1
|
Niu Y, Pemberton JG, Kim YJ, Balla T. Phosphatidylserine enrichment in the nuclear membrane regulates key enzymes of phosphatidylcholine synthesis. EMBO J 2024; 43:3414-3449. [PMID: 38918635 PMCID: PMC11329639 DOI: 10.1038/s44318-024-00151-z] [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: 03/12/2024] [Revised: 05/07/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Phosphatidylserine (PS) is an important anionic phospholipid that is synthesized within the endoplasmic reticulum (ER). While PS shows the highest enrichment and serves important functional roles in the plasma membrane (PM) but its role in the nucleus is poorly explored. Using three orthogonal approaches, we found that PS is also uniquely enriched in the inner nuclear membrane (INM) and the nuclear reticulum (NR). Nuclear PS is critical for supporting the translocation of CCTα and Lipin1α, two key enzymes important for phosphatidylcholine (PC) biosynthesis, from the nuclear matrix to the INM and NR in response to oleic acid treatment. We identified the PS-interacting regions within the M-domain of CCTα and M-Lip domain of Lipin1α, and show that lipid droplet formation is altered by manipulations of nuclear PS availability. Our studies reveal an unrecognized regulatory role of nuclear PS levels in the regulation of key PC synthesizing enzymes within the nucleus.
Collapse
Affiliation(s)
- Yang Niu
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
2
|
Yu J, Boehr DD. Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces. Front Mol Biosci 2023; 10:1306483. [PMID: 38099197 PMCID: PMC10720463 DOI: 10.3389/fmolb.2023.1306483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Recruitment of enzymes to intracellular membranes often modulates their catalytic activity, which can be important in cell signaling and membrane trafficking. Thus, re-localization is not only important for these enzymes to gain access to their substrates, but membrane interactions often allosterically regulate enzyme function by inducing conformational changes across different time and amplitude scales. Recent structural, biophysical and computational studies have revealed how key enzymes interact with lipid membrane surfaces, and how this membrane binding regulates protein structure and function. This review summarizes the recent progress in understanding regulatory mechanisms involved in enzyme-membrane interactions.
Collapse
Affiliation(s)
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| |
Collapse
|
3
|
Song Y, Wang R, Zhang Z, Liu X, Qi L, Shentu X, Yu X. Semi-rational engineering membrane binding domain of L-amino acid deaminase from Proteus vulgaris for enhanced α-ketoisocaproate. Front Microbiol 2022; 13:1025845. [PMID: 36246292 PMCID: PMC9561763 DOI: 10.3389/fmicb.2022.1025845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/16/2022] [Indexed: 12/01/2022] Open
Abstract
α-Keto acids are important raw materials for pharmaceuticals and functional foods, which could be produced from cheap feed stock by whole cell biocatalysts containing L-amino acid deaminases (L-AADs). However, the production capacity is limited by the low activity of L-AADs. The L-AAD mediated redox reaction employs the electron transport chain to transfer electrons from the reduced FADH2 to O2, implying that the interaction between L-AAD and the cell membrane affects its catalytic activity. To improve the catalytic activity of L-AAD from Proteus vulgaris, we redesigned the membrane-bound hydrophobic insertion sequences (INS, residues 325–375) by saturation mutagenesis and high-throughput screening. Mutants D340N and L363N exhibited higher affinity and catalytic efficiency for L-leucine, with half-life 1.62-fold and 1.28-fold longer than that of wild-type L-AAD. D340N catalyzed L-leucine to produce 81.21 g⋅L–1 α-ketoisocaproate, with a bioconversion rate of 89.06%, which was 17.57% higher than that of the wild-type. It is predicted that the mutations enhanced the interaction between the protein and the cell membrane.
Collapse
|
4
|
Olarte MJ, Swanson JMJ, Walther TC, Farese RV. The CYTOLD and ERTOLD pathways for lipid droplet-protein targeting. Trends Biochem Sci 2022; 47:39-51. [PMID: 34583871 PMCID: PMC8688270 DOI: 10.1016/j.tibs.2021.08.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/03/2023]
Abstract
Lipid droplets (LDs) are the main organelles for lipid storage, and their surfaces contain unique proteins with diverse functions, including those that facilitate the deposition and mobilization of LD lipids. Among organelles, LDs have an unusual structure with an organic, hydrophobic oil phase covered by a phospholipid monolayer. The unique properties of LD monolayer surfaces require proteins to localize to LDs by distinct mechanisms. Here we review the two pathways known to mediate direct LD protein localization: the CYTOLD pathway mediates protein targeting from the cytosol toLDs, and the ERTOLD pathway functions in protein targeting from the endoplasmic reticulum toLDs. We describe the emerging principles for each targeting pathway in animal cells and highlight open questions in the field.
Collapse
Affiliation(s)
- Maria-Jesus Olarte
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02124, USA.
