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Maeda M, Arakawa M, Komatsu Y, Saito K. Small GTPase ActIvitY ANalyzing (SAIYAN) system: A method to detect GTPase activation in living cells. J Cell Biol 2024; 223:e202403179. [PMID: 39101946 DOI: 10.1083/jcb.202403179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/10/2024] [Accepted: 07/11/2024] [Indexed: 08/06/2024] Open
Abstract
Small GTPases are essential in various cellular signaling pathways, and detecting their activation within living cells is crucial for understanding cellular processes. The current methods for detecting GTPase activation using fluorescent proteins rely on the interaction between the GTPase and its effector. Consequently, these methods are not applicable to factors, such as Sar1, where the effector also functions as a GTPase-activating protein. Here, we present a novel method, the Small GTPase ActIvitY ANalyzing (SAIYAN) system, for detecting the activation of endogenous small GTPases via fluorescent signals utilizing a split mNeonGreen system. We demonstrated Sar1 activation at the endoplasmic reticulum (ER) exit site and successfully detected its activation state in various cellular conditions. Utilizing the SAIYAN system in collagen-secreting cells, we discovered activated Sar1 localized both at the ER exit sites and ER-Golgi intermediate compartment (ERGIC) regions. Additionally, impaired collagen secretion confined the activated Sar1 at the ER exit sites, implying the importance of Sar1 activation through the ERGIC in collagen secretion.
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Affiliation(s)
- Miharu Maeda
- Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, Japan
| | - Masashi Arakawa
- Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, Japan
| | - Yukie Komatsu
- Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, Japan
| | - Kota Saito
- Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, Japan
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2
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Paul S, Audhya A, Cui Q. Delineating the shape of COat Protein complex-II coated membrane bud. PNAS NEXUS 2024; 3:pgae305. [PMID: 39108303 PMCID: PMC11302526 DOI: 10.1093/pnasnexus/pgae305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/10/2024] [Indexed: 08/16/2024]
Abstract
Curvature-generating proteins that direct membrane trafficking assemble on the surface of lipid bilayers to bud transport intermediates, which move protein and lipid cargoes from one cellular compartment to another. However, it remains unclear what controls the overall shape of the membrane bud once curvature induction has begun. In vitro experiments showed that excessive concentrations of the COPII protein Sar1 promoted the formation of membrane tubules from synthetic vesicles, while COPII-coated transport intermediates in cells are generally more spherical or lobed in shape. To understand the origin of these morphological differences, we employ atomistic, coarse-grained (CG), and continuum mesoscopic simulations of membranes in the presence of multiple curvature-generating proteins. We first characterize the membrane-bending ability of amphipathic peptides derived from the amino terminus of Sar1, as a function of interpeptide angle and concentration using an atomistic bicelle simulation protocol. Then, we employ CG simulations to reveal that Sec23 and Sec24 control the relative spacing between Sar1 protomers and form the inner-coat unit through an attachment with Sar1. Finally, using dynamical triangulated surface simulations based on the Helfrich Hamiltonian, we demonstrate that the uniform distribution of spacer molecules among curvature-generating proteins is crucial to the spherical budding of the membrane. Overall, our analyses suggest a new role for Sec23, Sec24, and cargo proteins in COPII-mediated membrane budding process in which they act as spacers to preserve a dispersed arrangement of Sar1 protomers and help determine the overall shape of the membrane bud.
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Affiliation(s)
- Sanjoy Paul
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA 02215, USA
- Departments of Physics and Biomedical Engineering, Boston University, Boston, MA 02215, USA
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3
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Kasberg W, Luong P, Minushkin K, Pustova I, Swift KA, Zhao M, Audhya A. TFG regulates inner COPII coat recruitment to facilitate anterograde secretory protein transport. Mol Biol Cell 2024; 35:ar113. [PMID: 38985515 PMCID: PMC11321049 DOI: 10.1091/mbc.e24-06-0282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
Coat protein complex II (COPII) governs the initial steps of biosynthetic secretory protein transport from the endoplasmic reticulum (ER), facilitating the movement of a wide variety of cargoes. Here, we demonstrate that Trk-fused gene (TFG) regulates the rate at which inner COPII coat proteins are concentrated at ER subdomains. Specifically, in cells lacking TFG, the GTPase-activating protein (GAP) Sec23 accumulates more rapidly at budding sites on the ER as compared with control cells, potentially altering the normal timing of GTP hydrolysis on Sar1. Under these conditions, anterograde trafficking of several secretory cargoes is delayed, irrespective of their predicted size. We propose that TFG controls the local, freely available pool of Sec23 during COPII coat formation and limits its capacity to prematurely destabilize COPII complexes on the ER. This function of TFG enables it to act akin to a rheostat, promoting the ordered recruitment of Sec23, which is critical for efficient secretory cargo export.
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Affiliation(s)
- William Kasberg
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Peter Luong
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Kayla Minushkin
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Iryna Pustova
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Kevin A. Swift
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Meixian Zhao
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
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4
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Mohr I, Mirzaiebadizi A, Sanyal SK, Chuenban P, Ahmadian MR, Ivanov R, Bauer P. Characterization of the small Arabidopsis thaliana GTPase and ADP-ribosylation factor-like 2 protein TITAN 5. J Cell Sci 2024; 137:jcs262315. [PMID: 39056156 DOI: 10.1242/jcs.262315] [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: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/28/2024] Open
Abstract
Small GTPases switch between GDP- and GTP-bound states during cell signaling. The ADP-ribosylation factor (ARF) family of small GTPases is involved in vesicle trafficking. Although evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. We characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5 (TTN5; also known as HALLIMASCH, ARL2 and ARLC1) from Arabidopsis thaliana, and two TTN5 proteins with point mutants in conserved residues, TTN5T30N and TTN5Q70L, that were expected to be unable to perform nucleotide exchange and GTP hydrolysis, respectively. TTN5 exhibited very rapid intrinsic nucleotide exchange and remarkably low GTP hydrolysis activity, functioning as a non-classical small GTPase being likely present in a GTP-loaded active form. We analyzed signals from YFP-TTN5 and HA3-TTN5 by in situ immunolocalization in Arabidopsis seedlings and through use of a transient expression system. Colocalization with endomembrane markers and pharmacological treatments suggests that TTN5 can be present at the plasma membrane and that it dynamically associates with membranes of vesicles, Golgi stacks and multivesicular bodies. Although TTN5Q70L mirrored wild-type TTN5 behavior, the TTN5T30N mutant differed in some aspects. Hence, the unusual rapid nucleotide exchange activity of TTN5 is linked with its membrane dynamics, and TTN5 likely has a role in vesicle transport within the endomembrane system.
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Affiliation(s)
- Inga Mohr
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Amin Mirzaiebadizi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Sibaji K Sanyal
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Pichaporn Chuenban
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
- Center for Plant Genome Engineering, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Düsseldorf, Germany
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5
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Pilic J, Gottschalk B, Bourgeois B, Habisch H, Koshenov Z, Oflaz FE, Erdogan YC, Miri SM, Yiğit EN, Aydın MŞ, Öztürk G, Eroglu E, Shoshan-Barmatz V, Madl T, Graier WF, Malli R. Hexokinase 1 forms rings that regulate mitochondrial fission during energy stress. Mol Cell 2024; 84:2732-2746.e5. [PMID: 38981483 DOI: 10.1016/j.molcel.2024.06.009] [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: 09/29/2023] [Revised: 04/30/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Metabolic enzymes can adapt during energy stress, but the consequences of these adaptations remain understudied. Here, we discovered that hexokinase 1 (HK1), a key glycolytic enzyme, forms rings around mitochondria during energy stress. These HK1-rings constrict mitochondria at contact sites with the endoplasmic reticulum (ER) and mitochondrial dynamics protein (MiD51). HK1-rings prevent mitochondrial fission by displacing the dynamin-related protein 1 (Drp1) from mitochondrial fission factor (Mff) and mitochondrial fission 1 protein (Fis1). The disassembly of HK1-rings during energy restoration correlated with mitochondrial fission. Mechanistically, we identified that the lack of ATP and glucose-6-phosphate (G6P) promotes the formation of HK1-rings. Mutations that affect the formation of HK1-rings showed that HK1-rings rewire cellular metabolism toward increased TCA cycle activity. Our findings highlight that HK1 is an energy stress sensor that regulates the shape, connectivity, and metabolic activity of mitochondria. Thus, the formation of HK1-rings may affect mitochondrial function in energy-stress-related pathologies.
