1
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Lange JDT, Stoller JR, Edwards KA, Friesen JA. Identification, characterization, and cellular localization of Leishmania major CTP:phosphocholine cytidylyltransferase. Biochem Biophys Res Commun 2024; 738:150548. [PMID: 39154553 DOI: 10.1016/j.bbrc.2024.150548] [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: 07/29/2024] [Revised: 08/01/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024]
Abstract
The eukaryotic parasite Leishmania is the causative agent of the disease leishmaniasis, the second largest parasitic killer in the world behind malaria. A large percentage of Leishmania membrane phospholipids is phosphatidylcholine (PC), formed via the Kennedy pathway, where the enzyme CTP: phosphocholine cytidylyltransferase (CCT) catalyzes the second, rate limiting step. Leishmania major CCT was expressed in non-pathogenic Leishmania tarentolae and exhibited activity that increased 10-fold in the presence of PC:oleate lipid vesicles. Confocal microscopy of L. tarentolae expressing L. major CCT fused to a red fluorescent protein revealed the enzyme is cytoplasmic but may associate with internal membranes. A truncated mutant of L. major CCT containing the catalytic domain was expressed in Escherichia coli and in vitro analysis of the enzyme showed catalysis was divalent cation-dependent and yielded a Vmax of 374 nmol/min/mg and Km values of 0.0648 mM and 3.74 mM, respectively, for the substrates CTP and phosphocholine.
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Affiliation(s)
- Justin D T Lange
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | - Jeanette R Stoller
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | - Kevin A Edwards
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA
| | - Jon A Friesen
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA.
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2
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Ludwig-Peisker O, Ansel E, Schweizer D, Jagannathan V, Loechel R, Leeb T. PCYT1A Missense Variant in Vizslas with Disproportionate Dwarfism. Genes (Basel) 2022; 13:genes13122354. [PMID: 36553621 PMCID: PMC9777673 DOI: 10.3390/genes13122354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Disproportionate dwarfism phenotypes represent a heterogeneous subset of skeletal dysplasias and have been described in many species including humans and dogs. In this study, we investigated Vizsla dogs that were affected by disproportionate dwarfism that we propose to designate as skeletal dysplasia 3 (SD3). The most striking skeletal changes comprised a marked shortening and deformation of the humerus and femur. An extended pedigree with six affected dogs suggested autosomal recessive inheritance. Combined linkage and homozygosity mapping localized a potential genetic defect to a ~4 Mb interval on chromosome 33. We sequenced the genome of an affected dog, and comparison with 926 control genomes revealed a single, private protein-changing variant in the critical interval, PCYT1A:XM_038583131.1:c.673T>C, predicted to cause an exchange of a highly conserved amino acid, XP_038439059.1:p.(Y225H). We observed perfect co-segregation of the genotypes with the phenotype in the studied family. When genotyping additional Vizslas, we encountered a single dog with disproportionate dwarfism that did not carry the mutant PCYT1A allele, which we hypothesize was due to heterogeneity. In the remaining 130 dogs, we observed perfect genotype-phenotype association, and none of the unaffected dogs were homozygous for the mutant PCYT1A allele. PCYT1A loss-of-function variants cause spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD) in humans. The skeletal changes in Vizslas were comparable to human patients. So far, no ocular phenotype has been recognized in dwarf Vizslas. We propose the PCYT1A missense variant as a candidate causative variant for SD3. Our data facilitate genetic testing of Vizslas to prevent the unintentional breeding of further affected puppies.
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Affiliation(s)
- Odette Ludwig-Peisker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Emily Ansel
- BluePearl Pet Hospital, Raleigh, NC 27616, USA
| | - Daniela Schweizer
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | | | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
- Correspondence: ; Tel.: +41-31-684-23-26
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3
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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.
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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.
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4
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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.
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Affiliation(s)
- Rosemary B Cornell
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A-1S6.
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5
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Molecular Docking Reveals the Binding Modes of Anticancer Alkylphospholipids and Lysophosphatidylcholine within the Catalytic Domain of Cytidine Triphosphate: Phosphocholine Cytidyltransferase. EUR J LIPID SCI TECH 2020. [DOI: 10.1002/ejlt.201900422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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6
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de Mendoza D, Pilon M. Control of membrane lipid homeostasis by lipid-bilayer associated sensors: A mechanism conserved from bacteria to humans. Prog Lipid Res 2019; 76:100996. [DOI: 10.1016/j.plipres.2019.100996] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 12/31/2022]
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7
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Knowles DG, Lee J, Taneva SG, Cornell RB. Remodeling of the interdomain allosteric linker upon membrane binding of CCTα pulls its active site close to the membrane surface. J Biol Chem 2019; 294:15531-15543. [PMID: 31488548 DOI: 10.1074/jbc.ra119.009850] [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: 01/10/2023] Open
Abstract
The rate-limiting step in the biosynthesis of the major membrane phospholipid, phosphatidylcholine, is catalyzed by CTP:phosphocholine cytidylyltransferase (CCT), which is regulated by reversible membrane binding of a long amphipathic helix (domain M). The M domain communicates with the catalytic domain via a conserved ∼20-residue linker, essential for lipid activation of CCT. Previous analysis of this region (denoted as the αEC/J) using MD simulations, cross-linking, mutagenesis, and solvent accessibility suggested that membrane binding of domain M promotes remodeling of the αEC/J into a more compact structure that is required for enzyme activation. Here, using tryptophan fluorescence quenching, we show that the allosteric linker lies superficially on the membrane surface. Analyses with truncated CCTs show that the αEC/J can interact with lipids independently of the M domain. We observed strong FRET between engineered tryptophans in the αEC/J and vesicles containing dansyl-phosphatidylethanolamine that depended on the native J sequence. These data are incompatible with the extended conformation of the αE helix observed in the previously determined crystal structure of inactive CCT but support a bent αE helix conformation stabilized by J segment interactions. Our results suggest that the membrane-adsorbed, folded allosteric linker may partially cover the active site cleft and pull it close to the membrane surface, where cytidyl transfer can occur efficiently in a relatively anhydrous environment.
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Affiliation(s)
- Daniel G Knowles
- 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
| | - Svetla G Taneva
- Department of Molecular Biology and Biochemistry, 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
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8
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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.
