1
|
Sai KV, Lee JY. Crossing the membrane - what does it take to flip a phospholipid? Structural and biochemical advances on P4-ATPase flippases. J Biol Chem 2024:107738. [PMID: 39233230 DOI: 10.1016/j.jbc.2024.107738] [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: 04/02/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/06/2024] Open
Abstract
Membrane asymmetry is critical for maintenance of several different processes such as cell signalling, apoptosis, and vesicular transport in various eukaryotic systems. Flippases of the P4-ATPase family are associated with flipping phospholipids from the luminal or exoplasmic leaflet to the cytosolic leaflet. P4-ATPases belong to the P-type ATPase family, which are activated by phosphorylation and couple ATPase activity to substrate translocation. These proteins possess a transmembrane domain responsible for substrate transport, while the cytosolic machinery perform the necessary ATP hydrolysis for this process. Several high-resolution structures of human or yeast P4-ATPases have recently been resolved, but a comprehensive overview of the changes for reaction cycle in different members was crucial for future research. In this review, we have compiled available data reflecting the reaction cycle-associated changes in conformation of P4-ATPases. Together, this will provide an improved understanding of the similarities and differences between these members, which will drive further structural, functional and computational studies to understand the mechanisms of these flippases.
Collapse
Affiliation(s)
- Kadambari Vijay Sai
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5
| | - Jyh-Yeuan Lee
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5.
| |
Collapse
|
2
|
Takatsu H, Nishimura N, Kosugi Y, Ogawa H, Nakayama K, Colin E, Platzer K, Abou Jamra R, Redler S, Prouteau C, Ziegler A, Shin HW. De Novo Missense Variations of ATP8B2 Impair Its Phosphatidylcholine Flippase Activity. Mol Cell Biol 2024:1-16. [PMID: 39219493 DOI: 10.1080/10985549.2024.2391829] [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: 04/01/2024] [Revised: 07/11/2024] [Accepted: 07/27/2024] [Indexed: 09/04/2024] Open
Abstract
P4-ATPases comprise a family of lipid flippases that translocate lipids from the exoplasmic (or luminal) to the cytoplasmic leaflet of biological membranes. Of the 14 known human P4-ATPases, ATP8B2 is a phosphatidylcholine flippase at the plasma membrane, but its physiological function is not well understood. Although ATP8B2 could interact with both CDC50A and CDC50B, it required only the CDC50A interaction for its exit from the endoplasmic reticulum and subsequent transport to the plasma membrane. Three de novo monoallelic missense variations of ATP8B2 were found in patients with intellectual disability. None of these variations affected the interaction of ATP8B2 with CDC50A or its localization to the plasma membrane. However, variations of either of two amino acid residues, which are conserved in all P4-ATPases, significantly reduced the phosphatidylcholine flippase activity of ATP8B2. Furthermore, mutations in the corresponding residues of ATP8B1 and ATP11C were found to decrease their flippase activities toward phosphatidylcholine and phosphatidylserine, respectively. These results indicate that the conserved amino acid residues are crucial for the enzymatic activities of the P4-ATPases.
Collapse
Affiliation(s)
- Hiroyuki Takatsu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Narumi Nishimura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Kosugi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Haruo Ogawa
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Estelle Colin
- Department of Medical Genetics, Angers University Hospital, Angers, France
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Silke Redler
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Clément Prouteau
- Department of Medical Genetics, Angers University Hospital, Angers, France
| | - Alban Ziegler
- Department of Medical Genetics, Angers University Hospital, Angers, France
| | - Hye-Won Shin
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Hou G, Wang X, Wang A, Yuan L, Zheng Q, Xiao H, Wang H. The role of secreted proteins in efferocytosis. Front Cell Dev Biol 2024; 11:1332482. [PMID: 38259511 PMCID: PMC10800375 DOI: 10.3389/fcell.2023.1332482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The clearance of apoptotic cells known as efferocytosis is the final stage of apoptosis, and includes the recognition, phagocytosis, and degradation of apoptotic cells. The maintenance of tissue homeostasis requires the daily elimination of billions of apoptotic cells from the human body via the process of efferocytosis. Accordingly, aberrations in efferocytosis underlie a growing list of diseases, including atherosclerosis, cancer, and infections. During the initial phase of apoptosis, "Eat-Me" signals are exposed and recognized by phagocytes either directly through phagocyte receptors or indirectly through secreted proteins that function as bridge molecules that cross-link dying cells to phagocytes. Here, we set out to provide a comprehensive review of the molecular mechanisms and biological significance of secreted proteins in apoptotic cell clearance. Specifically, it focuses on how these secreted proteins act as bridging molecules to facilitate the clearance process.
