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Du P, Li J, Hua M, Zhu L, Chen C, Zeng H. Potential Contributions of Human Endogenous Retroviruses in Innate Immune Memory. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1225-1233. [PMID: 39230265 DOI: 10.4049/jimmunol.2300411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/08/2024] [Indexed: 09/05/2024]
Abstract
The phenomenon wherein innate immune cells adopt long-term inflammatory phenotypes following the first stimuli is named trained immunity and can improve host defense against infections. Transcriptional and epigenetic reprogramming are critical mechanisms of trained immunity; however, the regulatory networks are not entirely clear at present. The human endogenous retroviruses (HERVs) provide large amounts of transcriptional regulators in the regulatory pathways. In this study, we analyzed published large omics data to explore the roles of such "dark matter" of the human genome in trained and tolerant macrophages. We collected 80 RNA sequencing data and 62 sequencing data to detect histone modifications and active regulatory regions from nine published studies on trained and tolerant macrophages. By analyzing the characteristics of transcription and epigenetic modification of HERVs, as well as their association with gene expression, we found that 15.3% of HERVs were transcribed nonrandomly from noncoding regions and enriched in specific HERV families and specific chromosomes, such as chromosomes 11, 15, 17, and 19, and they were highly related with the expression of adjacent genes. We found that 295 differentially expressed HERVs are located in 50-kbp flanking regions of 142 differentially expressed genes. We found epigenetic changes of these HERVs and that overlap with predicted enhancers and identified 35 enhancer-like HERVs. The related genes were highly involved in the activation and inflammatory responses, such as the TLR pathway. Other pathways including phosphoinositide signaling and transport of folate and K+ might be also related with trained immunity, which require further study. These results demonstrated that HERVs might play important roles in trained immunity.
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Affiliation(s)
- Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China; and
| | - Jiarui Li
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mingxi Hua
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liuluan Zhu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China; and
| | - Chen Chen
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hui Zeng
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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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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Ueshima R, Kikuma T, Sano K, Toda N, Greimel P, Takeda Y. Synthesis of azide-modified glycerophospholipid precursor analogs for detection of enzymatic reactions. Chembiochem 2024; 25:e202300699. [PMID: 38061997 DOI: 10.1002/cbic.202300699] [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: 10/13/2023] [Revised: 11/27/2023] [Indexed: 01/10/2024]
Abstract
Glycerophospholipids (GPLs) are major cell membrane components. Although various phosphorylated molecules are attached to lipid moieties as their headgroups, GPLs are biosynthesized from phosphatidic acid (PA) via its derivatives, diacylglycerol (DAG) or cytidine diphosphate diacylglycerol (CDP-DAG). A variety of molecular probes capable of introducing detection tags have been developed to investigate biological events involved in GPLs. In this study, we report the design, synthesis, and evaluation of novel analytical tools suitable to monitor the activity of GPL biosynthetic enzymes in vitro. Our synthetic targets, namely, azide-modified PA, azide-modified DAG, and azide-modified CDP-DAG, were successfully obtained from solketal as their common starting material. Moreover, using CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT), an enzyme that catalyzed the final reaction step in synthesizing phosphatidylinositol, we demonstrated that azide-modified CDP-DAG worked as a substrate for CDIPT.
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Affiliation(s)
- Rina Ueshima
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Takashi Kikuma
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Kanae Sano
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Nahoko Toda
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Peter Greimel
- RIKEN Center for Brain Science, Wako, 351-0198, Japan
| | - Yoichi Takeda
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
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Esposti MD. Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis. FEBS Lett 2023; 597:2484-2496. [PMID: 37507225 DOI: 10.1002/1873-3468.14708] [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: 02/21/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.
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Raina R, Banerjee A. Architects of the membrane: structures of eukaryotic choline phosphotransferase 1 and choline/ethanolamine phosphotransferase 1. Nat Struct Mol Biol 2023; 30:1247-1250. [PMID: 37696961 DOI: 10.1038/s41594-023-01073-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Affiliation(s)
- Rahul Raina
- Section on Structural and Chemical Biology, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anirban Banerjee
- Section on Structural and Chemical Biology, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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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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7
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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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8
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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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Puthenveetil R, Gómez-Navarro N, Banerjee A. Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases. Curr Opin Struct Biol 2022; 77:102463. [PMID: 36183446 PMCID: PMC9772126 DOI: 10.1016/j.sbi.2022.102463] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 12/24/2022]
Abstract
S-acylation is a reversible posttranslational modification, where a long-chain fatty acid is attached to a protein through a thioester linkage. Being the most abundant form of lipidation in humans, a family of twenty-three human zDHHC integral membrane enzymes catalyze this reaction. Previous structures of the apo and lipid bound zDHHCs shed light into the molecular details of the active site and binding pocket. Here, we delve further into the details of fatty acyl-CoA recognition by zDHHC acyltransferases using insights from the recent structure. We additionally review indirect evidence that suggests acyl-CoAs do not diffuse freely in the cytosol, but are channeled into specific pathways, and comment on the suggested mechanisms for fatty acyl-CoA compartmentalization and intracellular transport, to finally speculate about the potential mechanisms that underlie fatty acyl-CoA delivery to zDHHC enzymes.
