including (11 C)flumazenil positron emission tomography (PET) and transcranial magnetic stimulation (TMS). Thirty years after its discovery, encompassing extensive studies in both patients and the corresponding murine model, we are now running an open-label trial of taurine intervention, and are poised to undertake a phase II trial of the GABAB receptor antagonist SGS742.
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Affiliation(s)
- Kara R Vogel
- Section of Clinical Pharmacology, College of Pharmacy, Washington State University, Spokane, WA 99202-2131, USA.
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35
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Inhibition of serine palmitoyltransferase reduces Aβ and tau hyperphosphorylation in a murine model: a safe therapeutic strategy for Alzheimer's disease. Neurobiol Aging 2013; 34:2037-51. [PMID: 23528227 DOI: 10.1016/j.neurobiolaging.2013.02.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 01/31/2013] [Accepted: 02/09/2013] [Indexed: 12/14/2022]
Abstract
The contribution of the autosomal dominant mutations to the etiology of familial Alzheimer's disease (AD) is well characterized. However, the molecular mechanisms contributing to sporadic AD are less well understood. Increased ceramide levels have been evident in AD patients. We previously reported that increased ceramide levels, regulated by increased serine palmitoyltransferase (SPT), directly mediate amyloid β (Aβ) levels. Therefore, we inhibited SPT in an AD mouse model (TgCRND8) through subcutaneous administration of L-cylcoserine. The cortical Aβ₄₂ and hyperphosphorylated tau levels were down-regulated with the inhibition of SPT/ceramide. Positive correlations were observed among cortical SPT, ceramide, and Aβ₄₂ levels. With no evident toxic effects observed, inhibition of SPT could be a safe therapeutic strategy to ameliorate the AD pathology. We previously observed that miR-137, -181c, -9, and 29a/b post-transcriptionally regulate SPT levels, and the corresponding miRNA levels in the blood sera are potential diagnostic biomarkers for AD. Here, we observe a negative correlation between cortical Aβ₄₂ and sera Aβ₄₂, and a positive correlation between cortical miRNA levels and sera miRNA levels suggesting their potential as noninvasive diagnostic biomarkers.
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36
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Structural, mechanistic and regulatory studies of serine palmitoyltransferase. Biochem Soc Trans 2012; 40:547-54. [PMID: 22616865 DOI: 10.1042/bst20110769] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
SLs (sphingolipids) are composed of fatty acids and a polar head group derived from L-serine. SLs are essential components of all eukaryotic and many prokaryotic membranes but S1P (sphingosine 1-phosphate) is also a potent signalling molecule. Recent efforts have sought to inventory the large and chemically complex family of SLs (LIPID MAPS Consortium). Detailed understanding of SL metabolism may lead to therapeutic agents specifically directed at SL targets. We have studied the enzymes involved in SL biosynthesis; later stages are species-specific, but all core SLs are synthesized from the condensation of L-serine and a fatty acid thioester such as palmitoyl-CoA that is catalysed by SPT (serine palmitoyltransferase). SPT is a PLP (pyridoxal 5'-phosphate)-dependent enzyme that forms 3-KDS (3-ketodihydrosphingosine) through a decarboxylative Claisen-like condensation reaction. Eukaryotic SPTs are membrane-bound multi-subunit enzymes, whereas bacterial enzymes are cytoplasmic homodimers. We use bacterial SPTs (e.g. from Sphingomonas) to probe their structure and mechanism. Mutations in human SPT cause a neuropathy [HSAN1 (hereditary sensory and autonomic neuropathy type 1)], a rare SL metabolic disease. How these mutations perturb SPT activity is subtle and bacterial SPT mimics of HSAN1 mutants affect the enzyme activity and structure of the SPT dimer. We have also explored SPT inhibition using various inhibitors (e.g. cycloserine). A number of new subunits and regulatory proteins that have a direct impact on the activity of eukaryotic SPTs have recently been discovered. Knowledge gained from bacterial SPTs sheds some light on the more complex mammalian systems. In the present paper, we review historical aspects of the area and highlight recent key developments.