Collapse
Affiliation(s)
| | | | | | | | | | - Hui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Hui Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
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
| | | |
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
| |
Collapse
|
9
|
Chen S, Song X, Xiao Q, Wang L, Zhu X, Zou Y, Li G. Knockdown of TMEM30A in renal tubular epithelial cells leads to reduced glucose absorption. BMC Nephrol 2023; 24:250. [PMID: 37612668 PMCID: PMC10464243 DOI: 10.1186/s12882-023-03299-8] [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: 10/23/2022] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
The kidney reabsorbs large amounts of glucose through Na+-glucose cotransporter 2 (SGLT2). P4-ATPase acts together with the β-subunit TMEM30A to mediate the asymmetric distribution of phosphatidylserine (PS), phosphatidylethanolamine (PE), and other amino phospholipids, promoting plasma membrane and internal vesicle fusion, and facilitating vesicle protein transport. We observed reduced TMEM30A expression in renal tubules of DKD and IgA patients, suggesting a potential role of TMEM30A in renal tubular cells. To investigate the role of TMEM30A in renal tubules, we constructed a TMEM30A knockdown cell model by transfecting mouse kidney tubular epithelium cells (TCMK-1) with TMEM30A shRNA. Knockdown of TMEM30A in TCMK-1 cells attenuated vesicle transporter protein synthesis, resulting in reduced transport and expression of SGLT2, which in turn reduced glucose absorption. These data suggested that TMEM30A plays a crucial role in renal tubules.
Collapse
Affiliation(s)
- Sipei Chen
- Department of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2Nd Duan, 1St Circle Road, Qingyang District, Chengdu, 610072, Sichuan, China
| | - Xinrou Song
- Department of Nephrology, Chengdu Fifth People's Hospital, Chengdu, China
| | - Qiong Xiao
- Department of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2Nd Duan, 1St Circle Road, Qingyang District, Chengdu, 610072, Sichuan, China
| | - Li Wang
- Department of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2Nd Duan, 1St Circle Road, Qingyang District, Chengdu, 610072, Sichuan, China
| | - Xianjun Zhu
- Department of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2Nd Duan, 1St Circle Road, Qingyang District, Chengdu, 610072, Sichuan, China
| | - Yang Zou
- Department of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2Nd Duan, 1St Circle Road, Qingyang District, Chengdu, 610072, Sichuan, China
| | - Guisen Li
- Department of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2Nd Duan, 1St Circle Road, Qingyang District, Chengdu, 610072, Sichuan, China.