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Affiliation(s)
- Robbins Puthenveetil
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA. https://twitter.com/RoVeetil
| | - Natalia Gómez-Navarro
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA. https://twitter.com/NataliaGmez10
| | - Anirban Banerjee
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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10
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Kakar A, Sastré-Velásquez LE, Hess M, Galgóczy L, Papp C, Holzknecht J, Romanelli A, Váradi G, Malanovic N, Marx F. The Membrane Activity of the Amphibian Temporin B Peptide Analog TB_KKG6K Sheds Light on the Mechanism That Kills Candida albicans. mSphere 2022; 7:e0029022. [PMID: 35972132 PMCID: PMC9599520 DOI: 10.1128/msphere.00290-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Temporin B (TB) is a 13-amino-acid-long, cationic peptide secreted by the granular glands of the European frog Rana temporaria. We recently showed that the modified TB peptide analog TB_KKG6K rapidly killed planktonic and sessile Candida albicans at low micromolar concentrations and was neither hemolytic nor cytotoxic to mammalian cells in vitro. The present study aimed to shed light into its mechanism of action, with a focus on its fungal cell membrane activity. We utilized different fluorescent dyes to prove that it rapidly induces membrane depolarization and permeabilization. Studies on model membrane systems revealed that the TB analog undergoes hydrophobic and electrostatic membrane interactions, showing a preference for anionic lipids, and identified phosphatidylinositol and cardiolipin as possible peptide targets. Fluorescence microscopy using fluorescein isothiocyanate-labeled TB_KKG6K in the presence of the lipophilic dye FM4-64 indicated that the peptide compromises membrane integrity and rapidly enters C. albicans cells in an energy-independent manner. Peptide-treated cells analyzed by cryo-based electron microscopy exhibited no signs of cell lysis; however, subcellular structures had disintegrated, suggesting that intracellular activity may form part of the killing mechanism of the peptide. Taken together, this study proved that TB_KKG6K compromises C. albicans membrane function, which explains the previously observed rapid, fungicidal mode of action and supports its great potential as a future anti-Candida therapeutic. IMPORTANCE Fungal infections with the opportunistic human pathogen C. albicans are associated with high mortality rates in immunocompromised patients. This is partly due to the yeast's ability to rapidly develop resistance toward currently available antifungals. Small, cationic, membrane-active peptides are promising compounds to fight against resistance development, as many of them effectuate rapid fungal cell death. This fast killing is believed to hamper the development of resistance, as the fungi do not have sufficient time to adapt to the antifungal compound. We previously reported that the synthetic variant of the amphibian TB peptide, TB_KKG6K, rapidly kills C. albicans. In the current study, the mechanism of action of the TB analog was investigated. We show that this TB analog is membrane-active and impairs cell membrane function, highlighting its potential to be developed as an attractive alternative anti-C. albicans therapeutic that may hinder the development of resistance.
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Affiliation(s)
- Anant Kakar
- Biocenter, Institute of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Michael Hess
- Institute for Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - László Galgóczy
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Csaba Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Jeanett Holzknecht
- Biocenter, Institute of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Györgyi Váradi
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Nermina Malanovic
- Institute of Molecular Biosciences, Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Florentine Marx
- Biocenter, Institute of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
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11
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de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [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: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
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Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
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12
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Characterization of inositol lipid metabolism in gut-associated Bacteroidetes. Nat Microbiol 2022; 7:986-1000. [PMID: 35725777 PMCID: PMC9246714 DOI: 10.1038/s41564-022-01152-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/17/2022] [Indexed: 12/13/2022]
Abstract
Inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis. In Bacteria, however, inositol lipid production is relatively rare. Recently, the prominent human gut bacterium Bacteroides thetaiotaomicron (BT) was reported to produce inositol lipids and sphingolipids, but the pathways remain ambiguous and their prevalence unclear. Here, using genomic and biochemical approaches, we investigated the gene cluster for inositol lipid synthesis in BT using a previously undescribed strain with inducible control of sphingolipid synthesis. We characterized the biosynthetic pathway from myo-inositol-phosphate (MIP) synthesis to phosphoinositol dihydroceramide, determined the crystal structure of the recombinant BT MIP synthase enzyme and identified the phosphatase responsible for the conversion of bacterially-derived phosphatidylinositol phosphate (PIP-DAG) to phosphatidylinositol (PI-DAG). In vitro, loss of inositol lipid production altered BT capsule expression and antimicrobial peptide resistance. In vivo, loss of inositol lipids decreased bacterial fitness in a gnotobiotic mouse model. We identified a second putative, previously undescribed pathway for bacterial PI-DAG synthesis without a PIP-DAG intermediate, common in Prevotella. Our results indicate that inositol sphingolipid production is widespread in host-associated Bacteroidetes and has implications for symbiosis. The pathways responsible for inositol lipid production in human gut Bacteroides are characterized and these lipids are important for capsule expression and antimicrobial peptide resistance in vitro and colonization in vivo.
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13
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Ventura R, Martínez-Ruiz I, Hernández-Alvarez MI. Phospholipid Membrane Transport and Associated Diseases. Biomedicines 2022; 10:biomedicines10051201. [PMID: 35625937 PMCID: PMC9138374 DOI: 10.3390/biomedicines10051201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Phospholipids are the basic structure block of eukaryotic membranes, in both the outer and inner membranes, which delimit cell organelles. Phospholipids can also be damaged by oxidative stress produced by mitochondria, for instance, becoming oxidized phospholipids. These damaged phospholipids have been related to prevalent diseases such as atherosclerosis or non-alcoholic steatohepatitis (NASH) because they alter gene expression and induce cellular stress and apoptosis. One of the main sites of phospholipid synthesis is the endoplasmic reticulum (ER). ER association with other organelles through membrane contact sites (MCS) provides a close apposition for lipid transport. Additionally, an important advance in this small cytosolic gap are lipid transfer proteins (LTPs), which accelerate and modulate the distribution of phospholipids in other organelles. In this regard, LTPs can be established as an essential point within phospholipid circulation, as relevant data show impaired phospholipid transport when LTPs are defected. This review will focus on phospholipid function, metabolism, non-vesicular transport, and associated diseases.
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Affiliation(s)
- Raúl Ventura
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; (R.V.); (I.M.-R.)
| | - Inma Martínez-Ruiz
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; (R.V.); (I.M.-R.)
| | - María Isabel Hernández-Alvarez
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; (R.V.); (I.M.-R.)
