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Purohit V, Steussy CN, Rosales AR, Critchelow CJ, Schmidt T, Helquist P, Wiest O, Mesecar A, Cohen AE, Stauffacher CV. pH-dependent reaction triggering in PmHMGR crystals for time-resolved crystallography. Biophys J 2024; 123:622-637. [PMID: 38327055 PMCID: PMC10938121 DOI: 10.1016/j.bpj.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024] Open
Abstract
Serial crystallography and time-resolved data collection can readily be employed to investigate the catalytic mechanism of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl (HMG)-coenzyme-A (CoA) reductase (PmHMGR) by changing the environmental conditions in the crystal and so manipulating the reaction rate. This enzyme uses a complex mechanism to convert mevalonate to HMG-CoA using the co-substrate CoA and cofactor NAD+. The multi-step reaction mechanism involves an exchange of bound NAD+ and large conformational changes by a 50-residue subdomain. The enzymatic reaction can be run in both forward and reverse directions in solution and is catalytically active in the crystal for multiple reaction steps. Initially, the enzyme was found to be inactive in the crystal starting with bound mevalonate, CoA, and NAD+. To observe the reaction from this direction, we examined the effects of crystallization buffer constituents and pH on enzyme turnover, discovering a strong inhibition in the crystallization buffer and a controllable increase in enzyme turnover as a function of pH. The inhibition is dependent on ionic concentration of the crystallization precipitant ammonium sulfate but independent of its ionic composition. Crystallographic studies show that the observed inhibition only affects the oxidation of mevalonate but not the subsequent reactions of the intermediate mevaldehyde. Calculations of the pKa values for the enzyme active site residues suggest that the effect of pH on turnover is due to the changing protonation state of His381. We have now exploited the changes in ionic inhibition in combination with the pH-dependent increase in turnover as a novel approach for triggering the PmHMGR reaction in crystals and capturing information about its intermediate states along the reaction pathway.
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Affiliation(s)
- Vatsal Purohit
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Calvin N Steussy
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Anthony R Rosales
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
| | | | - Tim Schmidt
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
| | - Andrew Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana; Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana; Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana; Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, Indiana; Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana.
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2
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Chen Y, Liu Y, Wang Y, Zhang Y, Xie W, Zhang H, Weng Q, Xu M. Expression of cholesterol synthesis and steroidogenic markers in females of the Chinese brown frog ( Rana dybowskii) during prespawning and prehibernation. Am J Physiol Regul Integr Comp Physiol 2023; 325:R750-R758. [PMID: 37867473 DOI: 10.1152/ajpregu.00296.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 10/24/2023]
Abstract
The oviduct of the Chinese brown frog (Rana dybowskii) expands in prehibernation rather than in prespawning, which is one of the physiological phenomena that occur in the preparation for hibernation. Steroid hormones are known to regulate oviductal development. Cholesterol synthesis and steroidogenesis may play an important role in the expansion of the oviduct before hibernation. In this study, we investigated the expression patterns of the markers that are involved in the de novo steroid synthesis pathway in the oviduct of R. dybowskii during prespawning and prehibernation. According to histological analysis, the oviduct of R. dybowskii contains epithelial cells, glandular cells, and tubule lumens. During prehibernation, oviductal pipe diameter and weight were significantly larger than during prespawning. 3-Hydroxy-3-methylglutaryl CoA reductase (HMGCR), low-density lipoprotein receptor (LDLR), steroidogenic acute regulatory protein (StAR), cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc), and steroidogenic factor 1 (SF-1) were detected in epithelial cells in prehibernation and glandular cells during prespawning. HMGCR, LDLR, StAR, and P450scc protein expression levels were higher in prehibernation than during prespawning, but the SF-1 protein expression level did not significantly differ. HMGCR, LDLR, StAR, P450scc (CYP11A1), and SF-1 (NR5A1) mRNA expression levels were significantly higher in prehibernation compared with prespawning. The transcriptome results showed that the steroid synthesis pathway was highly expressed during prehibernation. Existing results indicate that the oviduct is able to synthesize steroid hormones using cholesterol, and that steroid hormones may affect the oviductal functions of R. dybowskii.