| |
Collapse
|
10
|
Kalli S, Vallieres C, Violet J, Sanders JW, Chapman J, Vincken JP, Avery SV, Araya-Cloutier C. Cellular Responses and Targets in Food Spoilage Yeasts Exposed to Antifungal Prenylated Isoflavonoids. Microbiol Spectr 2023; 11:e0132723. [PMID: 37428107 PMCID: PMC10433819 DOI: 10.1128/spectrum.01327-23] [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: 03/31/2023] [Accepted: 06/17/2023] [Indexed: 07/11/2023] Open
Abstract
Prenylated isoflavonoids are phytochemicals with promising antifungal properties. Recently, it was shown that glabridin and wighteone disrupted the plasma membrane (PM) of the food spoilage yeast Zygosaccharomyces parabailii in distinct ways, which led us to investigate further their modes of action (MoA). Transcriptomic profiling with Z. parabailii showed that genes encoding transmembrane ATPase transporters, including Yor1, and genes homologous to the pleiotropic drug resistance (PDR) subfamily in Saccharomyces cerevisiae were upregulated in response to both compounds. Gene functions involved in fatty acid and lipid metabolism, proteostasis, and DNA replication processes were overrepresented among genes upregulated by glabridin and/or wighteone. Chemogenomic analysis using the genome-wide deletant collection for S. cerevisiae further suggested an important role for PM lipids and PM proteins. Deletants of gene functions involved in biosynthesis of very-long-chain fatty acids (constituents of PM sphingolipids) and ergosterol were hypersensitive to both compounds. Using lipid biosynthesis inhibitors, we corroborated roles for sphingolipids and ergosterol in prenylated isoflavonoid action. The PM ABC transporter Yor1 and Lem3-dependent flippases conferred sensitivity and resistance, respectively, to the compounds, suggesting an important role for PM phospholipid asymmetry in their MoAs. Impaired tryptophan availability, likely linked to perturbation of the PM tryptophan permease Tat2, was evident in response to glabridin. Finally, substantial evidence highlighted a role of the endoplasmic reticulum (ER) in cellular responses to wighteone, including gene functions associated with ER membrane stress or with phospholipid biosynthesis, the primary lipid of the ER membrane. IMPORTANCE Preservatives, such as sorbic acid and benzoic acid, inhibit the growth of undesirable yeast and molds in foods. Unfortunately, preservative tolerance and resistance in food spoilage yeast, such as Zygosaccharomyces parabailii, is a growing challenge in the food industry, which can compromise food safety and increase food waste. Prenylated isoflavonoids are the main defense phytochemicals in the Fabaceae family. Glabridin and wighteone belong to this group of compounds and have shown potent antifungal activity against food spoilage yeasts. The present study demonstrated the mode of action of these compounds against food spoilage yeasts by using advanced molecular tools. Overall, the cellular actions of these two prenylated isoflavonoids share similarities (at the level of the plasma membrane) but also differences. Tryptophan import was specifically affected by glabridin, whereas endoplasmic reticulum membrane stress was specifically induced by wighteone. Understanding the mode of action of these novel antifungal agents is essential for their application in food preservation.
Collapse
Affiliation(s)
- Sylvia Kalli
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Cindy Vallieres
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Joseph Violet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - John Chapman
- Unilever Foods Innovation Centre, Wageningen, the Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Carla Araya-Cloutier
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, the Netherlands
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
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: 44] [Impact Index Per Article: 44.0] [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.
Collapse
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.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Kalavacherla T, Buschmann S, Schleker ESM, Michel H, Reinhart C. Purification and characterization of eukaryotic ATP-dependent transporters homologously expressed in Pichia pastoris for structural studies by cryo-electron microscopy. Protein Expr Purif 2023; 204:106230. [PMID: 36632890 DOI: 10.1016/j.pep.2023.106230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/01/2023] [Indexed: 01/09/2023]
Abstract
Membrane proteins play an essential role in all living organisms. Although there have been numerous efforts in the past to elucidate the structure and function of eukaryotic primary active transporters, knowledge about the majority of these membrane proteins is still minimal. This is often due to their low availability and complex handling. In this study, we homologously expressed three ATP-dependent transport proteins, STE6-2p, NEO1-p, and YPK9-p, in Pichia pastoris and subsequently optimized the solubilization and purification processes. Sequential use of different mild detergents and utilization of hydrophilic matrices in the purification procedure allowed us to obtain all three transporters monodisperse and in high purity, enabling initial structural analysis by cryo-electron microscopy. Using the respective substrates, we determined the specific activity of all target proteins using an ATPase assay. This study opens the door to further functional and structural studies of this pharmacologically important class of membrane proteins.