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- IBUB Universitat de Barcelona—Institut de Biomedicina de la Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence:
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14
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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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15
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Yang B, Yao H, Li D, Liu Z. The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface. Curr Res Struct Biol 2021; 3:312-323. [PMID: 34901881 PMCID: PMC8640168 DOI: 10.1016/j.crstbi.2021.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Phosphatidylglycerol is a crucial phospholipid found ubiquitously in biological membranes of prokaryotic and eukaryotic cells. The phosphatidylglycerol phosphate (PGP) synthase (PgsA), a membrane-embedded enzyme, catalyzes the primary reaction of phosphatidylglycerol biosynthesis. Mutations in pgsA frequently correlate with daptomycin resistance in Staphylococcus aureus and other prevalent infectious pathogens. Here we report the crystal structures of S. aureus PgsA (SaPgsA) captured at two distinct states of the catalytic process, with lipid substrate (cytidine diphosphate-diacylglycerol, CDP-DAG) or product (PGP) bound to the active site within a trifurcated amphipathic cavity. The hydrophilic head groups of CDP-DAG and PGP occupy two different pockets in the cavity, inducing local conformational changes. An elongated membrane-exposed surface groove accommodates the fatty acyl chains of CDP-DAG/PGP and opens a lateral portal for lipid entry/release. Remarkably, the daptomycin resistance-related mutations mostly cluster around the active site, causing reduction of enzymatic activity. Our results provide detailed mechanistic insights into the dynamic catalytic process of PgsA and structural frameworks beneficial for development of antimicrobial agents targeting PgsA from pathogenic bacteria. PgsA uses a trifurcated amphipathic cavity for binding of substrates or products. Conversion of CDP-DAG to PGP induces local conformational changes in PgsA. Daptomycin-resistant mutations of PgsA mostly lead to reduced catalytic activity. A structure-based five-state model is proposed for the synthesis of PGP by PgsA.
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Affiliation(s)
- Bowei Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hebang Yao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 201210, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 201210, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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16
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Crystal structures of phosphatidyl serine synthase PSS reveal the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases. Nat Commun 2021; 12:6982. [PMID: 34848707 PMCID: PMC8633023 DOI: 10.1038/s41467-021-27281-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 11/09/2021] [Indexed: 11/12/2022] Open
Abstract
Phospholipids are the major components of the membrane in all type of cells and organelles. They also are critical for cell metabolism, signal transduction, the immune system and other critical cell functions. The biosynthesis of phospholipids is a complex multi-step process with high-energy intermediates. Several enzymes in different metabolic pathways are involved in the initial phospholipid synthesis and its subsequent conversion. While the "Kennedy pathway" is the main pathway in mammalian cells, in bacteria and lower eukaryotes the precursor CDP-DAG is used in the de novo pathway by CDP-DAG alcohol O-phosphatidyl transferases to synthetize the basic lipids. Here we present the high-resolution structures of phosphatidyl serine synthase from Methanocaldococcus jannaschii crystallized in four different states. Detailed structural and functional analysis of the different structures allowed us to identify the substrate binding site and show how CDP-DAG, serine and two essential metal ions are bound and oriented relative to each other. In close proximity to the substrate binding site, two anions were identified that appear to be highly important for the reaction. The structural findings were confirmed by functional activity assays and suggest a model for the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases, which synthetize the phospholipids essential for the cells.
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17
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Knoll KE, Lindeque Z, Adeniji AA, Oosthuizen CB, Lall N, Loots DT. Elucidating the Antimycobacterial Mechanism of Action of Decoquinate Derivative RMB041 Using Metabolomics. Antibiotics (Basel) 2021; 10:693. [PMID: 34200519 PMCID: PMC8228794 DOI: 10.3390/antibiotics10060693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), still remains one of the leading causes of death from a single infectious agent worldwide. The high prevalence of this disease is mostly ascribed to the rapid development of drug resistance to the current anti-TB drugs, exacerbated by lack of patient adherence due to drug toxicity. The aforementioned highlights the urgent need for new anti-TB compounds with different antimycobacterial mechanisms of action to those currently being used. An N-alkyl quinolone; decoquinate derivative RMB041, has recently shown promising antimicrobial activity against Mtb, while also exhibiting low cytotoxicity and excellent pharmacokinetic characteristics. Its exact mechanism of action, however, is still unknown. Considering this, we used GCxGC-TOFMS and well described metabolomic approaches to analyze and compare the metabolic alterations of Mtb treated with decoquinate derivative RMB041 by comparison to non-treated Mtb controls. The most significantly altered pathways in Mtb treated with this drug include fatty acid metabolism, amino acid metabolism, glycerol metabolism, and the urea cycle. These changes support previous findings suggesting this drug acts primarily on the cell wall and secondarily on the DNA metabolism of Mtb. Additionally, we identified metabolic changes suggesting inhibition of protein synthesis and a state of dormancy.
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Affiliation(s)
- Kirsten E. Knoll
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Zander Lindeque
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Adetomiwa A. Adeniji
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Carel B. Oosthuizen
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
| | - Namrita Lall
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Du Toit Loots
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
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18
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Knoll KE, Lindeque Z, Adeniji AA, Oosthuizen CB, Lall N, Loots DT. Elucidating the Antimycobacterial Mechanism of Action of Ciprofloxacin Using Metabolomics. Microorganisms 2021; 9:microorganisms9061158. [PMID: 34071153 PMCID: PMC8228629 DOI: 10.3390/microorganisms9061158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 12/21/2022] Open
Abstract
In the interest of developing more effective and safer anti-tuberculosis drugs, we used a GCxGC-TOF-MS metabolomics research approach to investigate and compare the metabolic profiles of Mtb in the presence and absence of ciprofloxacin. The metabolites that best describe the differences between the compared groups were identified as markers characterizing the changes induced by ciprofloxacin. Malic acid was ranked as the most significantly altered metabolite marker induced by ciprofloxacin, indicative of an inhibition of the tricarboxylic acid (TCA) and glyoxylate cycle of Mtb. The altered fatty acid, myo-inositol, and triacylglycerol metabolism seen in this group supports previous observations of ciprofloxacin action on the Mtb cell wall. Furthermore, the altered pentose phosphate intermediates, glycerol metabolism markers, glucose accumulation, as well as the reduction in the glucogenic amino acids specifically, indicate a flux toward DNA (as well as cell wall) repair, also supporting previous findings of DNA damage caused by ciprofloxacin. This study further provides insights useful for designing network whole-system strategies for the identification of possible modes of action of various drugs and possibly adaptations by Mtb resulting in resistance.