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Affiliation(s)
- Johannes Pilic
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010 Graz, Austria
| | - Benjamin Gottschalk
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010 Graz, Austria
| | - Benjamin Bourgeois
- BioTechMed Graz, Mozartgasse 12/2, 8010 Graz, Austria; Otto Loewi Research Center, Medical Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Hansjörg Habisch
- Otto Loewi Research Center, Medical Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Zhanat Koshenov
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010 Graz, Austria
| | - Furkan E Oflaz
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010 Graz, Austria
| | - Yusuf C Erdogan
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010 Graz, Austria
| | - Seyed M Miri
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Türkiye; Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Türkiye
| | - Esra N Yiğit
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Türkiye; Department of Physiology, International School of Medicine, Istanbul Medipol University, 34810 Istanbul, Türkiye
| | - Mehmet Ş Aydın
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Türkiye
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Türkiye
| | - Emrah Eroglu
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Türkiye; Department of Physiology, International School of Medicine, Istanbul Medipol University, 34810 Istanbul, Türkiye
| | - Varda Shoshan-Barmatz
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel
| | - Tobias Madl
- BioTechMed Graz, Mozartgasse 12/2, 8010 Graz, Austria; Otto Loewi Research Center, Medical Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Wolfgang F Graier
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010 Graz, Austria; BioTechMed Graz, Mozartgasse 12/2, 8010 Graz, Austria
| | - Roland Malli
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/4, 8010 Graz, Austria; BioTechMed Graz, Mozartgasse 12/2, 8010 Graz, Austria; Center for Medical Research, CF Bioimaging, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.
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Park K, Ju S, Choi H, Gao P, Bang G, Choi JH, Jang J, Morris AJ, Kang BH, Hsu VW, Park SY. PITPβ promotes COPI vesicle fission through lipid transfer and membrane contact formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596058. [PMID: 38853868 PMCID: PMC11160616 DOI: 10.1101/2024.05.27.596058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Intracellular transport among organellar compartments occurs in two general ways, by membrane-bound carriers or membrane contacts. Specific circumstances that involve the coordination of these two modes of transport remain to be defined. Studying Coat Protein I (COPI) transport, we find that phosphatidylcholine with short acyl chains (sPC) is delivered through membrane contact from the endoplasmic reticulum (ER) to sites of COPI vesicle formation at the Golgi to support the fission stage. Phosphatidylinositol transfer protein beta (PITPβ) plays a key role in this process, with the elucidation of this role advancing a new understanding of how PITPβ acts, providing a mechanistic understanding of a specific circumstance when vesicular transport requires membrane contact, and contributing to a basic understanding of how transport carriers in a model intracellular pathway are formed.
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Affiliation(s)
- Kunyou Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sungeun Ju
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyewon Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Peng Gao
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jung Hoon Choi
- Department of Bio-Chemical Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jiwon Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Andrew J. Morris
- University of Arkansas for Medical Sciences and Central Arkansas Veterans Affairs Healthcare System, Little Rock, AR 72205, USA
| | - Byung-Ho Kang
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Victor W. Hsu
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
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7
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Levy E, Fallet-Bianco C, Auclair N, Patey N, Marcil V, Sané AT, Spahis S. Unraveling Chylomicron Retention Disease Enhances Insight into SAR1B GTPase Functions and Mechanisms of Actions, While Shedding Light of Intracellular Chylomicron Trafficking. Biomedicines 2024; 12:1548. [PMID: 39062121 PMCID: PMC11274388 DOI: 10.3390/biomedicines12071548] [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: 05/22/2024] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Over the past three decades, significant efforts have been focused on unraveling congenital intestinal disorders that disrupt the absorption of dietary lipids and fat-soluble vitamins. The primary goal has been to gain deeper insights into intra-enterocyte sites, molecular steps, and crucial proteins/regulatory pathways involved, while simultaneously identifying novel therapeutic targets and diagnostic tools. This research not only delves into specific and rare malabsorptive conditions, such as chylomicron retention disease (CRD), but also contributes to our understanding of normal physiology through the utilization of cutting-edge cellular and animal models alongside advanced research methodologies. This review elucidates how modern techniques have facilitated the decoding of CRD gene defects, the identification of dysfunctional cellular processes, disease regulatory mechanisms, and the essential role of coat protein complex II-coated vesicles and cargo receptors in chylomicron trafficking and endoplasmic reticulum (ER) exit sites. Moreover, experimental approaches have shed light on the multifaceted functions of SAR1B GTPase, wherein loss-of-function mutations not only predispose individuals to CRD but also exacerbate oxidative stress, inflammation, and ER stress, potentially contributing to clinical complications associated with CRD. In addition to dissecting the primary disease pathology, genetically modified animal models have emerged as invaluable assets in exploring various ancillary aspects, including responses to environmental challenges such as dietary alterations, gender-specific disparities in disease onset and progression, and embryonic lethality or developmental abnormalities. In summary, this comprehensive review provides an in-depth and contemporary analysis of CRD, offering a meticulous examination of the CRD current landscape by synthesizing the latest research findings and advancements in the field.
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Affiliation(s)
- Emile Levy
- Azrieli Research Center, CHU Ste-Justine and Department of Nutrition, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Catherine Fallet-Bianco
- Azrieli Research Center, CHU Ste-Justine and Pathology & Cell Biology, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Nickolas Auclair
- Azrieli Research Center, CHU Ste-Justine and Pharmacology, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Natalie Patey
- Azrieli Research Center, CHU Ste-Justine and Pathology & Cell Biology, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Valérie Marcil
- Azrieli Research Center, CHU Ste-Justine and Department of Nutrition, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | | | - Schohraya Spahis
- Azrieli Research Center, CHU Ste-Justine and Biochemistry & Molecular Medicine, Université de Montréal, Montreal, QC H3T 1C5, Canada;
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8
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Saxena S, Foresti O, Liu A, Androulaki S, Pena Rodriguez M, Raote I, Aridor M, Cui B, Malhotra V. Endoplasmic reticulum exit sites are segregated for secretion based on cargo size. Dev Cell 2024:S1534-5807(24)00387-3. [PMID: 38991587 DOI: 10.1016/j.devcel.2024.06.009] [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: 12/03/2023] [Revised: 04/08/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024]
Abstract
TANGO1, TANGO1-Short, and cTAGE5 form stable complexes at the endoplasmic reticulum exit sites (ERES) to preferably export bulky cargoes. Their C-terminal proline-rich domain (PRD) binds Sec23A and affects COPII assembly. The PRD in TANGO1-Short was replaced with light-responsive domains to control its binding to Sec23A in U2OS cells (human osteosarcoma). TANGO1-ShortΔPRD was dispersed in the ER membrane but relocated rapidly, reversibly, to pre-existing ERES by binding to Sec23A upon light activation. Prolonged binding between the two, concentrated ERES in the juxtanuclear region, blocked cargo export and relocated ERGIC53 into the ER, minimally impacting the Golgi complex organization. Bulky collagen VII and endogenous collagen I were collected at less than 47% of the stalled ERES, whereas small cargo molecules were retained uniformly at almost all the ERES. We suggest that ERES are segregated to handle cargoes based on their size, permitting cells to traffic them simultaneously for optimal secretion.
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Affiliation(s)
- Sonashree Saxena
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ombretta Foresti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Aofei Liu
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Stefania Androulaki
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Pena Rodriguez
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ishier Raote
- Institut Jacques Monod, Université Paris Cité, 75013 Paris, France
| | - Meir Aridor
- Department of Cell Biology, School of Medicine, University of Pittsburgh, 3500 Terrace Street, Pittsburgh, PA 15261, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA, USA; Wu-Tsai Neuroscience Institute and ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Vivek Malhotra
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.
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9
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Mohr I, Mirzaiebadizi A, Sanyal SK, Chuenban P, Ahmadian MR, Ivanov R, Bauer P. Characterization of the small Arabidopsis thaliana GTPase and ADP-ribosylation factor-like 2 protein TITAN 5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.27.538563. [PMID: 37162876 PMCID: PMC10168340 DOI: 10.1101/2023.04.27.538563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Small GTPases function by conformational switching ability between GDP- and GTP-bound states in rapid cell signaling events. The ADP-ribosylation factor (ARF) family is involved in vesicle trafficking. Though evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. Here, we characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5/HALLIMASCH/ARL2/ARLC1 (hereafter termed TTN5) from Arabidopsis thaliana. Two TTN5 variants were included in the study with point mutations at conserved residues, suspected to be functional for nucleotide exchange and GTP hydrolysis, TTN5T30N and TTN5Q70L. We found that TTN5 had a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanism. TTN5 acted as a non-classical small GTPase with a remarkably low GTP hydrolysis activity, suggesting it is likely present in GTP-loaded active form in the cell. We analyzed signals from yellow fluorescent protein (YFP)-tagged TTN5 and from in situ immunolocalization of hemagglutine-tagged HA3-TTN5 in Arabidopsis seedlings and in a transient expression system. Together with colocalization using endomembrane markers and pharmacological treatments the microscopic analysis suggests that TTN5 can be present at the plasma membrane and dynamically associated with membranes of vesicles, Golgi stacks and multivesicular bodies. While the TTN5Q70L variant showed similar GTPase activities and localization behavior as wild-type TTN5, the TTN5T30N mutant differed in some aspects. Hence, the unusual capacity of rapid nucleotide exchange activity of TTN5 is linked with cell membrane dynamics, likely associated with vesicle transport pathways in the endomembrane system.