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02124, USA.
| |
Collapse
|
5
|
Izrael R, Marton L, Nagy GN, Pálinkás HL, Kucsma N, Vértessy BG. Identification of a nuclear localization signal in the Plasmodium falciparum CTP: phosphocholine cytidylyltransferase enzyme. Sci Rep 2020; 10:19739. [PMID: 33184408 PMCID: PMC7665022 DOI: 10.1038/s41598-020-76829-1] [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: 08/04/2020] [Accepted: 11/02/2020] [Indexed: 12/30/2022] Open
Abstract
The phospholipid biosynthesis of the malaria parasite, Plasmodium falciparum is a key process for its survival and its inhibition is a validated antimalarial therapeutic approach. The second and rate-limiting step of the de novo phosphatidylcholine biosynthesis is catalysed by CTP: phosphocholine cytidylyltransferase (PfCCT), which has a key regulatory function within the pathway. Here, we investigate the functional impact of the key structural differences and their respective role in the structurally unique pseudo-heterodimer PfCCT protein in a heterologous cellular context using the thermosensitive CCT-mutant CHO-MT58 cell line. We found that a Plasmodium-specific lysine-rich insertion within the catalytic domain of PfCCT acts as a nuclear localization signal and its deletion decreases the nuclear propensity of the protein in the model cell line. We further showed that the putative membrane-binding domain also affected the nuclear localization of the protein. Moreover, activation of phosphatidylcholine biosynthesis by phospholipase C treatment induces the partial nuclear-to-cytoplasmic translocation of PfCCT. We additionally investigated the cellular function of several PfCCT truncated constructs in a CHO-MT58 based rescue assay. In absence of the endogenous CCT activity we observed that truncated constructs lacking the lysine-rich insertion, or the membrane-binding domain provided similar cell survival ratio as the full length PfCCT protein.
Collapse
Affiliation(s)
- Richard Izrael
- Institute of Enzymology, Research Centre for Natural Sciences, 1117, Budapest, Hungary.
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, 6720, Szeged, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111, Budapest, Hungary.
| | - Lívia Marton
- Institute of Enzymology, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Gergely N Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, 1117, Budapest, Hungary
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111, Budapest, Hungary
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hajnalka L Pálinkás
- Institute of Enzymology, Research Centre for Natural Sciences, 1117, Budapest, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, 6720, Szeged, Hungary
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111, Budapest, Hungary
| | - Nóra Kucsma
- Institute of Enzymology, Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, 1117, Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111, Budapest, Hungary.
| |
Collapse
|
6
|
Cornell RB. Membrane Lipids Assist Catalysis by CTP: Phosphocholine Cytidylyltransferase. J Mol Biol 2020; 432:5023-5042. [PMID: 32234309 DOI: 10.1016/j.jmb.2020.03.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
Abstract
While most of the articles in this issue review the workings of integral membrane enzymes, in this review, we describe the catalytic mechanism of an enzyme that contains a soluble catalytic domain but appears to catalyze its reaction on the membrane surface, anchored and assisted by a separate regulatory amphipathic helical domain and inter-domain linker. Membrane partitioning of CTP: phosphocholine cytidylyltransferase (CCT), a key regulatory enzyme of phosphatidylcholine metabolism, is regulated chiefly by changes in membrane phospholipid composition, and boosts the enzyme's catalytic efficiency >200-fold. Catalytic enhancement by membrane binding involves the displacement of an auto-inhibitory helix from the active site entrance-way and promotion of a new conformational ensemble for the inter-domain, allosteric linker that has an active role in the catalytic cycle. We describe the evidence for close contact between membrane lipid, a compact allosteric linker, and the CCT active site, and discuss potential ways that this interaction enhances catalysis.
Collapse
Affiliation(s)
- Rosemary B Cornell
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A-1S6.
| |
Collapse
|
7
|
Yue L, McPhee MJ, Gonzalez K, Charman M, Lee J, Thompson J, Winkler DFH, Cornell RB, Pelech S, Ridgway ND. Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets. Mol Biol Cell 2020; 31:1047-1059. [PMID: 32186954 PMCID: PMC7346725 DOI: 10.1091/mbc.e20-01-0014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
CTP:phosphocholine cytidylyltransferase-alpha (CCTα) and CCTβ catalyze the rate-limiting step in phosphatidylcholine (PC) biosynthesis. CCTα is activated by association of its α-helical M-domain with nuclear membranes, which is negatively regulated by phosphorylation of the adjacent P-domain. To understand how phosphorylation regulates CCT activity, we developed phosphosite-specific antibodies for pS319 and pY359+pS362 at the N- and C-termini of the P-domain, respectively. Oleate treatment of cultured cells triggered CCTα translocation to the nuclear envelope (NE) and nuclear lipid droplets (nLDs) and rapid dephosphorylation of pS319. Removal of oleate led to dissociation of CCTα from the NE and increased phosphorylation of S319. Choline depletion of cells also caused CCTα translocation to the NE and S319 dephosphorylation. In contrast, Y359 and S362 were constitutively phosphorylated during oleate addition and removal, and CCTα-pY359+pS362 translocated to the NE and nLDs of oleate-treated cells. Mutagenesis revealed that phosphorylation of S319 is regulated independently of Y359+S362, and that CCTα-S315D+S319D was defective in localization to the NE. We conclude that the P-domain undergoes negative charge polarization due to dephosphorylation of S319 and possibly other proline-directed sites and retention of Y359 and S362 phosphorylation, and that dephosphorylation of S319 and S315 is involved in CCTα recruitment to nuclear membranes.
