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Sun Z, Pan X, Li X, Jiang L, Hu P, Wang Y, Ye Y, Wu P, Zhao B, Xu J, Kong M, Pu Y, Zhao M, Hu J, Wang J, Chen G, Yuan C, Yu Y, Gao X, Zhao F, Pan A, Zheng Y. The Gut Microbiome Dynamically Associates with Host Glucose Metabolism throughout Pregnancy: Longitudinal Findings from a Matched Case-Control Study of Gestational Diabetes Mellitus. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205289. [PMID: 36683149 PMCID: PMC10074094 DOI: 10.1002/advs.202205289] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Though gut microbiome disturbance may be involved in the etiology of gestational diabetes mellitus (GDM), data on the gut microbiome's dynamic change during pregnancy and associations with gestational glucose metabolism are still inadequate. In this prospective study comprising 120 pairs of GDM patients and matched pregnant controls, a decrease in the diversity of gut microbial species and changes in the microbial community composition with advancing gestation are found in controls, while no such trends are observed in GDM patients. Multivariable analysis identifies 10 GDM-related species (e.g., Alistipes putredinis), and the integrated associations of these species with glycemic traits are modified by habitual intake of fiber-rich plant foods. In addition, the microbial metabolic potentials related to fiber fermentation (e.g., mannan degradation pathways) and their key enzymes consistently emerge as associated with both GDM status and glycemic traits. Microbial features especially those involved in fiber fermentation, provide an incremental predictive value in a prediction model with established risk factors of GDM. These data suggest that the gut microbiome remodeling with advancing gestation is different in GDM patients compared with controls, and dietary fiber fermentation contributes to the influence of gut microbiome on gestational glycemic regulation.
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Affiliation(s)
- Zhonghan Sun
- State Key Laboratory of Genetic EngineeringSchool of Life Sciences and Human Phenome InstituteFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary AnthropologyFudan UniversityShanghaiChina
| | - Xiong‐Fei Pan
- Section of Epidemiology and Population HealthMinistry of Education Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenWest China Second University Hospital & West China Biomedical Big Data CenterWest China HospitalSichuan University; Shuangliu Institute of Women's and Children's HealthShuangliu Maternal and Child Health HospitalChengduSichuanChina
| | - Xiao Li
- State Key Laboratory of Genetic EngineeringSchool of Life Sciences and Human Phenome InstituteFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary AnthropologyFudan UniversityShanghaiChina
| | - Limiao Jiang
- Department of Epidemiology & BiostatisticsSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
- Key Laboratory of Environment & Health (Huazhong University of Science and Technology)Ministry of EducationWuhanHubeiChina
| | - Ping Hu
- Key Laboratory of Environment & Health (Huazhong University of Science and Technology)Ministry of EducationWuhanHubeiChina
| | - Yi Wang
- Department of Epidemiology & BiostatisticsSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
- Key Laboratory of Environment & Health (Huazhong University of Science and Technology)Ministry of EducationWuhanHubeiChina
| | - Yi Ye
- Department of Epidemiology & BiostatisticsSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
- Key Laboratory of Environment & Health (Huazhong University of Science and Technology)Ministry of EducationWuhanHubeiChina
| | - Ping Wu
- Department of Epidemiology & BiostatisticsSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
- Key Laboratory of Environment & Health (Huazhong University of Science and Technology)Ministry of EducationWuhanHubeiChina
| | - Bin Zhao
- Antenatal Care ClinicsShuangliu Maternal and Child Health HospitalChengduChina
| | - Jianguo Xu
- Department of Clinical LaboratoriesShuangliu Maternal and Child Health HospitalChengduChina
| | - Mengmeng Kong
- State Key Laboratory of Genetic EngineeringSchool of Life Sciences and Human Phenome InstituteFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary AnthropologyFudan UniversityShanghaiChina
| | - Yanni Pu
- State Key Laboratory of Genetic EngineeringSchool of Life Sciences and Human Phenome InstituteFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary AnthropologyFudan UniversityShanghaiChina
| | - Manying Zhao
- State Key Laboratory of Genetic EngineeringSchool of Life Sciences and Human Phenome InstituteFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary AnthropologyFudan UniversityShanghaiChina