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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
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9
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Jiao H, Yin Y, Liu Z. Structures of the Mitochondrial CDP-DAG Synthase Tam41 Suggest a Potential Lipid Substrate Pathway from Membrane to the Active Site. Structure 2019; 27:1258-1269.e4. [PMID: 31178220 DOI: 10.1016/j.str.2019.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/14/2019] [Accepted: 04/29/2019] [Indexed: 11/18/2022]
Abstract
In mitochondria, CDP-diacylglycerol (CDP-DAG) is a crucial precursor for cardiolipin biosynthesis. Mitochondrial CDP-DAG is synthesized by the translocator assembly and maintenance protein 41 (Tam41) through an elusive process. Here we show that Tam41 adopts sequential catalytic mechanism, and report crystal structures of the bulk N-terminal region of Tam41 from Schizosaccharomyces pombe in the apo and CTP-bound state. The structure reveals that Tam41 contains a nucleotidyltransferase (NTase) domain and a winged helix domain. CTP binds to an "L"-shaped pocket sandwiched between the two domains. Rearrangement of a loop region near the active site is essential for opening the CTP-binding pocket. Docking of phosphatidic acid/CDP-DAG in the structure suggests a lipid entry/exit pathway connected to the "L"-shaped pocket. The C-terminal region of SpTam41 contains a positively charged amphipathic helix crucial for membrane association and participates in binding phospholipids. These results provide detailed insights into the mechanism of CDP-DAG biosynthesis in mitochondria.
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Affiliation(s)
- Haizhan Jiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, No. 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Yan Yin
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, No. 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, No. 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China.
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10
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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.
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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
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11
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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.
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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.
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12
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Haider A, Wei YC, Lim K, Barbosa AD, Liu CH, Weber U, Mlodzik M, Oras K, Collier S, Hussain MM, Dong L, Patel S, Alvarez-Guaita A, Saudek V, Jenkins BJ, Koulman A, Dymond MK, Hardie RC, Siniossoglou S, Savage DB. PCYT1A Regulates Phosphatidylcholine Homeostasis from the Inner Nuclear Membrane in Response to Membrane Stored Curvature Elastic Stress. Dev Cell 2018; 45:481-495.e8. [PMID: 29754800 PMCID: PMC5971203 DOI: 10.1016/j.devcel.2018.04.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/27/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022]
Abstract
Cell and organelle membranes consist of a complex mixture of phospholipids (PLs) that determine their size, shape, and function. Phosphatidylcholine (PC) is the most abundant phospholipid in eukaryotic membranes, yet how cells sense and regulate its levels in vivo remains unclear. Here we show that PCYT1A, the rate-limiting enzyme of PC synthesis, is intranuclear and re-locates to the nuclear membrane in response to the need for membrane PL synthesis in yeast, fly, and mammalian cells. By aligning imaging with lipidomic analysis and data-driven modeling, we demonstrate that yeast PCYT1A membrane association correlates with membrane stored curvature elastic stress estimates. Furthermore, this process occurs inside the nucleus, although nuclear localization signal mutants can compensate for the loss of endogenous PCYT1A in yeast and in fly photoreceptors. These data suggest an ancient mechanism by which nucleoplasmic PCYT1A senses surface PL packing defects on the inner nuclear membrane to control PC homeostasis.
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Affiliation(s)
- Afreen Haider
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yu-Chen Wei
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Koini Lim
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Antonio D Barbosa
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Che-Hsiung Liu
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Ursula Weber
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marek Mlodzik
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Kadri Oras
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Simon Collier
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - M Mahmood Hussain
- Departments of Cell Biology and Pediatrics, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Liang Dong
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Satish Patel
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Anna Alvarez-Guaita
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Vladimir Saudek
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Benjamin J Jenkins
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Albert Koulman
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Marcus K Dymond
- Division of Chemistry, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK
| | - Roger C Hardie
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Symeon Siniossoglou
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
| | - David B Savage
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
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13
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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.
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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
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14
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Park J, Kim H, Kim S, Lee D, Kim MS, Shin DH. Crystal structure of D-glycero-Β-D-manno-heptose-1-phosphate adenylyltransferase fromBurkholderia pseudomallei. Proteins 2017; 86:124-131. [DOI: 10.1002/prot.25398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Jimin Park
- College of Pharmacy; Ewha W. University; Seoul Republic of Korea
| | - Hyojin Kim
- College of Pharmacy; Ewha W. University; Seoul Republic of Korea
| | - Suwon Kim
- College of Pharmacy; Ewha W. University; Seoul Republic of Korea
| | - Daeun Lee
- College of Pharmacy; Ewha W. University; Seoul Republic of Korea
| | - Mi-Sun Kim
- College of Pharmacy; Ewha W. University; Seoul Republic of Korea
| | - Dong Hae Shin
- College of Pharmacy; Ewha W. University; Seoul Republic of Korea
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15
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Cho SH, Kim SY, Tomita T, Shiraishi T, Park JS, Sato S, Kudo F, Eguchi T, Funa N, Nishiyama M, Kuzuyama T. Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme. ACS Chem Biol 2017; 12:2209-2215. [PMID: 28727444 DOI: 10.1021/acschembio.7b00419] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fosfomycin is a wide-spectrum phosphonate antibiotic that is used clinically to treat cystitis, tympanitis, etc. Its biosynthesis starts with the formation of a carbon-phosphorus bond catalyzed by the phosphoenolpyruvate phosphomutase Fom1. We identified an additional cytidylyltransferase (CyTase) domain at the Fom1 N-terminus in addition to the phosphoenolpyruvate phosphomutase domain at the Fom1 C-terminus. Here, we demonstrate that Fom1 is bifunctional and that the Fom1 CyTase domain catalyzes the cytidylylation of the 2-hydroxyethylphosphonate (HEP) intermediate to produce cytidylyl-HEP. On the basis of this new function of Fom1, we propose a revised fosfomycin biosynthetic pathway that involves the transient CMP-conjugated intermediate. The identification of a biosynthetic mechanism via such transient cytidylylation of a biosynthetic intermediate fundamentally advances the understanding of phosphonate biosynthesis in nature. The crystal structure of the cytidylyl-HEP-bound CyTase domain provides a basis for the substrate specificity and reveals unique catalytic elements not found in other members of the CyTase family.