Collapse
Affiliation(s)
- Lambert Yue
- Department of Medicine, Division of Neurology, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Michael J McPhee
- Department of Pediatrics and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Kevin Gonzalez
- Department of Medicine, Division of Neurology, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Mark Charman
- Department of Pediatrics and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jonghwa Lee
- Department of Pediatrics and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jordan Thompson
- Department of Pediatrics and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Dirk F H Winkler
- Kinexus Bioinformatics Corporation, Vancouver, BC V6P 6T3, Canada
| | - Rosemary B Cornell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Steven Pelech
- Department of Medicine, Division of Neurology, University of British Columbia, Vancouver, BC V6T 2B5, Canada.,Kinexus Bioinformatics Corporation, Vancouver, BC V6P 6T3, Canada
| | - Neale D Ridgway
- Department of Pediatrics and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| |
Collapse
|
8
|
Taneva SG, Lee J, Knowles DG, Tishyadhigama C, Chen H, Cornell RB. Interdomain communication in the phosphatidylcholine regulatory enzyme, CCTα, relies on a modular αE helix. J Biol Chem 2019; 294:15517-15530. [PMID: 31488547 DOI: 10.1074/jbc.ra119.009849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/18/2019] [Indexed: 12/14/2022] Open
Abstract
CTP:phosphocholine cytidylyltransferase (CCT), the rate-limiting enzyme in phosphatidylcholine (PC) synthesis, is an amphitropic enzyme that regulates PC homeostasis. Recent work has suggested that CCTα activation by binding to a PC-deficient membrane involves conformational transitions in a helix pair (αE) that, along with a short linker of unknown structure (J segment), bridges the catalytic domains of the CCTα dimer to the membrane-binding (M) domains. In the soluble, inactive form, the αE helices are constrained into unbroken helices by contacts with two auto-inhibitory (AI) helices from domain M. In the active, membrane-bound form, the AI helices are displaced and engage the membrane. Molecular dynamics simulations have suggested that AI displacement is associated with hinge-like bending in the middle of the αE, positioning its C terminus closer to the active site. Here, we show that CCTα activation by membrane binding is sensitive to mutations in the αE and J segments, especially within or proximal to the αE hinge. Substituting Tyr-213 within this hinge with smaller uncharged amino acids that could destabilize interactions between the αE helices increased both constitutive and lipid-dependent activities, supporting a link between αE helix bending and stimulation of CCT activity. The solvent accessibilities of Tyr-213 and Tyr-216 suggested that these tyrosines move to new partially buried environments upon membrane binding of CCT, consistent with a folded αE/J structure. These data suggest that signal transduction through the modular αE helix pair relies on shifts in its conformational ensemble that are controlled by the AI helices and their displacement upon membrane binding.
Collapse
Affiliation(s)
- Svetla G Taneva
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jaeyong Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Daniel G Knowles
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Chanajai Tishyadhigama
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Hongwen Chen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Rosemary B Cornell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada .,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
9
|
Cornell RB, Taneva SG, Dennis MK, Tse R, Dhillon RK, Lee J. Disease-linked mutations in the phosphatidylcholine regulatory enzyme CCTα impair enzymatic activity and fold stability. J Biol Chem 2018; 294:1490-1501. [PMID: 30559292 DOI: 10.1074/jbc.ra118.006457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/05/2018] [Indexed: 11/06/2022] Open
Abstract
CTP:phosphocholine cytidylyltransferase (CCT) is the key regulatory enzyme in phosphatidylcholine (PC) synthesis and is activated by binding to PC-deficient membranes. Mutations in the gene encoding CCTα (PCYT1A) cause three distinct pathologies in humans: lipodystrophy, spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD), and isolated retinal dystrophy. Previous analyses showed that for some disease-linked PCYT1A variants steady state levels of CCTα and PC synthesis were reduced in patient fibroblasts, but other variants impaired PC synthesis with little effect on CCT levels. To explore the impact on CCT stability and function we expressed WT and mutant CCTs in COS-1 cells, which have very low endogenous CCT. Over-expression of two missense variants in the catalytic domain (V142M and P150A) generated aggregated enzymes that could not be refolded after solubilization by denaturation. Other mutations in the catalytic core that generated CCTs with reduced solubility could be purified. Five variants destabilized the catalytic domain-fold as assessed by lower transition temperatures for unfolding, and three of these manifested defects in substrate Km values. A mutation (R223S) in a signal-transducing linker between the catalytic and membrane-binding domains also impaired enzyme kinetics. E280del, a single amino acid deletion in the autoinhibitory helix increased the constitutive (lipid-independent) enzyme activity ∼4-fold. This helix also participates in membrane binding, and surprisingly E280del enhanced the enzyme's response to anionic lipid vesicles ∼4-fold. These in vitro analyses on purified mutant CCTs will complement future measurements of their impact on PC synthesis in cultured cells and in tissues with a stringent requirement for CCTα.
