1
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Pocognoni CA, Nawara T, Bhatt JM, Lee E, Jian X, Randazzo P, Sztul E. The lipid flippase ATP8A1 regulates the recruitment of ARF effectors to the trans-Golgi Network. Arch Biochem Biophys 2024; 758:110049. [PMID: 38879142 DOI: 10.1016/j.abb.2024.110049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/18/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
Formation of transport vesicles requires the coordinate activity of the coating machinery that selects cargo into the nascent vesicle and the membrane bending machinery that imparts curvature to the forming bud. Vesicle coating at the trans-Golgi Network (TGN) involves AP1, GGA2 and clathrin, which are recruited to membranes by activated ARF GTPases. The ARF activation at the TGN is mediated by the BIG1 and BIG2 guanine nucleotide exchange factors (GEFs). Membrane deformation at the TGN has been shown to be mediated by lipid flippases, including ATP8A1, that moves phospholipids from the inner to the outer leaflet of the TGN membrane. We probed a possible coupling between the coating and deformation machineries by testing for an interaction between BIG1, BIG2 and ATP8A1, and by assessing whether such an interaction may influence coating efficiency. Herein, we document that BIG1 and BIG2 co-localize with ATP8A1 in both, static and highly mobile TGN elements, and that BIG1 and BIG2 bind ATP8A1. We show that the interaction involves the catalytic Sec7 domain of the GEFs and the cytosolic C-terminal tail of ATP8A1. Moreover, we report that the expression of ATP8A1, but not ATP8A1 lacking the GEF-binding cytosolic tail, increases the generation of activated ARFs at the TGN and increases the selective recruitment of AP1, GGA2 and clathrin to TGN membranes. This occurs without increasing BIG1 or BIG2 levels at the TGN, suggesting that the binding of the ATP8A1 flippase tail to the Sec7 domain of BIG1/BIG2 increases their catalytic activity. Our results support a model in which a flippase component of the deformation machinery impacts the activity of the GEF component of the coating machinery.
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Affiliation(s)
- Cristian A Pocognoni
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mendoza 5500, Argentina.
| | - Tomasz Nawara
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, MCLM 731, Birmingham, AL, 35233-2008, USA
| | - Jay M Bhatt
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, MCLM 731, Birmingham, AL, 35233-2008, USA
| | - Eunjoo Lee
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, MCLM 731, Birmingham, AL, 35233-2008, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, MCLM 731, Birmingham, AL, 35233-2008, USA
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2
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Hou Y, Chen S, Peng L, Huang L, Zhang H, Zhang P, Yu M, Xiong L, Zhong X, Liu W, Zhu X, Wang L, Li Y, Li G. Tmem30a protects against podocyte injury through suppression of pyroptosis. iScience 2024; 27:109976. [PMID: 38868200 PMCID: PMC11166697 DOI: 10.1016/j.isci.2024.109976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/06/2024] [Accepted: 05/10/2024] [Indexed: 06/14/2024] Open
Abstract
Podocytopathies, such as focal segmental glomerulosclerosis (FSGS), are characterized by podocyte injury and can easily progress to end-stage kidney disease. However, the mechanisms underlying podocyte injury remain unclear. We observed podocyte injury along with pyroptosis in patients with FSGS. Bioinformatic analysis of public datasets revealed that transmembrane protein 30a (Tmem30a) might be associated with FSGS. The expression of Temem30a and the podocyte-related protein, nephrin, were significantly downregulated in patients with FSGS, adriamycin (ADR)-induced mice, and podocyte-specific Tmem30a lox P /loxP ; NPHS2-Cre mice, whereas the expression of NLR family pyrin domain containing 3 (NLRP3) and ASC, two pyroptosis-related proteins, were significantly upregulated. Meanwhile, the pyroptosis inhibitor MCC950 and disulfiram (DSF) increased Tmem30a and podocyte-related proteins expression, and inhibited pyroptosis-related proteins expression in ADR-induced mouse podocytes and Tmem30a knockdown (KD) mouse podocytes. Therefore, Tmem30a might protect against podocyte injury by inhibiting pyroptosis, suggesting a potential therapeutic target for podocytopathies.
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Affiliation(s)
- Yanpei Hou
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Sipei Chen
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Lei Peng
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Liming Huang
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Huijian Zhang
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Ping Zhang
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Min Yu
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Lin Xiong
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Xiang Zhong
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Wenjing Liu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Xianjun Zhu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Li Wang
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Yi Li
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
| | - Guisen Li
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 610072, China
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3
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Matsell E, Andersen JP, Molday RS. Functional and in silico analysis of ATP8A2 and other P4-ATPase variants associated with human genetic diseases. Dis Model Mech 2024; 17:dmm050546. [PMID: 38436085 PMCID: PMC11073571 DOI: 10.1242/dmm.050546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
P4-ATPases flip lipids from the exoplasmic to cytoplasmic leaflet of cell membranes, a property crucial for many biological processes. Mutations in P4-ATPases are associated with severe inherited and complex human disorders. We determined the expression, localization and ATPase activity of four variants of ATP8A2, the P4-ATPase associated with the neurodevelopmental disorder known as cerebellar ataxia, impaired intellectual development and disequilibrium syndrome 4 (CAMRQ4). Two variants, G447R and A772P, harboring mutations in catalytic domains, expressed at low levels and mislocalized in cells. In contrast, the E459Q variant in a flexible loop displayed wild-type expression levels, Golgi-endosome localization and ATPase activity. The R1147W variant expressed at 50% of wild-type levels but showed normal localization and activity. These results indicate that the G447R and A772P mutations cause CAMRQ4 through protein misfolding. The E459Q mutation is unlikely to be causative, whereas the R1147W may display a milder disease phenotype. Using various programs that predict protein stability, we show that there is a good correlation between the experimental expression of the variants and in silico stability assessments, suggesting that such analysis is useful in identifying protein misfolding disease-associated variants.
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Affiliation(s)
- Eli Matsell
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Robert S. Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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4
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Duan HD, Li H. Consensus, controversies, and conundrums of P4-ATPases: The emerging face of eukaryotic lipid flippases. J Biol Chem 2024; 300:107387. [PMID: 38763336 PMCID: PMC11225554 DOI: 10.1016/j.jbc.2024.107387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/21/2024] Open
Abstract
The cryo-EM resolution revolution has heralded a new era in our understanding of eukaryotic lipid flippases with a rapidly growing number of high-resolution structures. Flippases belong to the P4 family of ATPases (type IV P-type ATPases) that largely follow the reaction cycle proposed for the more extensively studied cation-transporting P-type ATPases. However, unlike the canonical P-type ATPases, no flippase cargos are transported in the phosphorylation half-reaction. Instead of being released into the intracellular or extracellular milieu, lipid cargos are transported to their destination at the inner leaflet of the membrane. Recent flippase structures have revealed multiple conformational states during the lipid transport cycle. Nonetheless, critical conformational states capturing the lipid cargo "in transit" are still missing. In this review, we highlight the amazing structural advances of these lipid transporters, discuss various perspectives on catalytic and regulatory mechanisms in the literature, and shed light on future directions in further deciphering the detailed molecular mechanisms of lipid flipping.
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Affiliation(s)
- H Diessel Duan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
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5
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Norris AC, Mansueto AJ, Jimenez M, Yazlovitskaya EM, Jain BK, Graham TR. Flipping the script: Advances in understanding how and why P4-ATPases flip lipid across membranes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119700. [PMID: 38382846 DOI: 10.1016/j.bbamcr.2024.119700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Type IV P-type ATPases (P4-ATPases) are a family of transmembrane enzymes that translocate lipid substrates from the outer to the inner leaflet of biological membranes and thus create an asymmetrical distribution of lipids within membranes. On the cellular level, this asymmetry is essential for maintaining the integrity and functionality of biological membranes, creating platforms for signaling events and facilitating vesicular trafficking. On the organismal level, this asymmetry has been shown to be important in maintaining blood homeostasis, liver metabolism, neural development, and the immune response. Indeed, dysregulation of P4-ATPases has been linked to several diseases; including anemia, cholestasis, neurological disease, and several cancers. This review will discuss the evolutionary transition of P4-ATPases from cation pumps to lipid flippases, the new lipid substrates that have been discovered, the significant advances that have been achieved in recent years regarding the structural mechanisms underlying the recognition and flipping of specific lipids across biological membranes, and the consequences of P4-ATPase dysfunction on cellular and physiological functions. Additionally, we emphasize the requirement for additional research to comprehensively understand the involvement of flippases in cellular physiology and disease and to explore their potential as targets for therapeutics in treating a variety of illnesses. The discussion in this review will primarily focus on the budding yeast, C. elegans, and mammalian P4-ATPases.
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Affiliation(s)
- Adriana C Norris
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Mariana Jimenez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Bhawik K Jain
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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6
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Yang S, Song C. Switching Go̅ -Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions. J Chem Theory Comput 2024; 20:2618-2629. [PMID: 38447049 DOI: 10.1021/acs.jctc.3c01222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Proteins are dynamic biomolecules that can transform between different conformational states when exerting physiological functions, which is difficult to simulate using all-atom methods. Coarse-grained (CG) Go̅-like models are widely used to investigate large-scale conformational transitions, which usually adopt implicit solvent models and therefore cannot explicitly capture the interaction between proteins and surrounding molecules, such as water and lipid molecules. Here, we present a new method, named Switching Go̅-Martini, to simulate large-scale protein conformational transitions between different states, based on the switching Go̅ method and the CG Martini 3 force field. The method is straightforward and efficient, as demonstrated by the benchmarking applications for multiple protein systems, including glutamine binding protein (GlnBP), adenylate kinase (AdK), and β2-adrenergic receptor (β2AR). Moreover, by employing the Switching Go̅-Martini method, we can not only unveil the conformational transition from the E2Pi-PL state to E1 state of the type 4 P-type ATPase (P4-ATPase) flippase ATP8A1-CDC50 but also provide insights into the intricate details of lipid transport.
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Affiliation(s)
- Song Yang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chen Song
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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7
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Dobson L, Gerdán C, Tusnády S, Szekeres L, Kuffa K, Langó T, Zeke A, Tusnády GE. UniTmp: unified resources for transmembrane proteins. Nucleic Acids Res 2024; 52:D572-D578. [PMID: 37870462 PMCID: PMC10767979 DOI: 10.1093/nar/gkad897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
The UNIfied database of TransMembrane Proteins (UniTmp) is a comprehensive and freely accessible resource of transmembrane protein structural information at different levels, from localization of protein segments, through the topology of the protein to the membrane-embedded 3D structure. We not only annotated tens of thousands of new structures and experiments, but we also developed a new system that can serve these resources in parallel. UniTmp is a unified platform that merges TOPDB (Topology Data Bank of Transmembrane Proteins), TOPDOM (database of conservatively located domains and motifs in proteins), PDBTM (Protein Data Bank of Transmembrane Proteins) and HTP (Human Transmembrane Proteome) databases and provides interoperability between the incorporated resources and an easy way to keep them regularly updated. The current update contains 9235 membrane-embedded structures, 9088 sequences with 536 035 topology-annotated segments and 8692 conservatively localized protein domains or motifs as well as 5466 annotated human transmembrane proteins. The UniTmp database can be accessed at https://www.unitmp.org.
