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Katelas DA, Cruz-Miron R, Arroyo-Olarte RD, Brouwers JF, Srivastav RK, Gupta N. Phosphatidylserine synthase in the endoplasmic reticulum of Toxoplasma is essential for its lytic cycle in human cells. J Lipid Res 2024; 65:100535. [PMID: 38522751 PMCID: PMC11166882 DOI: 10.1016/j.jlr.2024.100535] [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: 09/15/2023] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
Glycerophospholipids have emerged as a significant contributor to the intracellular growth of pathogenic protist Toxoplasma gondii. Phosphatidylserine (PtdSer) is one such lipid, attributed to the locomotion and motility-dependent invasion and egress events in its acutely infectious tachyzoite stage. However, the de novo synthesis of PtdSer and the importance of the pathway in tachyzoites remain poorly understood. We show that a base-exchange-type PtdSer synthase (PSS) located in the parasite's endoplasmic reticulum produces PtdSer, which is rapidly converted to phosphatidylethanolamine (PtdEtn) by PtdSer decarboxylase (PSD) activity. The PSS-PSD pathway enables the synthesis of several lipid species, including PtdSer (16:0/18:1) and PtdEtn (18:2/20:4, 18:1/18:2 and 18:2/22:5). The PSS-depleted strain exhibited a lower abundance of the major ester-linked PtdEtn species and concurrent accrual of host-derived ether-PtdEtn species. Most phosphatidylthreonine (PtdThr) species-an exclusive natural analog of PtdSer, also made in the endoplasmic reticulum-were repressed. PtdSer species, however, remained largely unaltered, likely due to the serine-exchange reaction of PtdThr synthase in favor of PtdSer upon PSS depletion. Not least, the loss of PSS abrogated the lytic cycle of tachyzoites, impairing the cell division, motility, and egress. In a nutshell, our data demonstrate a critical role of PSS in the biogenesis of PtdSer and PtdEtn species and its physiologically essential repurposing for the asexual reproduction of a clinically relevant intracellular pathogen.
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Affiliation(s)
- Dimitrios Alexandros Katelas
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany; Intracellular Parasite Education and Research Labs (iPEARL), Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-Pilani), Hyderabad, India
| | - Rosalba Cruz-Miron
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany; Intracellular Parasite Education and Research Labs (iPEARL), Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-Pilani), Hyderabad, India
| | - Ruben D Arroyo-Olarte
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany; Carrera de Médico Cirujano y Unidad de Biomedicina (UBIMED), FES-Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Jos F Brouwers
- Analysis Techniques in the Life Sciences, Centre of Expertise Perspective in Health, Avans University of Applied Sciences, Breda, The Netherlands
| | - Ratnesh Kumar Srivastav
- Intracellular Parasite Education and Research Labs (iPEARL), Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-Pilani), Hyderabad, India
| | - Nishith Gupta
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany; Intracellular Parasite Education and Research Labs (iPEARL), Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS-Pilani), Hyderabad, India.
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Alirezapour F, Mohammadi M, Khanmohammadi A. Zigzag boron nitride nanotube functionalization as a sensor for the recognition of group IIA (Mg 2+, Ca 2+) metal ions, quasi-metal (Si 2+, Ge 2+) ions, and transition metal (Cu 2+, Zn 2+) ions: a computational study. J Mol Model 2024; 30:174. [PMID: 38771381 DOI: 10.1007/s00894-024-05961-w] [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: 02/21/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
CONTEXT Boron nitride nanotubes (BNNTs) provide an exceptional and sophisticated platform for detecting metal ions with high surface area and remarkable chemical stability. Metal cations tend to bind to the surface of BNNTs, which leads to significant changes in the electrical properties of nanotubes. BNNT-based metal ion sensors have shown promising results in various applications, including water quality monitoring, biomedical research, industrial quality control, and environmental monitoring. In the present study, we have explored the electronic sensitivity of the BNNT to metal ions (Si2+, Ge2+, Cu2+, Zn2+, Mg2+, and Ca2+). The interaction between the ions with the pristine BNNT is performed in the solution phase. The results show that ion adsorption on the nanotube surface is exothermic and favorable. The density of states calculation is presented to investigate the electronic properties of the nanotube during the adsorption process. The results display that an increase in the electrical conductivity of the complexes accompanies the reduction in the energy gap. Based on the obtained data, the Si2+ and Ge2+ cations adsorbed on the BNNT with satisfactory Eg changes (%ΔE) can be promising candidates for better sensing ability. METHOD All calculations are conducted within the density functional theory (DFT) using the ωB97XD functional and 6-31G(d,p) basis set. The present approach incorporates the utilization of empirical atom-atom dispersion in conjunction with long-range correction. The calculations are performed using the quantum chemistry package GAMESS, and the obtained results are visualized by employing the GaussView 6.0.16 program.