Collapse
Affiliation(s)
- Rosemary B Cornell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada; Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada.
| | - Svetla G Taneva
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada
| | - Melissa K Dennis
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada
| | - Ronnie Tse
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada
| | - Randeep K Dhillon
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada
| | - Jaeyong Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada
| |
Collapse
|
10
|
Zhang C, Liu P. The New Face of the Lipid Droplet: Lipid Droplet Proteins. Proteomics 2018; 19:e1700223. [DOI: 10.1002/pmic.201700223] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/13/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Congyan Zhang
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Pingsheng Liu
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100049 China
| |
Collapse
|
11
|
Guca E, Nagy GN, Hajdú F, Marton L, Izrael R, Hoh F, Yang Y, Vial H, Vértessy BG, Guichou JF, Cerdan R. Structural determinants of the catalytic mechanism of Plasmodium CCT, a key enzyme of malaria lipid biosynthesis. Sci Rep 2018; 8:11215. [PMID: 30046154 PMCID: PMC6060094 DOI: 10.1038/s41598-018-29500-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/10/2018] [Indexed: 11/13/2022] Open
Abstract
The development of the malaria parasite, Plasmodium falciparum, in the human erythrocyte, relies on phospholipid metabolism to fulfil the massive need for membrane biogenesis. Phosphatidylcholine (PC) is the most abundant phospholipid in Plasmodium membranes. PC biosynthesis is mainly ensured by the de novo Kennedy pathway that is considered as an antimalarial drug target. The CTP:phosphocholine cytidylyltransferase (CCT) catalyses the rate-limiting step of the Kennedy pathway. Here we report a series of structural snapshots of the PfCCT catalytic domain in its free, substrate- and product-complexed states that demonstrate the conformational changes during the catalytic mechanism. Structural data show the ligand-dependent conformational variations of a flexible lysine. Combined kinetic and ligand-binding analyses confirm the catalytic roles of this lysine and of two threonine residues of the helix αE. Finally, we assessed the variations in active site residues between Plasmodium and mammalian CCT which could be exploited for future antimalarial drug design.
Collapse
Affiliation(s)
- Ewelina Guca
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, CNRS, Université de Montpellier, Montpellier, France.,Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Gergely N Nagy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.,Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX37BN, United Kingdom
| | - Fanni Hajdú
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Lívia Marton
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Richard Izrael
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - François Hoh
- CNRS UMR5048, Centre de Biochimie Structurale, Université de Montpellier, Montpellier, France.,INSERM U1054, Montpellier, France
| | - Yinshan Yang
- CNRS UMR5048, Centre de Biochimie Structurale, Université de Montpellier, Montpellier, France.,INSERM U1054, Montpellier, France
| | - Henri Vial
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, CNRS, Université de Montpellier, Montpellier, France
| | - Beata G Vértessy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Jean-François Guichou
- CNRS UMR5048, Centre de Biochimie Structurale, Université de Montpellier, Montpellier, France.,INSERM U1054, Montpellier, France
| | - Rachel Cerdan
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, CNRS, Université de Montpellier, Montpellier, France.
| |
Collapse
|
12
|
Ramezanpour M, Lee J, Taneva SG, Tieleman DP, Cornell RB. An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair. J Biol Chem 2018. [PMID: 29519816 DOI: 10.1074/jbc.ra118.002053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of α helices (αE) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys122 The impacts of the AI helix on active-site dynamics and positioning of Lys122 are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys122 side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased αE dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the αE element upon membrane binding of the AI helix. Moreover, when αE bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys122 and restraint of the pliable αE helices. We propose that membrane binding enables bending of the αE helices, bringing the active site closer to the membrane surface.
Collapse
Affiliation(s)
- Mohsen Ramezanpour
- From the Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 and
| | - Jaeyong Lee
- the Departments of Molecular Biology and Biochemistry and
| | | | - D Peter Tieleman
- From the Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 and
| | - Rosemary B Cornell
- the Departments of Molecular Biology and Biochemistry and .,Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
13
|
Bernfur K, Rutsdottir G, Emanuelsson C. The chloroplast-localized small heat shock protein Hsp21 associates with the thylakoid membranes in heat-stressed plants. Protein Sci 2017; 26:1773-1784. [PMID: 28608391 PMCID: PMC5563132 DOI: 10.1002/pro.3213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022]
Abstract
The small heat shock protein (sHsp) chaperones are crucial for cell survival and can prevent aggregation of client proteins that partially unfold under destabilizing conditions. Most investigations on the chaperone activity of sHsps are based on a limited set of thermosensitive model substrate client proteins since the endogenous targets are often not known. There is a high diversity among sHsps with a single conserved β‐sandwich fold domain defining the family, the α‐crystallin domain, whereas the N‐terminal and C‐terminal regions are highly variable in length and sequence among various sHsps and conserved only within orthologues. The endogenous targets are probably also varying among various sHsps, cellular compartments, cell type and organism. Here we have investigated Hsp21, a non‐metazoan sHsp expressed in the chloroplasts in green plants which experience huge environmental fluctuations not least in temperature. We describe how Hsp21 can also interact with the chloroplast thylakoid membranes, both when isolated thylakoid membranes are incubated with Hsp21 protein and when plants are heat‐stressed. The amount of Hsp21 associated with the thylakoid membranes was precisely determined by quantitative mass spectrometry after metabolic 15N‐isotope labeling of either recombinantly expressed and purified Hsp21 protein or intact Arabidopsis thaliana plants. We found that Hsp21 is among few proteins that become associated with the thylakoid membranes in heat‐stressed plants, and that approximately two thirds of the pool of chloroplast Hsp21 is affected. We conclude that for a complete picture of the role of sHsps in plant stress resistance also their association with the membranes should be considered.