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Affiliation(s)
- László Dobson
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Magyar Tudósok körútja 2, H-1117, Hungary
- Department of Bioinformatics, Semmelweis University, Budapest, Tűzoltó u. 7, H-1094, Hungary
| | - Csongor Gerdán
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Magyar Tudósok körútja 2, H-1117, Hungary
| | - Simon Tusnády
- Department of Bioinformatics, Semmelweis University, Budapest, Tűzoltó u. 7, H-1094, Hungary
| | - Levente Szekeres
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Magyar Tudósok körútja 2, H-1117, Hungary
| | - Katalin Kuffa
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Magyar Tudósok körútja 2, H-1117, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Pázmány P. stny. 1/C, H-1117, Hungary
| | - Tamás Langó
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Magyar Tudósok körútja 2, H-1117, Hungary
| | - András Zeke
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Magyar Tudósok körútja 2, H-1117, Hungary
| | - Gábor E Tusnády
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Magyar Tudósok körútja 2, H-1117, Hungary
- Department of Bioinformatics, Semmelweis University, Budapest, Tűzoltó u. 7, H-1094, Hungary
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8
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Villagrana R, López-Marqués RL. Plant P4-ATPase lipid flippases: How are they regulated? BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119599. [PMID: 37741575 DOI: 10.1016/j.bbamcr.2023.119599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/22/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
P4 ATPases are active membrane transporters that translocate lipids towards the cytosolic side of the biological membranes in eukaryotic cells. Due to their essential cellular functions, P4 ATPase activity is expected to be tightly controlled, but fundamental aspects of the regulation of plant P4 ATPases remain unstudied. In this mini-review, our knowledge of the regulatory mechanisms of yeast and mammalian P4 ATPases will be summarized, and sequence comparison and structural modelling will be used as a basis to discuss the putative regulation of the corresponding plant lipid transporters.
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Affiliation(s)
- Richard Villagrana
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Rosa Laura López-Marqués
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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9
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Mogensen LS, Mikkelsen SA, Tadini-Buoninsegni F, Holm R, Matsell E, Vilsen B, Molday RS, Andersen JP. On the track of the lipid transport pathway of the phospholipid flippase ATP8A2 - Mutation analysis of residues of the transmembrane segments M1, M2, M3 and M4. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119570. [PMID: 37678495 DOI: 10.1016/j.bbamcr.2023.119570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
P4-ATPases, also known as flippases, translocate specific lipids from the exoplasmic leaflet to the cytoplasmic leaflet of biological membranes, thereby generating an asymmetric lipid distribution essential for numerous cellular functions. A debated issue is which pathway within the protein the lipid substrate follows during the translocation. Here we present a comprehensive mutational screening of all amino acid residues in the transmembrane segments M1, M2, M3, and M4 of the flippase ATP8A2, thus allowing the functionally important residues in these transmembrane segments to be highlighted on a background of less important residues. Kinetic analysis of ATPase activity of 130 new ATP8A2 mutants, providing Vmax values as well as apparent affinities of the mutants for the lipid substrate, support a translocation pathway between M2 and M4 ("M2-M4 path"), extending from the entry site, where the lipid substrate binds from the exoplasmic leaflet, to a putative exit site at the cytoplasmic surface, formed by the divergence of M2 and M4. The effects of mutations in the M2-M4 path on the function of the entry site, including loss of lipid specificity in some mutants, suggest that the M2-M4 path and the entry site are conformationally coupled. Many of the residues of the M2-M4 path possess side chains with a potential for interacting with each other in a zipper-like mode, as well as with the head group of the lipid substrate, by ionic/hydrogen bonds. Thus, the translocation of the lipid substrate toward the cytoplasmic bilayer leaflet is comparable to unzipping a zipper of salt bridges/hydrogen bonds.
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Affiliation(s)
| | | | | | - Rikke Holm
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Eli Matsell
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bente Vilsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, Canada
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10
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Dieudonné T, Kümmerer F, Laursen MJ, Stock C, Flygaard RK, Khalid S, Lenoir G, Lyons JA, Lindorff-Larsen K, Nissen P. Activation and substrate specificity of the human P4-ATPase ATP8B1. Nat Commun 2023; 14:7492. [PMID: 37980352 PMCID: PMC10657443 DOI: 10.1038/s41467-023-42828-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/23/2023] [Indexed: 11/20/2023] Open
Abstract
Asymmetric distribution of phospholipids in eukaryotic membranes is essential for cell integrity, signaling pathways, and vesicular trafficking. P4-ATPases, also known as flippases, participate in creating and maintaining this asymmetry through active transport of phospholipids from the exoplasmic to the cytosolic leaflet. Here, we present a total of nine cryo-electron microscopy structures of the human flippase ATP8B1-CDC50A complex at 2.4 to 3.1 Å overall resolution, along with functional and computational studies, addressing the autophosphorylation steps from ATP, substrate recognition and occlusion, as well as a phosphoinositide binding site. We find that the P4-ATPase transport site is occupied by water upon phosphorylation from ATP. Additionally, we identify two different autoinhibited states, a closed and an outward-open conformation. Furthermore, we identify and characterize the PI(3,4,5)P3 binding site of ATP8B1 in an electropositive pocket between transmembrane segments 5, 7, 8, and 10. Our study also highlights the structural basis of a broad lipid specificity of ATP8B1 and adds phosphatidylinositol as a transport substrate for ATP8B1. We report a critical role of the sn-2 ester bond of glycerophospholipids in substrate recognition by ATP8B1 through conserved S403. These findings provide fundamental insights into ATP8B1 catalytic cycle and regulation, and substrate recognition in P4-ATPases.
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Affiliation(s)
- Thibaud Dieudonné
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Felix Kümmerer
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michelle Juknaviciute Laursen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Charlott Stock
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rasmus Kock Flygaard
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Guillaume Lenoir
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Joseph A Lyons
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Centre (iNANO) Aarhus University, Aarhus, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Poul Nissen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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11
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Palmgren M. P-type ATPases: Many more enigmas left to solve. J Biol Chem 2023; 299:105352. [PMID: 37838176 PMCID: PMC10654040 DOI: 10.1016/j.jbc.2023.105352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023] Open
Abstract
P-type ATPases constitute a large ancient super-family of primary active pumps that have diverse substrate specificities ranging from H+ to phospholipids. The significance of these enzymes in biology cannot be overstated. They are structurally related, and their catalytic cycles alternate between high- and low-affinity conformations that are induced by phosphorylation and dephosphorylation of a conserved aspartate residue. In the year 1988, all P-type sequences available by then were analyzed and five major families, P1 to P5, were identified. Since then, a large body of knowledge has accumulated concerning the structure, function, and physiological roles of members of these families, but only one additional family, P6 ATPases, has been identified. However, much is still left to be learned. For each family a few remaining enigmas are presented, with the intention that they will stimulate interest in continued research in the field. The review is by no way comprehensive and merely presents personal views with a focus on evolution.
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Affiliation(s)
- Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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12
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Čopič A, Dieudonné T, Lenoir G. Phosphatidylserine transport in cell life and death. Curr Opin Cell Biol 2023; 83:102192. [PMID: 37413778 DOI: 10.1016/j.ceb.2023.102192] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Phosphatidylserine (PS) is a negatively charged glycerophospholipid found mainly in the plasma membrane (PM) and in the late secretory/endocytic compartments, where it regulates cellular activity and can mediate apoptosis. Export of PS from the endoplasmic reticulum, its site of synthesis, to other compartments, and its transbilayer asymmetry must therefore be precisely regulated. We review recent findings on nonvesicular transport of PS by lipid transfer proteins (LTPs) at membrane contact sites, on PS flip-flop between membrane leaflets by flippases and scramblases, and on PS nanoclustering at the PM. We also discuss emerging data on cooperation between scramblases and LTPs, how perturbation of PS distribution can lead to disease, and the specific role of PS in viral infection.
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Affiliation(s)
- Alenka Čopič
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, 34293, Montpellier CEDEX 05, France.
| | - Thibaud Dieudonné
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette 91198, France
| | - Guillaume Lenoir
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette 91198, France
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13
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Bergman S, Cater RJ, Plante A, Mancia F, Khelashvili G. Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A. Nat Commun 2023; 14:3391. [PMID: 37296098 PMCID: PMC10250862 DOI: 10.1038/s41467-023-39088-y] [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: 12/28/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Major Facilitator Superfamily Domain containing 2 A (MFSD2A) is a transporter that is highly enriched at the blood-brain and blood-retinal barriers, where it mediates Na+-dependent uptake of ω-3 fatty acids in the form of lysolipids into the brain and eyes, respectively. Despite recent structural insights, it remains unclear how this process is initiated, and driven by Na+. Here, we perform Molecular Dynamics simulations which demonstrate that substrates enter outward facing MFSD2A from the outer leaflet of the membrane via lateral openings between transmembrane helices 5/8 and 2/11. The substrate headgroup enters first and engages in Na+ -bridged interactions with a conserved glutamic acid, while the tail is surrounded by hydrophobic residues. This binding mode is consistent with a "trap-and-flip" mechanism and triggers transition to an occluded conformation. Furthermore, using machine learning analysis, we identify key elements that enable these transitions. These results advance our molecular understanding of the MFSD2A transport cycle.
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Affiliation(s)
- Shana Bergman
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Rosemary J Cater
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Ambrose Plante
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA.
- Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA.
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14
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Nguyen C, Lei HT, Lai LTF, Gallenito MJ, Mu X, Matthies D, Gonen T. Lipid flipping in the omega-3 fatty-acid transporter. Nat Commun 2023; 14:2571. [PMID: 37156797 PMCID: PMC10167227 DOI: 10.1038/s41467-023-37702-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/28/2023] [Indexed: 05/10/2023] Open
Abstract
Mfsd2a is the transporter for docosahexaenoic acid (DHA), an omega-3 fatty acid, across the blood brain barrier (BBB). Defects in Mfsd2a are linked to ailments from behavioral and motor dysfunctions to microcephaly. Mfsd2a transports long-chain unsaturated fatty-acids, including DHA and α-linolenic acid (ALA), that are attached to the zwitterionic lysophosphatidylcholine (LPC) headgroup. Even with the recently determined structures of Mfsd2a, the molecular details of how this transporter performs the energetically unfavorable task of translocating and flipping lysolipids across the lipid bilayer remains unclear. Here, we report five single-particle cryo-EM structures of Danio rerio Mfsd2a (drMfsd2a): in the inward-open conformation in the ligand-free state and displaying lipid-like densities modeled as ALA-LPC at four distinct positions. These Mfsd2a snapshots detail the flipping mechanism for lipid-LPC from outer to inner membrane leaflet and release for membrane integration on the cytoplasmic side. These results also map Mfsd2a mutants that disrupt lipid-LPC transport and are associated with disease.
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Affiliation(s)
- Chi Nguyen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Hsiang-Ting Lei
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Louis Tung Faat Lai
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marc J Gallenito
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Xuelang Mu
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Doreen Matthies
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA.
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Departments of Physiology, University of California Los Angeles, Los Angeles, CA, 90095, USA.