Collapse
Affiliation(s)
- Tejaswi Kalavacherla
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany
| | - Sabine Buschmann
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany
| | - E Sabine M Schleker
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany
| | - Christoph Reinhart
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, D-60438, Frankfurt am Main, Germany.
| |
Collapse
|
15
|
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.
Collapse
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:
| |
Collapse
|
16
|
Functional Analysis of the P-Type ATPases Apt2-4 from Cryptococcus neoformans by Heterologous Expression in Saccharomyces cerevisiae. J Fungi (Basel) 2023; 9:jof9020202. [PMID: 36836316 PMCID: PMC9966271 DOI: 10.3390/jof9020202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Lipid flippases of the P4-ATPase family actively transport phospholipids across cell membranes, an activity essential for key cellular processes such as vesicle budding and membrane trafficking. Members of this transporter family have also been implicated in the development of drug resistance in fungi. The encapsulated fungal pathogen Cryptococcus neoformans contains four P4-ATPases, among which Apt2-4p are poorly characterized. Using heterologous expression in the flippase-deficient S. cerevisiae strain dnf1Δdnf2Δdrs2Δ, we tested their lipid flippase activity in comparison to Apt1p using complementation tests and fluorescent lipid uptake assays. Apt2p and Apt3p required the co-expression of the C. neoformans Cdc50 protein for activity. Apt2p/Cdc50p displayed a narrow substrate specificity, limited to phosphatidylethanolamine and -choline. Despite its inability to transport fluorescent lipids, the Apt3p/Cdc50p complex still rescued the cold-sensitive phenotype of dnf1Δdnf2Δdrs2Δ, suggesting a functional role for the flippase in the secretory pathway. Apt4p, the closest homolog to Saccharomyces Neo1p, which does not require a Cdc50 protein, was unable to complement several flippase-deficient mutant phenotypes, neither in the presence nor absence of a β-subunit. These results identify C. neoformans Cdc50 as an essential subunit for Apt1-3p and provide a first insight into the molecular mechanisms underlying their physiological functions.
Collapse
|
17
|
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.
Collapse
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
| | | |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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: 3] [Impact Index Per Article: 1.5] [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.
Collapse
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
| |
Collapse
|
20
|
Thorner J. TOR complex 2 is a master regulator of plasma membrane homeostasis. Biochem J 2022; 479:1917-1940. [PMID: 36149412 PMCID: PMC9555796 DOI: 10.1042/bcj20220388] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
As first demonstrated in budding yeast (Saccharomyces cerevisiae), all eukaryotic cells contain two, distinct multi-component protein kinase complexes that each harbor the TOR (Target Of Rapamycin) polypeptide as the catalytic subunit. These ensembles, dubbed TORC1 and TORC2, function as universal, centrally important sensors, integrators, and controllers of eukaryotic cell growth and homeostasis. TORC1, activated on the cytosolic surface of the lysosome (or, in yeast, on the cytosolic surface of the vacuole), has emerged as a primary nutrient sensor that promotes cellular biosynthesis and suppresses autophagy. TORC2, located primarily at the plasma membrane, plays a major role in maintaining the proper levels and bilayer distribution of all plasma membrane components (sphingolipids, glycerophospholipids, sterols, and integral membrane proteins). This article surveys what we have learned about signaling via the TORC2 complex, largely through studies conducted in S. cerevisiae. In this yeast, conditions that challenge plasma membrane integrity can, depending on the nature of the stress, stimulate or inhibit TORC2, resulting in, respectively, up-regulation or down-regulation of the phosphorylation and thus the activity of its essential downstream effector the AGC family protein kinase Ypk1. Through the ensuing effect on the efficiency with which Ypk1 phosphorylates multiple substrates that control diverse processes, membrane homeostasis is maintained. Thus, the major focus here is on TORC2, Ypk1, and the multifarious targets of Ypk1 and how the functions of these substrates are regulated by their Ypk1-mediated phosphorylation, with emphasis on recent advances in our understanding of these processes.