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Affiliation(s)
- Kirsten E. Knoll
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Zander Lindeque
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Adetomiwa A. Adeniji
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Carel B. Oosthuizen
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
| | - Namrita Lall
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Du Toit Loots
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
- Correspondence: ; Tel.: +27-(0)18-299-1818
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19
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Torres W, Chávez-Castillo M, Peréz-Vicuña JL, Carrasquero R, Díaz MP, Gomez Y, Ramírez P, Cano C, Rojas-Quintero J, Chacín M, Velasco M, de Sanctis JB, Bermudez V. Potential role of bioactive lipids in rheumatoid arthritis. Curr Pharm Des 2021; 27:4434-4451. [PMID: 34036919 DOI: 10.2174/1381612827666210525164734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 04/08/2021] [Indexed: 11/22/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease, which involves a pathological inflammatory response against articular cartilage in multiple joints throughout the body. It is a complex disorder associated with comorbidities such as depression, lymphoma, osteoporosis and cardiovascular disease (CVD), which significantly deteriorate patients' quality of life and prognosis. This has ignited a large initiative to elucidate the physiopathology of RA, aiming to identify new therapeutic targets and approaches in its multidisciplinary management. Recently, various lipid bioactive products have been proposed to have an essential role in this process; including eicosanoids, specialized pro-resolving mediators, phospholipids/sphingolipids, and endocannabinoids. Dietary interventions using omega-3 polyunsaturated fatty acids or treatment with synthetic endocannabinoids agonists have been shown to significantly ameliorate RA symptoms. Indeed, the modulation of lipid metabolism may be crucial in the pathophysiology and treatment of autoimmune diseases.
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Affiliation(s)
- Wheeler Torres
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo. Venezuela
| | - Mervin Chávez-Castillo
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo. Venezuela
| | - José L Peréz-Vicuña
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo. Venezuela
| | - Rubén Carrasquero
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo. Venezuela
| | - María P Díaz
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo. Venezuela
| | - Yosselin Gomez
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo. Venezuela
| | - Paola Ramírez
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo. Venezuela
| | - Clímaco Cano
- Endocrine and Metabolic Diseases Research Center. School of Medicine. University of Zulia. Maracaibo. Venezuela
| | - Joselyn Rojas-Quintero
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston. 0
| | - Maricarmen Chacín
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla. Colombia
| | - Manuel Velasco
- Universidad Central de Venezuela, Escuela de Medicina José María Vargas, Caracas. Venezuela
| | - Juan Bautista de Sanctis
- Institute of Molecular and Translational Medicine. Faculty of Medicine and Dentistry. Palacky University. Czech Republic
| | - Valmore Bermudez
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla. Colombia
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20
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Flores J, Cancino JC, Chavez-Galan L. Lipoarabinomannan as a Point-of-Care Assay for Diagnosis of Tuberculosis: How Far Are We to Use It? Front Microbiol 2021; 12:638047. [PMID: 33935997 PMCID: PMC8081860 DOI: 10.3389/fmicb.2021.638047] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is still a severe public health problem; the current diagnostic tests have limitations that delay treatment onset. Lipoarabinomannan (LAM) is a glycolipid that is a component of the cell wall of the bacillus Mycobacterium tuberculosis, the etiologic agent of TB. This glycolipid is excreted as a soluble form in urine. The World Health Organization has established that the design of new TB diagnostic methods is one of the priorities within the EndTB Strategy. LAM has been suggested as a biomarker to develop diagnostic tests based on its identification in urine, and it is one of the most prominent candidates to develop point-of-care diagnostic test because urine samples can be easily collected. Moreover, LAM can regulate the immune response in the host and can be found in the serum of TB patients, where it probably affects a wide variety of host cell populations, consequently influencing the quality of both innate and adaptive immune responses during TB infection. Here, we revised the evidence that supports that LAM could be used as a tool for the development of new point-of-care tests for TB diagnosis, and we discussed the mechanisms that could contribute to the low sensitivity of diagnostic testing.
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Affiliation(s)
- Julio Flores
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico.,Laboratory of Immunomicrobiology, Department of Microbiology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Juan Carlos Cancino
- Laboratory of Immunomicrobiology, Department of Microbiology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Leslie Chavez-Galan
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
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21
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Belcher Dufrisne M, Jorge CD, Timóteo CG, Petrou VI, Ashraf KU, Banerjee S, Clarke OB, Santos H, Mancia F. Structural and Functional Characterization of Phosphatidylinositol-Phosphate Biosynthesis in Mycobacteria. J Mol Biol 2020; 432:5137-5151. [PMID: 32389689 PMCID: PMC7483940 DOI: 10.1016/j.jmb.2020.04.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 01/05/2023]
Abstract
In mycobacteria, phosphatidylinositol (PI) acts as a common lipid anchor for key components of the cell wall, including the glycolipids phosphatidylinositol mannoside, lipomannan, and lipoarabinomannan. Glycolipids in Mycobacterium tuberculosis, the causative agent of tuberculosis, are important virulence factors that modulate the host immune response. The identity-defining step in PI biosynthesis in prokaryotes, unique to mycobacteria and few other bacterial species, is the reaction between cytidine diphosphate-diacylglycerol and inositol-phosphate to yield phosphatidylinositol-phosphate, the immediate precursor to PI. This reaction is catalyzed by the cytidine diphosphate-alcohol phosphotransferase phosphatidylinositol-phosphate synthase (PIPS), an essential enzyme for mycobacterial viability. Here we present structures of PIPS from Mycobacterium kansasii with and without evidence of donor and acceptor substrate binding obtained using a crystal engineering approach. PIPS from Mycobacterium kansasii is 86% identical to the ortholog from M. tuberculosis and catalytically active. Functional experiments guided by our structural results allowed us to further characterize the molecular determinants of substrate specificity and catalysis in a new mycobacterial species. This work provides a framework to strengthen our understanding of phosphatidylinositol-phosphate biosynthesis in the context of mycobacterial pathogens.