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Affiliation(s)
- Su-Hee Cho
- Biotechnology
Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Seung-Young Kim
- Department
of Food Science and Biotechnology, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Takeo Tomita
- Biotechnology
Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Taro Shiraishi
- Biotechnology
Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jin-Soo Park
- Biotechnology
Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shusuke Sato
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department
of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Nobutaka Funa
- Department
of Food Science and Biotechnology, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Makoto Nishiyama
- Biotechnology
Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology
Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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16
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Zhao X, Dauenpen M, Qu C, Qiu X. Genomic Analysis of Genes Involved in the Biosynthesis of Very Long Chain Polyunsaturated Fatty Acids inThraustochytriumsp. 26185. Lipids 2016; 51:1065-75. [DOI: 10.1007/s11745-016-4181-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 08/01/2016] [Indexed: 01/30/2023]
Affiliation(s)
- Xianming Zhao
- ; Food and Bioproduct Sciences; University of Saskatchewan; Saskatoon SK S7N 5A8 Canada
| | - Meesapyodsuk Dauenpen
- ; Food and Bioproduct Sciences; University of Saskatchewan; Saskatoon SK S7N 5A8 Canada
- ; National Research Council Canada; Saskatoon SK S7N 0W9 Canada
| | - Cunmin Qu
- ; Food and Bioproduct Sciences; University of Saskatchewan; Saskatoon SK S7N 5A8 Canada
| | - Xiao Qiu
- ; Food and Bioproduct Sciences; University of Saskatchewan; Saskatoon SK S7N 5A8 Canada
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17
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Brault JP, Friesen JA. Characterization of cytidylyltransferase enzyme activity through high performance liquid chromatography. Anal Biochem 2016; 510:26-32. [PMID: 27443959 DOI: 10.1016/j.ab.2016.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/13/2016] [Accepted: 07/15/2016] [Indexed: 11/26/2022]
Abstract
The cytidylyltransferases are a family of enzymes that utilize cytidine 5'-triphosphate (CTP) to synthesize molecules that are typically precursors to membrane phospholipids. The most extensively studied cytidylyltransferase is CTP:phosphocholine cytidylyltransferase (CCT), which catalyzes conversion of phosphocholine and CTP to cytidine diphosphocholine (CDP-choline), a step critical for synthesis of the membrane phospholipid phosphatidylcholine (PC). The current method used to determine catalytic activity of CCT measures production of radiolabeled CDP-choline from (14)C-labeled phosphocholine. The goal of this research was to develop a CCT enzyme assay that employed separation of non-radioactive CDP-choline from CTP. A C18 reverse phase column with a mobile phase of 0.1 M ammonium bicarbonate (98%) and acetonitrile (2%) (pH 7.4) resulted in separation of solutions of the substrate CTP from the product CDP-choline. A previously characterized truncated version of rat CCTα (denoted CCTα236) was used to test the HPLC enzyme assay by measuring CDP-choline product formation. The Vmax for CCTα236 was 3850 nmol/min/mg and K0.5 values for CTP and phosphocholine were 4.07 mM and 2.49 mM, respectively. The HPLC method was applied to glycerol 3-phosphate cytidylyltransferase (GCT) and CTP:2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase synthetase (CMS), members of the cytidylyltransferase family that produce CDP-glycerol and CDP-methylerythritol, respectively.
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Affiliation(s)
- James P Brault
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | - Jon A Friesen
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA.
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18
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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.
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19
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Boeszoermenyi A, Nagy HM, Arthanari H, Pillip CJ, Lindermuth H, Luna RE, Wagner G, Zechner R, Zangger K, Oberer M. Structure of a CGI-58 motif provides the molecular basis of lipid droplet anchoring. J Biol Chem 2015; 290:26361-72. [PMID: 26350461 PMCID: PMC4646293 DOI: 10.1074/jbc.m115.682203] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/29/2022] Open
Abstract
Triacylglycerols (TGs) stored in lipid droplets (LDs) are hydrolyzed in a highly regulated metabolic process called lipolysis to free fatty acids that serve as energy substrates for β-oxidation, precursors for membrane lipids and signaling molecules. Comparative gene identification-58 (CGI-58) stimulates the enzymatic activity of adipose triglyceride lipase (ATGL), which catalyzes the hydrolysis of TGs to diacylglycerols and free fatty acids. In adipose tissue, protein-protein interactions between CGI-58 and the LD coating protein perilipin 1 restrain the ability of CGI-58 to activate ATGL under basal conditions. Phosphorylation of perilipin 1 disrupts these interactions and mobilizes CGI-58 for the activation of ATGL. We have previously demonstrated that the removal of a peptide at the N terminus (residues 10–31) of CGI-58 abrogates CGI-58 localization to LDs and CGI-58-mediated activation of ATGL. Here, we show that this tryptophan-rich N-terminal peptide serves as an independent LD anchor, with its three tryptophans serving as focal points of the left (harboring Trp21 and Trp25) and right (harboring Trp29) anchor arms. The solution state NMR structure of a peptide comprising the LD anchor bound to dodecylphosphocholine micelles as LD mimic reveals that the left arm forms a concise hydrophobic core comprising tryptophans Trp21 and Trp25 and two adjacent leucines. Trp29 serves as the core of a functionally independent anchor arm. Consequently, simultaneous tryptophan alanine permutations in both arms abolish localization and activity of CGI-58 as opposed to tryptophan substitutions that occur in only one arm.
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Affiliation(s)
- Andras Boeszoermenyi
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria, the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Harald Manuel Nagy
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Haribabu Arthanari
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | | | - Hanna Lindermuth
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria, the Institute of Biophysics, Medical University of Graz, 8010 Graz, Austria
| | - Rafael Eulogio Luna
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Gerhard Wagner
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Rudolf Zechner
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Klaus Zangger
- the Institute of Chemistry, University of Graz, 8010 Graz, Austria, and
| | - Monika Oberer
- From the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria,
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20
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Accurate modeling of cation–π interactions in enzymes: a case study on the CDPCho:phosphocholine cytidylyltransferase complex. Struct Chem 2015. [DOI: 10.1007/s11224-015-0658-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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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.
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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
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22
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Marton L, Nagy GN, Ozohanics O, Lábas A, Krámos B, Oláh J, Vékey K, Vértessy BG. Molecular Mechanism for the Thermo-Sensitive Phenotype of CHO-MT58 Cell Line Harbouring a Mutant CTP:Phosphocholine Cytidylyltransferase. PLoS One 2015; 10:e0129632. [PMID: 26083347 PMCID: PMC4470507 DOI: 10.1371/journal.pone.0129632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/10/2015] [Indexed: 01/27/2023] Open
Abstract
Control and elimination of malaria still represents a major public health challenge. Emerging parasite resistance to current therapies urges development of antimalarials with novel mechanism of action. Phospholipid biosynthesis of the Plasmodium parasite has been validated as promising candidate antimalarial target. The most prevalent de novo pathway for synthesis of phosphatidylcholine is the Kennedy pathway. Its regulatory and often also rate limiting step is catalyzed by CTP:phosphocholine cytidylyltransferase (CCT). The CHO-MT58 cell line expresses a mutant variant of CCT, and displays a thermo-sensitive phenotype. At non-permissive temperature (40°C), the endogenous CCT activity decreases dramatically, blocking membrane synthesis and ultimately leading to apoptosis. In the present study we investigated the impact of the analogous mutation in a catalytic domain construct of Plasmodium falciparum CCT in order to explore the underlying molecular mechanism that explains this phenotype. We used temperature dependent enzyme activity measurements and modeling to investigate the functionality of the mutant enzyme. Furthermore, MS measurements were performed to determine the oligomerization state of the protein, and MD simulations to assess the inter-subunit interactions in the dimer. Our results demonstrate that the R681H mutation does not directly influence enzyme catalytic activity. Instead, it provokes increased heat-sensitivity by destabilizing the CCT dimer. This can possibly explain the significance of the PfCCT pseudoheterodimer organization in ensuring proper enzymatic function. This also provide an explanation for the observed thermo-sensitive phenotype of CHO-MT58 cell line.