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15
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Pazos I, Puig‐Tintó M, Betancur L, Cordero J, Jiménez‐Menéndez N, Abella M, Hernández AC, Duran AG, Adachi‐Fernández E, Belmonte‐Mateos C, Sabido‐Bozo S, Tosi S, Nezu A, Oliva B, Colombelli J, Graham TR, Yoshimori T, Muñiz M, Hamasaki M, Gallego O. The P4-ATPase Drs2 interacts with and stabilizes the multisubunit tethering complex TRAPPIII in yeast. EMBO Rep 2023; 24:e56134. [PMID: 36929574 PMCID: PMC10157312 DOI: 10.15252/embr.202256134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 03/17/2023] Open
Abstract
Multisubunit Tethering Complexes (MTCs) are a set of conserved protein complexes that tether vesicles at the acceptor membrane. Interactions with other components of the trafficking machinery regulate MTCs through mechanisms that are partially understood. Here, we systematically investigate the interactome that regulates MTCs. We report that P4-ATPases, a family of lipid flippases, interact with MTCs that participate in the anterograde and retrograde transport at the Golgi, such as TRAPPIII. We use the P4-ATPase Drs2 as a paradigm to investigate the mechanism and biological relevance of this interplay during transport of Atg9 vesicles. Binding of Trs85, the sole-specific subunit of TRAPPIII, to the N-terminal tail of Drs2 stabilizes TRAPPIII on membranes loaded with Atg9 and is required for Atg9 delivery during selective autophagy, a role that is independent of P4-ATPase canonical functions. This mechanism requires a conserved I(S/R)TTK motif that also mediates the interaction of the P4-ATPases Dnf1 and Dnf2 with MTCs, suggesting a broader role of P4-ATPases in MTC regulation.
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Affiliation(s)
- Irene Pazos
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Marta Puig‐Tintó
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Laura Betancur
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Jorge Cordero
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | | | - Marc Abella
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Altair C Hernández
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Ana G Duran
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Emi Adachi‐Fernández
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Carla Belmonte‐Mateos
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
| | - Susana Sabido‐Bozo
- Department of Cell BiologyUniversity of SevilleSevilleSpain
- Instituto de Biomedicina de Sevilla (IBiS)Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Sébastien Tosi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Akiko Nezu
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Baldomero Oliva
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
- Structural Bioinformatics Lab (GRIB‐IMIM)BarcelonaSpain
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Todd R Graham
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Manuel Muñiz
- Department of Cell BiologyUniversity of SevilleSevilleSpain
- Instituto de Biomedicina de Sevilla (IBiS)Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevilleSpain
| | - Maho Hamasaki
- Department of Genetics, Graduate School of MedicineOsaka UniversityOsakaJapan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Oriol Gallego
- Department of Medicine and Life Sciences (MELIS)Pompeu Fabra University (UPF)BarcelonaSpain
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16
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Sakuragi T, Nagata S. Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases. Nat Rev Mol Cell Biol 2023:10.1038/s41580-023-00604-z. [PMID: 37106071 PMCID: PMC10134735 DOI: 10.1038/s41580-023-00604-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2023] [Indexed: 04/29/2023]
Abstract
Cellular membranes function as permeability barriers that separate cells from the external environment or partition cells into distinct compartments. These membranes are lipid bilayers composed of glycerophospholipids, sphingolipids and cholesterol, in which proteins are embedded. Glycerophospholipids and sphingolipids freely move laterally, whereas transverse movement between lipid bilayers is limited. Phospholipids are asymmetrically distributed between membrane leaflets but change their location in biological processes, serving as signalling molecules or enzyme activators. Designated proteins - flippases and scramblases - mediate this lipid movement between the bilayers. Flippases mediate the confined localization of specific phospholipids (phosphatidylserine (PtdSer) and phosphatidylethanolamine) to the cytoplasmic leaflet. Scramblases randomly scramble phospholipids between leaflets and facilitate the exposure of PtdSer on the cell surface, which serves as an important signalling molecule and as an 'eat me' signal for phagocytes. Defects in flippases and scramblases cause various human diseases. We herein review the recent research on the structure of flippases and scramblases and their physiological roles. Although still poorly understood, we address the mechanisms by which they translocate phospholipids between lipid bilayers and how defects cause human diseases.
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Affiliation(s)
- Takaharu Sakuragi
- Biochemistry & Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Shigekazu Nagata
- Biochemistry & Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.
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17
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Chen KZ, Wang LL, Liu JY, Zhao JT, Huang SJ, Xiang MJ. P4-ATPase subunit Cdc50 plays a role in yeast budding and cell wall integrity in Candida glabrata. BMC Microbiol 2023; 23:99. [PMID: 37046215 PMCID: PMC10100066 DOI: 10.1186/s12866-023-02810-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/02/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND As highly-conserved types of lipid flippases among fungi, P4-ATPases play a significant role in various cellular processes. Cdc50 acts as the regulatory subunit of flippases, forming heterodimers with Drs2 to translocate aminophospholipids. Cdc50 homologs have been reported to be implicated in protein trafficking, drug susceptibility, and virulence in Saccharomyces cerevisiae, Candida albicans and Cryptococcus neoformans. It is likely that Cdc50 has an extensive influence on fungal cellular processes. The present study aimed to determine the function of Cdc50 in Candida glabrata by constructing a Δcdc50 null mutant and its complemented strain. RESULTS In Candida glabrata, the loss of Cdc50 led to difficulty in yeast budding, probably caused by actin depolarization. The Δcdc50 mutant also showed hypersensitivity to azoles, caspofungin, and cell wall stressors. Further experiments indicated hyperactivation of the cell wall integrity pathway in the Δcdc50 mutant, which elevated the major cell wall contents. An increase in exposure of β-(1,3)-glucan and chitin on the cell surface was also observed through flow cytometry. Interestingly, we observed a decrease in the phagocytosis rate when the Δcdc50 mutant was co-incubated with THP-1 macrophages. The Δcdc50 mutant also exhibited weakened virulence in nematode survival tests. CONCLUSION The results suggested that the lipid flippase subunit Cdc50 is implicated in yeast budding and cell wall integrity in C. glabrata, and thus have a broad influence on drug susceptibility and virulence. This work highlights the importance of lipid flippase, and offers potential targets for new drug research.
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Affiliation(s)
- Ke-Zhi Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu-Ling Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin-Yan Liu
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun-Tao Zhao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Si-Jia Huang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming-Jie Xiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Laboratory Medicine, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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18
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Mu J, Xue C, Fu L, Yu Z, Nie M, Wu M, Chen X, Liu K, Bu R, Huang Y, Yang B, Han J, Jiang Q, Chan KC, Zhou R, Li H, Huang A, Wang Y, Liu Z. Conformational cycle of human polyamine transporter ATP13A2. Nat Commun 2023; 14:1978. [PMID: 37031211 PMCID: PMC10082790 DOI: 10.1038/s41467-023-37741-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Dysregulation of polyamine homeostasis strongly associates with human diseases. ATP13A2, which is mutated in juvenile-onset Parkinson's disease and autosomal recessive spastic paraplegia 78, is a transporter with a critical role in balancing the polyamine concentration between the lysosome and the cytosol. Here, to better understand human ATP13A2-mediated polyamine transport, we use single-particle cryo-electron microscopy to solve high-resolution structures of human ATP13A2 in six intermediate states, including the putative E2 structure for the P5 subfamily of the P-type ATPases. These structures comprise a nearly complete conformational cycle spanning the polyamine transport process and capture multiple substrate binding sites distributed along the transmembrane regions, suggesting a potential polyamine transport pathway. Integration of high-resolution structures, biochemical assays, and molecular dynamics simulations allows us to obtain a better understanding of the structural basis of how hATP13A2 transports polyamines, providing a mechanistic framework for ATP13A2-related diseases.
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Affiliation(s)
- Jianqiang Mu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Chenyang Xue
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Lei Fu
- Shanghai Institute for Advanced Study, Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, 310027, Hangzhou, China
| | - Zongjun Yu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Minhan Nie
- School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, 510006, Guangzhou, China
| | - Mengqi Wu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Xinmeng Chen
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Kun Liu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Ruiqian Bu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Ying Huang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Baisheng Yang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Jianming Han
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Qianru Jiang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Kevin C Chan
- Shanghai Institute for Advanced Study, Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, 310027, Hangzhou, China
| | - Ruhong Zhou
- Shanghai Institute for Advanced Study, Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, 310027, Hangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, 510006, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, China
| | - Ancheng Huang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Yong Wang
- Shanghai Institute for Advanced Study, Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, 310027, Hangzhou, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, 314400, Haining, China.
| | - Zhongmin Liu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
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19
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Sim SI, Park E. P5-ATPases: Structure, substrate specificities, and transport mechanisms. Curr Opin Struct Biol 2023; 79:102531. [PMID: 36724561 DOI: 10.1016/j.sbi.2023.102531] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 02/01/2023]
Abstract
P5A- and P5B- ATPases, or collectively P5-ATPases, are eukaryotic-specific ATP-dependent transporters that are important for the function of the endoplasmic reticulum (ER) and endo-/lysosomes. However, their substrate specificities had remained enigmatic for many years. Recent cryo-electron microscopy (cryo-EM) and biochemical studies of P5-ATPases have revealed their substrate specificities and transport mechanisms, which were found to be markedly different from other members of the P-type ATPase superfamily. The P5A-ATPase extracts mistargeted or mis-inserted transmembrane helices from the ER membrane for protein quality control, while the P5B-ATPases mediate export of polyamines from late endo-/lysosomes into the cytosol. In this review, we discuss the mechanisms of their substrate recognition and transport based on the cryo-EM structures of the yeast and human P5-ATPases. We highlight how structural diversification of the transmembrane domain has enabled the P5-ATPase subfamily to adapt for transport of atypical substrates.
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Affiliation(s)
- Sue Im Sim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.
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20
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Xing Y, Peng K, Yi Q, Yu D, Shi H, Yang G, Yin S. TMEM30A is essential for hair cell polarity maintenance in postnatal mouse cochlea. Cell Mol Biol Lett 2023; 28:23. [PMID: 36959542 PMCID: PMC10035192 DOI: 10.1186/s11658-023-00437-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Phosphatidylserine is translocated to the inner leaflet of the phospholipid bilayer membrane by the flippase function of type IV P-tape ATPase (P4-ATPase), which is critical to maintain cellular stability and homeostasis. Transmembrane protein 30A (TMEM30A) is the β-subunit of P4-ATPase. Loss of P4-ATPase function causes sensorineural hearing loss and visual dysfunction in human. However, the function of TMEM30A in the auditory system is unclear. METHODS P4-ATPase subtype expression in the cochlea was detected by immunofluorescence staining and quantitative real-time polymerase chain reaction (qRT-PCR) at different developmental stages. Hair cell specific TMEM30A knockout mice and wild-type littermates were used for the following functional and morphological analysis. Auditory function was evaluated by auditory brainstem response. We investigated hair cell and stereocilia morphological changes by immunofluorescence staining. Scanning electron microscopy was applied to observe the stereocilia ultrastructure. Differentially expressed transcriptomes were analyzed based on RNA-sequencing data from knockout and wild-type mouse cochleae. Differentially expressed genes were verified by qRT-PCR. RESULTS TMEM30A and subtypes of P4-ATPase are expressed in the mouse cochlea in a temporal-dependent pattern. Deletion of TMEM30A in hair cells impaired hearing onset due to progressive hair cell loss. The disrupted kinocilia placement and irregular distribution of spectrin-α in cuticular plate indicated the hair cell planar polarity disruption in TMEM30A deletion hair cells. Hair cell degeneration begins at P7 and finishes around P14. Transcriptional analysis indicates that the focal adhesion pathway and stereocilium tip-related genes changed dramatically. Without the TMEM30A chaperone, excessive ATP8A2 accumulated in the cytoplasm, leading to overwhelming endoplasmic reticulum stress, which eventually contributed to hair cell death. CONCLUSIONS Deletion of TMEM30A led to disrupted planar polarity and stereocilia bundles, and finally led to hair cell loss and auditory dysfunction. TMEM30A is essential for hair cell polarity maintenance and membrane homeostasis. Our study highlights a pivotal role of TMEM30A in the postnatal development of hair cells and reveals the possible mechanisms underlying P4-ATPase-related genetic hearing loss.