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Affiliation(s)
- Meagan Belcher Dufrisne
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Carla D Jorge
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República-EAN, 2780-157 Oeiras, Portugal
| | - Cristina G Timóteo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República-EAN, 2780-157 Oeiras, Portugal
| | - Vasileios I Petrou
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Khuram U Ashraf
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Surajit Banerjee
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República-EAN, 2780-157 Oeiras, Portugal
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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22
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Origin and diversification of the cardiolipin biosynthetic pathway in the Eukarya domain. Biochem Soc Trans 2020; 48:1035-1046. [DOI: 10.1042/bst20190967] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022]
Abstract
Cardiolipin (CL) and its precursor phosphatidylglycerol (PG) are important anionic phospholipids widely distributed throughout all domains of life. They have key roles in several cellular processes by shaping membranes and modulating the activity of the proteins inserted into those membranes. They are synthesized by two main pathways, the so-called eukaryotic pathway, exclusively found in mitochondria, and the prokaryotic pathway, present in most bacteria and archaea. In the prokaryotic pathway, the first and the third reactions are catalyzed by phosphatidylglycerol phosphate synthase (Pgps) belonging to the transferase family and cardiolipin synthase (Cls) belonging to the hydrolase family, while in the eukaryotic pathway, those same reactions are catalyzed by unrelated homonymous enzymes: Pgps of the hydrolase family and Cls of the transferase family. Because of the enzymatic arrangement found in both pathways, it seems that the eukaryotic pathway evolved by convergence to the prokaryotic pathway. However, since mitochondria evolved from a bacterial endosymbiont, it would suggest that the eukaryotic pathway arose from the prokaryotic pathway. In this review, it is proposed that the eukaryote pathway evolved directly from a prokaryotic pathway by the neofunctionalization of the bacterial enzymes. Moreover, after the eukaryotic radiation, this pathway was reshaped by horizontal gene transfers or subsequent endosymbiotic processes.
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23
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Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase. J Mol Biol 2020; 432:5104-5123. [PMID: 32113953 DOI: 10.1016/j.jmb.2020.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
The lipid cubic phase (LCP) has been used extensively as a medium for crystallizing membrane proteins. It is an attractive environment in which to perform such studies because it incorporates a lipid bilayer. It is therefore considered a useful and a faithful biomembrane mimetic. Here, we bring together evidence that supports this view. Biophysical characterizations are described demonstrating that the cubic phase is a porous medium into and out of which water-soluble molecules can diffuse for binding to and reaction with reconstituted proteins. The proteins themselves are shown to be functionally reconstituted into and to have full mobility in the bilayered membrane, a prerequisite for LCP crystallogenesis. Spectroscopic methods have been used to characterize the conformation and disposition of proteins in the mesophase. Procedures for performing activity assays on enzymes directly in the cubic phase have been reported. Specific examples described here include a kinase and two transferases, where quantitative kinetics and mechanism-defining measurements were performed directly or via a coupled assay system. Finally, ligand-binding assays are described, where binding to proteins in the mesophase membrane was monitored directly by eye and indirectly by fluorescence quenching, enabling binding constant determinations for targets with affinity values in the micromolar and nanomolar range. These results make a convincing case that the lipid bilayer of the cubic mesophase is an excellent membrane mimetic and a suitable medium in which to perform not only crystallogenesis but also biochemical and biophysical characterizations of membrane proteins.
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Pemberton JG, Kim YJ, Balla T. Integrated regulation of the phosphatidylinositol cycle and phosphoinositide-driven lipid transport at ER-PM contact sites. Traffic 2019; 21:200-219. [PMID: 31650663 DOI: 10.1111/tra.12709] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/02/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022]
Abstract
Among the structural phospholipids that form the bulk of eukaryotic cell membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the common precursor for low-abundance regulatory lipids, collectively referred to as polyphosphoinositides (PPIn). The metabolic turnover of PPIn species has received immense attention because of the essential functions of these lipids as universal regulators of membrane biology and their dysregulation in numerous human pathologies. The diverse functions of PPIn lipids occur, in part, by orchestrating the spatial organization and conformational dynamics of peripheral or integral membrane proteins within defined subcellular compartments. The emerging role of stable contact sites between adjacent membranes as specialized platforms for the coordinate control of ion exchange, cytoskeletal dynamics, and lipid transport has also revealed important new roles for PPIn species. In this review, we highlight the importance of membrane contact sites formed between the endoplasmic reticulum (ER) and plasma membrane (PM) for the integrated regulation of PPIn metabolism within the PM. Special emphasis will be placed on non-vesicular lipid transport during control of the PtdIns biosynthetic cycle as well as toward balancing the turnover of the signaling PPIn species that define PM identity.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland
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25
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Díaz C, Pérez del Palacio J, Valero-Guillén PL, Mena García P, Pérez I, Vicente F, Martín C, Genilloud O, Sánchez Pozo A, Gonzalo-Asensio J. Comparative Metabolomics between Mycobacterium tuberculosis and the MTBVAC Vaccine Candidate. ACS Infect Dis 2019; 5:1317-1326. [PMID: 31099236 DOI: 10.1021/acsinfecdis.9b00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MTBVAC is a live attenuated M. tuberculosis vaccine constructed by genetic deletions in the phoP and fadD26 virulence genes. The MTBVAC vaccine is currently in phase 2 clinical trials with newborns and adults in South Africa, one of the countries with the highest incidence. Although MTBVAC has been extensively characterized by genomics, transcriptomics, lipidomics, and proteomics, its metabolomic profile is yet unknown. Accordingly, in this study we aim to identify differential metabolites between M. tuberculosis and MTBVAC. To this end, an untargeted metabolomics approach based on liquid chromatography coupled to high-resolution mass spectrometry was implemented in order to explore the main metabolic differences between M. tuberculosis and MTBVAC. As an outcome, we identified a set of 34 metabolites involved in diverse bacterial biosynthetic pathways. A consistent increase in the phosphatidylinositol species was observed in the vaccine candidate relative to its parental strain. This phenotype resulted in an increased production of phosphatidylinositol mannosides, a novel PhoP-regulated phenotype in the most widespread lineages of M. tuberculosis. This study represents a step ahead in our understanding of the MTBVAC vaccine, and some of the differential metabolites identified in this work might be used as potential vaccination biomarkers.