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Affiliation(s)
- Lívia Marton
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Gergely N. Nagy
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - Olivér Ozohanics
- Institute of Organic Chemistry, Research Centre for National Sciences, HAS, Budapest, Hungary
| | - Anikó Lábas
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Balázs Krámos
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Károly Vékey
- Institute of Organic Chemistry, Research Centre for National Sciences, HAS, Budapest, Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
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23
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Kofuji S, Kimura H, Nakanishi H, Nanjo H, Takasuga S, Liu H, Eguchi S, Nakamura R, Itoh R, Ueno N, Asanuma K, Huang M, Koizumi A, Habuchi T, Yamazaki M, Suzuki A, Sasaki J, Sasaki T. INPP4B Is a PtdIns(3,4,5)P3 Phosphatase That Can Act as a Tumor Suppressor. Cancer Discov 2015; 5:730-9. [PMID: 25883023 DOI: 10.1158/2159-8290.cd-14-1329] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/01/2015] [Indexed: 12/23/2022]
Abstract
UNLABELLED Inositol polyphosphate 4-phosphatase B (INPP4B) has been identified as a tumor suppressor mutated in human breast, ovary, and prostate cancers. The molecular mechanism underlying INPP4B's tumor-suppressive role is currently unknown. Here, we demonstrate that INPP4B restrains tumor development by dephosphorylating the PtdIns(3,4,5)P3 that accumulates in situations of PTEN deficiency. In vitro, INPP4B directly dephosphorylates PtdIns(3,4,5)P3. In vivo, neither inactivation of Inpp4b (Inpp4b(Δ/Δ)) nor heterozygous deletion of Pten (Pten(+/-)) in mice causes thyroid abnormalities, but a combination of these mutations induces malignant thyroid cancers with lung metastases. At the molecular level, simultaneous deletion of Inpp4b and Pten synergistically increases PtdIns(3,4,5)P3 levels and activates AKT downstream signaling proteins in thyroid cells. We propose that the PtdIns(3,4,5)P3 phosphatase activity of INPP4B can function as a "back-up" mechanism when PTEN is deficient, making INPP4B a potential novel therapeutic target for PTEN-deficient or PIK3CA-activated cancers. SIGNIFICANCE Although INPP4B expression is reduced in several types of human cancers, our work on Inpp4B-deficient mice provides the first evidence that INPP4B is a bona fide tumor suppressor whose function is particularly important in situations of PTEN deficiency. Our biochemical data demonstrate that INPP4B directly dephosphorylates PtdIns(3,4,5)P3.
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Affiliation(s)
- Satoshi Kofuji
- Research Center for Biosignal, Akita University, Akita, Japan. Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hirotaka Kimura
- Research Center for Biosignal, Akita University, Akita, Japan. Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | | | - Hiroshi Nanjo
- Department of Pathology, Akita University Graduate School of Medicine, Akita, Japan
| | - Shunsuke Takasuga
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hui Liu
- Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Satoshi Eguchi
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Ryotaro Nakamura
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Reietsu Itoh
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Noriko Ueno
- Research Center for Biosignal, Akita University, Akita, Japan
| | - Ken Asanuma
- Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan
| | - Mingguo Huang
- Research Center for Biosignal, Akita University, Akita, Japan. Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Atsushi Koizumi
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Tomonori Habuchi
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Masakazu Yamazaki
- Research Center for Biosignal, Akita University, Akita, Japan. Department of Cell Biology and Morphology, Akita University Graduate School of Medicine, Akita, Japan
| | - Akira Suzuki
- Division of Embryonic and Genetic Engineering, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Junko Sasaki
- Research Center for Biosignal, Akita University, Akita, Japan
| | - Takehiko Sasaki
- Research Center for Biosignal, Akita University, Akita, Japan. Department of Medical Biology, Akita University Graduate School of Medicine, Akita, Japan.
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24
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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.
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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.
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25
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Nagy GN, Marton L, Contet A, Ozohanics O, Ardelean LM, Révész Á, Vékey K, Irimie FD, Vial H, Cerdan R, Vértessy BG. Composite Aromatic Boxes for Enzymatic Transformations of Quaternary Ammonium Substrates. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Nagy GN, Marton L, Contet A, Ozohanics O, Ardelean LM, Révész A, Vékey K, Irimie FD, Vial H, Cerdan R, Vértessy BG. Composite aromatic boxes for enzymatic transformations of quaternary ammonium substrates. Angew Chem Int Ed Engl 2014; 53:13471-6. [PMID: 25283789 DOI: 10.1002/anie.201408246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 11/07/2022]
Abstract
Cation-π interactions to cognate ligands in enzymes have key roles in ligand binding and enzymatic catalysis. We have deciphered the key functional role of both charged and aromatic residues within the choline binding subsite of CTP:phosphocholine cytidylyltransferase and choline kinase from Plasmodium falciparum. Comparison of quaternary ammonium binding site structures revealed a general composite aromatic box pattern of enzyme recognition sites, well distinguished from the aromatic box recognition site of receptors.
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Affiliation(s)
- Gergely N Nagy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, 1111 Budapest (Hungary); Institute of Enzymology, Research Centre of National Sciences, HAS, 1117 Budapest (Hungary).