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Affiliation(s)
- Inga Mohr
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Amin Mirzaiebadizi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Sibaji K Sanyal
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Pichaporn Chuenban
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Düsseldorf, Germany
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10
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Johnson DH, Kou OH, Bouzos N, Zeno WF. Protein-membrane interactions: sensing and generating curvature. Trends Biochem Sci 2024; 49:401-416. [PMID: 38508884 PMCID: PMC11069444 DOI: 10.1016/j.tibs.2024.02.005] [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: 09/23/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024]
Abstract
Biological membranes are integral cellular structures that can be curved into various geometries. These curved structures are abundant in cells as they are essential for various physiological processes. However, curved membranes are inherently unstable, especially on nanometer length scales. To stabilize curved membranes, cells can utilize proteins that sense and generate membrane curvature. In this review, we summarize recent research that has advanced our understanding of interactions between proteins and curved membrane surfaces, as well as work that has expanded our ability to study curvature sensing and generation. Additionally, we look at specific examples of cellular processes that require membrane curvature, such as neurotransmission, clathrin-mediated endocytosis (CME), and organelle biogenesis.
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Affiliation(s)
- David H Johnson
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Orianna H Kou
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Nicoletta Bouzos
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Wade F Zeno
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA.
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11
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Mondal S, Cui Q. Sequence Sensitivity in Membrane Remodeling by Polyampholyte Condensates. J Phys Chem B 2024; 128:2087-2099. [PMID: 38407041 DOI: 10.1021/acs.jpcb.3c08149] [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: 02/27/2024]
Abstract
Intrinsically disordered peptides (IDPs) have been found to undergo liquid-liquid phase separation (LLPS) and produce complex coacervates that play numerous regulatory roles in the cell. Recent experimental studies have discovered that LLPS at or near the membrane surface helps in the biomolecular organization during signaling events and can significantly alter the membrane morphology. However, the molecular mechanism and microscopic details of such processes still remain unclear. Here we study the effect of polyampholyte and polyelectrolyte condensation on two different anionic membranes, as they represent a majority of naturally occurring IDPs. The polyampholytes are fifty-residue polymers, made of glutamate(E) and lysine(K) with different charge patterns. The polyelectrolytes are separate chains of E25 and K25. We first calibrate the MARTINI v3.0 force field and then perform long-time-scale coarse-grained molecular dynamics simulations. We find that condensates formed by all the polyampholytes get adsorbed on the membrane. However, the strong polyampholytes (i.e., blocky sequences) can remodel the membranes more prominently than the weaker ones (i.e., scrambled sequences). Condensates formed by the blocky sequences induce a significant negative curvature (∼0.1 nm-1) and local demixing of lipids, whereas those by the scrambled sequences tend to wet the membrane to a greater extent without generating significant curvature or demixing. We perform several microscopic analyses to characterize the nature of the interaction between membranes and these condensates. Our analyses of interaction energetics reveal that membrane remodeling and/or wetting are favored by enhanced interactions between polyampholytes with lipids and the counterions.
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Affiliation(s)
- Sayantan Mondal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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12
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Robinson CM, Duggan A, Forrester A. ER exit in physiology and disease. Front Mol Biosci 2024; 11:1352970. [PMID: 38314136 PMCID: PMC10835805 DOI: 10.3389/fmolb.2024.1352970] [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: 12/09/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
The biosynthetic secretory pathway is comprised of multiple steps, modifications and interactions that form a highly precise pathway of protein trafficking and secretion, that is essential for eukaryotic life. The general outline of this pathway is understood, however the specific mechanisms are still unclear. In the last 15 years there have been vast advancements in technology that enable us to advance our understanding of this complex and subtle pathway. Therefore, based on the strong foundation of work performed over the last 40 years, we can now build another level of understanding, using the new technologies available. The biosynthetic secretory pathway is a high precision process, that involves a number of tightly regulated steps: Protein folding and quality control, cargo selection for Endoplasmic Reticulum (ER) exit, Golgi trafficking, sorting and secretion. When deregulated it causes severe diseases that here we categorise into three main groups of aberrant secretion: decreased, excess and altered secretion. Each of these categories disrupts organ homeostasis differently, effecting extracellular matrix composition, changing signalling events, or damaging the secretory cells due to aberrant intracellular accumulation of secretory proteins. Diseases of aberrant secretion are very common, but despite this, there are few effective therapies. Here we describe ER exit sites (ERES) as key hubs for regulation of the secretory pathway, protein quality control and an integratory hub for signalling within the cell. This review also describes the challenges that will be faced in developing effective therapies, due to the specificity required of potential drug candidates and the crucial need to respect the fine equilibrium of the pathway. The development of novel tools is moving forward, and we can also use these tools to build our understanding of the acute regulation of ERES and protein trafficking. Here we review ERES regulation in context as a therapeutic strategy.
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Affiliation(s)
- Claire M Robinson
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Aislinn Duggan
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alison Forrester
- Research Unit of Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
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13
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Pang X, Zhang Y, Park K, Liao Z, Li J, Xu J, Hong MT, Yin G, Zhang T, Wang Y, Egelman EH, Fan J, Park SY, Hsu VW, Sun F. Structural elucidation of how ARF small GTPases induce membrane tubulation for vesicle fission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572083. [PMID: 38187566 PMCID: PMC10769218 DOI: 10.1101/2023.12.19.572083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The ADP-Ribosylation Factor (ARF) small GTPases have been found to act in vesicle fission through a direct ability to tubulate membrane. Here, we have used cryo-electron microscopy (EM) to solve the structure of an ARF6 protein lattice assembled on tubulated membrane to 3.9 Å resolution. ARF6 forms tetramers that polymerize into helical arrays to form this lattice. We identify, and confirm functionally, protein contacts critical for this lattice formation. The solved structure also suggests how the ARF amphipathic helix is positioned in the lattice for membrane insertion, and how a GTPase-activating protein (GAP) docks onto the lattice to catalyze ARF-GTP hydrolysis in completing membrane fission. As ARF1 and ARF6 are structurally conserved, we have also modeled ARF1 onto the ARF6 lattice, which has allowed us to pursue the reconstitution of Coat Protein I (COPI) vesicles to confirm more definitively that the ARF lattice acts in vesicle fission. Our findings are notable for having achieved the first detailed glimpse of how a small GTPase bends membrane and having provided a molecular understanding of how an ARF protein acts in vesicle fission.
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Affiliation(s)
- Xiaoyun Pang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Equal contribution
| | - Yan Zhang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Equal contribution
| | - Kunyou Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
- Equal contribution
| | - Zhenyu Liao
- City University of Hong Kong, Hong Kong, China
| | - Jian Li
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Jiashu Xu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minh-Triet Hong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Guoliang Yin
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tongming Zhang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyu Wang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, VA 22908 USA
| | - Jun Fan
- City University of Hong Kong, Hong Kong, China
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Victor W Hsu
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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14
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Xie P, Zhang H, Qin Y, Xiong H, Shi C, Zhou Z. Membrane Proteins and Membrane Curvature: Mutual Interactions and a Perspective on Disease Treatments. Biomolecules 2023; 13:1772. [PMID: 38136643 PMCID: PMC10741411 DOI: 10.3390/biom13121772] [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: 11/01/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The pathogenesis of various diseases often involves an intricate interplay between membrane proteins and membrane curvature. Understanding the underlying mechanisms of this interaction could offer novel perspectives on disease treatment. In this review, we provide an introduction to membrane curvature and its association with membrane proteins. Furthermore, we delve into the impact and potential implications of this interaction in the context of disease treatment. Lastly, we discuss the prospects and challenges associated with harnessing these interactions for effective disease management, aiming to provide fresh insights into therapeutic strategies.
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Affiliation(s)
| | | | | | | | | | - Zijian Zhou
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory & Center for Molecular Imaging and Translational Medicine, School of Public Health, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen 361102, China; (P.X.); (H.Z.); (Y.Q.); (H.X.); (C.S.)
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15
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Kasberg W, Luong P, Swift KA, Audhya A. Nutrient deprivation alters the rate of COPII subunit recruitment at ER subdomains to tune secretory protein transport. Nat Commun 2023; 14:8140. [PMID: 38066006 PMCID: PMC10709328 DOI: 10.1038/s41467-023-44002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Co-assembly of the multilayered coat protein complex II (COPII) with the Sar1 GTPase at subdomains of the endoplasmic reticulum (ER) enables secretory cargoes to be concentrated efficiently within nascent transport intermediates, which subsequently deliver their contents to ER-Golgi intermediate compartments. Here, we define the spatiotemporal accumulation of native COPII subunits and secretory cargoes at ER subdomains under differing nutrient availability conditions using a combination of CRISPR/Cas9-mediated genome editing and live cell imaging. Our findings demonstrate that the rate of inner COPII coat recruitment serves as a determinant for the pace of cargo export, irrespective of COPII subunit expression levels. Moreover, increasing inner COPII coat recruitment kinetics is sufficient to rescue cargo trafficking deficits caused by acute nutrient limitation. Our findings are consistent with a model in which the rate of inner COPII coat addition acts as an important control point to regulate cargo export from the ER.
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Affiliation(s)
- William Kasberg
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Peter Luong
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Kevin A Swift
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA.