Collapse
Affiliation(s)
- Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, U.S.A
| |
Collapse
|
21
|
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
| | | |
Collapse
|
22
|
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.
Collapse
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:
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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: 16] [Impact Index Per Article: 8.0] [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.
Collapse
|
25
|
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: 12] [Impact Index Per Article: 6.0] [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.
Collapse
|
26
|
Fischer S, Weber LM, Liefke R. Evolutionary adaptation of the Polycomb repressive complex 2. Epigenetics Chromatin 2022; 15:7. [PMID: 35193659 PMCID: PMC8864842 DOI: 10.1186/s13072-022-00439-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/08/2022] [Indexed: 12/31/2022] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is an essential chromatin regulatory complex involved in repressing the transcription of diverse developmental genes. PRC2 consists of a core complex; possessing H3K27 methyltransferase activity and various associated factors that are important to modulate its function. During evolution, the composition of PRC2 and the functionality of PRC2 components have changed considerably. Here, we compare the PRC2 complex members of Drosophila and mammals and describe their adaptation to altered biological needs. We also highlight how the PRC2.1 subcomplex has gained multiple novel functions and discuss the implications of these changes for the function of PRC2 in chromatin regulation.
Collapse
Affiliation(s)
- Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043, Marburg, Germany
| | - Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043, Marburg, Germany
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043, Marburg, Germany. .,Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, 35043, Marburg, Germany.
| |
Collapse
|
27
|
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: 7] [Impact Index Per Article: 2.3] [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.
Collapse
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.
| |
Collapse
|
28
|
Tomita A, Daiho T, Kusakizako T, Yamashita K, Ogasawara S, Murata T, Nishizawa T, Nureki O. Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2. Mol Cell 2021; 81:4799-4809.e5. [PMID: 34798056 DOI: 10.1016/j.molcel.2021.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/26/2021] [Accepted: 11/01/2021] [Indexed: 01/11/2023]
Abstract
The cytoplasmic polyamine maintains cellular homeostasis by chelating toxic metal cations, regulating transcriptional activity, and protecting DNA. ATP13A2 was identified as a lysosomal polyamine exporter responsible for polyamine release into the cytosol, and its dysfunction is associated with Alzheimer's disease and other neural degradation diseases. ATP13A2 belongs to the P5 subfamily of the P-type ATPase family, but its mechanisms remain unknown. Here, we report the cryoelectron microscopy (cryo-EM) structures of human ATP13A2 under four different conditions, revealing the structural coupling between the polyamine binding and the dephosphorylation. Polyamine is bound at the luminal tunnel and recognized through numerous electrostatic and π-cation interactions, explaining its broad specificity. The unique N-terminal domain is anchored to the lipid membrane to stabilize the E2P conformation, thereby accelerating the E1P-to-E2P transition. These findings reveal the distinct mechanism of P5B ATPases, thereby paving the way for neuroprotective therapy by activating ATP13A2.
Collapse
Affiliation(s)
- Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Daiho
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Tsurumi, Yokohama 230-0045, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
29
|
Sim SI, von Bülow S, Hummer G, Park E. Structural basis of polyamine transport by human ATP13A2 (PARK9). Mol Cell 2021; 81:4635-4649.e8. [PMID: 34715013 DOI: 10.1016/j.molcel.2021.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/17/2021] [Accepted: 08/11/2021] [Indexed: 02/03/2023]
Abstract
Polyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have suggested that ATP13A2 and its close homologs, collectively known as P5B-ATPases, are polyamine transporters at endo-/lysosomes. Loss-of-function mutations of ATP13A2 in humans cause hereditary early-onset Parkinson's disease. To understand the polyamine transport mechanism of ATP13A2, we determined high-resolution cryoelectron microscopy (cryo-EM) structures of human ATP13A2 in five distinct conformational intermediates, which together, represent a near-complete transport cycle of ATP13A2. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, in which polyamines may exit within the cytosolic leaflet of the membrane. Our study provides important mechanistic insights into polyamine transport and a framework to understand the functions and mechanisms of P5B-ATPases.