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27
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Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets. PLoS Comput Biol 2014; 10:e1003733. [PMID: 25033262 PMCID: PMC4102429 DOI: 10.1371/journal.pcbi.1003733] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 06/04/2014] [Indexed: 01/25/2023] Open
Abstract
Over the past several years fungal infections have shown an increasing incidence in the susceptible population, and caused high mortality rates. In parallel, multi-resistant fungi are emerging in human infections. Therefore, the identification of new potential antifungal targets is a priority. The first task of this study was to analyse the protein domain and domain architecture content of the 137 fungal proteomes (corresponding to 111 species) available in UniProtKB (UniProt KnowledgeBase) by January 2013. The resulting list of core and exclusive domain and domain architectures is provided in this paper. It delineates the different levels of fungal taxonomic classification: phylum, subphylum, order, genus and species. The analysis highlighted Aspergillus as the most diverse genus in terms of exclusive domain content. In addition, we also investigated which domains could be considered promiscuous in the different organisms. As an application of this analysis, we explored three different ways to detect potential targets for antifungal drugs. First, we compared the domain and domain architecture content of the human and fungal proteomes, and identified those domains and domain architectures only present in fungi. Secondly, we looked for information regarding fungal pathways in public repositories, where proteins containing promiscuous domains could be involved. Three pathways were identified as a result: lovastatin biosynthesis, xylan degradation and biosynthesis of siroheme. Finally, we classified a subset of the studied fungi in five groups depending on their occurrence in clinical samples. We then looked for exclusive domains in the groups that were more relevant clinically and determined which of them had the potential to bind small molecules. Overall, this study provides a comprehensive analysis of the available fungal proteomes and shows three approaches that can be used as a first step in the detection of new antifungal targets. Some fungi have become pathogenic to plants and in a lesser extent to animals. Under certain conditions their presence in the human body can prove a threat for human health, especially for immunocompromised patients. Yet, some fungi can also infect healthy individuals. The low sensitivity of the antifungal drugs available together with the clinically observed resistance of some fungi raises the demand for new alternative treatments. Proteins are biological molecules which perform essential functions within the living organisms. Many of those functions are attributed to the varying folded structure of each protein. These configurations are composed of functional units -also called domains- each one independently responsible for a fraction of the overall biological function. Understanding how the different block combinations are distributed across members of the same or similar families of organisms is important. For instance, exclusive domain combinations can hold particular acquired functions. Blocks displaying a high mobility can play major roles for the organism's survival. The biological goal of this study was to analyse the functional implications of protein domains and domain combinations in the available fungal proteomes. This information can be used to highlight proteins and pathways that could be potentially used as drug targets.
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28
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Payne F, Lim K, Girousse A, Brown RJ, Kory N, Robbins A, Xue Y, Sleigh A, Cochran E, Adams C, Dev Borman A, Russel-Jones D, Gorden P, Semple RK, Saudek V, O'Rahilly S, Walther TC, Barroso I, Savage DB. Mutations disrupting the Kennedy phosphatidylcholine pathway in humans with congenital lipodystrophy and fatty liver disease. Proc Natl Acad Sci U S A 2014; 111:8901-6. [PMID: 24889630 PMCID: PMC4066527 DOI: 10.1073/pnas.1408523111] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Phosphatidylcholine (PC) is the major glycerophospholipid in eukaryotic cells and is an essential component in all cellular membranes. The biochemistry of de novo PC synthesis by the Kennedy pathway is well established, but less is known about the physiological functions of PC. We identified two unrelated patients with defects in the Kennedy pathway due to biallellic loss-of-function mutations in phosphate cytidylyltransferase 1 alpha (PCYT1A), the rate-limiting enzyme in this pathway. The mutations lead to a marked reduction in PCYT1A expression and PC synthesis. The phenotypic consequences include some features, such as severe fatty liver and low HDL cholesterol levels, that are predicted by the results of previously reported liver-specific deletion of murine Pcyt1a. Both patients also had lipodystrophy, severe insulin resistance, and diabetes, providing evidence for an additional and essential role for PCYT1A-generated PC in the normal function of white adipose tissue and insulin action.
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Affiliation(s)
- Felicity Payne
- Metabolic Disease Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Koini Lim
- University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom
| | - Amandine Girousse
- University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom
| | - Rebecca J Brown
- Diabetes Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nora Kory
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520
| | - Ann Robbins
- University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom
| | - Yali Xue
- Metabolic Disease Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Alison Sleigh
- Wolfson Brain Imaging Centre, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Elaine Cochran
- Diabetes Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Claire Adams
- University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom
| | - Arundhati Dev Borman
- Moorfields Eye Hospital National Health Service Trust, London EC1V 2PD, United Kingdom; and
| | - David Russel-Jones
- Centre for Endocrinology, Diabetes and Research, Royal Surrey County Hospital, Guildford GU2 7XX, United Kingdom
| | - Phillip Gorden
- Diabetes Endocrinology and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Robert K Semple
- University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom
| | - Vladimir Saudek
- University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom
| | - Stephen O'Rahilly
- University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom;
| | - Tobias C Walther
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06520
| | - Inês Barroso
- Metabolic Disease Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom;University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom;
| | - David B Savage
- University of Cambridge, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Cambridge CB2 0QQ, United Kingdom;
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29
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Pavlovic Z, Singh RK, Bakovic M. A novel murine CTP:phosphoethanolamine cytidylyltransferase splice variant is a post-translational repressor and an indicator that both cytidylyltransferase domains are required for activity. Gene 2014; 543:58-68. [PMID: 24703999 DOI: 10.1016/j.gene.2014.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/20/2014] [Accepted: 04/01/2014] [Indexed: 11/27/2022]
Abstract
CTP:phosphoethanolamine cytidylyltransferase (Pcyt2) has an important regulatory function in biosynthesis of the membrane phospholipid phosphatidylethanolamine. We previously determined that the full-length Pcyt2α and its splice variant Pcyt2β are the main active isoforms of this enzyme. Here we report that mouse Pcyt2 could be spliced at Introns 7 and 8 to produce a unique third isoform, Pcyt2γ, in which the second cytidylyltransferase domain at the C-terminus becomes deleted. Pcyt2γ is ubiquitously expressed in embryonic and adult mouse tissues, and is the most abundant in the kidney, skeletal muscle and testis. Pcyt2γ splicing mechanism dominates over Pcyt2β exon-skipping mechanism in most examined tissues. Although Pcyt2γ maintains the N-terminal cytidylyltransferase domain as most cytidylyltransferases, the lack of the C-terminal cytidylyltransferase domain causes a complete loss of catalytic activity. However, Pcyt2γ interacts with the active isoform, Pcyt2α, and significantly reduces Pcyt2α homodimerization and activity. The inactive N-domain (H35Y, H35A) and C-domain (H244Y, H244A) mutants of Pcyt2α also reduce Pcyt2α homodimerization and activity. This study revealed the importance of both cytidylyltransferase (35)HYGH and (244)HIGH motifs for the activity of murine Pcyt2α and established that the naturally occurring splice variant Pcyt2γ has a function to restrain the enzyme activity through the formation of unproductive enzyme complexes.