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16
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Artlett CM, Connolly LM. TANGO1 Dances to Export of Procollagen from the Endoplasmic Reticulum. FIBROSIS (HONG KONG, CHINA) 2023; 1:10008. [PMID: 38650832 PMCID: PMC11034787 DOI: 10.35534/fibrosis.2023.10008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The endoplasmic reticulum (ER) to Golgi secretory pathway is an elegantly complex process whereby protein cargoes are manufactured, folded, and distributed from the ER to the cisternal layers of the Golgi stack before they are delivered to their final destinations. The export of large bulky cargoes such as procollagen and its trafficking to the Golgi is a sophisticated mechanism requiring TANGO1 (Transport ANd Golgi Organization protein 1. It is also called MIA3 (Melanoma Inhibitory Activity protein 3). TANGO1 has two prominent isoforms, TANGO1-Long and TANGO1-Short, and each isoform has specific functions. On the luminal side, TANGO1-Long has an HSP47 recruitment domain and uses this protein to collect collagen. It can also tether its paralog isoforms cTAGE5 and TALI and along with these proteins enlarges the vesicle to accommodate procollagen. Recent studies show that TANGO1-Long combines retrograde membrane flow with anterograde cargo transport. This complex mechanism is highly activated in fibrosis and promotes the excessive deposition of collagen in the tissues. The therapeutic targeting of TANGO1 may prove successful in the control of fibrotic disorders. This review focuses on TANGO1 and its complex interaction with other procollagen export factors that modulate increased vesicle size to accommodate the export of procollagen.
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Affiliation(s)
- Carol M. Artlett
- Drexel University College of Medicine, Drexel University, Philadelphia, PA 19129, USA
| | - Lianne M. Connolly
- Drexel University College of Medicine, Drexel University, Philadelphia, PA 19129, USA
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17
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Kasberg W, Luong P, Hanna MG, Minushkin K, Tsao A, Shankar R, Block S, Audhya A. The Sar1 GTPase is dispensable for COPII-dependent cargo export from the ER. Cell Rep 2023; 42:112635. [PMID: 37300835 PMCID: PMC10592460 DOI: 10.1016/j.celrep.2023.112635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/21/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Coat protein complex II (COPII) plays an integral role in the packaging of secretory cargoes within membrane-enclosed transport carriers that leave the endoplasmic reticulum (ER) from discrete subdomains. Lipid bilayer remodeling necessary for this process is driven initially by membrane penetration mediated by the Sar1 GTPase and further stabilized by assembly of a multilayered complex of several COPII proteins. However, the relative contributions of these distinct factors to transport carrier formation and protein trafficking remain unclear. Here, we demonstrate that anterograde cargo transport from the ER continues in the absence of Sar1, although the efficiency of this process is dramatically reduced. Specifically, secretory cargoes are retained nearly five times longer at ER subdomains when Sar1 is depleted, but they ultimately remain capable of being translocated to the perinuclear region of cells. Taken together, our findings highlight alternative mechanisms by which COPII promotes transport carrier biogenesis.
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Affiliation(s)
- William Kasberg
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Peter Luong
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Michael G Hanna
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Kayla Minushkin
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Annabelle Tsao
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Raakhee Shankar
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Samuel Block
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.
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18
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Anila MM, Ghosh R, Różycki B. Membrane curvature sensing by model biomolecular condensates. SOFT MATTER 2023; 19:3723-3732. [PMID: 37190858 DOI: 10.1039/d3sm00131h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Biomolecular condensates (BCs) are fluid droplets that form in biological cells by liquid-liquid phase separation. Their major components are intrinsically disordered proteins. Vast attention has been given in recent years to BCs inside the cytosol and nucleus. BCs at the cell membrane have not been studied to the same extent so far. However, recent studies provide increasingly more examples of interfaces between BCs and membranes which function as platforms for diverse biomolecular processes. Galectin-3, for example, is known to mediate clathrin-independent endocytosis and has been recently shown to undergo liquid-liquid phase separation, but the function of BCs of galectin-3 in endocytic pit formation is unknown. Here, we use dissipative particle dynamics simulations to study a generic coarse-grained model for BCs interacting with lipid membranes. In analogy to galectin-3, we consider polymers comprising two segments - one of them mediates multivalent attractive interactions between the polymers, and the other one has affinity for association with specific lipid head groups. When these polymers are brought into contact with a multi-component membrane, they spontaneously assemble into droplets and, simultaneously, induce lateral separation of lipids within the membrane. Interestingly, we find that if the membrane is bent, the polymer droplets localize at membrane regions curved inward. Although the polymers have no particular shape or intrinsic curvature, they appear to sense membrane curvature when clustered at the membrane. Our results indicate toward a generic mechanism of membrane curvature sensing by BCs involved in such processes as endocytosis.
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Affiliation(s)
- Midhun Mohan Anila
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Rikhia Ghosh
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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19
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Van der Verren SE, Zanetti G. The small GTPase Sar1, control centre of COPII trafficking. FEBS Lett 2023; 597:865-882. [PMID: 36737236 DOI: 10.1002/1873-3468.14595] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Sar1 is a small GTPase of the ARF family. Upon exchange of GDP for GTP, Sar1 associates with the endoplasmic reticulum (ER) membrane and recruits COPII components, orchestrating cargo concentration and membrane deformation. Many aspects of the role of Sar1 and regulation of its GTP cycle remain unclear, especially as complexity increases in higher organisms that secrete a wider range of cargoes. This review focusses on the regulation of GTP hydrolysis and its role in coat assembly, as well as the mechanism of Sar1-induced membrane deformation and scission. Finally, we highlight the additional specialisation in higher eukaryotes and the outstanding questions on how Sar1 functions are orchestrated.
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Affiliation(s)
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College London, UK
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20
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Li L, Ji J, Song F, Hu J. Intercellular Receptor-ligand Binding: Effect of Protein-membrane Interaction. J Mol Biol 2023; 435:167787. [PMID: 35952805 DOI: 10.1016/j.jmb.2022.167787] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 02/04/2023]
Abstract
Gaining insights into the intercellular receptor-ligand binding is of great importance for understanding numerous physiological and pathological processes, and stimulating new strategies in drug design and discovery. In contrast to the in vitro protein interaction in solution, the anchored receptor and ligand molecules interact with membrane in situ, which affects the intercellular receptor-ligand binding. Here, we review theoretical, simulation and experimental works regarding the regulatory effects of protein-membrane interactions on intercellular receptor-ligand binding mainly from the following aspects: membrane fluctuations, membrane curvature, glycocalyx, and lipid raft. In addition, we discuss biomedical significances and possible research directions to advance the field and highlight the importance of understanding of coupling effects of these factors in pharmaceutical development.
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Affiliation(s)
- Long Li
- Kuang Yaming Honors School and Institute for Brain Sciences, Nanjing University, 210023 Nanjing, China; State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, 100190 Beijing, China
| | - Jing Ji
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, 100190 Beijing, China; School of Engineering Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jinglei Hu
- Kuang Yaming Honors School and Institute for Brain Sciences, Nanjing University, 210023 Nanjing, China.
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21
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Tang VT, Ginsburg D. Cargo selection in endoplasmic reticulum-to-Golgi transport and relevant diseases. J Clin Invest 2023; 133:163838. [PMID: 36594468 PMCID: PMC9797344 DOI: 10.1172/jci163838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Most proteins destined for the extracellular space or various intracellular compartments must traverse the intracellular secretory pathway. The first step is the recruitment and transport of cargoes from the endoplasmic reticulum (ER) lumen to the Golgi apparatus by coat protein complex II (COPII), consisting of five core proteins. Additional ER transmembrane proteins that aid cargo recruitment are referred to as cargo receptors. Gene duplication events have resulted in multiple COPII paralogs present in the mammalian genome. Here, we review the functions of each COPII protein, human disorders associated with each paralog, and evidence for functional conservation between paralogs. We also provide a summary of current knowledge regarding two prototypical cargo receptors in mammals, LMAN1 and SURF4, and their roles in human health and disease.
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Affiliation(s)
- Vi T. Tang
- Department of Molecular and Integrative Physiology,,Life Sciences Institute
| | - David Ginsburg
- Life Sciences Institute,,Department of Internal Medicine,,Department of Human Genetics,,Department of Pediatrics and Communicable Diseases, and,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
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22
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Kustigian L, Gong X, Gai W, Thongchol J, Zhang J, Puchalla J, Carr CM, Rye HS. GTP-stimulated membrane fission by the N-BAR protein AMPH-1. Traffic 2023; 24:34-47. [PMID: 36435193 PMCID: PMC9825645 DOI: 10.1111/tra.12875] [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: 01/17/2022] [Revised: 10/24/2022] [Accepted: 11/19/2022] [Indexed: 11/28/2022]
Abstract
Membrane-enclosed transport carriers sort biological molecules between stations in the cell in a dynamic process that is fundamental to the physiology of eukaryotic organisms. While much is known about the formation and release of carriers from specific intracellular membranes, the mechanism of carrier formation from the recycling endosome, a compartment central to cellular signaling, remains to be resolved. In Caenorhabditis elegans, formation of transport carriers from the recycling endosome requires the dynamin-like, Eps15-homology domain (EHD) protein, RME-1, functioning with the Bin/Amphiphysin/Rvs (N-BAR) domain protein, AMPH-1. Here we show, using a free-solution single-particle technique known as burst analysis spectroscopy (BAS), that AMPH-1 alone creates small, tubular-vesicular products from large, unilamellar vesicles by membrane fission. Membrane fission requires the amphipathic H0 helix of AMPH-1 and is slowed in the presence of RME-1. Unexpectedly, AMPH-1-induced membrane fission is stimulated in the presence of GTP. Furthermore, the GTP-stimulated membrane fission activity seen for AMPH-1 is recapitulated by the heterodimeric N-BAR amphiphysin protein from yeast, Rvs161/167p, strongly suggesting that GTP-stimulated membrane fission is a general property of this important class of N-BAR proteins.