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Affiliation(s)
- Caridad Díaz
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 34, 18016 Granada, Spain
| | - José Pérez del Palacio
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 34, 18016 Granada, Spain
| | - Pedro Luis Valero-Guillén
- Departamento de Genética y Microbiología, Facultad de Medicina, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria (IMIB), Campus de Espinardo, 30100 Murcia, Spain
| | - Patricia Mena García
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 34, 18016 Granada, Spain
| | - Irene Pérez
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón,
C/Domingo Miral s/n, 50019 Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisca Vicente
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 34, 18016 Granada, Spain
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón,
C/Domingo Miral s/n, 50019 Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Paseo Isabel la Católica 1-3, 50009 Zaragoza, Spain
| | - Olga Genilloud
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 34, 18016 Granada, Spain
| | - Antonio Sánchez Pozo
- Departamento de Bioquímica y Biología Molecular II, Facultad de Farmacia, Universidad de Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón,
C/Domingo Miral s/n, 50019 Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), C/Mariano Esquillor, Edificio I + D, Campus Río Ebro, 50018 Zaragoza, Spain
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26
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Blunsom NJ, Cockcroft S. Phosphatidylinositol synthesis at the endoplasmic reticulum. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1865:158471. [PMID: 31173893 DOI: 10.1016/j.bbalip.2019.05.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/23/2022]
Abstract
Phosphatidylinositol (PI) is a minor phospholipid with a characteristic fatty acid profile; it is highly enriched in stearic acid at the sn-1 position and arachidonic acid at the sn-2 position. PI is phosphorylated into seven specific derivatives, and individual species are involved in a vast array of cellular functions including signalling, membrane traffic, ion channel regulation and actin dynamics. De novo PI synthesis takes place at the endoplasmic reticulum where phosphatidic acid (PA) is converted to PI in two enzymatic steps. PA is also produced at the plasma membrane during phospholipase C signalling, where hydrolysis of phosphatidylinositol (4,5) bisphosphate (PI(4,5)P2) leads to the production of diacylglycerol which is rapidly phosphorylated to PA. This PA is transferred to the ER to be also recycled back to PI. For the synthesis of PI, CDP-diacylglycerol synthase (CDS) converts PA to the intermediate, CDP-DG, which is then used by PI synthase to make PI. The de novo synthesised PI undergoes remodelling to acquire its characteristic fatty acid profile, which is altered in p53-mutated cancer cells. In mammals, there are two CDS enzymes at the ER, CDS1 and CDS2. In this review, we summarise the de novo synthesis of PI at the ER and the enzymes involved in its subsequent remodelling to acquire its characteristic acyl chains. We discuss how CDS, the rate limiting enzymes in PI synthesis are regulated by different mechanisms. During phospholipase C signalling, the CDS1 enzyme is specifically upregulated by cFos via protein kinase C.
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Affiliation(s)
- Nicholas J Blunsom
- Dept. of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, London WC1E 6JJ, UK
| | - Shamshad Cockcroft
- Dept. of Neuroscience, Physiology and Pharmacology, Division of Biosciences, University College London, London WC1E 6JJ, UK.
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27
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Grāve K, Bennett MD, Högbom M. Structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis. Commun Biol 2019; 2:175. [PMID: 31098408 PMCID: PMC6506517 DOI: 10.1038/s42003-019-0427-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/16/2019] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis causes over one million yearly deaths, and drug resistance is rapidly developing. Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) is an integral membrane enzyme involved in biosynthesis of inositol-derived phospholipids required for formation of the mycobacterial cell wall, and a potential drug target. Here we present three crystal structures of M. tuberculosis PgsA1: in absence of substrates (2.9 Å), in complex with Mn2+ and citrate (1.9 Å), and with the CDP-DAG substrate (1.8 Å). The structures reveal atomic details of substrate binding as well as coordination and dynamics of the catalytic metal site. In addition, molecular docking supported by mutagenesis indicate a binding mode for the second substrate, D-myo-inositol-3-phosphate. Together, the data describe the structural basis for M. tuberculosis phosphatidylinositol phosphate synthesis and suggest a refined general catalytic mechanism-including a substrate-induced carboxylate shift-for Class I CDP-alcohol phosphotransferases, enzymes essential for phospholipid biosynthesis in all domains of life.