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Affiliation(s)
- Yuan Chen
- Laboratory of Animal Physiology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, People's Republic of China
| | - Yuning Liu
- Laboratory of Animal Physiology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - Yankun Wang
- Laboratory of Animal Physiology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, People's Republic of China
| | - Yue Zhang
- Laboratory of Animal Physiology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, People's Republic of China
| | - Wenqian Xie
- Laboratory of Animal Physiology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - Haolin Zhang
- Laboratory of Animal Physiology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - Qiang Weng
- Laboratory of Animal Physiology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - Meiyu Xu
- Laboratory of Animal Physiology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, People's Republic of China
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3
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Du B, Sun M, Hui W, Xie C, Xu X. Recent Advances on Key Enzymes of Microbial Origin in the Lycopene Biosynthesis Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12927-12942. [PMID: 37609695 DOI: 10.1021/acs.jafc.3c03942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Lycopene is a common carotenoid found mainly in ripe red fruits and vegetables that is widely used in the food industry due to its characteristic color and health benefits. Microbial synthesis of lycopene is gradually replacing the traditional methods of plant extraction and chemical synthesis as a more economical and productive manufacturing strategy. The biosynthesis of lycopene is a typical multienzyme cascade reaction, and it is important to understand the characteristics of each key enzyme involved and how they are regulated. In this paper, the catalytic characteristics of the key enzymes involved in the lycopene biosynthesis pathway and related studies are first discussed in detail. Then, the strategies applied to the key enzymes of lycopene synthesis, including fusion proteins, enzyme screening, combinatorial engineering, CRISPR/Cas9-based gene editing, DNA assembly, and scaffolding technologies are purposefully illustrated and compared in terms of both traditional and emerging multienzyme regulatory strategies. Finally, future developments and regulatory options for multienzyme synthesis of lycopene and similar secondary metabolites are also discussed.
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Affiliation(s)
- Bangmian Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Mengjuan Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Wenyang Hui
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Chengjia Xie
- School of Chemical Engineering, Yangzhou Polytechnic Institute, Yangzhou 225127, Jiangsu Province, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
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4
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Bose S, Steussy CN, López-Pérez D, Schmidt T, Kulathunga SC, Seleem MN, Lipton M, Mesecar AD, Rodwell VW, Stauffacher CV. Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor. Commun Biol 2023; 6:360. [PMID: 37012403 PMCID: PMC10070635 DOI: 10.1038/s42003-023-04639-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/28/2023] [Indexed: 04/05/2023] Open
Abstract
HMG-CoA reductase (HMGR), a rate-limiting enzyme of the mevalonate pathway in Gram-positive pathogenic bacteria, is an attractive target for development of novel antibiotics. In this study, we report the crystal structures of HMGR from Enterococcus faecalis (efHMGR) in the apo and liganded forms, highlighting several unique features of this enzyme. Statins, which inhibit the human enzyme with nanomolar affinity, perform poorly against the bacterial HMGR homologs. We also report a potent competitive inhibitor (Chembridge2 ID 7828315 or compound 315) of the efHMGR enzyme identified by a high-throughput, in-vitro screening. The X-ray crystal structure of efHMGR in complex with 315 was determined to 1.27 Å resolution revealing that the inhibitor occupies the mevalonate-binding site and interacts with several key active site residues conserved among bacterial homologs. Importantly, 315 does not inhibit the human HMGR. Our identification of a selective, non-statin inhibitor of bacterial HMG-CoA reductases will be instrumental in lead optimization and development of novel antibacterial drug candidates.
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Affiliation(s)
- Sucharita Bose
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post Bellary Road, Bangalore, 560065, India
| | - C Nicklaus Steussy
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Daneli López-Pérez
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
- Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Tim Schmidt
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Samadhi C Kulathunga
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, 625 Harrison Street, West Lafayette, IN, 47907, USA
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, 205 Duck Pond Drive, Blacksburg, VA, 24061, USA
| | - Mark Lipton
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN, 47907, USA
| | - Victor W Rodwell
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN, 47907, USA
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.