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Affiliation(s)
- Zvezdan Pavlovic
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada.
| | - Ratnesh Kumar Singh
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Marica Bakovic
- Department of Human Health and Nutritional Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
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30
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Tian S, Ohtsuka J, Wang S, Nagata K, Tanokura M, Ohta A, Horiuchi H, Fukuda R. Human CTP:phosphoethanolamine cytidylyltransferase: enzymatic properties and unequal catalytic roles of CTP-binding motifs in two cytidylyltransferase domains. Biochem Biophys Res Commun 2014; 449:26-31. [PMID: 24802409 DOI: 10.1016/j.bbrc.2014.04.131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 04/25/2014] [Indexed: 10/25/2022]
Abstract
CTP:phosphoethanolamine cytidylyltransferase (ECT) is a key enzyme in the CDP-ethanolamine branch of the Kennedy pathway, which is the primary pathway of phosphatidylethanolamine (PE) synthesis in mammalian cells. Here, the enzymatic properties of recombinant human ECT (hECT) were characterized. The catalytic reaction of hECT obeyed Michaelis-Menten kinetics with respect to both CTP and phosphoethanolamine. hECT is composed of two tandem cytidylyltransferase (CT) domains as ECTs of other organisms. The histidines, especially the first histidine, in the CTP-binding motif HxGH in the N-terminal CT domain were critical for its catalytic activity in vitro, while those in the C-terminal CT domain were not. Overexpression of the wild-type hECT and hECT mutants containing amino acid substitutions in the HxGH motif in the C-terminal CT domain suppressed the growth defect of the Saccharomyces cerevisiae mutant of ECT1 encoding ECT in the absence of a PE supply via the decarboxylation of phosphatidylserine, but overexpression of hECT mutants of the N-terminal CT domain did not. These results suggest that the N-terminal CT domain of hECT contributes to its catalytic reaction, but C-terminal CT domain does not.
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Affiliation(s)
- Siqi Tian
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jun Ohtsuka
- Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shipeng Wang
- Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akinori Ohta
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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31
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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.
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Affiliation(s)
- Guillaume Drin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and CNRS, 06560 Valbonne, France;
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32
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Pavlovic Z, Zhu L, Pereira L, Singh RK, Cornell RB, Bakovic M. Isoform-specific and protein kinase C-mediated regulation of CTP:phosphoethanolamine cytidylyltransferase phosphorylation. J Biol Chem 2014; 289:9053-64. [PMID: 24519946 DOI: 10.1074/jbc.m113.544932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CTP:phosphoethanolamine cytidylyltransferase (Pcyt2) is the main regulatory enzyme for de novo biosynthesis of phosphatidylethanolamine by the CDP-ethanolamine pathway. There are two isoforms of Pcyt2, -α and -β; however, very little is known about their specific roles in this important metabolic pathway. We previously demonstrated increased phosphatidylethanolamine biosynthesis subsequent to elevated activity and phosphorylation of Pcyt2α and -β in MCF-7 breast cancer cells grown under conditions of serum deficiency. Mass spectroscopy analyses of Pcyt2 provided evidence for isoform-specific as well as shared phosphorylations. Pcyt2β was specifically phosphorylated at the end of the first cytidylyltransferase domain. Pcyt2α was phosphorylated within the α-specific motif that is spliced out in Pcyt2β and on two PKC consensus serine residues, Ser-215 and Ser-223. Single and double mutations of PKC consensus sites reduced Pcyt2α phosphorylation, activity, and phosphatidylethanolamine synthesis by 50-90%. The phosphorylation and activity of endogenous Pcyt2 were dramatically increased with phorbol esters and reduced by specific PKC inhibitors. In vitro translated Pcyt2α was phosphorylated by PKCα, PKCβI, and PKCβII. Pcyt2α Ser-215 was also directly phosphorylated with PKCα. Mapping of the Pcyt2α- and -β-phosphorylated sites to the solved structure of a human Pcyt2β showed that they clustered within and flanking the central linker region that connects the two catalytic domains and is a novel regulatory segment not present in other cytidylyltransferases. This study is the first to demonstrate differences in phosphorylation between Pcyt2 isoforms and to uncover the role of the PKC-regulated phosphorylation.
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Affiliation(s)
- Zvezdan Pavlovic
- From the Department of Human Health and Nutritional Sciences, University of Guelph, Ontario N1G 2W1 and
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33
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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
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34
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Yamamoto G, Baratela W, Almeida T, Lazar M, Afonso C, Oyamada M, Suzuki L, Oliveira L, Ramos E, Kim C, Passos-Bueno M, Bertola D. Mutations in PCYT1A cause spondylometaphyseal dysplasia with cone-rod dystrophy. Am J Hum Genet 2014; 94:113-9. [PMID: 24387991 DOI: 10.1016/j.ajhg.2013.11.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 11/22/2013] [Indexed: 01/31/2023] Open
Abstract
Spondylometaphyseal dysplasia with cone-rod dystrophy is a rare autosomal-recessive disorder characterized by severe short stature, progressive lower-limb bowing, flattened vertebral bodies, metaphyseal involvement, and visual impairment caused by cone-rod dystrophy. Whole-exome sequencing of four individuals affected by this disorder from two Brazilian families identified two previously unreported homozygous mutations in PCYT1A. This gene encodes the alpha isoform of the phosphate cytidylyltransferase 1 choline enzyme, which is responsible for converting phosphocholine into cytidine diphosphate-choline, a key intermediate step in the phosphatidylcholine biosynthesis pathway. A different enzymatic defect in this pathway has been previously associated with a muscular dystrophy with mitochondrial structural abnormalities that does not have cartilage and/or bone or retinal involvement. Thus, the deregulation of the phosphatidylcholine pathway may play a role in multiple genetic diseases in humans, and further studies are necessary to uncover its precise pathogenic mechanisms and the entirety of its phenotypic spectrum.
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35
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Hoover-Fong J, Sobreira N, Jurgens J, Modaff P, Blout C, Moser A, Kim OH, Cho TJ, Cho SY, Kim SJ, Jin DK, Kitoh H, Park WY, Ling H, Hetrick KN, Doheny KF, Valle D, Pauli RM. Mutations in PCYT1A, encoding a key regulator of phosphatidylcholine metabolism, cause spondylometaphyseal dysplasia with cone-rod dystrophy. Am J Hum Genet 2014; 94:105-12. [PMID: 24387990 DOI: 10.1016/j.ajhg.2013.11.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 11/22/2013] [Indexed: 12/30/2022] Open
Affiliation(s)
- Julie Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Greenberg Center for Skeletal Dysplasias, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Julie Jurgens
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Peggy Modaff
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Carrie Blout
- McKusick-Nathans Institute of Genetic Medicine, Greenberg Center for Skeletal Dysplasias, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ann Moser
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ok-Hwa Kim
- Department of Radiology, Ajou University Hospital, Suwon, Kyunggi 443-721, Korea
| | - Tae-Joon Cho
- Division of Pediatric Orthopaedics, Seoul National University Children's Hospital, Seoul 110-744, Korea
| | - Sung Yoon Cho
- Department of Pediatrics, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-Do 471-701, Korea
| | - Sang Jin Kim
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Korea
| | - Dong-Kyu Jin
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Korea
| | - Hiroshi Kitoh
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 135-710, Korea; Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Hua Ling
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Kurt N Hetrick
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - David Valle
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Richard M Pauli
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
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36
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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.