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Affiliation(s)
- Yazhi Xing
- Department of Otolaryngology Head & Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1301 Research Bldg, 600 Yishan Rd, Shanghai, China
- Otolaryngology Institute of Shanghai Jiao Tong University, 600 Yishan Rd, Shanghai, 200233, China
| | - Kun Peng
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Qian Yi
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Dongzhen Yu
- Department of Otolaryngology Head & Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1301 Research Bldg, 600 Yishan Rd, Shanghai, China
- Otolaryngology Institute of Shanghai Jiao Tong University, 600 Yishan Rd, Shanghai, 200233, China
| | - Haibo Shi
- Department of Otolaryngology Head & Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1301 Research Bldg, 600 Yishan Rd, Shanghai, China
- Otolaryngology Institute of Shanghai Jiao Tong University, 600 Yishan Rd, Shanghai, 200233, China
| | - Guang Yang
- Department of Otolaryngology Head & Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1301 Research Bldg, 600 Yishan Rd, Shanghai, China.
- Otolaryngology Institute of Shanghai Jiao Tong University, 600 Yishan Rd, Shanghai, 200233, China.
| | - Shankai Yin
- Department of Otolaryngology Head & Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1301 Research Bldg, 600 Yishan Rd, Shanghai, China
- Otolaryngology Institute of Shanghai Jiao Tong University, 600 Yishan Rd, Shanghai, 200233, China
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21
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Tsuchiya M, Tachibana N, Nagao K, Tamura T, Hamachi I. Organelle-selective click labeling coupled with flow cytometry allows pooled CRISPR screening of genes involved in phosphatidylcholine metabolism. Cell Metab 2023:S1550-4131(23)00050-5. [PMID: 36917984 DOI: 10.1016/j.cmet.2023.02.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 03/14/2023]
Abstract
Cellular lipid synthesis and transport are governed by intricate protein networks. Although genetic screening should contribute to deciphering the regulatory networks of lipid metabolism, technical challenges remain-especially for high-throughput readouts of lipid phenotypes. Here, we coupled organelle-selective click labeling of phosphatidylcholine (PC) with flow cytometry-based CRISPR screening technologies to convert organellar PC phenotypes into a simple fluorescence readout for genome-wide screening. This technique, named O-ClickFC, was successfully applied in genome-scale CRISPR-knockout screens to identify previously reported genes associated with PC synthesis (PCYT1A, ACACA), vesicular membrane trafficking (SEC23B, RAB5C), and non-vesicular transport (PITPNB, STARD7). Moreover, we revealed previously uncharacterized roles of FLVCR1 as a choline uptake facilitator, CHEK1 as a post-translational regulator of the PC-synthetic pathway, and CDC50A as responsible for the translocation of PC to the outside of the plasma membrane bilayer. These findings demonstrate the versatility of O-ClickFC as an unprecedented platform for genetic dissection of cellular lipid metabolism.
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Affiliation(s)
- Masaki Tsuchiya
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; PRESTO (Precursory Research for Embryonic Science and Technology), JST, Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
| | - Nobuhiko Tachibana
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; PRESTO (Precursory Research for Embryonic Science and Technology), JST, Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
| | - Kohjiro Nagao
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Misasaginakauchi-cho, Yamashina-ku, Kyoto 607-8414, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology), JST, Sanbancho, Chiyodaku, Tokyo 102-0075, Japan.
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22
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Meng T, Chen X, He Z, Huang H, Lin S, Liu K, Bai G, Liu H, Xu M, Zhuang H, Zhang Y, Waqas A, Liu Q, Zhang C, Sun XD, Huang H, Umair M, Yan Y, Feng D. ATP9A deficiency causes ADHD and aberrant endosomal recycling via modulating RAB5 and RAB11 activity. Mol Psychiatry 2023; 28:1219-1231. [PMID: 36604604 PMCID: PMC9816018 DOI: 10.1038/s41380-022-01940-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 12/10/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023]
Abstract
ATP9A, a lipid flippase of the class II P4-ATPases, is involved in cellular vesicle trafficking. Its homozygous variants are linked to neurodevelopmental disorders in humans. However, its physiological function, the underlying mechanism as well as its pathophysiological relevance in humans and animals are still largely unknown. Here, we report two independent families in which the nonsense mutations c.433C>T/c.658C>T/c.983G>A (p. Arg145*/p. Arg220*/p. Trp328*) in ATP9A (NM_006045.3) cause autosomal recessive hypotonia, intellectual disability (ID) and attention deficit hyperactivity disorder (ADHD). Atp9a null mice show decreased muscle strength, memory deficits and hyperkinetic movement disorder, recapitulating the symptoms observed in patients. Abnormal neurite morphology and impaired synaptic transmission are found in the primary motor cortex and hippocampus of the Atp9a null mice. ATP9A is also required for maintaining neuronal neurite morphology and the viability of neural cells in vitro. It mainly localizes to endosomes and plays a pivotal role in endosomal recycling pathway by modulating small GTPase RAB5 and RAB11 activation. However, ATP9A pathogenic mutants have aberrant subcellular localization and cause abnormal endosomal recycling. These findings provide strong evidence that ATP9A deficiency leads to neurodevelopmental disorders and synaptic dysfunctions in both humans and mice, and establishes novel regulatory roles for ATP9A in RAB5 and RAB11 activity-dependent endosomal recycling pathway and neurological diseases.
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Affiliation(s)
- Tian Meng
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China.,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, China.,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China
| | - Xiaoting Chen
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Zhengjie He
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China.,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, China
| | - Haofeng Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Shiyin Lin
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Kunru Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Guo Bai
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Hao Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, China.,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China.,Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511500, China
| | - Mindong Xu
- Key Laboratory of Neuroscience, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Haixia Zhuang
- Department of Anesthesiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yunlong Zhang
- Key Laboratory of Neuroscience, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ahmed Waqas
- Department of Zoology, Division of Science and Technology, University of Education, Lahore, 54000, Pakistan
| | - Qian Liu
- Department of Cerebrovascular Disease Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Chuan Zhang
- Medical Genetics Center, Gansu Provincial Maternity and Child-care Hospital; Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, 730050, China
| | - Xiang-Dong Sun
- Key Laboratory of Neuroscience, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Huansen Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, 11481, Saudi Arabia. .,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, 22209, Pakistan.
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, China.
| | - Du Feng
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China. .,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, China. .,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China.
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23
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Zhang H, Zhang Y, Xu P, Bai C. Exploring the Phospholipid Transport Mechanism of ATP8A1-CDC50. Biomedicines 2023; 11:biomedicines11020546. [PMID: 36831082 PMCID: PMC9953615 DOI: 10.3390/biomedicines11020546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
P4-ATPase translocates lipids from the exoplasmic to the cytosolic plasma membrane leaflet to maintain lipid asymmetry distribution in eukaryotic cells. P4-ATPase is associated with severe neurodegenerative and metabolic diseases such as neurological and motor disorders. Thus, it is important to understand its transport mechanism. However, even with progress in X-ray diffraction and cryo-electron microscopy techniques, it is difficult to obtain the dynamic information of the phospholipid transport process in detail. There are still some problems required to be resolved: (1) when does the lipid transport happen? (2) How do the key residues on the transmembrane helices contribute to the free energy of important states? In this work, we explore the phospholipid transport mechanism using a coarse-grained model and binding free energy calculations. We obtained the free energy landscape by coupling the protein conformational changes and the phospholipid transport event, taking ATP8A1-CDC50 (the typical subtype of P4-ATPase) as the research object. According to the results, we found that the phospholipid would bind to the ATP8A1-CDC50 at the early stage when ATP8A1-CDC50 changes from E2P to E2Pi-PL state. We also found that the electrostatic effects play crucial roles in the phospholipid transport process. The information obtained from this work could help us in designing novel drugs for P-type flippase disorders.
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Affiliation(s)
- Honghui Zhang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yue Zhang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Peiyi Xu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
- Correspondence:
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24
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Tadini-Buoninsegni F, Mikkelsen SA, Mogensen LS, Holm R, Molday RS, Andersen JP. Electrogenic reaction step and phospholipid translocation pathway of the mammalian P4-ATPase ATP8A2. FEBS Lett 2023; 597:495-503. [PMID: 35945663 DOI: 10.1002/1873-3468.14459] [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: 06/16/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022]
Abstract
ATP8A2 is a mammalian P4-ATPase (flippase) that translocates the negatively charged lipid substrate phosphatidylserine from the exoplasmic leaflet to the cytoplasmic leaflet of cellular membranes. Using an electrophysiological method based on solid supported membranes, we investigated the electrogenicity of specific reaction steps of ATP8A2 and explored a potential phospholipid translocation pathway involving residues with positively charged side chains. Changes to the current signals caused by mutations show that the main electrogenic event occurs in connection with the release of the bound phosphatidylserine to the cytoplasmic leaflet and support the hypothesis that the phospholipid interacts with specific lysine and arginine residues near the cytoplasmic border of the lipid bilayer during the translocation and reorientation required for insertion into the cytoplasmic leaflet.
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Affiliation(s)
| | | | | | - Rikke Holm
- Department of Biomedicine, Aarhus University, Denmark
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.,Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, Canada
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25
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Heger T, Stock C, Laursen MJ, Habeck M, Dieudonné T, Nissen P. eGFP as an All-in-One Tag for Purification of Membrane Proteins. Methods Mol Biol 2023; 2652:171-186. [PMID: 37093475 DOI: 10.1007/978-1-0716-3147-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Within the last decade, cryo-electron microscopy has revolutionized our understanding of membrane proteins, but they still represent challenging targets for biochemical and structural studies. The first obstacle is often to obtain high production levels of correctly folded target protein. In these cases, the use of eGFP tags is an efficient strategy, as it allows rapid screenings of expression systems, constructs, and detergents for solubilization. Additionally, eGFP tags can now be used for affinity purification with recently developed nanobodies. Here we present a series of methods based on enhanced green fluorescent protein (eGFP) fluorescence to efficiently screen for production and stabilization of detergent-solubilized eGFP-tagged membrane proteins produced in S. cerevisiae via in-gel fluorescence SDS-PAGE and fluorescence-detection size-exclusion chromatography (FSEC). Additionally, we present a protocol describing the production of affinity resin based on eGFP-binding nanobodies produced in E. coli. We showcase the purification of human ATP7B, a copper transporting P-type ATPase, as an example of the applicability of the methods.