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5
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Arjmand G, Haeri MR. Antibacterial Effect of Some Eukaryotic Sterol Biosynthesis Inhibitors. Adv Biomed Res 2022; 11:90. [PMID: 36518857 PMCID: PMC9744079 DOI: 10.4103/abr.abr_291_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/24/2022] [Accepted: 03/12/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Isoprenoids and their derivatives are building blocks for the synthesis of biomolecules with important biological functions such as cholesterol in eukaryotes and lipid carrier undecaprenol, which is involved in cell wall biosynthesis in bacteria. With the global threat of multidrug-resistant bacteria, there is a need for finding new metabolic targets for killing bacteria. In the present study, we examined the impact of eukaryotic sterol biosynthesis inhibitors on the growth of four pathogenic bacteria. MATERIALS AND METHODS Antibacterial effect of HMG CoA reductase inhibitor (simvastatin), farnesyl pyrophosphate synthase inhibitor (alendronate), squalene epoxidase inhibitor (terbinafine), and lanosterol demethylase inhibitor (ketoconazole) were studied against four pathogenic bacteria: two gram-positive bacteria, Staphylococcus aureus and Enterococcus faecalis and two gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa. Broth microdilution method was used for assessing the antibacterial susceptibility of the components using 96 well plats. MIC and MBC were determined visibly. RESULTS MIC of Ketoconazole for Staphylococcus aureus and Enterococcus faecalis were 0.166 and 1 mg/mL, respectively. Terbinafine had a weak inhibitory effect on Staphylococcus aureus (MIC: 8 mg/mL). Ketoconazole and terbinafine had no inhibitory effect on gram-negative bacteria. MBC of Simvastatin for both Staphylococcus aureus and Enterococcus faecalis was 0.5 mg/mL and of Alendronate for Pseudomonas aeruginosa was 6.6 mg/mL. CONCLUSION Our results show that farnesyl pyrophosphate synthase and class II HMG-CoA reductases inhibitors (ketoconazole and simvastatin) have reasonable antibacterial activity against gram-positive bacteria. These two enzymes provide suitable targets for designing new antibiotics based on modifying the chemical structure of currently used drugs to obtain maximum activity.
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Affiliation(s)
- Ghasem Arjmand
- Department of Biochemistry, Faculty of Science, Payam Noor University, Tehran Branch, Tehran, Iran
| | - Mohammad Reza Haeri
- Department of Clinical Biochemistry, Faculty of Medicine, Qom University of Medical Sciences, Qom, Iran,Address for correspondence: Dr. Mohammad Reza Haeri, Department of Clinical Biochemistry, Faculty of Medicine, Qom University of Medical Sciences, Qom, Iran. E-mail:
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6
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Haywood J, Breese KJ, Zhang J, Waters MT, Bond CS, Stubbs KA, Mylne JS. A fungal tolerance trait and selective inhibitors proffer HMG-CoA reductase as a herbicide mode-of-action. Nat Commun 2022; 13:5563. [PMID: 36137996 PMCID: PMC9500038 DOI: 10.1038/s41467-022-33185-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/07/2022] [Indexed: 12/02/2022] Open
Abstract
Decades of intense herbicide use has led to resistance in weeds. Without innovative weed management practices and new herbicidal modes of action, the unabated rise of herbicide resistance will undoubtedly place further stress upon food security. HMGR (3-hydroxy-3-methylglutaryl-coenzyme A reductase) is the rate limiting enzyme of the eukaryotic mevalonate pathway successfully targeted by statins to treat hypercholesterolemia in humans. As HMGR inhibitors have been shown to be herbicidal, HMGR could represent a mode of action target for the development of herbicides. Here, we present the crystal structure of a HMGR from Arabidopsis thaliana (AtHMG1) which exhibits a wider active site than previously determined structures from different species. This plant conserved feature enables the rational design of specific HMGR inhibitors and we develop a tolerance trait through sequence analysis of fungal gene clusters. These results suggest HMGR to be a viable herbicide target modifiable to provide a tolerance trait.
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Affiliation(s)
- Joel Haywood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA, 6102, Australia.
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia.
| | - Karen J Breese
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Jingjing Zhang
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Mark T Waters
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Joshua S Mylne
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA, 6102, Australia.
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia.
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7
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Gesto DS, Pereira CMS, Cerqueira NMFS, Sousa SF. An Atomic-Level Perspective of HMG-CoA-Reductase: The Target Enzyme to Treat Hypercholesterolemia. Molecules 2020; 25:molecules25173891. [PMID: 32859023 PMCID: PMC7503714 DOI: 10.3390/molecules25173891] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 12/19/2022] Open
Abstract
This review provides an updated atomic-level perspective regarding the enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoAR), linking the more recent data on this enzyme with a structure/function interpretation. This enzyme catalyzes one of the most important steps in cholesterol biosynthesis and is regarded as one of the most important drug targets in the treatment of hypercholesterolemia. Taking this into consideration, we review in the present article several aspects of this enzyme, including its structure and biochemistry, its catalytic mechanism and different reported and proposed approaches for inhibiting this enzyme, including the commercially available statins or the possibility of using dimerization inhibitors.