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Affiliation(s)
- Jaeyong Lee
- From the Departments of Molecular Biology and Biochemistry and
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37
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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.
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Affiliation(s)
- Gergely N Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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38
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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.
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Affiliation(s)
- Thomas A Lagace
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada.
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39
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Campanacci V, Mukherjee S, Roy CR, Cherfils J. Structure of the Legionella effector AnkX reveals the mechanism of phosphocholine transfer by the FIC domain. EMBO J 2013; 32:1469-77. [PMID: 23572077 DOI: 10.1038/emboj.2013.82] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 03/12/2013] [Indexed: 11/09/2022] Open
Abstract
The FIC motif and the eukaryotic-like ankyrin repeats are found in many bacterial type IV effectors, yet little is known about how these domains enable bacteria to modulate host cell functions. Bacterial FIC domains typically bind ATP and transfer adenosine monophosphate moiety onto target proteins. The ankyrin repeat-containing protein AnkX encoded by the intracellular pathogen Legionella pneumophila is unique in that its FIC domain binds to CDP-choline and transfers a phosphocholine residue onto proteins in the Rab1 GTPase family. By determining the structures of unbound AnkX and AnkX with bound CDP-choline, CMP/phosphocholine and CMP, we demonstrate that the orientation of substrate binding in relation to the catalytic FIC motif enables this protein to function as a phosphocholinating enzyme rather than a nucleotidyl transferase. Additionally, the structure reveals that the ankyrin repeats mediate scaffolding interactions that resemble those found in protein-protein interactions, but are unprecedented in intramolecular interactions. Together with phosphocholination experiments, our structures unify a general phosphoryl transferase mechanism common to all FIC enzymes that should be conserved from bacteria to human.
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Affiliation(s)
- Valérie Campanacci
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, Gif-sur-Yvette, France
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40
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Fujisawa I, Kitamura Y, Okamoto R, Murayama K, Kato R, Aoki K. Crystal structure of pyrogallol[4]arene complex with phosphocholine: A molecular recognition model for phosphocholine through cation–π interaction. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.01.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Biochemical characterization of Plasmodium falciparum CTP:phosphoethanolamine cytidylyltransferase shows that only one of the two cytidylyltransferase domains is active. Biochem J 2013. [DOI: 10.1042/bj20121480] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The intra-erythrocytic proliferation of the human malaria parasite Plasmodium falciparum requires massive synthesis of PE (phosphatidylethanolamine) that together with phosphatidylcholine constitute the bulk of the malaria membrane lipids. PE is mainly synthesized de novo by the CDP:ethanolamine-dependent Kennedy pathway. We previously showed that inhibition of PE biosynthesis led to parasite death. In the present study we characterized PfECT [P. falciparum CTP:phosphoethanolamine CT (cytidylyltransferase)], which we identified as the rate-limiting step of the PE metabolic pathway in the parasite. The cellular localization and expression of PfECT along the parasite life cycle were studied using polyclonal antibodies. Biochemical analyses showed that the enzyme activity follows Michaelis–Menten kinetics. PfECT is composed of two CT domains separated by a linker region. Activity assays on recombinant enzymes upon site-directed mutagenesis revealed that the N-terminal CT domain was the only catalytically active domain of PfECT. Concordantly, three-dimensional homology modelling of PfECT showed critical amino acid differences between the substrate-binding sites of the two CT domains. PfECT was predicted to fold as an intramolecular dimer suggesting that the inactive C-terminal domain is important for dimer stabilization. Given the absence of PE synthesis in red blood cells, PfECT represents a potential antimalarial target opening the way for a rational conception of bioactive compounds.
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Huang HKH, Taneva SG, Lee J, Silva LP, Schriemer DC, Cornell RB. The membrane-binding domain of an amphitropic enzyme suppresses catalysis by contact with an amphipathic helix flanking its active site. J Mol Biol 2012; 425:1546-64. [PMID: 23238251 DOI: 10.1016/j.jmb.2012.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 11/24/2012] [Accepted: 12/03/2012] [Indexed: 11/29/2022]
Abstract
CTP:phosphocholine cytidylyltransferase (CCT), the regulatory enzyme in the synthesis of phosphatidylcholine, is activated by binding membranes using a lipid-induced amphipathic helix (domain M). Domain M functions to silence catalysis when CCT is not membrane engaged. The silencing mechanism is unknown. We used photo-cross-linking and mass spectrometry to identify contacts between domain M and other CCT domains in its soluble form. Each of four sites in domain M forged cross-links to the same set of peptides that flank the active site and overlap at helix αE at the base of the active site. These cross-links were broken in the presence of activating lipid vesicles. Mutagenesis of domain M revealed that multiple hydrophobic residues within a putative auto-inhibitory (AI) motif contribute to the contact with helix αE and silencing. Helix αE was confirmed as the docking site for domain M by deuterium exchange analysis. We compared the dynamics and fold stability of CCT domains by site-directed fluorescence anisotropy and urea denaturation. The results suggest a bipartite structure for domain M: a disordered N-terminal portion and an ordered C-terminal AI motif with an unfolding transition identical with that of helix αE. Reduction in hydrophobicity of the AI motif decreased its order and fold stability, as did deletion of the catalytic domain. These results support a model in which catalytic silencing is mediated by the docking of an amphipathic AI motif onto the amphipathic helices αE. An unstructured leash linking αE with the AI motif may facilitate both the silencing contact and its membrane-triggered disruption.
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Affiliation(s)
- Harris K-H Huang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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43
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Phosphatidylcholine and the CDP-choline cycle. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:523-32. [PMID: 23010477 DOI: 10.1016/j.bbalip.2012.09.009] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 09/16/2012] [Indexed: 11/20/2022]
Abstract
The CDP-choline pathway of phosphatidylcholine (PtdCho) biosynthesis was first described more than 50 years ago. Investigation of the CDP-choline pathway in yeast provides a basis for understanding the CDP-choline pathway in mammals. PtdCho is considered as an intermediate in a cycle of synthesis and degradation, and the activity of a CDP-choline cycle is linked to subcellular membrane lipid movement. The components of the mammalian CDP-choline pathway include choline transport, choline kinase, phosphocholine cytidylyltransferase, and choline phosphotransferase activities. The protein isoforms and biochemical mechanisms of regulation of the pathway enzymes are related to their cell- and tissue-specific functions. Regulated PtdCho turnover mediated by phospholipases or neuropathy target esterase participates in the mammalian CDP-choline cycle. Knockout mouse models define the biological functions of the CDP-choline cycle in mammalian cells and tissues. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.