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Affiliation(s)
- Kristīne Grāve
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, SE-106 91 Stockholm, Sweden
| | - Matthew D. Bennett
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, SE-106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, SE-106 91 Stockholm, Sweden
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28
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López-Cortés A, Paz-Y-Miño C, Cabrera-Andrade A, Barigye SJ, Munteanu CR, González-Díaz H, Pazos A, Pérez-Castillo Y, Tejera E. Gene prioritization, communality analysis, networking and metabolic integrated pathway to better understand breast cancer pathogenesis. Sci Rep 2018; 8:16679. [PMID: 30420728 PMCID: PMC6232116 DOI: 10.1038/s41598-018-35149-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/16/2018] [Indexed: 12/30/2022] Open
Abstract
Consensus strategy was proved to be highly efficient in the recognition of gene-disease association. Therefore, the main objective of this study was to apply theoretical approaches to explore genes and communities directly involved in breast cancer (BC) pathogenesis. We evaluated the consensus between 8 prioritization strategies for the early recognition of pathogenic genes. A communality analysis in the protein-protein interaction (PPi) network of previously selected genes was enriched with gene ontology, metabolic pathways, as well as oncogenomics validation with the OncoPPi and DRIVE projects. The consensus genes were rationally filtered to 1842 genes. The communality analysis showed an enrichment of 14 communities specially connected with ERBB, PI3K-AKT, mTOR, FOXO, p53, HIF-1, VEGF, MAPK and prolactin signaling pathways. Genes with highest ranking were TP53, ESR1, BRCA2, BRCA1 and ERBB2. Genes with highest connectivity degree were TP53, AKT1, SRC, CREBBP and EP300. The connectivity degree allowed to establish a significant correlation between the OncoPPi network and our BC integrated network conformed by 51 genes and 62 PPi. In addition, CCND1, RAD51, CDC42, YAP1 and RPA1 were functional genes with significant sensitivity score in BC cell lines. In conclusion, the consensus strategy identifies both well-known pathogenic genes and prioritized genes that need to be further explored.
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Affiliation(s)
- Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Mariscal Sucre Avenue, 170129, Quito, Ecuador.
- RNASA-IMEDIR, Computer Sciences Faculty, University of Coruna, 15071, Coruna, Spain.
| | - César Paz-Y-Miño
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Mariscal Sucre Avenue, 170129, Quito, Ecuador
| | - Alejandro Cabrera-Andrade
- Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de las Américas, Avenue de los Granados, 170125, Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de las Américas, Avenue de los Granados, 170125, Quito, Ecuador
| | - Stephen J Barigye
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Cristian R Munteanu
- RNASA-IMEDIR, Computer Sciences Faculty, University of Coruna, 15071, Coruna, Spain
- INIBIC, Institute of Biomedical Research, CHUAC, UDC, 15006, Coruna, Spain
| | - Humberto González-Díaz
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940, Leioa, Biscay, Spain
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Biscay, Spain
| | - Alejandro Pazos
- RNASA-IMEDIR, Computer Sciences Faculty, University of Coruna, 15071, Coruna, Spain
- INIBIC, Institute of Biomedical Research, CHUAC, UDC, 15006, Coruna, Spain
| | - Yunierkis Pérez-Castillo
- Grupo de Bio-Quimioinformática, Universidad de las Américas, Avenue de los Granados, 170125, Quito, Ecuador
- Escuela de Ciencias Físicas y Matemáticas, Universidad de las Américas, Avenue de los Granados, 170125, Quito, Ecuador
| | - Eduardo Tejera
- Grupo de Bio-Quimioinformática, Universidad de las Américas, Avenue de los Granados, 170125, Quito, Ecuador.
- Facultad de Ingeniería y Ciencias Agropecuarias, Universidad de las Américas, Avenue de los Granados, 170125, Quito, Ecuador.
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29
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Cheng W, Doyle DA, El Arnaout T. The N-acyltransferase Lnt: Structure-function insights from recent simultaneous studies. Int J Biol Macromol 2018; 117:870-877. [PMID: 29859843 DOI: 10.1016/j.ijbiomac.2018.05.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 02/05/2023]
Abstract
Bacterial lipoproteins have been researched for decades due to their roles in a large number of biological functions. There were no structures of their main three membrane processing enzymes, until 2016 for Lgt and LspA, and then 2017 for Lnt with not one but three simultaneous, independent publications. We have analyzed the recent findings for this apolipoprotein N-acyltransferase Lnt, with comparisons between the novel structures, and with soluble nitrilases, to determine the significance of unique features in terms of substrate's recognition and binding mechanism influenced by exclusive residues, two transmembrane helices, and a flexible loop.
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Affiliation(s)
- Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Declan A Doyle
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Toufic El Arnaout
- School of Food Science and Environmental Health, Dublin Institute of Technology, Marlborough St, Dublin 1, Ireland.
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30
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Li Z, Tang Y, Wu Y, Zhao S, Bao J, Luo Y, Li D. Structural insights into the committed step of bacterial phospholipid biosynthesis. Nat Commun 2017; 8:1691. [PMID: 29167463 PMCID: PMC5700162 DOI: 10.1038/s41467-017-01821-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/18/2017] [Indexed: 11/09/2022] Open
Abstract
The membrane-integral glycerol 3-phosphate (G3P) acyltransferase PlsY catalyses the committed and essential step in bacterial phospholipid biosynthesis by acylation of G3P, forming lysophosphatidic acid. It contains no known acyltransferase motifs, lacks eukaryotic homologs, and uses the unusual acyl-phosphate as acyl donor, as opposed to acyl-CoA or acyl-carrier protein for other acyltransferases. Previous studies have identified several PlsY inhibitors as potential antimicrobials. Here we determine the crystal structure of PlsY at 1.48 Å resolution, revealing a seven-transmembrane helix fold. Four additional substrate- and product-bound structures uncover the atomic details of its relatively inflexible active site. Structure and mutagenesis suggest a different acylation mechanism of ‘substrate-assisted catalysis’ that, unlike other acyltransferases, does not require a proteinaceous catalytic base to complete. The structure data and a high-throughput enzymatic assay developed in this work should prove useful for virtual and experimental screening of inhibitors against this vital bacterial enzyme. The first step in bacterial phospholipid biosynthesis is the acylation of glycerol 3-phosphate to form lysophosphatidic acid. Here, the authors present the high resolution crystal structure of the glycerol 3-phosphate acyltransferase PlsY, a membrane protein and give insights into its catalytical mechanism.