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Affiliation(s)
- Lauren Kustigian
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
- Current address: GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, Pennsylvania 19426, USA
| | - Xue Gong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Wei Gai
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Jirapat Thongchol
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Jason Puchalla
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Chavela M. Carr
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77845, USA
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23
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Kozlov MM, Taraska JW. Generation of nanoscopic membrane curvature for membrane trafficking. Nat Rev Mol Cell Biol 2023; 24:63-78. [PMID: 35918535 DOI: 10.1038/s41580-022-00511-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Curved membranes are key features of intracellular organelles, and their generation involves dynamic protein complexes. Here we describe the fundamental mechanisms such as the hydrophobic insertion, scaffolding and crowding mechanisms these proteins use to produce membrane curvatures and complex shapes required to form intracellular organelles and vesicular structures involved in endocytosis and secretion. For each mechanism, we discuss its cellular functions as well as the underlying physical principles and the specific membrane properties required for the mechanism to be feasible. We propose that the integration of individual mechanisms into a highly controlled, robust process of curvature generation often relies on the assembly of proteins into coats. How cells unify and organize the curvature-generating factors at the nanoscale is presented for three ubiquitous coats central for membrane trafficking in eukaryotes: clathrin-coated pits, caveolae, and COPI and COPII coats. The emerging theme is that these coats arrange and coordinate curvature-generating factors in time and space to dynamically shape membranes to accomplish membrane trafficking within cells.
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Affiliation(s)
- Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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24
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Gao YQ, Chao DY. Localization and circulation: vesicle trafficking in regulating plant nutrient homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1350-1363. [PMID: 36321185 DOI: 10.1111/tpj.16020] [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: 07/23/2022] [Revised: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Nutrient homeostasis is essential for plant growth and reproduction. Plants, therefore, have evolved tightly regulated mechanisms for the uptake, translocation, distribution, and storage of mineral nutrients. Considering that inorganic nutrient transport relies on membrane-based transporters and channels, vesicle trafficking, one of the fundamental cell biological processes, has become a hotspot of plant nutrition studies. In this review, we summarize recent advances in the study of how vesicle trafficking regulates nutrient homeostasis to contribute to the adaptation of plants to heterogeneous environments. We also discuss new perspectives on future studies, which may inspire researchers to investigate new approaches to improve the human diet and health by changing the nutrient quality of crops.
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Affiliation(s)
- Yi-Qun Gao
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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25
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Melero A, Boulanger J, Kukulski W, Miller EA. Ultrastructure of COPII vesicle formation in yeast characterized by correlative light and electron microscopy. Mol Biol Cell 2022; 33:ar122. [PMID: 36001360 PMCID: PMC9634970 DOI: 10.1091/mbc.e22-03-0103] [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] [Indexed: 01/18/2023] Open
Abstract
Traffic of proteins out of the endoplasmic reticulum (ER) is driven by the COPII coat, a layered protein scaffold that mediates the capture of cargo proteins and the remodeling of the ER membrane into spherical vesicular carriers. Although the components of this machinery have been genetically defined, and the mechanisms of coat assembly extensively explored in vitro, understanding the physical mechanisms of membrane remodeling in cells remains a challenge. Here we use correlative light and electron microscopy (CLEM) to visualize the nanoscale ultrastructure of membrane remodeling at ER exit sites (ERES) in yeast cells. Using various COPII mutants, we have determined the broad contribution that each layer of the coat makes to membrane remodeling. Our data suggest that inner coat components define the radius of curvature, whereas outer coat components facilitate membrane fission. The organization of the coat in conjunction with membrane biophysical properties determines the ultrastructure of vesicles and thus the efficiency of protein transport.
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Affiliation(s)
- Alejandro Melero
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- *Address correspondence to: Elizabeth A. Miller (); Alejandro Melero ()
| | - Jerome Boulanger
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Elizabeth A. Miller
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- *Address correspondence to: Elizabeth A. Miller (); Alejandro Melero ()
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26
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Pathway engineering facilitates efficient protein expression in Pichia pastoris. Appl Microbiol Biotechnol 2022; 106:5893-5912. [PMID: 36040488 DOI: 10.1007/s00253-022-12139-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
Pichia pastoris has been recognized as an important platform for the production of various heterologous proteins in recent years. The strong promoter AOX1, induced by methanol, with the help of the α-pre-pro signal sequence, can lead to a high expression level of extracellular protein. However, this combination was not always efficient, as protein secretion in P. pastoris involves numerous procedures mediated by several cellular proteins, including folding assisted by endoplasmic reticulum (ER) molecular chaperones, degradation through ubiquitination, and an efficient vesicular transport system. Efficient protein expression requires the cooperation of various intracellular pathways. This article summarizes the process of protein secretion, modification, and transportation in P. pastoris. In addition, the roles played by the key proteins in these processes and the corresponding co-expression effects are also listed. It is expected to lay the foundation for the industrial protein production of P. pastoris. KEY POINTS: • Mechanisms of chaperones in protein folding and their co-expression effects are summarized. • Protein glycosylation modifications are comprehensively reviewed. • Current dilemmas in the overall protein secretion pathway of Pichia pastoris and corresponding solutions are demonstrated.
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Mondal S, Cui Q. Coacervation of poly-electrolytes in the presence of lipid bilayers: mutual alteration of structure and morphology. Chem Sci 2022; 13:7933-7946. [PMID: 35865903 PMCID: PMC9258347 DOI: 10.1039/d2sc02013k] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
Many intrinsically disordered peptides have been shown to undergo liquid-liquid phase separation and form complex coacervates, which play various regulatory roles in the cell. Recent experimental studies found that such phase separation processes may also occur at the lipid membrane surface and help organize biomolecules during signaling events; in some cases, phase separation of proteins at the membrane surface was also observed to lead to significant remodeling of the membrane morphology. The molecular mechanisms that govern the interactions between complex coacervates and lipid membranes and the impacts of such interactions on their structure and morphology, however, remain unclear. Here we study the coacervation of poly-glutamate (E30) and poly-lysine (K30) in the presence of lipid bilayers of different compositions. We carry out explicit-solvent coarse-grained molecular dynamics simulations by using the MARTINI (v3.0) force-field. We find that more than 20% anionic lipids are required for the coacervate to form stable contact with the bilayer. Upon wetting, the coacervate induces negative curvature to the bilayer and facilitates local lipid demixing, without any peptide insertion. The magnitude of negative curvature, extent of lipid demixing, and asphericity of the coacervate increase with the concentration of anionic lipids. Overall, we observe a decrease in the number of contacts among the polyelectrolytes as the droplet spreads over the bilayer. Therefore, unlike previous suggestions, interactions among polyelectrolytes do not constitute a driving force for the membrane bending upon wetting by the coacervate. Rather, analysis of interaction energy components suggests that bending of the membrane is favored by enhanced interactions between polyelectrolytes with lipids as well as with counterions. Kinetic studies reveal that, at the studied polyelectrolyte concentrations, the coacervate formation precedes bilayer wetting.
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Affiliation(s)
- Sayantan Mondal
- Department of Chemistry, Boston University 590 Commonwealth Avenue Boston MA 02215 USA (+1)-617-353-6189
| | - Qiang Cui
- Department of Chemistry, Boston University 590 Commonwealth Avenue Boston MA 02215 USA (+1)-617-353-6189
- Department of Physics, Boston University 590 Commonwealth Avenue Boston MA 02215 USA
- Department of Biomedical Engineering, Boston University 44 Cummington Mall Boston MA 02215 USA
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28
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Circularized fluorescent nanodiscs for probing protein-lipid interactions. Commun Biol 2022; 5:507. [PMID: 35618817 PMCID: PMC9135701 DOI: 10.1038/s42003-022-03443-4] [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: 12/28/2021] [Accepted: 05/03/2022] [Indexed: 12/29/2022] Open
Abstract
Protein–lipid interactions are vital for numerous transmembrane signaling pathways. However, simple tools to characterize these interactions remain scarce and are much needed to advance our understanding of signal transduction across lipid bilayers. To tackle this challenge, we herein engineer nanodisc as a robust fluorescent sensor for reporting membrane biochemical reactions. We circularize nanodiscs via split GFP and thereby create an intensity-based fluorescent sensor (isenND) for detecting membrane binding and remodeling events. We show that isenND responds robustly and specifically to the action of a diverse array of membrane-interacting proteins and peptides, ranging from synaptotagmin and synuclein involved in neurotransmission to viral fusion peptides of HIV-1 and SARS-CoV-2. Together, isenND can serve as a versatile biochemical reagent useful for basic and translational research of membrane biology. A fluorescent probe for detecting membrane protein binding and remodeling events is presented, which relies on split-GFP technology to generate circularized nanodiscs useful in membrane protein biophysics and structural biology.