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Affiliation(s)
- Diana S. Gesto
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
| | - Carlos M. S. Pereira
- UCIBIO/REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.M.S.P.); (N.M.F.S.C.)
| | - Nuno M. F. S. Cerqueira
- UCIBIO/REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.M.S.P.); (N.M.F.S.C.)
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.M.S.P.); (N.M.F.S.C.)
- Correspondence:
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8
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[Blood lipid metabolic profile of overweight/obese boys aged 9-12 years]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020. [PMID: 32800035 PMCID: PMC7441509 DOI: 10.7499/j.issn.1008-8830.2005077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To study the features of blood lipid metabolic profile in overweight/obese boys aged 9-12 years and the possible mechanism of overweight/obesity in children. METHODS According to body mass index (BMI), 72 boys, aged 9-12 years, were divided into a control group with 42 boys and an overweight/obesity group with 30 boys. Fasting venous blood samples were collected early in the morning. BMI, waist-hip ratio, body composition, and blood lipids were measured. Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry technique was used to analyze the serum lipid compounds. A statistical analysis and visualization of the data were performed. RESULTS Compared with the control group, the overweight/obesity group had significantly higher waist-hip ratio, body fat percentage, and triglyceride level (P<0.05) and a significantly lower level of high-density lipoprotein cholesterol (P<0.05). The metabolomic analysis identified 150 differentially expressed lipid compounds between the two groups, mainly glycerolipids (40.7%), glycerophospholipids (24.7%), fatty acyls (10.7%), and sphingolipids (7.3%). The levels of most of glycerolipids were significantly upregulated in the overweight/obesity group, while those of most of glycerophospholipids and sphingolipids were downregulated in this group. Key lipids with differential expression were enriched into two KEGG metabolic pathways, i.e., ether lipid metabolism pathway and terpenoid backbone biosynthesis pathway (P<0.05), and might further affected the biosynthesis and metabolism of downstream coenzyme Q and other terpenoids (P=0.06). CONCLUSIONS Disordered lipid metabolic profile is observed in overweight/obese boys aged 9-12 years, with increases in most glycerolipids and reductions in glycerophospholipids and sphingolipids. Overweight/obese boys may have disorders in ether lipid metabolism and biosynthesis of terpenoid and even coenzyme Q.
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9
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Liang CY, Cao YP, Yan Y. [Blood lipid metabolic profile of overweight/obese boys aged 9-12 years]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:874-881. [PMID: 32800035 PMCID: PMC7441509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/13/2020] [Indexed: 08/02/2024]
Abstract
OBJECTIVE To study the features of blood lipid metabolic profile in overweight/obese boys aged 9-12 years and the possible mechanism of overweight/obesity in children. METHODS According to body mass index (BMI), 72 boys, aged 9-12 years, were divided into a control group with 42 boys and an overweight/obesity group with 30 boys. Fasting venous blood samples were collected early in the morning. BMI, waist-hip ratio, body composition, and blood lipids were measured. Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry technique was used to analyze the serum lipid compounds. A statistical analysis and visualization of the data were performed. RESULTS Compared with the control group, the overweight/obesity group had significantly higher waist-hip ratio, body fat percentage, and triglyceride level (P<0.05) and a significantly lower level of high-density lipoprotein cholesterol (P<0.05). The metabolomic analysis identified 150 differentially expressed lipid compounds between the two groups, mainly glycerolipids (40.7%), glycerophospholipids (24.7%), fatty acyls (10.7%), and sphingolipids (7.3%). The levels of most of glycerolipids were significantly upregulated in the overweight/obesity group, while those of most of glycerophospholipids and sphingolipids were downregulated in this group. Key lipids with differential expression were enriched into two KEGG metabolic pathways, i.e., ether lipid metabolism pathway and terpenoid backbone biosynthesis pathway (P<0.05), and might further affected the biosynthesis and metabolism of downstream coenzyme Q and other terpenoids (P=0.06). CONCLUSIONS Disordered lipid metabolic profile is observed in overweight/obese boys aged 9-12 years, with increases in most glycerolipids and reductions in glycerophospholipids and sphingolipids. Overweight/obese boys may have disorders in ether lipid metabolism and biosynthesis of terpenoid and even coenzyme Q.