| | - Jianying Hu
- State Key Laboratory of Genetic EngineeringSchool of Life Sciences and Human Phenome InstituteFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary AnthropologyFudan UniversityShanghaiChina
| | - Jinfeng Wang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
| | - Guo‐Chong Chen
- Department of Nutrition and Food HygieneSchool of Public HealthSoochow UniversitySuzhouChina
| | - Changzheng Yuan
- School of Public HealthZhejiang University School of MedicineHangzhouZhejiangChina
| | - Yongfu Yu
- School of Public HealthFudan UniversityShanghaiChina
| | - Xiang Gao
- School of Public HealthFudan UniversityShanghaiChina
| | - Fangqing Zhao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
| | - An Pan
- Department of Epidemiology & BiostatisticsSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
- Key Laboratory of Environment & Health (Huazhong University of Science and Technology)Ministry of EducationWuhanHubeiChina
| | - Yan Zheng
- State Key Laboratory of Genetic EngineeringSchool of Life Sciences and Human Phenome InstituteFudan UniversityShanghaiChina
- School of Public HealthFudan UniversityShanghaiChina
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Lu H, Li R, Yang P, Luo W, Chen S, Bilal M, Xu H, Gu C, Liu S, Zhao Y, Geng C, Zhao L. iTRAQ-BASED Proteomic Analysis of the Mechanism of Fructose on Improving Fengycin Biosynthesis in Bacillus Amyloliquefaciens. Molecules 2021; 26:molecules26206309. [PMID: 34684889 PMCID: PMC8539540 DOI: 10.3390/molecules26206309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
Fengycin, as a lipopeptide produced by Bacillus subtilis, displays potent activity against filamentous fungi, including Aspergillus flavus and Soft-rot fungus, which exhibits a wide range of potential applications in food industries, agriculture, and medicine. To better clarify the regulatory mechanism of fructose on fengycin biosynthesis, the iTRAQ-based proteomic analysis was utilized to investigate the differentially expressed proteins of B. amyloliquefaciens fmb-60 cultivated in ML (without fructose) and MLF (with fructose) medium. The results indicated that a total of 811 proteins, including 248 proteins with differential expression levels (162 which were upregulated (fold > 2) and 86, which were downregulated (fold < 0.5) were detected, and most of the proteins are associated with cellular metabolism, biosynthesis, and biological regulation process. Moreover, the target genes’ relative expression was conducted using quantitative real-time PCR to validate the proteomic analysis results. Based on the results of proteome analysis, the supposed pathways of fructose enhancing fengycin biosynthesis in B. amyloliquefaciens fmb-60 can be summarized as improvement of the metabolic process, including cellular amino acid and amide, fatty acid biosynthesis, peptide and protein, nucleotide and nucleobase-containing compound, drug/toxin, cofactor, and vitamin; reinforcement of peptide/protein translation, modification, biological process, and response to a stimulus. In conclusion, this study represents a comprehensive and systematic investigation of the fructose mechanism on improving fengycin biosynthesis in B. amyloliquefaciens, which will provide a road map to facilitate the potential application of fengycin or its homolog in defending against filamentous fungi.
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Affiliation(s)
- Hedong Lu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
| | - Ruili Li
- College of Food Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 250003, China;
| | - Panping Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
| | - Weibo Luo
- Institute of Food and Marine Bio-Resources, College of Biological Science and Technology, Fuzhou University, Fuzhou 350108, China; (W.L.); (S.C.)
| | - Shunxian Chen
- Institute of Food and Marine Bio-Resources, College of Biological Science and Technology, Fuzhou University, Fuzhou 350108, China; (W.L.); (S.C.)
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
| | - Hai Xu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
| | - Chengyuan Gu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
| | - Shuai Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
| | - Chengxin Geng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
- Correspondence: (C.G.); (L.Z.); Tel.: +86-517-83559107 (C.G.); +86-517-83559216 (L.Z.)
| | - Li Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (P.Y.); (M.B.); (H.X.); (C.G.); (S.L.); (Y.Z.)
- Correspondence: (C.G.); (L.Z.); Tel.: +86-517-83559107 (C.G.); +86-517-83559216 (L.Z.)