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Affiliation(s)
- Zhenjian Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yannan Tang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China
| | - Yitian Luo
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 333 Middle Huaxia Road, Shanghai, 201210, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, China.
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31
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Dufrisne MB, Petrou VI, Clarke OB, Mancia F. Structural basis for catalysis at the membrane-water interface. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1368-1385. [PMID: 27913292 DOI: 10.1016/j.bbalip.2016.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 11/27/2022]
Abstract
The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments - the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Meagan Belcher Dufrisne
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Vasileios I Petrou
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Oliver B Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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32
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Structural basis of phosphatidyl-myo-inositol mannosides biosynthesis in mycobacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1355-1367. [PMID: 27826050 DOI: 10.1016/j.bbalip.2016.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/29/2016] [Accepted: 11/02/2016] [Indexed: 11/22/2022]
Abstract
Phosphatidyl-myo-inositol mannosides (PIMs) are glycolipids of unique chemical structure found in the inner and outer membranes of the cell envelope of all Mycobacterium species. The PIM family of glycolipids comprises phosphatidyl-myo-inositol mono-, di-, tri-, tetra-, penta-, and hexamannosides with different degrees of acylation. PIMs are considered not only essential structural components of the cell envelope but also the precursors of lipomannan and lipoarabinomannan, two major lipoglycans implicated in host-pathogen interactions. Since the description of the complete chemical structure of PIMs, major efforts have been committed to defining the molecular bases of its biosynthetic pathway. The structural characterization of the integral membrane phosphatidyl-myo-inositol phosphate synthase (PIPS), and that of three enzymes working at the protein-membrane interface, the phosphatidyl-myo-inositol mannosyltransferases A and B, and the acyltransferase PatA, established the basis of the early steps of the PIM pathway at the molecular level. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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33
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Chauhan N, Farine L, Pandey K, Menon AK, Bütikofer P. Lipid topogenesis--35years on. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:757-766. [PMID: 26946259 DOI: 10.1016/j.bbalip.2016.02.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 12/28/2022]
Abstract
Glycerophospholipids are the principal fabric of cellular membranes. The pathways by which these lipids are synthesized were elucidated mainly through the work of Kennedy and colleagues in the late 1950s and early 1960s. Subsequently, attention turned to cell biological aspects of lipids: Where in the cell are lipids synthesized? How are lipids integrated into membranes to form a bilayer? How are they sorted and transported from their site of synthesis to other cellular destinations? These topics, collectively termed 'lipid topogenesis', were the subject of a review article in 1981 by Bell, Ballas and Coleman. We now assess what has been learned about early events of lipid topogenesis, i.e. "lipid synthesis, the integration of lipids into membranes, and lipid translocation across membranes", in the 35 years since the publication of this important review. We highlight the recent elucidation of the X-ray structures of key membrane enzymes of glycerophospholipid synthesis, progress on identifying lipid scramblase proteins needed to equilibrate lipids across membranes, and new complexities in the subcellular location and membrane topology of phosphatidylinositol synthesis revealed through a comparison of two unicellular model eukaryotes. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
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Affiliation(s)
- Neha Chauhan
- Department of Biochemistry, Weill Cornell Medical College, New York 10065, USA
| | - Luce Farine
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, New York 10065, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York 10065, USA.
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
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34
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Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, Li C, Kloss B, Bruni R, Kloppmann E, Rost B, Manzini MC, Shapiro L, Mancia F. Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis. Nat Commun 2016; 7:10175. [PMID: 26729507 PMCID: PMC4728340 DOI: 10.1038/ncomms10175] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/11/2015] [Indexed: 11/08/2022] Open
Abstract
The attachment of a sugar to a hydrophobic polyisoprenyl carrier is the first step for all extracellular glycosylation processes. The enzymes that perform these reactions, polyisoprenyl-glycosyltransferases (PI-GTs) include dolichol phosphate mannose synthase (DPMS), which generates the mannose donor for glycosylation in the endoplasmic reticulum. Here we report the 3.0 Å resolution crystal structure of GtrB, a glucose-specific PI-GT from Synechocystis, showing a tetramer in which each protomer contributes two helices to a membrane-spanning bundle. The active site is 15 Å from the membrane, raising the question of how water-soluble and membrane-embedded substrates are brought into apposition for catalysis. A conserved juxtamembrane domain harbours disease mutations, which compromised activity in GtrB in vitro and in human DPM1 tested in zebrafish. We hypothesize a role of this domain in shielding the polyisoprenyl-phosphate for transport to the active site. Our results reveal the basis of PI-GT function, and provide a potential molecular explanation for DPM1-related disease.
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Affiliation(s)
- Chiara Ardiccioni
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Oliver B. Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - David Tomasek
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
| | - Habon A. Issa
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Desiree C. von Alpen
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Heather L. Pond
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Surajit Banerjee
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Qun Liu
- New York Structural Biology Center, X4 Beamlines, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chijun Li
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York 10027, USA
| | - Renato Bruni
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York 10027, USA
| | - Edda Kloppmann
- Department of Informatics, Bioinformatics and Computational Biology, Garching 85748, Germany
- Institute for Advanced Study (TUM-IAS), TUM (Technische Universität München), Garching 85748, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology, Garching 85748, Germany
- Institute for Advanced Study (TUM-IAS), TUM (Technische Universität München), Garching 85748, Germany
| | - M. Chiara Manzini
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia 20037, USA
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia 20037, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA
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