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10
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Marsafari M, Xu P. Debottlenecking mevalonate pathway for antimalarial drug precursor amorphadiene biosynthesis in Yarrowia lipolytica. Metab Eng Commun 2020; 10:e00121. [PMID: 31956504 PMCID: PMC6957783 DOI: 10.1016/j.mec.2019.e00121] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/13/2019] [Accepted: 12/31/2019] [Indexed: 11/17/2022] Open
Abstract
World Health Organization reports that half of the population in developing countries are at risk of malaria infection. Artemisinin, the most potent anti-malaria drug, is a sesquiterpene endoperoxide extracted from the plant Artemisia annua. Due to scalability and economics issues, plant extraction or chemical synthesis could not provide a sustainable route for large-scale manufacturing of artemisinin. The price of artemisinin has been fluctuating from 200$/Kg to 1100$/Kg, due to geopolitical and climate factors. Microbial fermentation was considered as a promising method to stabilize the artemisinin supply chain. Yarrowia lipolytica, is an oleaginous yeast with proven capacity to produce large quantity of lipids and oleochemicals. In this report, the lipogenic acetyl-CoA pathways and the endogenous mevalonate pathway of Y. lipolytica were harnessed for amorphadiene production. Gene overexpression indicate that HMG-CoA and acetyl-CoA supply are two limiting bottlenecks for amorphadiene production. We have identified the optimal HMG-CoA reductase and determined the optimal gene copy number for the precursor pathways. Amorphadiene production was improved further by either inhibiting fatty acids synthase or activating the fatty acid degradation pathway. With co-expression of mevalonate kinase (encoded by Erg12), a push-and-pull strategy enabled the engineered strain to produce 171.5 mg/L of amorphadiene in shake flasks. These results demonstrate that balancing carbon flux and manipulation of precursor competing pathways are key factors to improve amorphadiene biosynthesis in oleaginous yeast; and Y. lipolytica is a promising microbial host to expand nature’s biosynthetic capacity, allowing us to quickly access antimalarial drug precursors. Endogenous acetyl-CoA and mevalonate pathway were harnessed for amorphadiene synthesis. Expression of native untruncated HMG-CoA reductase (HMG1) removes rate-limiting steps. Balancing ADS, HMG1 and MVK activity effectively pull FPP flux toward amorphadiene. Activation of fatty acid degradation pushes carbon flux toward HMG-CoA pathways. A push-and-pull strategy boosts amorphadiene production to 171.5 mg/L in shake flasks.
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Affiliation(s)
- Monireh Marsafari
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
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11
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Peacock RB, Hicks CW, Walker AM, Dewing SM, Lewis KM, Abboud JC, Stewart SWA, Kang C, Watson JM. Structural and Functional Characterization of Dynamic Oligomerization in Burkholderia cenocepacia HMG-CoA Reductase. Biochemistry 2019; 58:3960-3970. [PMID: 31469273 DOI: 10.1021/acs.biochem.9b00494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR), in most organisms, catalyzes the four-electron reduction of the thioester (S)-HMG-CoA to the primary alcohol (R)-mevalonate, utilizing NADPH as the hydride donor. In some organisms, including the opportunistic lung pathogen Burkholderia cenocepacia, it catalyzes the reverse reaction, utilizing NAD+ as a hydride acceptor in the oxidation of mevalonate. B. cenocepacia HMGR has been previously shown to exist as an ensemble of multiple non-additive oligomeric states, each with different levels of enzymatic activity, suggesting that the enzyme exhibits characteristics of the morpheein model of allostery. We have characterized a number of factors, including pH, substrate concentration, and enzyme concentration, that modulate the structural transitions that influence the interconversion among the multiple oligomers. We have also determined the crystal structure of B. cenocepacia HMGR in the hexameric state bound to coenzyme A and ADP. This hexameric assembly provides important clues about how the transition among oligomers might occur, and why B. cenocepacia HMGR, unique among characterized HMGRs, exhibits morpheein-like behavior.