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29
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Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions. J Membr Biol 2022; 255:237-259. [PMID: 35451616 PMCID: PMC9028910 DOI: 10.1007/s00232-022-00237-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022]
Abstract
Cellular membranes are highly dynamic in shape. They can rapidly and precisely regulate their shape to perform various cellular functions. The protein’s ability to sense membrane curvature is essential in various biological events such as cell signaling and membrane trafficking. As they are bound, these curvature-sensing proteins may also change the local membrane shape by one or more curvature driving mechanisms. Established curvature-sensing/driving mechanisms rely on proteins with specific structural features such as amphipathic helices and intrinsically curved shapes. However, the recent discovery and characterization of many proteins have shattered the protein structure–function paradigm, believing that the protein functions require a unique structural feature. Typically, such structure-independent functions are carried either entirely by intrinsically disordered proteins or hybrid proteins containing disordered regions and structured domains. It is becoming more apparent that disordered proteins and regions can be potent sensors/inducers of membrane curvatures. In this article, we outline the basic features of disordered proteins and regions, the motifs in such proteins that encode the function, membrane remodeling by disordered proteins and regions, and assays that may be employed to investigate curvature sensing and generation by ordered/disordered proteins.
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30
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Zhang L, Wang Y, Dong Y, Pant A, Liu Y, Masserman L, Xu Y, McLaughlin RN, Bai J. The endophilin curvature-sensitive motif requires electrostatic guidance to recycle synaptic vesicles in vivo. Dev Cell 2022; 57:750-766.e5. [PMID: 35303431 PMCID: PMC8969179 DOI: 10.1016/j.devcel.2022.02.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/21/2022] [Accepted: 02/22/2022] [Indexed: 12/29/2022]
Abstract
Curvature-sensing mechanisms assist proteins in executing particular actions on various membrane organelles. Here, we investigate the functional specificity of curvature-sensing amphipathic motifs in Caenorhabditis elegans through the study of endophilin, an endocytic protein for synaptic vesicle recycling. We generate chimeric endophilin proteins by replacing the endophilin amphipathic motif H0 with other curvature-sensing amphipathic motifs. We find that the role of amphipathic motifs cannot simply be extrapolated from the identity of their parental proteins. For example, the amphipathic motif of the nuclear pore complex protein NUP133 functionally replaces the synaptic role of endophilin H0. Interestingly, non-functional endophilin chimeras have similar defects-producing fewer synaptic vesicles but more endosomes-and this indicates that the curvature-sensing motifs in these chimeras have a common deficiency for reforming synaptic vesicles. Finally, we convert non-functional endophilin chimeras into functional proteins by changing the cationic property of amphipathic motifs, successfully reprogramming the functional specificity of curvature-sensing motifs in vivo.
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Affiliation(s)
- Lin Zhang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yu Wang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, P.R. China; Fudan University, Shanghai 200433, P.R. China
| | - Yongming Dong
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Aaradhya Pant
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yan Liu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Laura Masserman
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ye Xu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Jihong Bai
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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31
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Wang L, Zhang J, Wang D, Song C. Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins. PLoS Comput Biol 2022; 18:e1009972. [PMID: 35353812 PMCID: PMC9000120 DOI: 10.1371/journal.pcbi.1009972] [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: 03/11/2021] [Revised: 04/11/2022] [Accepted: 02/25/2022] [Indexed: 11/20/2022] Open
Abstract
One of the unique traits of membrane proteins is that a significant fraction of their hydrophobic amino acids is exposed to the hydrophobic core of lipid bilayers rather than being embedded in the protein interior, which is often not explicitly considered in the protein structure and function predictions. Here, we propose a characteristic and predictive quantity, the membrane contact probability (MCP), to describe the likelihood of the amino acids of a given sequence being in direct contact with the acyl chains of lipid molecules. We show that MCP is complementary to solvent accessibility in characterizing the outer surface of membrane proteins, and it can be predicted for any given sequence with a machine learning-based method by utilizing a training dataset extracted from MemProtMD, a database generated from molecular dynamics simulations for the membrane proteins with a known structure. As the first of many potential applications, we demonstrate that MCP can be used to systematically improve the prediction precision of the protein contact maps and structures. The distribution of residues on protein surfaces is largely determined by the surrounding environment. For soluble proteins, most of the residues on the outer surface are hydrophilic, and people use the quantity “solvent accessibility” to describe and predict these surface residues. In contrast, for membrane proteins that are embedded in a lipid bilayer, many of their surface residues are hydrophobic and membrane-contacting, but there is yet a widely-accepted quantity for the description or prediction of this characteristic property. Here, we propose a new quantity termed “membrane contact probability (MCP)”, which can be used to describe and predict the membrane-contacting surface residues of proteins. We also propose a machine learning-based method to predict MCP from protein sequences, utilizing the dataset generated by physics-based computer simulations. We demonstrate that a quantity such as MCP is helpful for protein structure prediction, and we believe that it will find broad applications in the structure and function studies of membrane proteins.
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Affiliation(s)
- Lei Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
| | - Jiangguo Zhang
- School of Life Sciences, Peking University, Beijing, China
| | - Dali Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail:
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32
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Mehrani A, Stagg SM. Probing intracellular vesicle trafficking and membrane remodelling by cryo-EM. J Struct Biol 2022; 214:107836. [PMID: 35101600 PMCID: PMC8923612 DOI: 10.1016/j.jsb.2022.107836] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 11/25/2022]
Abstract
Protein transport between the membranous compartments of the eukaryotic cells is mediated by the constant fission and fusion of the membrane-bounded vesicles from a donor to an acceptor membrane. While there are many membrane remodelling complexes in eukaryotes, COPII, COPI, and clathrin-coated vesicles are the three principal classes of coat protein complexes that participate in vesicle trafficking in the endocytic and secretory pathways. These vesicle-coat proteins perform two key functions: deforming lipid bilayers into vesicles and encasing selective cargoes. The three trafficking complexes share some commonalities in their structural features but differ in their coat structures, mechanisms of cargo sorting, vesicle formation, and scission. While the structures of many of the proteins involved in vesicle formation have been determined in isolation by X-ray crystallography, elucidating the proteins' structures together with the membrane is better suited for cryogenic electron microscopy (cryo-EM). In recent years, advances in cryo-EM have led to solving the structures and mechanisms of several vesicle trafficking complexes and associated proteins.
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Affiliation(s)
- Atousa Mehrani
- Department of Chemistry and Biochemistry, Florida State University
| | - Scott M. Stagg
- Department of Biological Sciences, Florida State University,Institute of Molecular Biophysics, Florida State University
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33
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Li T, Guo Y. ADP-Ribosylation Factor Family of Small GTP-Binding Proteins: Their Membrane Recruitment, Activation, Crosstalk and Functions. Front Cell Dev Biol 2022; 10:813353. [PMID: 35186926 PMCID: PMC8850633 DOI: 10.3389/fcell.2022.813353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Members of the ADP-ribosylation factor (ARF) family of guanine-nucleotide binding proteins play critical roles in various cellular processes, especially in regulating the secretory, and endocytic pathways. The fidelity of intracellular vesicular trafficking depends on proper activations and precise subcellular distributions of ARF family proteins regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Here we review recent progress in understanding the membrane recruitment, activation, crosstalk, and functions of ARF family proteins.
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Affiliation(s)
- Tiantian Li
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yusong Guo
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Yusong Guo,
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34
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Liu X, Stenhammar J, Wennerström H, Sparr E. Vesicles Balance Osmotic Stress with Bending Energy That Can Be Released to Form Daughter Vesicles. J Phys Chem Lett 2022; 13:498-507. [PMID: 35005979 PMCID: PMC8785185 DOI: 10.1021/acs.jpclett.1c03369] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
The bending energy of the lipid membrane is central to biological processes involving vesicles, such as endocytosis and exocytosis. To illustrate the role of bending energy in these processes, we study the response of single-component giant unilamellar vesicles (GUVs) subjected to external osmotic stress by glucose addition. For osmotic pressures exceeding 0.15 atm, an abrupt shape change from spherical to prolate occurs, showing that the osmotic pressure is balanced by the free energy of membrane bending. After equilibration, the external glucose solution was exchanged for pure water, yielding rapid formation of monodisperse daughter vesicles inside the GUVs through an endocytosis-like process. Our theoretical analysis shows that this process requires significant free energies stored in the deformed membrane to be kinetically allowed. The results indicate that bending energies stored in GUVs are much higher than previously implicated, with potential consequences for vesicle fusion/fission and the osmotic regulation in living cells.