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Affiliation(s)
- Fahimeh Alirezapour
- Department of Chemistry, Payame Noor University (PNU), P. O. Box 19395-4697, Tehran, Iran.
| | - Marziyeh Mohammadi
- Department of Chemistry, Faculty of Science, Vali-E-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Azadeh Khanmohammadi
- Department of Chemistry, Payame Noor University (PNU), P. O. Box 19395-4697, Tehran, Iran
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Zhou Y, Phelps GA, Mangrum MM, McLeish J, Phillips EK, Lou J, Ancajas CF, Rybak JM, Oelkers PM, Lee RE, Best MD, Reynolds TB. The small molecule CBR-5884 inhibits the Candida albicans phosphatidylserine synthase. mBio 2024; 15:e0063324. [PMID: 38587428 PMCID: PMC11077991 DOI: 10.1128/mbio.00633-24] [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: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
Systemic infections by Candida spp. are associated with high mortality rates, partly due to limitations in current antifungals, highlighting the need for novel drugs and drug targets. The fungal phosphatidylserine synthase, Cho1, from Candida albicans is a logical antifungal drug target due to its importance in virulence, absence in the host, and conservation among fungal pathogens. Inhibitors of Cho1 could serve as lead compounds for drug development, so we developed a target-based screen for inhibitors of purified Cho1. This enzyme condenses serine and cytidyldiphosphate-diacylglycerol (CDP-DAG) into phosphatidylserine (PS) and releases cytidylmonophosphate (CMP). Accordingly, we developed an in vitro nucleotidase-coupled malachite-green-based high throughput assay for purified C. albicans Cho1 that monitors CMP production as a proxy for PS synthesis. Over 7,300 molecules curated from repurposing chemical libraries were interrogated in primary and dose-responsivity assays using this platform. The screen had a promising average Z' score of ~0.8, and seven compounds were identified that inhibit Cho1. Three of these, ebselen, LOC14, and CBR-5884, exhibited antifungal effects against C. albicans cells, with fungicidal inhibition by ebselen and fungistatic inhibition by LOC14 and CBR-5884. Only CBR-5884 showed evidence of disrupting in vivo Cho1 function by inducing phenotypes consistent with the cho1∆∆ mutant, including a reduction of cellular PS levels. Kinetics curves and computational docking indicate that CBR-5884 competes with serine for binding to Cho1 with a Ki of 1,550 ± 245.6 nM. Thus, this compound has the potential for development into an antifungal compound. IMPORTANCE Fungal phosphatidylserine synthase (Cho1) is a logical antifungal target due to its crucial role in the virulence and viability of various fungal pathogens, and since it is absent in humans, drugs targeted at Cho1 are less likely to cause toxicity in patients. Using fungal Cho1 as a model, there have been two unsuccessful attempts to discover inhibitors for Cho1 homologs in whole-cell screens prior to this study. The compounds identified in these attempts do not act directly on the protein, resulting in the absence of known Cho1 inhibitors. The significance of our research is that we developed a high-throughput target-based assay and identified the first Cho1 inhibitor, CBR-5884, which acts both on the purified protein and its function in the cell. This molecule acts as a competitive inhibitor with a Ki value of 1,550 ± 245.6 nM and, thus, has the potential for development into a new class of antifungals targeting PS synthase.