Collapse
Affiliation(s)
- Sue Im Sim
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
30
|
Zhao P, Zhao C, Chen D, Yun C, Li H, Bai L. Structure and activation mechanism of the hexameric plasma membrane H +-ATPase. Nat Commun 2021; 12:6439. [PMID: 34750373 PMCID: PMC8575881 DOI: 10.1038/s41467-021-26782-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022] Open
Abstract
The S. cerevisiae plasma membrane H+-ATPase, Pma1, is a P3A-type ATPase and the primary protein component of the membrane compartment of Pma1 (MCP). Like other plasma membrane H+-ATPases, Pma1 assembles and functions as a hexamer, a property unique to this subfamily among the larger family of P-type ATPases. It has been unclear how Pma1 organizes the yeast membrane into MCP microdomains, or why it is that Pma1 needs to assemble into a hexamer to establish the membrane electrochemical proton gradient. Here we report a high-resolution cryo-EM study of native Pma1 hexamers embedded in endogenous lipids. Remarkably, we found that the Pma1 hexamer encircles a liquid-crystalline membrane domain composed of 57 ordered lipid molecules. The Pma1-encircled lipid patch structure likely serves as the building block of the MCP. At pH 7.4, the carboxyl-terminal regulatory α-helix binds to the phosphorylation domains of two neighboring Pma1 subunits, locking the hexamer in the autoinhibited state. The regulatory helix becomes disordered at lower pH, leading to activation of the Pma1 hexamer. The activation process is accompanied by a 6.7 Å downward shift and a 40° rotation of transmembrane helices 1 and 2 that line the proton translocation path. The conformational changes have enabled us to propose a detailed mechanism for ATP-hydrolysis-driven proton pumping across the plasma membrane. Our structures will facilitate the development of antifungal drugs that target this essential protein.
Collapse
Affiliation(s)
- Peng Zhao
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chaoran Zhao
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Dandan Chen
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Caihong Yun
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China.
| |
Collapse
|
31
|
Bai L, Jain BK, You Q, Duan HD, Takar M, Graham TR, Li H. Structural basis of the P4B ATPase lipid flippase activity. Nat Commun 2021; 12:5963. [PMID: 34645814 PMCID: PMC8514546 DOI: 10.1038/s41467-021-26273-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
P4 ATPases are lipid flippases that are phylogenetically grouped into P4A, P4B and P4C clades. The P4A ATPases are heterodimers composed of a catalytic α-subunit and accessory β-subunit, and the structures of several heterodimeric flippases have been reported. The S. cerevisiae Neo1 and its orthologs represent the P4B ATPases, which function as monomeric flippases without a β-subunit. It has been unclear whether monomeric flippases retain the architecture and transport mechanism of the dimeric flippases. Here we report the structure of a P4B ATPase, Neo1, in its E1-ATP, E2P-transition, and E2P states. The structure reveals a conserved architecture as well as highly similar functional intermediate states relative to dimeric flippases. Consistently, structure-guided mutagenesis of residues in the proposed substrate translocation path disrupted Neo1’s ability to establish membrane asymmetry. These observations indicate that evolutionarily distant P4 ATPases use a structurally conserved mechanism for substrate transport. The P4 ATPase lipid flippases play a crucial role in membrane biogenesis. Here the authors report the structure of the monomeric P4B ATPase Neo1 in several states, clarifying the mechanism of substrate transport.