Collapse
Affiliation(s)
- Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
| | - Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
| |
Collapse
|
14
|
Cummins DJ, Espada A, Novick SJ, Molina-Martin M, Stites RE, Espinosa JF, Broughton H, Goswami D, Pascal BD, Dodge JA, Chalmers MJ, Griffin PR. Two-Site Evaluation of the Repeatability and Precision of an Automated Dual-Column Hydrogen/Deuterium Exchange Mass Spectrometry Platform. Anal Chem 2016; 88:6607-14. [PMID: 27224086 DOI: 10.1021/acs.analchem.6b01650] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) is an information-rich biophysical method for the characterization of protein dynamics. Successful applications of differential HDX-MS include the characterization of protein-ligand binding. A single differential HDX-MS data set (protein ± ligand) is often comprised of more than 40 individual HDX-MS experiments. To eliminate laborious manual processing of samples, and to minimize random and gross errors, automated systems for HDX-MS analysis have become routine in many laboratories. However, an automated system, while less prone to random errors introduced by human operators, may have systematic errors that go unnoticed without proper detection. Although the application of automated (and manual) HDX-MS has become common, there are only a handful of studies reporting the systematic evaluation of the performance of HDX-MS experiments, and no reports have been published describing a cross-site comparison of HDX-MS experiments. Here, we describe an automated HDX-MS platform that operates with a parallel, two-trap, two-column configuration that has been installed in two remote laboratories. To understand the performance of the system both within and between laboratories, we have designed and completed a test-retest repeatability study for differential HDX-MS experiments implemented at each of two laboratories, one in Florida and the other in Spain. This study provided sufficient data to do both within and between laboratory variability assessments. Initial results revealed a systematic run-order effect within one of the two systems. Therefore, the study was repeated, and this time the conclusion was that the experimental conditions were successfully replicated with minimal systematic error.
Collapse
Affiliation(s)
- David J Cummins
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Alfonso Espada
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Scott J Novick
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Manuel Molina-Martin
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Ryan E Stites
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Juan Felix Espinosa
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Howard Broughton
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Devrishi Goswami
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Bruce D Pascal
- The Scripps Research institute, Informatics Core, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jeffrey A Dodge
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Patrick R Griffin
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| |
Collapse
|
15
|
Lagace TA. Phosphatidylcholine: Greasing the Cholesterol Transport Machinery. Lipid Insights 2016; 8:65-73. [PMID: 27081313 PMCID: PMC4821435 DOI: 10.4137/lpi.s31746] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/26/2016] [Accepted: 02/23/2016] [Indexed: 01/19/2023] Open
Abstract
Negative feedback regulation of cholesterol metabolism in mammalian cells ensures a proper balance of cholesterol with other membrane lipids, principal among these being the major phospholipid phosphatidylcholine (PC). Processes such as cholesterol biosynthesis and efflux, cholesteryl ester storage in lipid droplets, and uptake of plasma lipoproteins are tuned to the cholesterol/PC ratio. Cholesterol-loaded macrophages in atherosclerotic lesions display increased PC biosynthesis that buffers against elevated cholesterol levels and may also facilitate cholesterol trafficking to enhance cholesterol sensing and efflux. These same mechanisms could play a generic role in homeostatic responses to acute changes in membrane free cholesterol levels. Here, I discuss the established and emerging roles of PC metabolism in promoting intracellular cholesterol trafficking and membrane lipid homeostasis.
Collapse
Affiliation(s)
- Thomas A Lagace
- Department of Pathology and Laboratory Medicine, University of Ottawa Heart Institute, Ottawa, ON, Canada
| |
Collapse
|
16
|
Targeting Fat: Mechanisms of Protein Localization to Lipid Droplets. Trends Cell Biol 2016; 26:535-546. [PMID: 26995697 DOI: 10.1016/j.tcb.2016.02.007] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
How proteins specifically localize to the phospholipid monolayer surface of lipid droplets (LDs) is being unraveled. We review here the major known pathways of protein targeting to LDs and suggest a classification framework based on the localization origin for the protein. Class I proteins often have a membrane-embedded, hydrophobic 'hairpin' motif, and access LDs from the endoplasmic reticulum (ER) either during LD formation or after formation via ER-LD membrane bridges. Class II proteins access the LD surface from the cytosol and bind through amphipathic helices or other hydrophobic domains. Other proteins require lipid modifications or protein-protein interactions to bind to LDs. We summarize knowledge for targeting and removal of the different classes, and highlight areas needing investigation.