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Affiliation(s)
- Tomáš Heger
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Charlott Stock
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michelle Juknaviciute Laursen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michael Habeck
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Thibaud Dieudonné
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Poul Nissen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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26
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Li J, Zhao Y, Wang N. Physiological and Pathological Functions of TMEM30A: An Essential Subunit of P4-ATPase Phospholipid Flippases. J Lipids 2023; 2023:4625567. [PMID: 37200892 PMCID: PMC10188266 DOI: 10.1155/2023/4625567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/28/2023] [Accepted: 04/15/2023] [Indexed: 05/20/2023] Open
Abstract
Phospholipids are asymmetrically distributed across mammalian plasma membrane. The function of P4-ATPases is to maintain the abundance of phosphatidylserine (PS) and phosphatidylethanolamine (PE) in the inner leaflet as lipid flippases. Transmembrane protein 30A (TMEM30A, also named CDC50A), as an essential β subunit of most P4-ATPases, facilitates their transport and functions. With TMEM30A knockout mice or cell lines, it is found that the loss of TMEM30A has huge influences on the survival of mice and cells because of PS exposure-triggered apoptosis signaling. TMEM30A is a promising target for drug discovery due to its significant roles in various systems and diseases. In this review, we summarize the functions of TMEM30A in different systems, present current understanding of the protein structures and mechanisms of TMEM30A-P4-ATPase complexes, and discuss how these fundamental aspects of TMEM30A may be applied to disease treatment.
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Affiliation(s)
- Jingyi Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Yue Zhao
- Clinical Medical Laboratory, Wenjiang Hospital of Sichuan Provincial People's Hospital, Chengdu, China
| | - Na Wang
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
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27
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Multiple sub-state structures of SERCA2b reveal conformational overlap at transition steps during the catalytic cycle. Cell Rep 2022; 41:111760. [PMID: 36476867 DOI: 10.1016/j.celrep.2022.111760] [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: 01/12/2022] [Revised: 09/06/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) pumps Ca2+ into the endoplasmic reticulum (ER). Herein, we present cryo-electron microscopy (EM) structures of three intermediates of SERCA2b: Ca2+-bound phosphorylated (E1P·2Ca2+) and Ca2+-unbound dephosphorylated (E2·Pi) intermediates and another between the E2P and E2·Pi states. Our cryo-EM analysis demonstrates that the E1P·2Ca2+ state exists in low abundance and preferentially transitions to an E2P-like structure by releasing Ca2+ and that the Ca2+ release gate subsequently undergoes stepwise closure during the dephosphorylation processes. Importantly, each intermediate adopts multiple sub-state structures including those like the next one in the catalytic series, indicating conformational overlap at transition steps, as further substantiated by atomistic molecular dynamic simulations of SERCA2b in a lipid bilayer. The present findings provide insight into how enzymes accelerate catalytic cycles.
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28
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Jain BK, Wagner AS, Reynolds TB, Graham TR. Lipid Transport by Candida albicans Dnf2 Is Required for Hyphal Growth and Virulence. Infect Immun 2022; 90:e0041622. [PMID: 36214556 PMCID: PMC9670988 DOI: 10.1128/iai.00416-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is a common cause of human mucosal yeast infections, and invasive candidiasis can be fatal. Antifungal medications are limited, but those targeting the pathogen cell wall or plasma membrane have been effective. Therefore, virulence factors controlling membrane biogenesis are potential targets for drug development. P4-ATPases contribute to membrane biogenesis by selecting and transporting specific lipids from the extracellular leaflet to the cytoplasmic leaflet of the bilayer to generate lipid asymmetry. A subset of heterodimeric P4-ATPases, including Dnf1-Lem3 and Dnf2-Lem3 from Saccharomyces cerevisiae, transport phosphatidylcholine (PC), phosphatidylethanolamine (PE), and the sphingolipid glucosylceramide (GlcCer). GlcCer is a critical lipid for Candida albicans polarized growth and virulence, but the role of GlcCer transporters in virulence has not been explored. Here, we show that the Candida albicans Dnf2 (CaDnf2) requires association with CaLem3 to form a functional transporter and flip fluorescent derivatives of GlcCer, PC, and PE across the plasma membrane. Mutation of conserved substrate-selective residues in the membrane domain strongly abrogates GlcCer transport and partially disrupts PC transport by CaDnf2. Candida strains harboring dnf2-null alleles (dnf2ΔΔ) or point mutations that disrupt substrate recognition exhibit defects in yeast-to-hypha growth transition, filamentous growth, and virulence in systemically infected mice. The influence of CaDNF1 deletion on the morphological phenotypes is negligible, although the dnf1ΔΔ dnf2ΔΔ strain was less virulent than the dnf2ΔΔ strain. These results indicate that the transport of GlcCer and/or PC by plasma membrane P4-ATPases is important for the pathogenicity of Candida albicans.
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Affiliation(s)
- Bhawik K. Jain
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Andrew S. Wagner
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Todd B. Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Todd R. Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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29
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Di Cera E, Mohammed BM, Pelc LA, Stojanovski BM. Cryo-EM structures of coagulation factors. Res Pract Thromb Haemost 2022; 6:e12830. [PMID: 36349261 PMCID: PMC9630041 DOI: 10.1002/rth2.12830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/08/2022] [Accepted: 09/22/2022] [Indexed: 11/05/2022] Open
Abstract
A State of the Art lecture titled "Cryo-EM structures of coagulation factors" was presented at the ISTH Congress in 2022. Cryogenic electron microscopy (cryo-EM) is a revolutionary technique capable of solving the structure of high molecular weight proteins and their complexes, unlike nuclear magnetic resonance (NMR), and under conditions not biased by crystal contacts, unlike X-ray crystallography. These features are particularly relevant to the analysis of coagulation factors that are too big for NMR and often recalcitrant to X-ray investigation. Using cryo-EM, we have solved the structures of coagulation factors V and Va, prothrombinase on nanodiscs, and the prothrombin-prothrombinase complex. These structures have advanced basic knowledge in the field of thrombosis and hemostasis, especially on the function of factor V and the molecular mechanism for prothrombin activation, and set the stage for exciting new lines of investigation. Finally, we summarize relevant new data on this topic presented during the 2022 ISTH Congress.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSt. LouisMissouriUSA
| | - Bassem M. Mohammed
- Edward A. Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSt. LouisMissouriUSA
| | - Leslie A. Pelc
- Edward A. Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSt. LouisMissouriUSA
| | - Bosko M. Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular BiologySaint Louis University School of MedicineSt. LouisMissouriUSA
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30
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Wang W, Wu S, Cen Z, Zhang Y, Chen Y, Huang Y, Cillo AR, Prokopec JS, Quarato G, Vignali DAA, Stewart-Ornstein J, Li S, Lu B, Gong YN. Mobilizing phospholipids on tumor plasma membrane implicates phosphatidylserine externalization blockade for cancer immunotherapy. Cell Rep 2022; 41:111582. [PMID: 36323258 PMCID: PMC9671066 DOI: 10.1016/j.celrep.2022.111582] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 06/06/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
In "healthy" tumor cells, phosphatidylserine (PS) is predominately localized in the inner plasma membrane leaflet. During apoptosis, PS relocates to the outer leaflet. Herein, we established PSout tumor models with tumor cells lacking PS flippase component CDC50A, constantly exposing PS but alive. PSout tumors developed bigger than wild-type (WT) tumors, featuring M2 polarized tumor-associated macrophages (TAMs) and fewer tumor-antigen-specific T cells. The PS receptor TIM-3 is responsible for PS recognition. Employing an opposite tumor model, PSin, with tumor cells lacking the PS scramblase Xkr8 and unable to expose PS during otherwise normal apoptosis, we find that the accumulated apoptotic tumor cells produce and release cyclic GAMP (cGAMP) to immune cells to activate the STING pathway, leading to TAM M1 polarization, suppressed interleukin (IL)-10 secretion, and natural killer (NK) cell cytotoxicity. Silencing Xkr8 in vivo by either short hairpin RNA (shRNA) or small interfering RNA (siRNA) to achieve a PS externalization blockade provides robust therapeutic anti-tumor efficiency.
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Affiliation(s)
- Weihong Wang
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Shaoxian Wu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Zhanpeng Cen
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; School of Medicine, Tsinghua University, Beijing, China
| | - Yixin Zhang
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Yuang Chen
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
| | - Yixian Huang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
| | - Anthony R Cillo
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Joshua S Prokopec
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Giovanni Quarato
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dario A A Vignali
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, 5115 Center Avenue, Pittsburgh, PA 15213, USA
| | - Jacob Stewart-Ornstein
- Department of Computational and Systems Biology, Hillman Cancer Center and University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Song Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA
| | - Binfeng Lu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, 5115 Center Avenue, Pittsburgh, PA 15213, USA.
| | - Yi-Nan Gong
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, 5115 Center Avenue, Pittsburgh, PA 15213, USA.
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31
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Ipsen JØ, Sørensen DM. ATP hydrolytic activity of purified Spf1p correlate with micellar lipid fluidity and is dependent on conserved residues in transmembrane helix M1. PLoS One 2022; 17:e0274908. [PMID: 36264897 PMCID: PMC9584430 DOI: 10.1371/journal.pone.0274908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
P5A ATPases are expressed in the endoplasmic reticulum (ER) of all eukaryotic cells, and their disruption results in pleiotropic phenotypes related to severe ER stress. They were recently proposed to function in peptide translocation although their specificity have yet to be confirmed in reconstituted assays using the purified enzyme. A general theme for P-type ATPases is that binding and transport of substrates is coupled to hydrolysis of ATP in a conserved allosteric mechanism, however several independent reports have shown purified Spf1p to display intrinsic spontaneous ATP hydrolytic activity after purification. It has never been determined to what extend this spontaneous activity is caused by uncoupling of the enzyme. In this work we have purified a functional tagged version of the Saccharomyces cerevisiae P5A ATPase Spf1p and have observed that the intrinsic ATP hydrolytic activity of the purified and re-lipidated protein can be stimulated by specific detergents (C12E8, C12E10 and Tween20) in mixed lipid/detergent micelles in the absence of any apparent substrate. We further show that this increase in activity correlate with the reaction temperature and the anisotropic state of the mixed lipid/detergent micelles and further that this correlation relies on three highly conserved phenylalanine residues in M1. This suggests that at least part of the intrinsic ATP hydrolytic activity is allosterically coupled to movements in the TM domain in the purified preparations. It is suggested that free movement of the M1 helix represent an energetic constraint on catalysis and that this constraint likely is lost in the purified preparations resulting in protein with intrinsic spontaneous ATP hydrolytic activity. Removal of the N-terminal part of the protein apparently removes this activity.