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Affiliation(s)
- Xiaoyan Liu
- Physical Chemistry, Lund University, 221 00 Lund, Sweden
| | | | | | - Emma Sparr
- Physical Chemistry, Lund University, 221 00 Lund, Sweden
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35
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Zhang Y, Wang J, Ruan Y, Yang Y, Cheng Y, Wang F, Zhang C, Xu Y, Liu L, Yu M, Ren B, Wang J, Zhao B, Yang R, Xiong J, Wang J, Zhang J, Jian R, Liu Y, Tian Y. Genome-wide CRISPR screen identifies Puf60 as a novel stemness gene of mouse Embryonic Stem Cells. Stem Cells Dev 2022; 31:132-142. [PMID: 35019759 DOI: 10.1089/scd.2021.0309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mechanisms underlying self-renewal of embryonic stem cells (ESCs) hold great value in the clinical translation of stem cell biology and regenerative medicine research. To study the mechanisms in ESC self-renewal, screening and identification of key genes maintaining ESC self-renewal were performed by a genome-wide CRISPR-Cas9 knockout virus library. The mouse ESC R1 were infected with CRISPR-Cas9 knockout virus library and cultured for 14 days. The variation of sgRNA ratio was analyzed by high-throughput sequencing, followed by bioinformatics analysis to profile the altered genes. Our results showed 1375 genes with increased sgRNA ratio were found to be mainly involved in signal transduction, cell differentiation and cell apoptosis; 2929 genes with decreased sgRNA ratio were mainly involved in cell cycle regulation, RNA splicing, and biological metabolic processes. We further confirmed our screen specificity by confirming Puf60, U2af2, Wdr75 and Usp16 as novel positive regulators in mESC self-renewal. Meanwhile, further analysis showed the relevance between Puf60 expression and tumor. In conclusion, our study screened key genes maintaining ESC self-renewal and successful identified Puf60, U2af2, Wdr75 and Usp16 as novel positive regulators in mESC self-renewal, which provided theoretical basis and research clues for a better understanding of ESC self-renewal regulation.
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Affiliation(s)
- Yue Zhang
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, 30# Gaotanyan St., Shapingba District, Chongqing 400038, China, Chongqing, China, 400038;
| | - Jiaqi Wang
- Army Medical University, 12525, Institude of Immunulogy PLA & Department of Immunology, Army Medical University, Chongqing 400038, China, Chongqing, China;
| | - Yan Ruan
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Yi Yang
- Army Medical University, 12525, Experimental Center of Basic Medicine, College of Basic Medical Sciences, Chongqing, China;
| | - Yuda Cheng
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Fengsheng Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Chen Zhang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Yixiao Xu
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China;
| | - Lianlian Liu
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Meng Yu
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Bangqi Ren
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China;
| | - Jiangjun Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Binyu Zhao
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Ran Yang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Jiaxiang Xiong
- Army Medical University, 12525, Experimental Center of Basic Medicine, College of Basic Medical Sciences, Chongqing, China;
| | - Jiali Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, China;
| | - Junlei Zhang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, China;
| | - Rui Jian
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology,, Chongqing, China;
| | - Yong Liu
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China;
| | - Yanping Tian
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology,, Chongqing, China;
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36
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A tango for coats and membranes: New insights into ER-to-Golgi traffic. Cell Rep 2022; 38:110258. [DOI: 10.1016/j.celrep.2021.110258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/17/2021] [Accepted: 12/21/2021] [Indexed: 12/30/2022] Open
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37
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Ohashi Y. Activation Mechanisms of the VPS34 Complexes. Cells 2021; 10:cells10113124. [PMID: 34831348 PMCID: PMC8624279 DOI: 10.3390/cells10113124] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/18/2023] Open
Abstract
Phosphatidylinositol-3-phosphate (PtdIns(3)P) is essential for cell survival, and its intracellular synthesis is spatially and temporally regulated. It has major roles in two distinctive cellular pathways, namely, the autophagy and endocytic pathways. PtdIns(3)P is synthesized from phosphatidylinositol (PtdIns) by PIK3C3C/VPS34 in mammals or Vps34 in yeast. Pathway-specific VPS34/Vps34 activity is the consequence of the enzyme being incorporated into two mutually exclusive complexes: complex I for autophagy, composed of VPS34/Vps34-Vps15/Vps15-Beclin 1/Vps30-ATG14L/Atg14 (mammals/yeast), and complex II for endocytic pathways, in which ATG14L/Atg14 is replaced with UVRAG/Vps38 (mammals/yeast). Because of its involvement in autophagy, defects in which are closely associated with human diseases such as cancer and neurodegenerative diseases, developing highly selective drugs that target specific VPS34/Vps34 complexes is an essential goal in the autophagy field. Recent studies on the activation mechanisms of VPS34/Vps34 complexes have revealed that a variety of factors, including conformational changes, lipid physicochemical parameters, upstream regulators, and downstream effectors, greatly influence the activity of these complexes. This review summarizes and highlights each of these influences as well as clarifying key questions remaining in the field and outlining future perspectives.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Francis Crick Avenue, Cambridge CB2 0QH, UK
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38
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Adams EJ, Khoriaty R, Kiseleva A, Cleuren ACA, Tomberg K, van der Ent MA, Gergics P, Tang VT, Zhu G, Hoenerhoff MJ, O'Shea KS, Saunders TL, Ginsburg D. Murine SEC24D can substitute functionally for SEC24C during embryonic development. Sci Rep 2021; 11:21100. [PMID: 34702932 PMCID: PMC8548507 DOI: 10.1038/s41598-021-00579-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022] Open
Abstract
The COPII component SEC24 mediates the recruitment of transmembrane cargos or cargo adaptors into newly forming COPII vesicles on the ER membrane. Mammalian genomes encode four Sec24 paralogs (Sec24a-d), with two subfamilies based on sequence homology (SEC24A/B and C/D), though little is known about their comparative functions and cargo-specificities. Complete deficiency for Sec24d results in very early embryonic lethality in mice (before the 8 cell stage), with later embryonic lethality (E7.5) observed in Sec24c null mice. To test the potential overlap in function between SEC24C/D, we employed dual recombinase mediated cassette exchange to generate a Sec24cc-d allele, in which the C-terminal 90% of SEC24C has been replaced by SEC24D coding sequence. In contrast to the embryonic lethality at E7.5 of SEC24C-deficiency, Sec24cc-d/c-d pups survive to term, though dying shortly after birth. Sec24cc-d/c-d pups are smaller in size, but exhibit no other obvious developmental abnormality by pathologic evaluation. These results suggest that tissue-specific and/or stage-specific expression of the Sec24c/d genes rather than differences in cargo export function explain the early embryonic requirements for SEC24C and SEC24D.
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Affiliation(s)
- Elizabeth J Adams
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Constellation Pharmaceuticals, Cambridge, MA, 02142, USA
| | - Rami Khoriaty
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Univeristy of Michigan Rogel Cancer Center, Ann Arbor, MI, 48109, USA.
| | - Anna Kiseleva
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Audrey C A Cleuren
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kärt Tomberg
- Departement of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Peter Gergics
- Departement of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vi T Tang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Guojing Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mark J Hoenerhoff
- In Vivo Animal Core, Unit of Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - K Sue O'Shea
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Thomas L Saunders
- Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David Ginsburg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA.
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39
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Jalal ASB, Tran NT, Wu LJ, Ramakrishnan K, Rejzek M, Gobbato G, Stevenson CEM, Lawson DM, Errington J, Le TBK. CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc. Mol Cell 2021; 81:3623-3636.e6. [PMID: 34270916 DOI: 10.1101/2021.02.11.430593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/25/2021] [Accepted: 06/18/2021] [Indexed: 05/25/2023]
Abstract
ATP- and GTP-dependent molecular switches are extensively used to control functions of proteins in a wide range of biological processes. However, CTP switches are rarely reported. Here, we report that a nucleoid occlusion protein Noc is a CTPase enzyme whose membrane-binding activity is directly regulated by a CTP switch. In Bacillus subtilis, Noc nucleates on 16 bp NBS sites before associating with neighboring non-specific DNA to form large membrane-associated nucleoprotein complexes to physically occlude assembly of the cell division machinery. By in vitro reconstitution, we show that (1) CTP is required for Noc to form the NBS-dependent nucleoprotein complex, and (2) CTP binding, but not hydrolysis, switches Noc to a membrane-active state. Overall, we suggest that CTP couples membrane-binding activity of Noc to nucleoprotein complex formation to ensure productive recruitment of DNA to the bacterial cell membrane for nucleoid occlusion activity.
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Affiliation(s)
- Adam S B Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | | | - Martin Rejzek
- Chemistry Platform, John Innes Centre, Norwich, NR4 7UH, UK
| | - Giulia Gobbato
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
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40
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Recent developments in membrane curvature sensing and induction by proteins. Biochim Biophys Acta Gen Subj 2021; 1865:129971. [PMID: 34333084 DOI: 10.1016/j.bbagen.2021.129971] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding. SCOPE OF REVIEW We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins. MAJOR CONCLUSIONS Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood. GENERAL SIGNIFICANCE The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.
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41
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Raote I, Saxena S, Campelo F, Malhotra V. TANGO1 marshals the early secretory pathway for cargo export. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183700. [PMID: 34293283 DOI: 10.1016/j.bbamem.2021.183700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/13/2022]
Abstract
TANGO1 protein facilitates the endoplasmic reticulum (ER) export of large cargoes that cannot be accommodated in 60 nm transport vesicles. It assembles into a ring in the plane of the ER membrane to create a distinct domain. Its lumenal portion collects and sorts folded cargoes while its cytoplasmic domains collar COPII coats, recruit retrograde COPI-coated membranes that fuse within the TANGO1 ring, thus opening a tunnel for cargo transfer from the ER into a growing export conduit. This mode of cargo transfer bypasses the need for vesicular intermediates and is used to export the most abundant and bulky cargoes. The evolution of TANGO1 and its activities defines the difference between yeast and animal early secretory pathways.