Collapse
|
17
|
Membrane lipid compositional sensing by the inducible amphipathic helix of CCT. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1861:847-861. [PMID: 26747646 DOI: 10.1016/j.bbalip.2015.12.022] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 11/21/2022]
Abstract
The amphipathic helical (AH) membrane binding motif is recognized as a major device for lipid compositional sensing. We explore the function and mechanism of sensing by the lipid biosynthetic enzyme, CTP:phosphocholine cytidylyltransferase (CCT). As the regulatory enzyme in phosphatidylcholine (PC) synthesis, CCT contributes to membrane PC homeostasis. CCT directly binds and inserts into the surface of bilayers that are deficient in PC and therefore enriched in lipids that enhance surface charge and/or create lipid packing voids. These two membrane physical properties induce the folding of the CCT M domain into a ≥60 residue AH. Membrane binding activates catalysis by a mechanism that has been partially deciphered. We review the evidence for CCT compositional sensing, and the membrane and protein determinants for lipid selective membrane-interactions. We consider the factors that promote the binding of CCT isoforms to the membranes of the ER, nuclear envelope, or lipid droplets, but exclude CCT from other organelles and the plasma membrane. The CCT sensing mechanism is compared with several other proteins that use an AH motif for membrane compositional sensing. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
Collapse
|
18
|
Cornell RB, Ridgway ND. CTP:phosphocholine cytidylyltransferase: Function, regulation, and structure of an amphitropic enzyme required for membrane biogenesis. Prog Lipid Res 2015; 59:147-71. [PMID: 26165797 DOI: 10.1016/j.plipres.2015.07.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022]
Abstract
CTP:phosphocholine cytidylyltransferase (CCT) catalyzes a rate-limiting and regulated step in the CDP-choline pathway for the synthesis of phosphatidylcholine (PC) and PC-derived lipids. Control of CCT activity is multi-layered, and includes direct regulation by reversible membrane binding involving a built-in lipid compositional sensor. Thus CCT contributes to phospholipid compositional homeostasis. CCT also modifies the curvature of its target membrane. Knowledge of CCT structure and regulation of its catalytic function are relatively advanced compared to many lipid metabolic enzymes, and are reviewed in detail. Recently the genetic origins of two human developmental and lipogenesis disorders have been traced to mutations in the gene for CCTα.
Collapse
Affiliation(s)
- Rosemary B Cornell
- Department of Molecular Biology and Biochemistry and the Department of Chemistry, Simon Fraser University, Burnaby, B.C. V5A-1S6, Canada.
| | - Neale D Ridgway
- Departments of Pediatrics, and Biochemistry and Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia B3H-4H7, Canada
| |
Collapse
|
19
|
Jing R, Sun J, Wang Y, Li M. Domain position prediction based on sequence information by using fuzzy mean operator. Proteins 2015; 83:1462-9. [PMID: 26009844 DOI: 10.1002/prot.24833] [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: 02/13/2015] [Revised: 04/23/2015] [Accepted: 05/17/2015] [Indexed: 11/09/2022]
Abstract
The prediction of protein domain region is an advantageous process on the study of protein structure and function. In this study, we proposed a new method, which is composed of fuzzy mean operator and region division, to predict the particular positions of domains in a target protein based on its sequence. The whole sequence is aligned and scored by using fuzzy mean operator, and the final determination of domain region position is realized by region division. A published benchmark is used for the comparison with previous researches. In addition, we generate two extra datasets to examine the stability of this method. Finally, the prediction accuracy of independent test dataset achieved by our method was up to 84.13%. We wish that this method could be useful for related researches.
Collapse
Affiliation(s)
- Runyu Jing
- Chemical Information Center (CIC), College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Jing Sun
- Chemical Information Center (CIC), College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yuelong Wang
- Chemical Information Center (CIC), College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Menglong Li
- Chemical Information Center (CIC), College of Chemistry, Sichuan University, Chengdu, 610064, China
| |
Collapse
|
20
|
Craddock CP, Adams N, Bryant FM, Kurup S, Eastmond PJ. PHOSPHATIDIC ACID PHOSPHOHYDROLASE Regulates Phosphatidylcholine Biosynthesis in Arabidopsis by Phosphatidic Acid-Mediated Activation of CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE Activity. THE PLANT CELL 2015; 27:1251-64. [PMID: 25862304 PMCID: PMC4558698 DOI: 10.1105/tpc.15.00037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/19/2015] [Indexed: 05/04/2023]
Abstract
Regulation of membrane lipid biosynthesis is critical for cell function. We previously reported that disruption of PHOSPHATIDIC ACID PHOSPHOHYDROLASE1 (PAH1) and PAH2 stimulates net phosphatidylcholine (PC) biosynthesis and proliferation of the endoplasmic reticulum (ER) in Arabidopsis thaliana. Here, we show that this response is caused specifically by a reduction in the catalytic activity of the protein and positively correlates with an accumulation of its substrate, phosphatidic acid (PA). The accumulation of PC in pah1 pah2 is suppressed by disruption of CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE1 (CCT1), which encodes a key enzyme in the nucleotide pathway for PC biosynthesis. The activity of recombinant CCT1 is stimulated by lipid vesicles containing PA. Truncation of CCT1, to remove the predicted C-terminal amphipathic lipid binding domain, produced a constitutively active enzyme. Overexpression of native CCT1 in Arabidopsis has no significant effect on PC biosynthesis or ER morphology, but overexpression of the truncated constitutively active version largely replicates the pah1 pah2 phenotype. Our data establish that membrane homeostasis is regulated by lipid composition in Arabidopsis and reveal a mechanism through which the abundance of PA, mediated by PAH activity, modulates CCT activity to govern PC content.