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Pallapati AR, Sirigiri SD, Jain S, Ratnala V, Roy I. Lysine245 plays a crucial role in stability and function of glycerol 3-phosphate dehydrogenase (Gpd1) in Saccharomyces cerevisiae. J Cell Biochem 2021; 122:1726-1736. [PMID: 34369003 DOI: 10.1002/jcb.30125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/10/2021] [Accepted: 07/16/2021] [Indexed: 11/07/2022]
Abstract
Glycerol 3-phosphate dehydrogenase (Gpd1 isoform) catalyzes the rate limiting step of glycerol synthesis and is a critical component of the osmo-responsive machinery in yeast. The three-dimensional structure of the enzyme is similar to the enzyme from many other organisms, including humans. A recent study with the human enzyme has proposed K120 (K152 in yeast) to be in the correct orientation for catalysis; K204 (K245 in yeast) is out of plane and is not a participant in the catalytic cycle. The current work was carried out to establish the role of K245 in the catalytic cycle of yeast Gpd1. K245A mutant was found to possess lower catalytic activity. Osmotically stressed cells expressing Gpd1 (K245A) showed no change in intracellular glycerol as compared with wild-type cells which showed ~60% increase. Fluorescence microscopy, native polyacrylamide gel electrophoresis (PAGE) analysis, fluorescence spectroscopy, and Thioflavin T spectrofluorimetry showed a relatively unstable, aggregation- and degradation-prone conformation for the mutant. In silico studies showed an aggregation "hotspot" around K245. This study establishes the requirement of K245 for conformational stability and functional adaptation of Gpd1 in Saccharomyces cerevisiae.
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Affiliation(s)
- Anusha R Pallapati
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
| | - Sri D Sirigiri
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
| | - Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
| | - Vamsi Ratnala
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
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He Q, Toh JD, Ero R, Qiao Z, Kumar V, Serra A, Tan J, Sze SK, Gao YG. The unusual di-domain structure of Dunaliella salina glycerol-3-phosphate dehydrogenase enables direct conversion of dihydroxyacetone phosphate to glycerol. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:153-164. [PMID: 31762135 DOI: 10.1111/tpj.14619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/31/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Dunaliella has been extensively studied due to its intriguing adaptation to high salinity. Its di-domain glycerol-3-phosphate dehydrogenase (GPDH) isoform is likely to underlie the rapid production of the osmoprotectant glycerol. Here, we report the structure of the chimeric Dunaliella salina GPDH (DsGPDH) protein featuring a phosphoserine phosphatase-like domain fused to the canonical glycerol-3-phosphate (G3P) dehydrogenase domain. Biochemical assays confirm that DsGPDH can convert dihydroxyacetone phosphate (DHAP) directly to glycerol, whereas a separate phosphatase protein is required for this conversion process in most organisms. The structure of DsGPDH in complex with its substrate DHAP and co-factor nicotinamide adenine dinucleotide (NAD) allows the identification of the residues that form the active sites. Furthermore, the structure reveals an intriguing homotetramer form that likely contributes to the rapid biosynthesis of glycerol.
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Affiliation(s)
- Qinghua He
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, College of Life Science and Technology, Southwest Minzu University, Chengdu, 610041, China
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Joel Dewei Toh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore City, 138673, Singapore
| | - Rya Ero
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 639798, Singapore
| | - Zhu Qiao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 639798, Singapore
| | - Veerendra Kumar
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore City, 138673, Singapore
| | - Aida Serra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Jackie Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore City, 138673, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 639798, Singapore
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5
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Costa CHSD, Bichara TW, Gomes GC, Dos Santos AM, da Costa KS, Lima AHLE, Alves CN, Lameira J. Unraveling the conformational dynamics of glycerol 3-phosphate dehydrogenase, a nicotinamide adenine dinucleotide-dependent enzyme of Leishmania mexicana. J Biomol Struct Dyn 2020; 39:2044-2055. [PMID: 32174264 DOI: 10.1080/07391102.2020.1742206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Allosteric changes modulate the enzymatic activity, leading to activation or inhibition of the molecular target. Understanding the induced fit accommodation mechanism of a ligand in its lowest-free energy state and the subsequent conformational changes induced in the protein are important questions for drug design. In the present study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were applied to analyze the glycerol-3-phosphate dehydrogenase of Leishmania mexicana (LmGPDH) conformational changes induced by its cofactor and substrate binding. GPDH is a nicotinamide adenine dinucleotide (NAD)-dependent enzyme, which has been reported as an interesting target for drug discovery and development against leishmaniasis. Despite its relevance for glycolysis and pentose phosphate pathways, the structural flexibility and conformational motions of LmGPDH in complex with NADH and dihydroxyacetone phosphate (DHAP) remain unexplored. Here, we analyzed the conformational dynamics of the enzyme-NADH complex (cofactor), and the enzyme-NADH-DHAP complex (adduct), mapped the hydrogen-bond interactions for the complexes and pointed some structural determinants of the enzyme that emerge from these contacts to NADH and DHAP. Finally, we proposed a consistent mechanism for the conformational changes on the first step of the reversible redox conversion of dihydroxyacetone phosphate to glycerol 3-phosphate, indicating key residues and interactions that could be further explored in drug discovery.