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Affiliation(s)
- Johan Ørskov Ipsen
- Center for Membrane Pumps in Cells and Disease—PUMPKIN, Danish National Research Foundation, Copenhagen, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Danny Mollerup Sørensen
- Center for Membrane Pumps in Cells and Disease—PUMPKIN, Danish National Research Foundation, Copenhagen, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
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Miyata Y, Yamada K, Nagata S, Segawa K. Two types of type IV P-type ATPases independently re-establish the asymmetrical distribution of phosphatidylserine in plasma membranes. J Biol Chem 2022; 298:102527. [PMID: 36162506 PMCID: PMC9597894 DOI: 10.1016/j.jbc.2022.102527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022] Open
Abstract
Phospholipids are asymmetrically distributed between the lipid bilayer of plasma membranes in which phosphatidylserine (PtdSer) is confined to the inner leaflet. ATP11A and ATP11C, type IV P-Type ATPases in plasma membranes, flip PtdSer from the outer to the inner leaflet, but involvement of other P4-ATPases is unclear. We herein demonstrated that once PtdSer was exposed on the cell surface of ATP11A−/−ATP11C−/− mouse T cell line (W3), its internalization to the inner leaflet of plasma membranes was negligible at 15 °C. However, ATP11A−/−ATP11C−/− cells internalized the exposed PtdSer at 37 °C, a temperature at which trafficking of intracellular membranes was active. In addition to ATP11A and 11C, W3 cells expressed ATP8A1, 8B2, 8B4, 9A, 9B, and 11B, with ATP8A1 and ATP11B being present at recycling endosomes. Cells deficient in four P4-ATPases (ATP8A1, 11A, 11B, and 11C) (QKO) did not constitutively expose PtdSer on the cell surface but lost the ability to re-establish PtdSer asymmetry within 1 hour, even at 37 °C. The expression of ATP11A or ATP11C conferred QKO cells with the ability to rapidly re-establish PtdSer asymmetry at 15 °C and 37 °C, while cells expressing ATP8A1 or ATP11B required a temperature of 37 °C to achieve this function, and a dynamin inhibitor blocked this process. These results revealed that mammalian cells are equipped with two independent mechanisms to re-establish its asymmetry: the first is a rapid process involving plasma membrane flippases, ATP11A and ATP11C, while the other is mediated by ATP8A1 and ATP11B, which require an endocytosis process.
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Affiliation(s)
- Yugo Miyata
- Department of Medical Chemistry, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Kyoko Yamada
- Laboratory of Biochemistry & Immunology, World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Shigekazu Nagata
- Laboratory of Biochemistry & Immunology, World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
| | - Katsumori Segawa
- Department of Medical Chemistry, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan; Laboratory of Biochemistry & Immunology, World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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Shin HW, Takatsu H. Regulatory Roles of N- and C-Terminal Cytoplasmic Regions of P4-ATPases. Chem Pharm Bull (Tokyo) 2022; 70:524-532. [DOI: 10.1248/cpb.c22-00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hye-Won Shin
- Graduate School of Pharmaceutical Sciences, Kyoto University
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Fruergaard MU, Dach I, Andersen JL, Ozol M, Shasavar A, Quistgaard EM, Poulsen H, Fedosova NU, Nissen P. The Na,K-ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state. J Biol Chem 2022; 298:102317. [PMID: 35926706 PMCID: PMC9485054 DOI: 10.1016/j.jbc.2022.102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 10/29/2022] Open
Abstract
The Na+,K+-ATPase generates electrochemical gradients of Na+ and K+ across the plasma membrane via a functional cycle that includes various phosphoenzyme intermediates. However, the structure and function of these intermediates and how metal fluorides mimick them require further investigation. Here, we describe a 4.0 Å resolution crystal structure and functional properties of the pig kidney Na+,K+-ATPase stabilized by the inhibitor beryllium fluoride (denoted E2-BeFx). E2-BeFx is expected to mimic properties of the E2P phosphoenzyme, yet with unknown characteristics of ion and ligand binding. The structure resembles the E2P form obtained by phosphorylation from inorganic phosphate (Pi) and stabilized by cardiotonic steroids, including a low-affinity Mg2+ site near ion binding site II. Our anomalous Fourier analysis of the crystals soaked in Rb+ (a K+ congener) followed by a low-resolution rigid-body refinement (6.9-7.5 Å) revealed pre-occlusion transitions leading to activation of the dephosphorylation reaction. We show that the Mg2+ location indicates a site of initial K+ recognition and acceptance upon binding to the outward-open E2P state after Na+ release. Furthermore, using binding and activity studies, we find that the BeFx-inhibited enzyme is also able to bind ADP/ATP and Na+. These results relate the E2-BeFx complex to a transient K+- and ADP-sensitive E*P intermediate of the functional cycle of the Na+,K+-ATPase, prior to E2P.
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Affiliation(s)
- Marlene U Fruergaard
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Ingrid Dach
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Jacob L Andersen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark; Department of Biomedicine, Aarhus University, DK - 8000 Aarhus C, Denmark
| | - Mette Ozol
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Azadeh Shasavar
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Esben M Quistgaard
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Hanne Poulsen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Natalya U Fedosova
- Department of Biomedicine, Aarhus University, DK - 8000 Aarhus C, Denmark.
| | - Poul Nissen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark.
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CDC50 Orthologues in Plasmodium falciparum Have Distinct Roles in Merozoite Egress and Trophozoite Maturation. mBio 2022; 13:e0163522. [PMID: 35862778 PMCID: PMC9426505 DOI: 10.1128/mbio.01635-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In model organisms, type IV ATPases (P4-ATPases) require cell division control protein 50 (CDC50) chaperones for their phospholipid flipping activity. In the malaria parasite Plasmodium falciparum, guanylyl cyclase alpha (GCα) is an integral membrane protein that is essential for release (egress) of merozoites from their host erythrocytes. GCα is unusual in that it contains both a C-terminal cyclase domain and an N-terminal P4-ATPase domain of unknown function. We sought to investigate whether any of the three CDC50 orthologues (termed A, B, and C) encoded by P. falciparum are required for GCα function. Using gene tagging and conditional gene disruption, we demonstrate that CDC50B and CDC50C but not CDC50A are expressed in the clinically important asexual blood stages and that CDC50B is a binding partner of GCα whereas CDC50C is the binding partner of another putative P4-ATPase, phospholipid-transporting ATPase 2 (ATP2). Our findings indicate that CDC50B has no essential role for intraerythrocytic parasite maturation but modulates the rate of parasite egress by interacting with GCα for optimal cGMP synthesis. In contrast, CDC50C is essential for blood stage trophozoite maturation. Additionally, we find that the CDC50C-ATP2 complex may influence parasite endocytosis of host cell hemoglobin and consequently hemozoin formation.
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Zhang Y, Zhu X, Zhang H, Yan J, Xu P, Wu P, Wu S, Bai C. Mechanism Study of Proteins under Membrane Environment. MEMBRANES 2022; 12:membranes12070694. [PMID: 35877897 PMCID: PMC9322369 DOI: 10.3390/membranes12070694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022]
Abstract
Membrane proteins play crucial roles in various physiological processes, including molecule transport across membranes, cell communication, and signal transduction. Approximately 60% of known drug targets are membrane proteins. There is a significant need to deeply understand the working mechanism of membrane proteins in detail, which is a challenging work due to the lack of available membrane structures and their large spatial scale. Membrane proteins carry out vital physiological functions through conformational changes. In the current study, we utilized a coarse-grained (CG) model to investigate three representative membrane protein systems: the TMEM16A channel, the family C GPCRs mGlu2 receptor, and the P4-ATPase phospholipid transporter. We constructed the reaction pathway of conformational changes between the two-end structures. Energy profiles and energy barriers were calculated. These data could provide reasonable explanations for TMEM16A activation, the mGlu2 receptor activation process, and P4-ATPase phospholipid transport. Although they all belong to the members of membrane proteins, they behave differently in terms of energy. Our work investigated the working mechanism of membrane proteins and could give novel insights into other membrane protein systems of interest.
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Affiliation(s)
- Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Xiaohong Zhu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Honghui Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Junfang Yan
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Peiyi Xu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Peng Wu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518055, China;
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
- Correspondence: (S.W.); (C.B.)
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
- Chenzhu Biotechnology Co., Ltd., Hangzhou 310005, China
- Correspondence: (S.W.); (C.B.)
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37
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Zhang Y, Inaba K. Structural basis of the conformational and functional regulation of human SERCA2b, the ubiquitous endoplasmic reticulum calcium pump. Bioessays 2022; 44:e2200052. [PMID: 35560336 DOI: 10.1002/bies.202200052] [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: 03/06/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 11/06/2022]
Abstract
Sarco/endoplasmic reticulum Ca2+ ATPase 2b (SERCA2b), a member of the SERCA family, is expressed ubiquitously and transports Ca2+ into the sarco/endoplasmic reticulum using the energy provided by ATP binding and hydrolysis. The crystal structure of SERCA2b in its Ca2+ - and ATP-bound (E1∙2Ca2+ -ATP) state and cryo-electron microscopy (cryo-EM) structures of the protein in its E1∙2Ca2+ -ATP and Ca2+ -unbound phosphorylated (E2P) states have provided essential insights into how the overall conformation and ATPase activity of SERCA2b is regulated by the transmembrane helix 11 and the subsequent luminal extension loop, both of which are specific to this isoform. More recently, our cryo-EM analysis has revealed that SERCA2b likely adopts open and closed conformations of the cytosolic domains in the Ca2+ -bound but ATP-free (E1∙2Ca2+ ) state, and that the closed conformation represents a state immediately prior to ATP binding. This review article summarizes the unique mechanisms underlying the conformational and functional regulation of SERCA2b.
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Affiliation(s)
- Yuxia Zhang
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan.,Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Japan
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38
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Shi D, An K, Zhang H, Xu P, Bai C. Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines. ENTROPY 2022; 24:e24050620. [PMID: 35626506 PMCID: PMC9140642 DOI: 10.3390/e24050620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 12/14/2022]
Abstract
Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but also related to the conformational transition dynamics and the corresponding energy profiles. With the rapid development of crystallographic techniques, the spatial scale of resolved structures is reaching up to thousands of residues, and the concomitant conformational changes become more and more complicated, posing a great challenge for computational biology research. Previously, a coarse-grained (CG) model aiming at conformational free energy evaluation was developed and showed excellent ability to reproduce the energy profiles by accurate electrostatic interaction calculations. In this study, we extended the application of the CG model to a series of large-scale protein machine systems. The spike protein trimer of SARS-CoV-2, ATP citrate lyase (ACLY) tetramer, and P4-ATPases systems were carefully studied and discussed as examples. It is indicated that the CG model is effective to depict the energy profiles of the conformational pathway between two endpoint structures, especially for large-scale systems. Both the energy change and energy barrier between endpoint structures provide reasonable mechanism explanations for the associated biological processes, including the opening of receptor binding domain (RBD) of spike protein, the phospholipid transportation of P4-ATPase, and the loop translocation of ACLY. Taken together, the CG model provides a suitable alternative in mechanistic studies related to conformational change in large-scale protein machines.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Ke An
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Honghui Zhang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
| | - Peiyi Xu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China; (D.S.); (K.A.); (H.Z.); (P.X.)