Collapse
Affiliation(s)
- Christian P Craddock
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Nicolette Adams
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Fiona M Bryant
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Smita Kurup
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Peter J Eastmond
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| |
Collapse
|
21
|
Contet A, Pihan E, Lavigne M, Wengelnik K, Maheshwari S, Vial H, Douguet D, Cerdan R. Plasmodium falciparum CTP:phosphocholine cytidylyltransferase possesses two functional catalytic domains and is inhibited by a CDP-choline analog selected from a virtual screening. FEBS Lett 2015; 589:992-1000. [PMID: 25771858 DOI: 10.1016/j.febslet.2015.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
Abstract
Phosphatidylcholine is the major lipid component of the malaria parasite membranes and is required for parasite multiplication in human erythrocytes. Plasmodium falciparum CTP:phosphocholine cytidylyltransferase (PfCCT) is the rate-limiting enzyme of the phosphatidylcholine biosynthesis pathway and thus considered as a potential antimalarial target. In contrast to its mammalian orthologs, PfCCT contains a duplicated catalytic domain. Here, we show that both domains are catalytically active with similar kinetic parameters. A virtual screening strategy allowed the identification of a drug-size molecule competitively inhibiting the enzyme. This compound also prevented phosphatidylcholine biosynthesis in parasites and exerted an antimalarial effect. This study constitutes the first step towards a rationalized design of future new antimalarial agents targeting PfCCT.
Collapse
Affiliation(s)
- Alicia Contet
- Université Montpellier, CNRS, Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, Place Eugène Bataillon, 34095 Montpellier, France
| | - Emilie Pihan
- CNRS, Université Nice Sophia-Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660, route des Lucioles, Sophia Antipolis, 06560 Valbonne, France
| | - Marina Lavigne
- Université Montpellier, CNRS, Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, Place Eugène Bataillon, 34095 Montpellier, France
| | - Kai Wengelnik
- Université Montpellier, CNRS, Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, Place Eugène Bataillon, 34095 Montpellier, France
| | - Sweta Maheshwari
- Université Montpellier, CNRS, Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, Place Eugène Bataillon, 34095 Montpellier, France
| | - Henri Vial
- Université Montpellier, CNRS, Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, Place Eugène Bataillon, 34095 Montpellier, France
| | - Dominique Douguet
- CNRS, Université Nice Sophia-Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660, route des Lucioles, Sophia Antipolis, 06560 Valbonne, France.
| | - Rachel Cerdan
- Université Montpellier, CNRS, Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, Place Eugène Bataillon, 34095 Montpellier, France.
| |
Collapse
|
22
|
Affiliation(s)
- Gregory
F. Pirrone
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - Roxana E. Iacob
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - John R. Engen
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| |
Collapse
|
23
|
Abstract
Lipids are unevenly distributed within and between cell membranes, thus defining organelle identity. Such distribution relies on local metabolic branches and mechanisms that move lipids. These processes are regulated by feedback mechanisms that decipher topographical information in organelle membranes and then regulate lipid levels or flows. In the endoplasmic reticulum, the major lipid source, transcriptional regulators and enzymes sense changes in membrane features to modulate lipid production. At the Golgi apparatus, lipid-synthesizing, lipid-flippase, and lipid-transport proteins (LTPs) collaborate to control lipid balance and distribution within the membrane to guarantee remodeling processes crucial for vesicular trafficking. Open questions exist regarding LTPs, which are thought to be lipid sensors that regulate lipid synthesis or carriers that transfer lipids between organelles across long distances or in contact sites. A novel model is that LTPs, by exchanging two different lipids, exploit one lipid gradient between two distinct membranes to build a second lipid gradient.