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Affiliation(s)
- Yue Zhou
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Gregory A. Phelps
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mikayla M. Mangrum
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jemma McLeish
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Elise K. Phillips
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jinchao Lou
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | | | - Jeffrey M. Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Peter M. Oelkers
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, Michigan, USA
| | - Richard E. Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Michael D. Best
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Todd B. Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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4
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Ong LL, Jan HM, Le HHT, Yang TC, Kuo CY, Feng AF, Mong KKT, Lin CH. Membrane lipid remodeling eradicates Helicobacter pylori by manipulating the cholesteryl 6'-acylglucoside biosynthesis. J Biomed Sci 2024; 31:44. [PMID: 38685037 PMCID: PMC11057186 DOI: 10.1186/s12929-024-01031-8] [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: 01/03/2024] [Accepted: 04/14/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Helicobacter pylori, the main cause of various gastric diseases, infects approximately half of the human population. This pathogen is auxotrophic for cholesterol which it converts to various cholesteryl α-glucoside derivatives, including cholesteryl 6'-acyl α-glucoside (CAG). Since the related biosynthetic enzymes can be translocated to the host cells, the acyl chain of CAG likely comes from its precursor phosphatidylethanolamine (PE) in the host membranes. This work aims at examining how the acyl chain of CAG and PE inhibits the membrane functions, especially bacterial adhesion. METHODS Eleven CAGs that differ in acyl chains were used to study the membrane properties of human gastric adenocarcinoma cells (AGS cells), including lipid rafts clustering (monitored by immunofluorescence with confocal microscopy) and lateral membrane fluidity (by the fluorescence recovery after photobleaching). Cell-based and mouse models were employed to study the degree of bacterial adhesion, the analyses of which were conducted by using flow cytometry and immunofluorescence staining, respectively. The lipidomes of H. pylori, AGS cells and H. pylori-AGS co-cultures were analyzed by Ultraperformance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC-MS/MS) to examine the effect of PE(10:0)2, PE(18:0)2, PE(18:3)2, or PE(22:6)2 treatments. RESULTS CAG10:0, CAG18:3 and CAG22:6 were found to cause the most adverse effect on the bacterial adhesion. Further LC-MS analysis indicated that the treatment of PE(10:0)2 resulted in dual effects to inhibit the bacterial adhesion, including the generation of CAG10:0 and significant changes in the membrane compositions. The initial (1 h) lipidome changes involved in the incorporation of 10:0 acyl chains into dihydro- and phytosphingosine derivatives and ceramides. In contrast, after 16 h, glycerophospholipids displayed obvious increase in their very long chain fatty acids, monounsaturated and polyunsaturated fatty acids that are considered to enhance membrane fluidity. CONCLUSIONS The PE(10:0)2 treatment significantly reduced bacterial adhesion in both AGS cells and mouse models. Our approach of membrane remodeling has thus shown great promise as a new anti-H. pylori therapy.
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Affiliation(s)
- Lih-Lih Ong
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001, University Road, Eastern District, Hsinchu, 300093, Taiwan
- Institute of Chemistry, Academia Sinica, No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan
| | - Hau-Ming Jan
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Hong-Hanh Thi Le
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan
| | - Tsai-Chen Yang
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan
| | - Chou-Yu Kuo
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan
| | - Ai-Feng Feng
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001, University Road, Eastern District, Hsinchu, 300093, Taiwan
| | - Kwok-Kong Tony Mong
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001, University Road, Eastern District, Hsinchu, 300093, Taiwan.
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan.
- Department of Chemistry and Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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Singh S, Dransfeld U, Ambaw Y, Lopez-Scarim J, Farese RV, Walther TC. PLD3 and PLD4 synthesize S,S-BMP, a key phospholipid enabling lipid degradation in lysosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586175. [PMID: 38562702 PMCID: PMC10983895 DOI: 10.1101/2024.03.21.586175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Bis(monoacylglycero)phosphate (BMP) is an abundant lysosomal phospholipid required for degradation of lipids, in particular gangliosides. Alterations in BMP levels are associated with neurodegenerative diseases. Unlike typical glycerophospholipids, lysosomal BMP has two chiral glycerol carbons in the S (rather than the R) stereo-conformation, protecting it from lysosomal degradation. How this unusual and yet crucial S,S-stereochemistry is achieved is unknown. Here we report that phospholipases D3 and D4 (PLD3 and PLD4) synthesize lysosomal S,S-BMP, with either enzyme catalyzing the critical glycerol stereo-inversion reaction in vitro. Deletion of PLD3 or PLD4 markedly reduced BMP levels in cells or in murine tissues where either enzyme is highly expressed (brain for PLD3; spleen for PLD4), leading to gangliosidosis and lysosomal abnormalities. PLD3 mutants associated with neurodegenerative diseases, including Alzheimer's disease risk, diminished PLD3 catalytic activity. We conclude that PLD3/4 enzymes synthesize lysosomal S,S-BMP, a crucial lipid for maintaining brain health.