Collapse
Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China.
| | - Bhawik K Jain
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Qinglong You
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - H Diessel Duan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Mehmet Takar
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| |
Collapse
|
32
|
López-Marqués RL. Lipid flippases as key players in plant adaptation to their environment. NATURE PLANTS 2021; 7:1188-1199. [PMID: 34531559 DOI: 10.1038/s41477-021-00993-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Lipid flippases (P4 ATPases) are active transporters that catalyse the translocation of lipids between the two sides of the biological membranes in the secretory pathway. This activity modulates biological membrane properties, contributes to vesicle formation, and is the trigger for lipid signalling events, which makes P4 ATPases essential for eukaryotic cell survival. Plant P4 ATPases (also known as aminophospholipid ATPases (ALAs)) are crucial for plant fertility and proper development, and are involved in key adaptive responses to biotic and abiotic stress, including chilling tolerance, heat adaptation, nutrient deficiency responses and pathogen defence. While ALAs present many analogies to mammalian and yeast P4 ATPases, they also show characteristic features as the result of their independent evolution. In this Review, the main properties, roles, regulation and mechanisms of action of ALA proteins are discussed.
Collapse
Affiliation(s)
- Rosa L López-Marqués
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
| |
Collapse
|
33
|
Ristovski M, Farhat D, Bancud SEM, Lee JY. Lipid Transporters Beam Signals from Cell Membranes. MEMBRANES 2021; 11:562. [PMID: 34436325 PMCID: PMC8399137 DOI: 10.3390/membranes11080562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
Lipid composition in cellular membranes plays an important role in maintaining the structural integrity of cells and in regulating cellular signaling that controls functions of both membrane-anchored and cytoplasmic proteins. ATP-dependent ABC and P4-ATPase lipid transporters, two integral membrane proteins, are known to contribute to lipid translocation across the lipid bilayers on the cellular membranes. In this review, we will highlight current knowledge about the role of cholesterol and phospholipids of cellular membranes in regulating cell signaling and how lipid transporters participate this process.
Collapse
Affiliation(s)
- Miliça Ristovski
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (M.R.); (D.F.); (S.E.M.B.)
- Translational and Molecular Medicine Program, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Danny Farhat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (M.R.); (D.F.); (S.E.M.B.)
- Biomedical Sciences Program, Faculty of Science, University of Ottawa, Ottawa, ON K1H 6N5, Canada
| | - Shelly Ellaine M. Bancud
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (M.R.); (D.F.); (S.E.M.B.)
- Translational and Molecular Medicine Program, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jyh-Yeuan Lee
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (M.R.); (D.F.); (S.E.M.B.)
| |
Collapse
|
34
|
Structural Basis of Substrate-Independent Phosphorylation in a P4-ATPase Lipid Flippase. J Mol Biol 2021; 433:167062. [PMID: 34023399 DOI: 10.1016/j.jmb.2021.167062] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 11/21/2022]
Abstract
P4-ATPases define a eukaryotic subfamily of the P-type ATPases, and are responsible for the transverse flip of specific lipids from the extracellular or luminal leaflet to the cytosolic leaflet of cell membranes. The enzymatic cycle of P-type ATPases is divided into autophosphorylation and dephosphorylation half-reactions. Unlike most other P-type ATPases, P4-ATPases transport their substrate during dephosphorylation only, i.e. the phosphorylation half-reaction is not associated with transport. To study the structural basis of the distinct mechanisms of P4-ATPases, we have determined cryo-EM structures of Drs2p-Cdc50p from Saccharomyces cerevisiae covering multiple intermediates of the cycle. We identify several structural motifs specific to Drs2p and P4-ATPases in general that decrease movements and flexibility of domains as compared to other P-type ATPases such as Na+/K+-ATPase or Ca2+-ATPase. These motifs include the linkers that connect the transmembrane region to the actuator (A) domain, which is responsible for dephosphorylation. Additionally, mutation of Tyr380, which interacts with conserved Asp340 of the distinct DGET dephosphorylation loop of P4-ATPases, highlights a functional role of these P4-ATPase specific motifs in the A-domain. Finally, the transmembrane (TM) domain, responsible for transport, also undergoes less extensive conformational changes, which is ensured both by a longer segment connecting TM helix 4 with the phosphorylation site, and possible stabilization by the auxiliary subunit Cdc50p. Collectively these adaptions in P4-ATPases are responsible for phosphorylation becoming transport-independent.
Collapse
|