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Affiliation(s)
| | | | | | | | | | | | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém, PA, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém, PA, Brazil
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6
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Saryi NAA, Hutchinson JD, Al-Hejjaj MY, Sedelnikova S, Baker P, Hettema EH. Pnc1 piggy-back import into peroxisomes relies on Gpd1 homodimerisation. Sci Rep 2017; 7:42579. [PMID: 28209961 PMCID: PMC5314374 DOI: 10.1038/srep42579] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/29/2016] [Indexed: 12/17/2022] Open
Abstract
Peroxisomes are eukaryotic organelles that posttranslationally import proteins via one of two conserved peroxisomal targeting signal (PTS1 or 2) mediated pathways. Oligomeric proteins can be imported via these pathways but evidence is accumulating that at least some PTS1-containing monomers enter peroxisomes before they assemble into oligomers. Some proteins lacking a PTS are imported by piggy-backing onto PTS-containing proteins. One of these proteins is the nicotinamidase Pnc1, that is co-imported with the PTS2-containing enzyme Glycerol-3-phosphate dehydrogenase 1, Gpd1. Here we show that Pnc1 co-import requires Gpd1 to form homodimers. A mutation that interferes with Gpd1 homodimerisation does not prevent Gpd1 import but prevents Pnc1 co-import. A suppressor mutation that restores Gpd1 homodimerisation also restores Pnc1 co-import. In line with this, Pnc1 interacts with Gpd1 in vivo only when Gpd1 can form dimers. Redirection of Gpd1 from the PTS2 import pathway to the PTS1 import pathway supports Gpd1 monomer import but not Gpd1 homodimer import and Pnc1 co-import. Our results support a model whereby Gpd1 may be imported as a monomer or a dimer but only the Gpd1 dimer facilitates co-transport of Pnc1 into peroxisomes.
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Affiliation(s)
- Nadal A Al Saryi
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - John D Hutchinson
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Murtakab Y Al-Hejjaj
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Svetlana Sedelnikova
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Patrick Baker
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Ewald H Hettema
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
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7
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Carbone V, Schofield LR, Zhang Y, Sang C, Dey D, Hannus IM, Martin WF, Sutherland-Smith AJ, Ronimus RS. Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase. J Biol Chem 2015; 290:21690-704. [PMID: 26175150 DOI: 10.1074/jbc.m115.647461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 01/23/2023] Open
Abstract
One of the most critical events in the origins of cellular life was the development of lipid membranes. Archaea use isoprenoid chains linked via ether bonds to sn-glycerol 1-phosphate (G1P), whereas bacteria and eukaryotes use fatty acids attached via ester bonds to enantiomeric sn-glycerol 3-phosphate. NAD(P)H-dependent G1P dehydrogenase (G1PDH) forms G1P and has been proposed to have played a crucial role in the speciation of the Archaea. We present here, to our knowledge, the first structures of archaeal G1PDH from the hyperthermophilic methanogen Methanocaldococcus jannaschii with bound substrate dihydroxyacetone phosphate, product G1P, NADPH, and Zn(2+) cofactor. We also biochemically characterized the enzyme with respect to pH optimum, cation specificity, and kinetic parameters for dihydroxyacetone phosphate and NAD(P)H. The structures provide key evidence for the reaction mechanism in the stereospecific addition for the NAD(P)H-based pro-R hydrogen transfer and the coordination of the Zn(2+) cofactor during catalysis. Structure-based phylogenetic analyses also provide insight into the origins of G1PDH.
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Affiliation(s)
- Vincenzo Carbone
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Linley R Schofield
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Yanli Zhang
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Carrie Sang
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Debjit Dey
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Ingegerd M Hannus
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University, University of Düsseldorf, 40225 Düsseldorf, Germany, and
| | | | - Ron S Ronimus
- From AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand,
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