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Affiliation(s)
- Shubham Singh
- Cell Biology Program, Sloan Kettering Institute, MSKCC, New York, NY, USA
| | - Ulrich Dransfeld
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yohannes Ambaw
- Cell Biology Program, Sloan Kettering Institute, MSKCC, New York, NY, USA
| | - Joshua Lopez-Scarim
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Robert V. Farese
- Cell Biology Program, Sloan Kettering Institute, MSKCC, New York, NY, USA
| | - Tobias C. Walther
- Cell Biology Program, Sloan Kettering Institute, MSKCC, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
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6
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Song P, Zhao L, Zhu L, Sha G, Dong W. BsR1, a broad-spectrum antibacterial peptide with potential for plant protection. Microbiol Spectr 2023; 11:e0257823. [PMID: 37948344 PMCID: PMC10714738 DOI: 10.1128/spectrum.02578-23] [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: 06/20/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE This study addresses the critical need for new antibacterial drugs in the face of bacterial multidrug resistance resulting from antibiotic overuse. It highlights the significance of antimicrobial peptides as essential components of innate immunity in animals and plants, which have been proven effective against multidrug-resistant bacteria and are difficult to develop resistance against. This study successfully synthesizes a broad-spectrum antibacterial peptide, BsR1, with strong inhibitory activities against various Gram-positive and Gram-negative bacteria. BsR1 demonstrates favorable stability and a mode of action that damages bacterial cell membranes, leading to cell death. It also exhibits biological safety and shows potential in enhancing disease resistance in rice. This research offers a novel approach and potential medication for antibacterial drug development, presenting a valuable tool in combating pathogenic microorganisms, particularly in plants.
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Affiliation(s)
- Pei Song
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Li Zhao
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Li Zhu
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Gan Sha
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Wubei Dong
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
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7
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Wang L, Zhou M. Structure of a eukaryotic cholinephosphotransferase-1 reveals mechanisms of substrate recognition and catalysis. Nat Commun 2023; 14:2753. [PMID: 37179328 PMCID: PMC10182977 DOI: 10.1038/s41467-023-38003-9] [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: 11/08/2022] [Accepted: 04/03/2023] [Indexed: 05/15/2023] Open
Abstract
Phosphatidylcholine (PC) is the most abundant phospholipid in eukaryotic cell membranes. In eukaryotes, two highly homologous enzymes, cholinephosphotransferase-1 (CHPT1) and choline/ethanolamine phosphotransferase-1 (CEPT1) catalyze the final step of de novo PC synthesis. CHPT1/CEPT1 joins two substrates, cytidine diphosphate-choline (CDP-choline) and diacylglycerol (DAG), to produce PC, and Mg2+ is required for the reaction. However, mechanisms of substrate recognition and catalysis remain unresolved. Here we report structures of a CHPT1 from Xenopus laevis (xlCHPT1) determined by cryo-electron microscopy to an overall resolution of ~3.2 Å. xlCHPT1 forms a homodimer, and each protomer has 10 transmembrane helices (TMs). The first 6 TMs carve out a cone-shaped enclosure in the membrane in which the catalysis occurs. The enclosure opens to the cytosolic side, where a CDP-choline and two Mg2+ are coordinated. The structures identify a catalytic site unique to eukaryotic CHPT1/CEPT1 and suggest an entryway for DAG. The structures also reveal an internal pseudo two-fold symmetry between TM3-6 and TM7-10, and suggest that CHPT1/CEPT1 may have evolved from their distant prokaryotic ancestors through gene duplication.
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Affiliation(s)
- Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
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8
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Wang Z, Yang M, Yang Y, He Y, Qian H. Structural basis for catalysis of human choline/ethanolamine phosphotransferase 1. Nat Commun 2023; 14:2529. [PMID: 37137909 PMCID: PMC10156783 DOI: 10.1038/s41467-023-38290-2] [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: 11/01/2022] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) are two primary components of the eukaryotic membrane and play essential roles in the maintenance of membrane integrity, lipid droplet biogenesis, autophagosome formation, and lipoprotein formation and secretion. Choline/ethanolamine phosphotransferase 1 (CEPT1) catalyzes the last step of the biosynthesis of PC and PE in the Kennedy pathway by transferring the substituted phosphate group from CDP-choline/ethanolamine to diacylglycerol. Here, we present the cryo-EM structures of human CEPT1 and its complex with CDP-choline at resolutions of 3.7 Å and 3.8 Å, respectively. CEPT1 is a dimer with 10 transmembrane segments (TMs) in each protomer. TMs 1-6 constitute a conserved catalytic domain with an interior hydrophobic chamber accommodating a PC-like density. Structural observations and biochemical characterizations suggest that the hydrophobic chamber coordinates the acyl tails during the catalytic process. The PC-like density disappears in the structure of the complex with CDP-choline, suggesting a potential substrate-triggered product release mechanism.