- Correspondence:
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Tancer RJ, Wang Y, Pawar S, Xue C, Wiedman GR. Development of Antifungal Peptides against Cryptococcus neoformans; Leveraging Knowledge about the cdc50Δ Mutant Susceptibility for Lead Compound Development. Microbiol Spectr 2022; 10:e0043922. [PMID: 35377230 PMCID: PMC9045296 DOI: 10.1128/spectrum.00439-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 12/20/2022] Open
Abstract
Cryptococcus neoformans is a major fungal pathogen that often causes life-threatening meningitis in immunocompromised populations. This yeast pathogen is highly resistant to the echinocandin drug caspofungin. Previous studies showed that Cryptococcus lipid translocase (flippase) is required for the caspofungin resistance of that fungus. Mutants with a deleted subunit of lipid flippase, Cdc50, showed increased sensitivity to caspofungin. Here we designed an antifungal peptide targeting the P4-ATPase function. We synthesized stable peptides based on the Cdc50 loop region to identify peptides that can sensitize caspofungin by blocking flippase function and found that myristylated peptides based on the "AS15 sequence" was effective at high concentrations. A modified peptide, "AW9-Ma" showed a MIC of 64 μg/mL against H99 wild type and a fractional inhibitory concentration (FIC) index value of 0.5 when used in combination with caspofungin. Most notably, in the presence of the AW9-Ma peptide, C. neoformans wild type was highly sensitive to caspofungin with a MIC of 4 μg/mL, the same as the cdc50Δ mutant. Further assays with flow cytometry showed inhibition of the lipid flippase enzyme activity and significant accumulation of phosphatidylserine on the cell membrane surface. Using a fluorescently labeled peptide, we confirmed that the peptide co-localized with mCherry-tagged P4-ATPase protein Apt1 in C. neoformans. Structure-activity relationship studies of the AW9 sequence showed that two lysine residues on the peptide are likely responsible for the interaction with the P4-ATPase, hence critical for its antifungal activity. IMPORTANCE The authors have developed a lead compound peptide antifungal drug targeting a protein from the organism Cryptococcus neoformans. Binding of the drug to the target fungal protein causes charged lipid molecules to be retained on the surface. This peptide works in synergy with the existing antifungal drug caspofungin. Echinocandin drugs like caspofungin are one of the few classes of existing antifungals. Due to the high concentrations needed, caspofungin is rarely used to treat C. neoformans infections. The authors believe that their new compound provides a way to lower the concentration of caspofungin needed to treat such infections, thus opening the possibility for greater utility of these antifungal.
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Affiliation(s)
- Robert J. Tancer
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey, USA
| | - Yina Wang
- Public Health Research Institute, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Siddhi Pawar
- Public Health Research Institute, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Chaoyang Xue
- Public Health Research Institute, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Gregory R. Wiedman
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey, USA
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Dieudonné T, Herrera SA, Laursen MJ, Lejeune M, Stock C, Slimani K, Jaxel C, Lyons JA, Montigny C, Pomorski TG, Nissen P, Lenoir G. Autoinhibition and regulation by phosphoinositides of ATP8B1, a human lipid flippase associated with intrahepatic cholestatic disorders. eLife 2022; 11:75272. [PMID: 35416773 PMCID: PMC9045818 DOI: 10.7554/elife.75272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/12/2022] [Indexed: 11/24/2022] Open
Abstract
P4-ATPases flip lipids from the exoplasmic to the cytosolic leaflet, thus maintaining lipid asymmetry in eukaryotic cell membranes. Mutations in several human P4-ATPase genes are associated with severe diseases, for example in ATP8B1 causing progressive familial intrahepatic cholestasis, a rare inherited disorder progressing toward liver failure. ATP8B1 forms a binary complex with CDC50A and displays a broad specificity to glycerophospholipids, but regulatory mechanisms are unknown. Here, we report functional studies and the cryo-EM structure of the human lipid flippase ATP8B1-CDC50A at 3.1 Å resolution. We find that ATP8B1 is autoinhibited by its N- and C-terminal tails, which form extensive interactions with the catalytic sites and flexible domain interfaces. Consistently, ATP hydrolysis is unleashed by truncation of the C-terminus, but also requires phosphoinositides, most markedly phosphatidylinositol-3,4,5-phosphate (PI(3,4,5)P3), and removal of both N- and C-termini results in full activation. Restored inhibition of ATP8B1 truncation constructs with a synthetic peptide mimicking the C-terminal segment further suggests molecular communication between N- and C-termini in the autoinhibition and demonstrates that the regulatory mechanism can be interfered with by exogenous compounds. A recurring (G/A)(Y/F)AFS motif of the C-terminal segment suggests that this mechanism is employed widely across P4-ATPase lipid flippases in plasma membrane and endomembranes.
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Affiliation(s)
- Thibaud Dieudonné
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Sara Abad Herrera
- Department of Molecular Biochemistry, Ruhr University Bochum, Bochum, Germany
| | | | - Maylis Lejeune
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Charlott Stock
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kahina Slimani
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Christine Jaxel
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Joseph A Lyons
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Cédric Montigny
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | | | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Guillaume Lenoir
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
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41
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Structural insights into the activation of autoinhibited human lipid flippase ATP8B1 upon substrate binding. Proc Natl Acad Sci U S A 2022; 119:e2118656119. [PMID: 35349344 PMCID: PMC9168909 DOI: 10.1073/pnas.2118656119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ATP8B1 is a P4 ATPase that maintains membrane asymmetry by transporting phospholipids across the cell membrane. Disturbance of lipid asymmetry will lead to the imbalance of the cell membrane and eventually, cell death. Thus, defects in ATP8B1 are usually associated with severe human diseases, such as intrahepatic cholestasis. The present structures of ATP8B1 complexed with its auxiliary noncatalytic partners CDC50A and CDC50B reveal an autoinhibited state of ATP8B1 that could be released upon substrate binding. Moreover, release of this autoinhibition could be facilitated by the bile acids, which are key factors that alter the membrane asymmetry of hepatocytes. This enabled us to figure out a feedback loop of bile acids and lipids across the cell membrane. The human P4 ATPase ATP8B1 in complex with the auxiliary noncatalytic protein CDC50A or CDC50B mediates the transport of cell-membrane lipids from the outer to the inner membrane leaflet, which is crucial to maintain the asymmetry of membrane lipids. Its dysfunction usually leads to an imbalance of bile-acid circulation and eventually causes intrahepatic cholestasis diseases. Here, we found that both ATP8B1–CDC50A and ATP8B1–CDC50B possess a higher ATPase activity in the presence of the most favored substrate phosphatidylserine (PS), and, moreover, that the PS-stimulated activity could be augmented upon the addition of bile acids. The 3.4-Å cryo-electron microscopy structures of ATP8B1–CDC50A and ATP8B1–CDC50B enabled us to capture a phosphorylated and autoinhibited state, with the N- and C-terminal tails separately inserted into the cytoplasmic interdomain clefts of ATP8B1. The PS-bound ATP8B1–CDC50A structure at 4.0-Å resolution indicated that the autoinhibited state could be released upon PS binding. Structural analysis combined with mutagenesis revealed the residues that determine the substrate specificity and a unique positively charged loop in the phosphorylated domain of ATP8B1 for the recruitment of bile acids. Together, we supplemented the Post–Albers transport cycle of P4 ATPases with an extra autoinhibited state of ATP8B1, which could be activated upon substrate binding. These findings not only provide structural insights into the ATP8B1-mediated restoration of human membrane lipid asymmetry during bile-acid circulation, but also advance our understanding of the molecular mechanism of P4 ATPases.
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Conformational changes of a phosphatidylcholine flippase in lipid membranes. Cell Rep 2022; 38:110518. [PMID: 35294892 DOI: 10.1016/j.celrep.2022.110518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/06/2022] [Accepted: 02/18/2022] [Indexed: 11/20/2022] Open
Abstract
Type 4 P-type ATPases (P4-ATPases) actively and selectively translocate phospholipids across membrane bilayers. Driven by ATP hydrolysis, P4-ATPases undergo conformational changes during lipid flipping. It is unclear how the active flipping states of P4-ATPases are regulated in the lipid membranes, especially for phosphatidylcholine (PC)-flipping P4-ATPases whose substrate, PC, is a substantial component of membranes. Here, we report the cryoelectron microscopy structures of a yeast PC-flipping P4-ATPase, Dnf1, in lipid environments. In native yeast lipids, Dnf1 adopts a conformation in which the lipid flipping pathway is disrupted. Only when the lipid composition is changed can Dnf1 be captured in the active conformations that enable lipid flipping. These results suggest that, in the native membrane, Dnf1 may stay in an idle conformation that is unable to support the trans-membrane movement of lipids. Dnf1 may have altered conformational preferences in membranes with different lipid compositions.
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Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases. Nat Commun 2022; 13:1213. [PMID: 35260556 PMCID: PMC8904598 DOI: 10.1038/s41467-022-28832-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FoF1 ATP synthase. When powered by ATP hydrolysis, the V1 domain rotates the central rotor against the A3B3 hexamer, composed of three catalytic AB dimers adopting different conformations (ABopen, ABsemi, and ABclosed). Here, we report the atomic models of 18 catalytic intermediates of the V1 domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not rotate immediately after binding of ATP to the V1. Instead, three events proceed simultaneously with the 120˚ rotation of the shaft: hydrolysis of ATP in ABsemi, zipper movement in ABopen by the binding ATP, and unzipper movement in ABclosed with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in ABsemi, rather than the power stroke model proposed previously for F1-ATPase. The rotary ATPases use a rotary catalytic mechanism to drive transmembrane proton movement powered by ATP hydrolysis. Here, the authors report a collection of V/A-ATPase V1 domain structures, providing insights into rotary mechanism of the enzyme and potentially other rotary motor proteins driven by ATP hydrolysis.
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Bitter RM, Oh S, Deng Z, Rahman S, Hite RK, Yuan P. Structure of the Wilson disease copper transporter ATP7B. SCIENCE ADVANCES 2022; 8:eabl5508. [PMID: 35245129 PMCID: PMC8896786 DOI: 10.1126/sciadv.abl5508] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/10/2022] [Indexed: 05/31/2023]
Abstract
ATP7A and ATP7B, two homologous copper-transporting P1B-type ATPases, play crucial roles in cellular copper homeostasis, and mutations cause Menkes and Wilson diseases, respectively. ATP7A/B contains a P-type ATPase core consisting of a membrane transport domain and three cytoplasmic domains, the A, P, and N domains, and a unique amino terminus comprising six consecutive metal-binding domains. Here, we present a cryo-electron microscopy structure of frog ATP7B in a copper-free state. Interacting with both the A and P domains, the metal-binding domains are poised to exert copper-dependent regulation of ATP hydrolysis coupled to transmembrane copper transport. A ring of negatively charged residues lines the cytoplasmic copper entrance that is presumably gated by a conserved basic residue sitting at the center. Within the membrane, a network of copper-coordinating ligands delineates a stepwise copper transport pathway. This work provides the first glimpse into the structure and function of ATP7 proteins and facilitates understanding of disease mechanisms and development of rational therapies.
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Affiliation(s)
- Ryan M. Bitter
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - SeCheol Oh
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suhaila Rahman
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard K. Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
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Bisio H, Krishnan A, Marq JB, Soldati-Favre D. Toxoplasma gondii phosphatidylserine flippase complex ATP2B-CDC50.4 critically participates in microneme exocytosis. PLoS Pathog 2022; 18:e1010438. [PMID: 35325010 PMCID: PMC8982854 DOI: 10.1371/journal.ppat.1010438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 04/05/2022] [Accepted: 03/11/2022] [Indexed: 12/22/2022] Open
Abstract
Regulated microneme secretion governs motility, host cell invasion and egress in the obligate intracellular apicomplexans. Intracellular calcium oscillations and phospholipid dynamics critically regulate microneme exocytosis. Despite its importance for the lytic cycle of these parasites, molecular mechanistic details about exocytosis are still missing. Some members of the P4-ATPases act as flippases, changing the phospholipid distribution by translocation from the outer to the inner leaflet of the membrane. Here, the localization and function of the repertoire of P4-ATPases was investigated across the lytic cycle of Toxoplasma gondii. Of relevance, ATP2B and the non-catalytic subunit cell division control protein 50.4 (CDC50.4) form a stable heterocomplex at the parasite plasma membrane, essential for microneme exocytosis. This complex is responsible for flipping phosphatidylserine, which presumably acts as a lipid mediator for organelle fusion with the plasma membrane. Overall, this study points toward the importance of phosphatidylserine asymmetric distribution at the plasma membrane for microneme exocytosis. Biological membranes display diverse functions, including membrane fusion, which are conferred by a defined composition and organization of proteins and lipids. Apicomplexan parasites possess specialized secretory organelles (micronemes), implicated in motility, invasion and egress from host cells. Microneme exocytosis is already known to depend on phosphatidic acid for its fusion with the plasma membrane. Here we identify a type P4-ATPase and its CDC50 chaperone (ATP2B-CDC50.4) that act as a flippase and contribute to the enrichment of phosphatidylserine (PS) in the inner leaflet of the parasite plasma membrane. The disruption of PS asymmetric distribution at the plasma membrane impacts microneme exocytosis. Overall, our results shed light on the importance of membrane homeostasis and lipid composition in controlling microneme secretion.