Collapse
Affiliation(s)
- Guillaume Drin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and CNRS, 06560 Valbonne, France;
| |
Collapse
|
24
|
Chong SSY, Taneva SG, Lee JMC, Cornell RB. The Curvature Sensitivity of a Membrane-Binding Amphipathic Helix Can Be Modulated by the Charge on a Flanking Region. Biochemistry 2014; 53:450-61. [DOI: 10.1021/bi401457r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sharon S. Y. Chong
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Svetla G. Taneva
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Joseph M. C. Lee
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Rosemary B. Cornell
- Department
of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| |
Collapse
|
25
|
Lee J, Taneva SG, Holland BW, Tieleman DP, Cornell RB. Structural basis for autoinhibition of CTP:phosphocholine cytidylyltransferase (CCT), the regulatory enzyme in phosphatidylcholine synthesis, by its membrane-binding amphipathic helix. J Biol Chem 2013; 289:1742-55. [PMID: 24275660 DOI: 10.1074/jbc.m113.526970] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CTP:phosphocholine cytidylyltransferase (CCT) interconverts between an inactive soluble and active membrane-bound form in response to changes in membrane lipid composition. Activation involves disruption of an inhibitory interaction between the αE helices at the base of the active site and an autoinhibitory (AI) segment in the regulatory M domain and membrane insertion of the M domain as an amphipathic helix. We show that in the CCT soluble form the AI segment functions to suppress kcat and elevate the Km for CTP. The crystal structure of a CCT dimer composed of the catalytic and AI segments reveals an AI-αE interaction as a cluster of four amphipathic helices (two αE and two AI helices) at the base of the active sites. This interaction corroborates mutagenesis implicating multiple hydrophobic residues within the AI segment that contribute to its silencing function. The AI-αE interaction directs the turn at the C-terminal end of the AI helix into backbone-to-backbone contact with a loop (L2) at the opening to the active site, which houses the key catalytic residue, lysine 122. Molecular dynamics simulations suggest that lysine 122 side-chain orientations are constrained by contacts with the AI helix-turn, which could obstruct its engagement with substrates. This work deciphers how the CCT regulatory amphipathic helix functions as a silencing device.
Collapse
Affiliation(s)
- Jaeyong Lee
- From the Departments of Molecular Biology and Biochemistry and
| | | | | | | | | |
Collapse
|
26
|
Nagy GN, Marton L, Krámos B, Oláh J, Révész Á, Vékey K, Delsuc F, Hunyadi-Gulyás É, Medzihradszky KF, Lavigne M, Vial H, Cerdan R, Vértessy BG. Evolutionary and mechanistic insights into substrate and product accommodation of CTP:phosphocholine cytidylyltransferase from Plasmodium falciparum. FEBS J 2013; 280:3132-48. [PMID: 23578277 DOI: 10.1111/febs.12282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 03/08/2013] [Accepted: 03/26/2013] [Indexed: 12/31/2022]
Abstract
The enzyme CTP:phosphocholine cytidylyltransferase (CCT) is essential in the lipid biosynthesis of Plasmodia (Haemosporida), presenting a promising antimalarial target. Here, we identified two independent gene duplication events of CCT within Apicomplexa and characterized a truncated construct of Plasmodium falciparum CCT that forms a dimer resembling the molecular architecture of CCT enzymes from other sources. Based on biophysical and enzyme kinetics methods, our data show that the CDP-choline product of the CCT enzymatic reaction binds to the enzyme considerably stronger than either substrate (CTP or choline phosphate). Interestingly, in the presence of Mg²⁺ , considered to be a cofactor of the enzyme, the binding of the CTP substrate is attenuated by a factor of 5. The weaker binding of CTP:Mg²⁺ , similarly to the related enzyme family of aminoacyl tRNA synthetases, suggests that, with lack of Mg²⁺ , positively charged side chain(s) of CCT may contribute to CTP accommodation. Thermodynamic investigations by isothermal titration calorimetry and fluorescent spectroscopy studies indicate that accommodation of the choline phosphate moiety in the CCT active site is different when it appears on its own as one of the substrates or when it is linked to the CDP-choline product. A tryptophan residue within the active site is identified as a useful internal fluorescence sensor of enzyme-ligand binding. Results indicate that the catalytic mechanism of Plasmodium falciparum CCT may involve conformational changes affecting the choline subsite of the enzyme.
Collapse
Affiliation(s)
- Gergely N Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Lagace TA, Ridgway ND. The role of phospholipids in the biological activity and structure of the endoplasmic reticulum. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2499-510. [PMID: 23711956 DOI: 10.1016/j.bbamcr.2013.05.018] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/09/2013] [Accepted: 05/15/2013] [Indexed: 01/22/2023]
Abstract
The endoplasmic reticulum (ER) is an interconnected network of tubular and planar membranes that supports the synthesis and export of proteins, carbohydrates and lipids. Phospholipids, in particular phosphatidylcholine (PC), are synthesized in the ER where they have essential functions including provision of membranes required for protein synthesis and export, cholesterol homeostasis, and triacylglycerol storage and secretion. Coordination of these biological processes is essential, as highlighted by findings that link phospholipid metabolism in the ER with perturbations in lipid storage/secretion and stress responses, ultimately contributing to obesity/diabetes, atherosclerosis and neurological disorders. Phospholipid synthesis is not uniformly distributed in the ER but is localized at membrane interfaces or contact zones with other organelles, and in dynamic, proliferating ER membranes. The topology of phospholipid synthesis is an important consideration when establishing the etiology of diseases that arise from ER dysfunction. This review will highlight our current understanding of the contribution of phospholipid synthesis to proper ER function, and how alterations contribute to aberrant stress responses and disease. This article is part of a Special Issue entitled: Functional and structural diversity of endoplasmic reticulum.
Collapse
Affiliation(s)
- Thomas A Lagace
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada.
| | | |
Collapse
|
28
|
|