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Affiliation(s)
- Zhenhua Wang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Meng Yang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Yufan Yang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Yonglin He
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Hongwu Qian
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
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9
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Zhou Y, Syed JH, Semchonok DA, Wright E, Kyrilis FL, Hamdi F, Kastritis PL, Bruce BD, Reynolds TB. Solubilization, purification, and characterization of the hexameric form of phosphatidylserine synthase from Candida albicans. J Biol Chem 2023:104756. [PMID: 37116705 DOI: 10.1016/j.jbc.2023.104756] [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: 12/16/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023] Open
Abstract
Phosphatidylserine (PS) synthase from Candida albicans, encoded by the CHO1 gene, has been identified as a potential drug target for new antifungals against systemic candidiasis. Rational drug design or small molecule screening are effective ways to identify specific inhibitors of Cho1, but both will be facilitated by protein purification. Due to the transmembrane nature of Cho1, methods were needed to solubilize and purify the native form of Cho1. Here, we used six non-ionic detergents and three styrene maleic acids (SMAs) to solubilize an HA-tagged Cho1 protein from the total microsomal fractions. Blue native PAGE (BN-PAGE) and immunoblot analysis revealed a single band corresponding to Cho1 in all detergent-solubilized fractions, while two bands were present in the SMA2000-solubilized fraction. Our enzymatic assay suggests that digitonin- or DDM-solubilized enzyme has the most PS synthase activity. Pull-downs of HA-tagged Cho1 in the digitonin-solubilized fraction reveal an apparent MW of Cho1 consistent with a hexamer. Furthermore, negative-staining electron microscopy analysis and AlphaFold2 structure prediction modeling suggest the hexamer is composed of a trimer of dimers. We purified Cho1 protein to near-homogeneity as a hexamer using affinity chromatography and TEV protease treatment, and optimized Cho1 enzyme activity for manganese and detergent concentrations, temperature (24°C), and pH (8.0). The purified Cho1 has a Km for its substrate CDP-diacylglycerol of 72.20 μM with a Vmax of 0.079 nmol/(μg*min) while exhibiting a sigmoidal kinetic curve for its other substrate serine, indicating cooperative binding. Purified hexameric Cho1 can potentially be used in downstream structure determination and small drug screening.
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Affiliation(s)
- Yue Zhou
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States
| | - Jawhar H Syed
- Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Edward Wright
- Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Barry D Bruce
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States; Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States
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10
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Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
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Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
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Zhou Y, Cassilly CD, Reynolds TB. Mapping the Substrate-Binding Sites in the Phosphatidylserine Synthase in Candida albicans. Front Cell Infect Microbiol 2022; 11:765266. [PMID: 35004345 PMCID: PMC8727905 DOI: 10.3389/fcimb.2021.765266] [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: 08/26/2021] [Accepted: 11/29/2021] [Indexed: 12/02/2022] Open
Abstract
The fungal phosphatidylserine (PS) synthase, a membrane protein encoded by the CHO1 gene, is a potential drug target for pathogenic fungi, such as Candida albicans. However, both substrate-binding sites of C. albicans Cho1 have not been characterized. Cho1 has two substrates: cytidyldiphosphate-diacylglycerol (CDP-DAG) and serine. Previous studies identified a conserved CDP-alcohol phosphotransferase (CAPT) binding motif, which is present within Cho1. We tested the CAPT motif for its role in PS synthesis by mutating conserved residues using alanine substitution mutagenesis. PS synthase assays revealed that mutations in all but one conserved amino acid within the CAPT motif resulted in decreased Cho1 function. In contrast, there were no clear motifs in Cho1 for binding serine. Therefore, to identify the serine binding site, PS synthase sequences from three fungi were aligned with sequences of a similar enzyme, phosphatidylinositol (PI) synthase, from the same fungi. This revealed a motif that was unique to PS synthases. Using alanine substitution mutagenesis, we found that some of the residues in this motif are required for Cho1 function. Two alanine substitution mutants, L184A and R189A, exhibited contrasting impacts on PS synthase activity, and were characterized for their Michaelis-Menten kinetics. The L184A mutant displayed enhanced PS synthase activity and showed an increased Vmax. In contrast, R189A showed decreased PS synthase activity and increased Km for serine, suggesting that residue R189 is involved in serine binding. These results help to characterize PS synthase substrate binding, and should direct rational approaches for finding Cho1 inhibitors that may lead to better antifungals.
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Affiliation(s)
- Yue Zhou
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Chelsi D Cassilly
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, United States
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