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Niu Y, Pemberton JG, Kim YJ, Balla T. Phosphatidylserine enrichment in the nuclear membrane regulates key enzymes of phosphatidylcholine synthesis. EMBO J 2024; 43:3414-3449. [PMID: 38918635 PMCID: PMC11329639 DOI: 10.1038/s44318-024-00151-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/07/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Phosphatidylserine (PS) is an important anionic phospholipid that is synthesized within the endoplasmic reticulum (ER). While PS shows the highest enrichment and serves important functional roles in the plasma membrane (PM) but its role in the nucleus is poorly explored. Using three orthogonal approaches, we found that PS is also uniquely enriched in the inner nuclear membrane (INM) and the nuclear reticulum (NR). Nuclear PS is critical for supporting the translocation of CCTα and Lipin1α, two key enzymes important for phosphatidylcholine (PC) biosynthesis, from the nuclear matrix to the INM and NR in response to oleic acid treatment. We identified the PS-interacting regions within the M-domain of CCTα and M-Lip domain of Lipin1α, and show that lipid droplet formation is altered by manipulations of nuclear PS availability. Our studies reveal an unrecognized regulatory role of nuclear PS levels in the regulation of key PC synthesizing enzymes within the nucleus.
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Affiliation(s)
- Yang Niu
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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Yu J, Boehr DD. Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces. Front Mol Biosci 2023; 10:1306483. [PMID: 38099197 PMCID: PMC10720463 DOI: 10.3389/fmolb.2023.1306483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Recruitment of enzymes to intracellular membranes often modulates their catalytic activity, which can be important in cell signaling and membrane trafficking. Thus, re-localization is not only important for these enzymes to gain access to their substrates, but membrane interactions often allosterically regulate enzyme function by inducing conformational changes across different time and amplitude scales. Recent structural, biophysical and computational studies have revealed how key enzymes interact with lipid membrane surfaces, and how this membrane binding regulates protein structure and function. This review summarizes the recent progress in understanding regulatory mechanisms involved in enzyme-membrane interactions.
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Affiliation(s)
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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Tumor protein D54 binds intracellular nanovesicles via an extended amphipathic region. J Biol Chem 2022; 298:102136. [PMID: 35714773 PMCID: PMC9270247 DOI: 10.1016/j.jbc.2022.102136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Tumor Protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54 and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical (e.g. COPI and COPII) transport vesicles. Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by four amphipathic helices (AH1-4), which could fold upon binding to lipid membranes. Limited proteolysis, circular dichroism (CD) spectroscopy, tryptophan fluorescence, and cysteine mutagenesis coupled to covalent binding of a membrane sensitive probe showed that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. Furthermore, site-directed mutagenesis indicated that AH2 and AH3 have a predominant role in TPD54 binding to membranes both in cells and using model liposomes. We found that AH3 has the physicochemical features of an Amphipathic Lipid Packing Sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Accordingly, we observed that binding of TPD54 to liposomes is very sensitive to membrane curvature and lipid unsaturation. We conclude that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and -independent mechanisms.
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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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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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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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