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Affiliation(s)
- Riley B Peacock
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Chad W Hicks
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Alexander M Walker
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Sophia M Dewing
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Kevin M Lewis
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Jean-Claude Abboud
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Samuel W A Stewart
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - ChulHee Kang
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Jeffrey M Watson
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
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12
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Vögeli B, Shima S, Erb TJ, Wagner T. Crystal structure of archaeal HMG-CoA reductase: insights into structural changes of the C-terminal helix of the class-I enzyme. FEBS Lett 2019; 593:543-553. [PMID: 30702149 DOI: 10.1002/1873-3468.13331] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 01/04/2019] [Accepted: 01/22/2019] [Indexed: 11/08/2022]
Abstract
3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) catalyses the last step in mevalonate biosynthesis. HMGR is the target of statin inhibitors that regulate cholesterol concentration in human blood. Here, we report the properties and structures of HMGR from an archaeon Methanothermococcus thermolithotrophicus (mHMGR). The structures of the apoenzyme and the NADPH complex are highly similar to those of human HMGR. A notable exception is C-terminal helix (Lα10-11) that is straight in both mHMGR structures. This helix is kinked and closes the active site in the human enzyme ternary complex, pointing to a substrate-induced structural rearrangement of C-terminal in class-I HMGRs during the catalytic cycle.
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Affiliation(s)
- Bastian Vögeli
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Seigo Shima
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tristan Wagner
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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13
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Costa CHS, Oliveira ARS, Dos Santos AM, da Costa KS, Lima AHLE, Alves CN, Lameira J. Computational study of conformational changes in human 3-hydroxy-3-methylglutaryl coenzyme reductase induced by substrate binding. J Biomol Struct Dyn 2019; 37:4374-4383. [PMID: 30470158 DOI: 10.1080/07391102.2018.1549508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is mainly involved in the regulation of cholesterol biosynthesis. HMGR catalyses the reduction of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonate at the expense of two NADPH molecules in a two-step reversible reaction. In the present study, we constructed a model of human HMGR (hHMGR) to explore the conformational changes of HMGR in complex with HMG-CoA and NADPH. In addition, we analysed the complete sequence of the Flap domain using molecular dynamics (MD) simulations and principal component analysis (PCA). The simulations revealed that the Flap domain plays an important role in catalytic site activation and substrate binding. The apo form of hHMGR remained in an open state, while a substrate-induced closure of the Flap domain was observed for holo hHMGR. Our study also demonstrated that the phosphorylation of Ser872 induces significant conformational changes in the Flap domain that lead to a complete closure of the active site, suggesting three principal conformations for the first stage of hHMGR catalysis. Our results were consistent with previous proposed models for the catalytic mechanism of hHMGR. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Alberto M Dos Santos
- Institute of Biological Sciences, Federal University of Pará , Belém , Pará , Brazil
| | - Kauê Santana da Costa
- Institute of Biodiversity, Federal University of West of Pará , Santarém , Pará , Brazil
| | | | - Cláudio N Alves
- Institute of Natural Sciences, Federal University of Pará , Belém , Pará , Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará , Belém , Pará , Brazil
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14
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Ragwan ER, Arai E, Kung Y. New Crystallographic Snapshots of Large Domain Movements in Bacterial 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase. Biochemistry 2018; 57:5715-5725. [PMID: 30199631 DOI: 10.1021/acs.biochem.8b00869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR) catalyzes the first committed step of the mevalonate pathway, which is used across biology in the biosynthesis of countless metabolites. HMGR consumes 2 equiv of the cofactor NAD(P)H to perform the four-electron reduction of HMG-CoA to mevalonate toward the production of steroids and isoprenoids, the largest class of natural products. Recent structural data have shown that HMGR contains a highly mobile C-terminal domain (CTD) that is believed to adopt many different conformations to permit binding and dissociation of the substrate, cofactors, and products at specific points during the reaction cycle. Here, we have characterized the HMGR from Delftia acidovorans as an NADH-specific enzyme and determined crystal structures of the enzyme in unbound, mevalonate-bound, and NADH- and citrate-bound states. Together, these structures depict ligand binding in both the active site and the cofactor-binding site while illustrating how a conserved helical motif confers NAD(P)H cofactor specificity. Unexpectedly, the NADH-bound structure also reveals a new conformation of the CTD, in which the domain has "flipped" upside-down, while directly binding the cofactor. By capturing these structural snapshots, this work not only expands the known range of HMGR domain movement but also provides valuable insight into the catalytic mechanism of this biologically important enzyme.
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Affiliation(s)
- Edwin R Ragwan
- Department of Chemistry , Bryn Mawr College , 101 North Merion Avenue , Bryn Mawr , Pennsylvania 19010 , United States
| | - Eri Arai
- Department of Chemistry , Bryn Mawr College , 101 North Merion Avenue , Bryn Mawr , Pennsylvania 19010 , United States
| | - Yan Kung
- Department of Chemistry , Bryn Mawr College , 101 North Merion Avenue , Bryn Mawr , Pennsylvania 19010 , United States
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