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37
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Bourquin F, Capitani G, Grütter MG. PLP-dependent enzymes as entry and exit gates of sphingolipid metabolism. Protein Sci 2012; 20:1492-508. [PMID: 21710479 DOI: 10.1002/pro.679] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sphingolipids are membrane constituents as well as signaling molecules involved in many essential cellular processes. Serine palmitoyltransferase (SPT) and sphingosine-1-phosphate lyase (SPL), both PLP (pyridoxal 5'-phosphate)-dependent enzymes, function as entry and exit gates of the sphingolipid metabolism. SPT catalyzes the condensation of serine and a fatty acid into 3-keto-dihydrosphingosine, whereas SPL degrades sphingosine-1-phosphate (S1P) into phosphoethanolamine and a long-chain aldehyde. The recently solved X-ray structures of prokaryotic homologs of SPT and SPL combined with functional studies provide insight into the structure-function relationship of the two enzymes. Despite carrying out different reactions, the two enzymes reveal striking similarities in the overall fold, topology, and residues crucial for activity. Unlike their eukaryotic counterparts, bacterial SPT and SPL lack a transmembrane helix, making them targets of choice for biochemical characterization because the use of detergents can be avoided. Both human enzymes are linked to severe diseases or disorders and might therefore serve as targets for the development of therapeutics aiming at the modulation of their activity. This review gives an overview of the sphingolipid metabolism and of the available biochemical studies of prokaryotic SPT and SPL, and discusses the major similarities and differences to the corresponding eukaryotic enzymes.
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Affiliation(s)
- Florence Bourquin
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
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38
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Lowther J, Beattie AE, Langridge-Smith PRR, Clarke DJ, Campopiano DJ. l-Penicillamine is a mechanism-based inhibitor of serine palmitoyltransferase by forming a pyridoxal-5′-phosphate-thiazolidine adduct. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20020a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Shi C, Geders TW, Park SW, Wilson DJ, Boshoff HI, Orisadipe A, Barry CE, Schnappinger D, Finzel BC, Aldrich CC. Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis. J Am Chem Soc 2011; 133:18194-201. [PMID: 21988601 PMCID: PMC3222238 DOI: 10.1021/ja204036t] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BioA catalyzes the second step of biotin biosynthesis, and this enzyme represents a potential target to develop new antitubercular agents. Herein we report the design, synthesis, and biochemical characterization of a mechanism-based inhibitor (1) featuring a 3,6-dihydropyrid-2-one heterocycle that covalently modifies the pyridoxal 5'-phosphate (PLP) cofactor of BioA through aromatization. The structure of the PLP adduct was confirmed by MS/MS and X-ray crystallography at 1.94 Å resolution. Inactivation of BioA by 1 was time- and concentration-dependent and protected by substrate. We used a conditional knock-down mutant of M. tuberculosis to demonstrate the antitubercular activity of 1 correlated with BioA expression, and these results provide support for the designed mechanism of action.
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Affiliation(s)
- Ce Shi
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
| | - Todd W. Geders
- Department of Medicinal Chemistry, University of Minnesota, MN, 55455, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, United States
| | - Daniel J. Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
| | - Helena I. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Abayomi Orisadipe
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, United States
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, MN, 55455, United States
| | - Courtney C. Aldrich
- Center for Drug Design, Academic Health Center, University of Minnesota, MN, 55455, United States
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40
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Merrill AH. Sphingolipid and glycosphingolipid metabolic pathways in the era of sphingolipidomics. Chem Rev 2011; 111:6387-422. [PMID: 21942574 PMCID: PMC3191729 DOI: 10.1021/cr2002917] [Citation(s) in RCA: 527] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Indexed: 12/15/2022]
Affiliation(s)
- Alfred H Merrill
- School of Biology, and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
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41
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Lowther J, Charmier G, Raman MC, Ikushiro H, Hayashi H, Campopiano DJ. Role of a conserved arginine residue during catalysis in serine palmitoyltransferase. FEBS Lett 2011; 585:1729-34. [PMID: 21514297 DOI: 10.1016/j.febslet.2011.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 04/04/2011] [Accepted: 04/05/2011] [Indexed: 10/18/2022]
Abstract
All sphingolipid-producing organisms require the pyridoxal 5'-phosphate (PLP)-dependent serine palmitoyltransferase (SPT) to catalyse the first reaction on the de novo sphingolipid biosynthetic pathway. SPT is a member of the alpha oxoamine synthase (AOS) family that catalyses a Claisen-like condensation of palmitoyl-CoA and L-serine to form 3-ketodihydrosphingosine (KDS). Protein sequence alignment across various species reveals an arginine residue, not involved in PLP binding, to be strictly conserved in all prokaryotic SPTs, the lcb2 subunits of eukaryotic SPTs and all members of the AOS family. Here we use UV-vis spectroscopy and site-directed mutagenesis, in combination with a substrate analogue, to show that the equivalent residue (R370) in the SPT from Sphingomonas wittichii is required to form the key PLP:L-serine quinonoid intermediate that condenses with palmitoyl-CoA and thus plays an essential role enzyme catalysis.
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Affiliation(s)
- Jonathan Lowther
- School of Chemistry, EaStCHEM, University of Edinburgh, Edinburgh, Scotland, UK
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