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Ding Z, Taneva SG, Huang HKH, Campbell SA, Semenec L, Chen N, Cornell RB. A 22-mer segment in the structurally pliable regulatory domain of metazoan CTP: phosphocholine cytidylyltransferase facilitates both silencing and activating functions. J Biol Chem 2012; 287:38980-91. [PMID: 22988242 DOI: 10.1074/jbc.m112.402081] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
CTP:phosphocholine cytidylyltransferase (CCT), an amphitropic enzyme that regulates phosphatidylcholine synthesis, is composed of a catalytic head domain and a regulatory tail. The tail region has dual functions as a regulator of membrane binding/enzyme activation and as an inhibitor of catalysis in the unbound form of the enzyme, suggesting conformational plasticity. These functions are well conserved in CCTs across diverse phyla, although the sequences of the tail regions are not. CCT regulatory tails of diverse origins are composed of a long membrane lipid-inducible amphipathic helix (m-AH) followed by a highly disordered segment, reminiscent of the Parkinson disease-linked protein, α-synuclein, which we show shares a novel sequence motif with vertebrate CCTs. To unravel features required for silencing, we created chimeric enzymes by fusing the catalytic domain of rat CCTα to the regulatory tail of CCTs from Drosophila, Caenorhabditis elegans, or Saccharomyces cerevisiae or to α-synuclein. Only the tail domains of the two invertebrate CCTs were competent for both suppression of catalytic activity and for activation by lipid vesicles. Thus, both silencing and activating functions of the m-AH can tolerate significant changes in length and sequence. We identified a highly amphipathic 22-residue segment in the m-AH with features conserved among animal CCTs but not yeast CCT or α-synuclein. Deletion of this segment from rat CCT increased the lipid-independent V(max) by 10-fold, equivalent to the effect of deleting the entire tail, and severely weakened membrane binding affinity. However, membrane binding was required for additional increases in catalytic efficiency. Thus, full activation of CCT may require not only loss of a silencing conformation in the m-AH but a gain of an activating conformation, promoted by membrane binding.
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Affiliation(s)
- Ziwei Ding
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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The amphipathic helix of an enzyme that regulates phosphatidylcholine synthesis remodels membranes into highly curved nanotubules. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1173-86. [DOI: 10.1016/j.bbamem.2012.01.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/09/2012] [Accepted: 01/10/2012] [Indexed: 11/20/2022]
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Dennis MK, Taneva SG, Cornell RB. The intrinsically disordered nuclear localization signal and phosphorylation segments distinguish the membrane affinity of two cytidylyltransferase isoforms. J Biol Chem 2011; 286:12349-60. [PMID: 21303909 DOI: 10.1074/jbc.m110.201715] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Membrane phosphatidylcholine homeostasis is maintained in part by a sensing device in the key regulatory enzyme, CTP:phosphocholine cytidylyltransferase (CCT). CCT responds to decreases in membrane phosphatidylcholine content by reversible membrane binding and activation. Two prominent isoforms, CCTα and -β2, have nearly identical catalytic domains and very similar membrane binding amphipathic helical (M) domains but have divergent and structurally disordered N-terminal (N) and C-terminal phosphorylation (P) regions. We found that the binding affinity of purified CCTβ2 for anionic membranes was weaker than CCTα by more than an order of magnitude. Using chimeric CCTs, insertion/deletion mutants, and truncated CCTs, we show that the stronger affinity of CCTα can be attributed in large part to the electrostatic membrane binding function of the polybasic nuclear localization signal (NLS) motif, present in the unstructured N-terminal segment of CCTα but lacking in CCTβ2. The membrane partitioning of CCTβ2 in cells enriched with the lipid activator, oleic acid, was also weaker than that of CCTα and was elevated by incorporation of the NLS motif. Thus, the polybasic NLS can function as a secondary membrane binding motif not only in vitro but in the context of cell membranes. A comparison of phosphorylated, dephosphorylated, and region P-truncated forms showed that the in vitro membrane affinity of CCTβ2 is more sensitive than CCTα to phosphorylation status, which antagonizes membrane binding of both isoforms. These data provide a model wherein the primary membrane binding motif, an amphipathic helical domain, works in collaboration with other intrinsically disordered segments that modulate membrane binding strength. The NLS reinforces, whereas the phosphorylated tail antagonizes the attraction of domain M for anionic membranes.
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Affiliation(s)
- Melissa K Dennis
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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Gersting SW, Staudigl M, Truger MS, Messing DD, Danecka MK, Sommerhoff CP, Kemter KF, Muntau AC. Activation of phenylalanine hydroxylase induces positive cooperativity toward the natural cofactor. J Biol Chem 2010; 285:30686-97. [PMID: 20667834 PMCID: PMC2945563 DOI: 10.1074/jbc.m110.124016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/29/2010] [Indexed: 11/06/2022] Open
Abstract
Protein misfolding with loss-of-function of the enzyme phenylalanine hydroxylase (PAH) is the molecular basis of phenylketonuria in many individuals carrying missense mutations in the PAH gene. PAH is complexly regulated by its substrate L-Phenylalanine and its natural cofactor 6R-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)). Sapropterin dihydrochloride, the synthetic form of BH(4), was recently approved as the first pharmacological chaperone to correct the loss-of-function phenotype. However, current knowledge about enzyme function and regulation in the therapeutic setting is scarce. This illustrates the need for comprehensive analyses of steady state kinetics and allostery beyond single residual enzyme activity determinations to retrace the structural impact of missense mutations on the phenylalanine hydroxylating system. Current standard PAH activity assays are either indirect (NADH) or discontinuous due to substrate and product separation before detection. We developed an automated fluorescence-based continuous real-time PAH activity assay that proved to be faster and more efficient but as precise and accurate as standard methods. Wild-type PAH kinetic analyses using the new assay revealed cooperativity of activated PAH toward BH(4), a previously unknown finding. Analyses of structurally preactivated variants substantiated BH(4)-dependent cooperativity of the activated enzyme that does not rely on the presence of l-Phenylalanine but is determined by activating conformational rearrangements. These findings may have implications for an individualized therapy, as they support the hypothesis that the patient's metabolic state has a more significant effect on the interplay of the drug and the conformation and function of the target protein than currently appreciated.
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Affiliation(s)
- Søren W. Gersting
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Michael Staudigl
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Marietta S. Truger
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Dunja D. Messing
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Marta K. Danecka
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Christian P. Sommerhoff
- the Department of Clinical Chemistry and Clinical Biochemistry, Surgical Clinic, Ludwig-Maximilians-University, Munich 80336, Germany
| | - Kristina F. Kemter
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
| | - Ania C. Muntau
- From the Department of Molecular Pediatrics, Dr. von Hauner Children's Hospital, Munich 80337 and
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