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Affiliation(s)
- Hugo Bisio
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aarti Krishnan
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Baptiste Marq
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- * E-mail:
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Lambert E, Mehdipour AR, Schmidt A, Hummer G, Perez C. Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nat Commun 2022; 13:1022. [PMID: 35197476 PMCID: PMC8866510 DOI: 10.1038/s41467-022-28361-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/23/2022] [Indexed: 02/08/2023] Open
Abstract
Transport of lipids across membranes is fundamental for diverse biological pathways in cells. Multiple ion-coupled transporters take part in lipid translocation, but their mechanisms remain largely unknown. Major facilitator superfamily (MFS) lipid transporters play central roles in cell wall synthesis, brain development and function, lipids recycling, and cell signaling. Recent structures of MFS lipid transporters revealed overlapping architectural features pointing towards a common mechanism. Here we used cysteine disulfide trapping, molecular dynamics simulations, mutagenesis analysis, and transport assays in vitro and in vivo, to investigate the mechanism of LtaA, a proton-dependent MFS lipid transporter essential for lipoteichoic acid synthesis in the pathogen Staphylococcus aureus. We reveal that LtaA displays asymmetric lateral openings with distinct functional relevance and that cycling through outward- and inward-facing conformations is essential for transport activity. We demonstrate that while the entire amphipathic central cavity of LtaA contributes to lipid binding, its hydrophilic pocket dictates substrate specificity. We propose that LtaA catalyzes lipid translocation by a ‘trap-and-flip’ mechanism that might be shared among MFS lipid transporters. LtaA catalyzes glycolipid translocation by a ‘trap-and-flip’ mechanism, pointing to a shared mechanistic model among MFS lipid transporters. Asymmetric lateral openings allow access of the entire lipid substrate to the amphipathic central cavity.
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Affiliation(s)
| | | | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gerhard Hummer
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Camilo Perez
- Biozentrum, University of Basel, Basel, Switzerland.
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Wang J, Yu C, Zhuang J, Qi W, Jiang J, Liu X, Zhao W, Cao Y, Wu H, Qi J, Zhao RC. The role of phosphatidylserine on the membrane in immunity and blood coagulation. Biomark Res 2022; 10:4. [PMID: 35033201 PMCID: PMC8760663 DOI: 10.1186/s40364-021-00346-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/17/2022] Open
Abstract
The negatively charged aminophospholipid, phosphatidylserine (PtdSer), is located in the inner leaflet of the plasma membrane in normal cells, and may be exposed to the outer leaflet under some immune and blood coagulation processes. Meanwhile, Ptdser exposed to apoptotic cells can be recognized and eliminated by various immune cells, whereas on the surface of activated platelets Ptdser interacts with coagulation factors prompting enhanced production of thrombin which significantly facilitates blood coagulation. In the case where PtdSer fails in exposure or mistakenly occurs, there are occurrences of certain immunological and haematological diseases, such as the Scott syndrome and Systemic lupus erythematosus. Besides, viruses (e.g., Human Immunodeficiency Virus (HIV), Ebola virus (EBOV)) can invade host cells through binding the exposed PtdSer. Most recently, the Corona Virus Disease 2019 (COVID-19) has been similarly linked to PtdSer or its receptors. Therefore, it is essential to comprehensively understand PtdSer and its functional characteristics. Therefore, this review summarizes Ptdser, its eversion mechanism; interaction mechanism, particularly with its immune receptors and coagulation factors; recognition sites; and its function in immune and blood processes. This review illustrates the potential aspects for the underlying pathogenic mechanism of PtdSer-related diseases, and the discovery of new therapeutic strategies as well.
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Affiliation(s)
- Jiao Wang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | - Changxin Yu
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Junyi Zhuang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Wenxin Qi
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Jiawen Jiang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Xuanting Liu
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Wanwei Zhao
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Yiyang Cao
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Hao Wu
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Jingxuan Qi
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Robert Chunhua Zhao
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, No. 5 Dongdansantiao, Beijing, 100005, China.
- Centre of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences, Beijing, China.
- Beijing Key Laboratory of New Drug Development and Clinical Trial of Stem Cell Therapy (BZ0381), Beijing, China.
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Alipoor SD, Mirsaeidi M. SARS-CoV-2 cell entry beyond the ACE2 receptor. Mol Biol Rep 2022; 49:10715-10727. [PMID: 35754059 PMCID: PMC9244107 DOI: 10.1007/s11033-022-07700-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/09/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Angiotensin-converting enzyme 2 (ACE2) is known as the major viral entry site for SARS-CoV-2. However, viral tissue tropism and high rate of infectivity do not directly correspond with the level of ACE2 expression in the organs. It may suggest involvement of other receptors or accessory membrane proteins in SARSCoV-2 cell entry. METHODS AND RESULTS A systematic search was carried out in PubMed/Medline, EMBASE, and Cochrane Library for studies reporting SARS-CoV-2 cell entry. We used a group of the MeSH terms including "cell entry", "surface receptor", "ACE2", and "SARS-CoV-2". We reviewed all selected papers published in English up to end of February 2022. We found several receptors or auxiliary membrane proteins (including CD147, NRP-1, CD26, AGTR2, Band3, KREMEN1, ASGR1, ANP, TMEM30A, CLEC4G, and LDLRAD3) along with ACE2 that facilitate virus entry and transmission. Expression of Band3 protein on the surface of erythrocytes and evidence of binding with S protein of SARS-CoV-2 may explain asymptomatic hypoxemia during COVID19 infection. The variants of SARS-CoV-2 including the B.1.1.7 (Alpha), B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.617.2+ (Delta+), and B.1.1.529 (Omicron) may have different potency to bond with these receptors. CONCLUSIONS The high rate of infectivity of SARS-CoV-2 may be due to its ability to enter the host cell through a group of cell surface receptors. These receptors are potential targets to develop novel therapeutic agents for SARS-CoV-2.
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Affiliation(s)
- Shamila D. Alipoor
- grid.419420.a0000 0000 8676 7464Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic, Engineering and Biotechnology, Tehran, Iran
| | - Mehdi Mirsaeidi
- grid.15276.370000 0004 1936 8091Division of Pulmonary, Critical Care, and Sleep Disease, College of Medicine-Jacksonville, University of Florida, Jacksonville, FL USA
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49
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Egea PF. Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, Funnels. Front Cell Dev Biol 2021; 9:784367. [PMID: 34912813 PMCID: PMC8667587 DOI: 10.3389/fcell.2021.784367] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic cells are characterized by their exquisite compartmentalization resulting from a cornucopia of membrane-bound organelles. Each of these compartments hosts a flurry of biochemical reactions and supports biological functions such as genome storage, membrane protein and lipid biosynthesis/degradation and ATP synthesis, all essential to cellular life. Acting as hubs for the transfer of matter and signals between organelles and throughout the cell, membrane contacts sites (MCSs), sites of close apposition between membranes from different organelles, are essential to cellular homeostasis. One of the now well-acknowledged function of MCSs involves the non-vesicular trafficking of lipids; its characterization answered one long-standing question of eukaryotic cell biology revealing how some organelles receive and distribute their membrane lipids in absence of vesicular trafficking. The endoplasmic reticulum (ER) in synergy with the mitochondria, stands as the nexus for the biosynthesis and distribution of phospholipids (PLs) throughout the cell by contacting nearly all other organelle types. MCSs create and maintain lipid fluxes and gradients essential to the functional asymmetry and polarity of biological membranes throughout the cell. Membrane apposition is mediated by proteinaceous tethers some of which function as lipid transfer proteins (LTPs). We summarize here the current state of mechanistic knowledge of some of the major classes of LTPs and tethers based on the available atomic to near-atomic resolution structures of several "model" MCSs from yeast but also in Metazoans; we describe different models of lipid transfer at MCSs and analyze the determinants of their specificity and directionality. Each of these systems illustrate fundamental principles and mechanisms for the non-vesicular exchange of lipids between eukaryotic membrane-bound organelles essential to a wide range of cellular processes such as at PL biosynthesis and distribution, lipid storage, autophagy and organelle biogenesis.
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Affiliation(s)
- Pascal F Egea
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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50
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Nakanishi H, Hayashida K, Nishizawa T, Oshima A, Abe K. Cryo-EM of the ATP11C flippase reconstituted in Nanodiscs shows a distended phospholipid bilayer inner membrane around transmembrane helix 2. J Biol Chem 2021; 298:101498. [PMID: 34922944 PMCID: PMC8733269 DOI: 10.1016/j.jbc.2021.101498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/26/2022] Open
Abstract
ATP11C is a member of the P4-ATPase flippase family that mediates translocation of phosphatidylserine (PtdSer) across the lipid bilayer. In order to characterize the structure and function of ATP11C in a model natural lipid environment, we revisited and optimized a quick procedure for reconstituting ATP11C into Nanodiscs using methyl-β-cyclodextrin as a reagent for the detergent removal. ATP11C was efficiently reconstituted with the endogenous lipid, or the mixture of endogenous lipid and synthetic dioleoylphosphatidylcholine (DOPC)/dioleoylphosphatidylserine (DOPS), all of which retained the ATPase activity. We obtained 3.4 Å and 3.9 Å structures using single-particle cryo-electron microscopy (cryo-EM) of AlF- and BeF-stabilized ATP11C transport intermediates, respectively, in a bilayer containing DOPS. We show that the latter exhibited a distended inner membrane around ATP11C transmembrane helix 2, possibly reflecting the perturbation needed for phospholipid release to the lipid bilayer. Our structures of ATP11C in the lipid membrane indicate that the membrane boundary varies upon conformational changes of the enzyme and is no longer flat around the protein, a change that likely contributes to phospholipid translocation across the membrane leaflets.
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Affiliation(s)
- Hanayo Nakanishi
- Cellular and Structural Physiology Institute, Nagoya University, 464-8601, Japan
| | - Kenichi Hayashida
- Cellular and Structural Physiology Institute, Nagoya University, 464-8601, Japan
| | - Tomohiro Nishizawa
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute, Nagoya University, 464-8601, Japan; Graduate School of Pharmaceutical Sciences, Nagoya University, 464-8601, Japan; Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, 464-8601, Japan; Graduate School of Pharmaceutical Sciences, Nagoya University, 464-8601, Japan.
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