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Affiliation(s)
- Ishier Raote
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.
| | - Sonashree Saxena
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain.
| | - Vivek Malhotra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
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42
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Jalal ASB, Tran NT, Wu LJ, Ramakrishnan K, Rejzek M, Gobbato G, Stevenson CEM, Lawson DM, Errington J, Le TBK. CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc. Mol Cell 2021; 81:3623-3636.e6. [PMID: 34270916 PMCID: PMC8429893 DOI: 10.1016/j.molcel.2021.06.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/25/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
ATP- and GTP-dependent molecular switches are extensively used to control functions of proteins in a wide range of biological processes. However, CTP switches are rarely reported. Here, we report that a nucleoid occlusion protein Noc is a CTPase enzyme whose membrane-binding activity is directly regulated by a CTP switch. In Bacillus subtilis, Noc nucleates on 16 bp NBS sites before associating with neighboring non-specific DNA to form large membrane-associated nucleoprotein complexes to physically occlude assembly of the cell division machinery. By in vitro reconstitution, we show that (1) CTP is required for Noc to form the NBS-dependent nucleoprotein complex, and (2) CTP binding, but not hydrolysis, switches Noc to a membrane-active state. Overall, we suggest that CTP couples membrane-binding activity of Noc to nucleoprotein complex formation to ensure productive recruitment of DNA to the bacterial cell membrane for nucleoid occlusion activity. CTP is required for Noc to form a higher-order nucleoprotein complex on DNA CTP binding switches DNA-entrapped Noc to a membrane-active state CTP hydrolysis likely reverses the association between Noc-DNA and the membrane The membrane-targeting helix adopts an autoinhibitory conformation in apo-Noc
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Affiliation(s)
- Adam S B Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | | | - Martin Rejzek
- Chemistry Platform, John Innes Centre, Norwich, NR4 7UH, UK
| | - Giulia Gobbato
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
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43
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Joiner AMN, Phillips BP, Yugandhar K, Sanford EJ, Smolka MB, Yu H, Miller EA, Fromme JC. Structural basis of TRAPPIII-mediated Rab1 activation. EMBO J 2021; 40:e107607. [PMID: 34018207 PMCID: PMC8204860 DOI: 10.15252/embj.2020107607] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022] Open
Abstract
The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo-EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α-helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.
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Affiliation(s)
- Aaron MN Joiner
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | | | - Kumar Yugandhar
- Department of Computational Biology/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Ethan J Sanford
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Haiyuan Yu
- Department of Computational Biology/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | | | - J Christopher Fromme
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
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44
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Dautt-Castro M, Rosendo-Vargas M, Casas-Flores S. The Small GTPases in Fungal Signaling Conservation and Function. Cells 2021; 10:cells10051039. [PMID: 33924947 PMCID: PMC8146680 DOI: 10.3390/cells10051039] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Monomeric GTPases, which belong to the Ras superfamily, are small proteins involved in many biological processes. They are fine-tuned regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Several families have been identified in organisms from different kingdoms. Overall, the most studied families are Ras, Rho, Rab, Ran, Arf, and Miro. Recently, a new family named Big Ras GTPases was reported. As a general rule, the proteins of all families have five characteristic motifs (G1–G5), and some specific features for each family have been described. Here, we present an exhaustive analysis of these small GTPase families in fungi, using 56 different genomes belonging to different phyla. For this purpose, we used distinct approaches such as phylogenetics and sequences analysis. The main functions described for monomeric GTPases in fungi include morphogenesis, secondary metabolism, vesicle trafficking, and virulence, which are discussed here. Their participation during fungus–plant interactions is reviewed as well.
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45
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Joiner AMN, Fromme JC. Structural basis for the initiation of COPII vesicle biogenesis. Structure 2021; 29:859-872.e6. [PMID: 33831355 DOI: 10.1016/j.str.2021.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/09/2021] [Accepted: 03/16/2021] [Indexed: 12/19/2022]
Abstract
The first stage of the eukaryotic secretory pathway is the packaging of cargo proteins into coat protein complex II (COPII) vesicles exiting the ER. The cytoplasmic COPII vesicle coat machinery is recruited to the ER membrane by the activated, GTP-bound, form of the conserved Sar1 GTPase. Activation of Sar1 on the surface of the ER by Sec12, a membrane-anchored GEF (guanine nucleotide exchange factor), is therefore the initiating step of the secretory pathway. Here we report the structure of the complex between Sar1 and the cytoplasmic GEF domain of Sec12, both from Saccharomyces cerevisiae. This structure, representing a key nucleotide-free activation intermediate, reveals how the potassium ion-binding K loop disrupts the nucleotide-binding site of Sar1. We propose an unexpected orientation of the GEF domain relative to the membrane surface and postulate a mechanism for how Sec12 facilitates membrane insertion of the amphipathic helix exposed by Sar1 upon GTP binding.
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Affiliation(s)
- Aaron M N Joiner
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850, USA.
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46
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Hutchings J, Stancheva VG, Brown NR, Cheung ACM, Miller EA, Zanetti G. Structure of the complete, membrane-assembled COPII coat reveals a complex interaction network. Nat Commun 2021; 12:2034. [PMID: 33795673 PMCID: PMC8016994 DOI: 10.1038/s41467-021-22110-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/12/2021] [Indexed: 01/02/2023] Open
Abstract
COPII mediates Endoplasmic Reticulum to Golgi trafficking of thousands of cargoes. Five essential proteins assemble into a two-layer architecture, with the inner layer thought to regulate coat assembly and cargo recruitment, and the outer coat forming cages assumed to scaffold membrane curvature. Here we visualise the complete, membrane-assembled COPII coat by cryo-electron tomography and subtomogram averaging, revealing the full network of interactions within and between coat layers. We demonstrate the physiological importance of these interactions using genetic and biochemical approaches. Mutagenesis reveals that the inner coat alone can provide membrane remodelling function, with organisational input from the outer coat. These functional roles for the inner and outer coats significantly move away from the current paradigm, which posits membrane curvature derives primarily from the outer coat. We suggest these interactions collectively contribute to coat organisation and membrane curvature, providing a structural framework to understand regulatory mechanisms of COPII trafficking and secretion.
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Affiliation(s)
- Joshua Hutchings
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Nick R Brown
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
- The Francis Crick Institute, London, UK
| | - Alan C M Cheung
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
- School of Biochemistry, University of Bristol, Bristol, UK
| | | | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK.
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47
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Fu M, Franquelim HG, Kretschmer S, Schwille P. Non‐Equilibrium Large‐Scale Membrane Transformations Driven by MinDE Biochemical Reaction Cycles. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Meifang Fu
- Dept. Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Henri G. Franquelim
- Dept. Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Simon Kretschmer
- Dept. Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
- Department of Bioengineering and Therapeutic Science University of California San Francisco San Francisco CA USA
| | - Petra Schwille
- Dept. Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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48
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Fu M, Franquelim HG, Kretschmer S, Schwille P. Non-Equilibrium Large-Scale Membrane Transformations Driven by MinDE Biochemical Reaction Cycles. Angew Chem Int Ed Engl 2021; 60:6496-6502. [PMID: 33285025 PMCID: PMC7986748 DOI: 10.1002/anie.202015184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 12/11/2022]
Abstract
The MinDE proteins from E. coli have received great attention as a paradigmatic biological pattern-forming system. Recently, it has surfaced that these proteins do not only generate oscillating concentration gradients driven by ATP hydrolysis, but that they can reversibly deform giant vesicles. In order to explore the potential of Min proteins to actually perform mechanical work, we introduce a new model membrane system, flat vesicle stacks on top of a supported lipid bilayer. MinDE oscillations can repeatedly deform these flat vesicles into tubules and promote progressive membrane spreading through membrane adhesion. Dependent on membrane and buffer compositions, Min oscillations further induce robust bud formation. Altogether, we demonstrate that under specific conditions, MinDE self-organization can result in work performed on biomimetic systems and achieve a straightforward mechanochemical coupling between the MinDE biochemical reaction cycle and membrane transformation.
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Affiliation(s)
- Meifang Fu
- Dept. Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Henri G. Franquelim
- Dept. Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Simon Kretschmer
- Dept. Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
- Department of Bioengineering and Therapeutic ScienceUniversity of California San FranciscoSan FranciscoCAUSA
| | - Petra Schwille
- Dept. Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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49
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Measuring protein insertion areas in lipid monolayers by fluorescence correlation spectroscopy. Biophys J 2021; 120:1333-1342. [PMID: 33609496 DOI: 10.1016/j.bpj.2021.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/21/2021] [Accepted: 02/10/2021] [Indexed: 11/22/2022] Open
Abstract
Membrane insertion of protein domains is an important step in many membrane remodeling processes, for example, in vesicular transport. The membrane area taken up by the protein insertion influences the protein binding affinity as well as the mechanical stress induced in the membrane and thereby its curvature. To our knowledge, this is the first optical measurement of this quantity on a system in equilibrium with direct determination of the number of inserted protein and no further assumptions concerning the binding thermodynamics. Whereas macroscopic total area changes in lipid monolayers are typically measured on a Langmuir film balance, finding the number of inserted proteins without perturbing the system and quantitating any small area changes has posed a challenge. Here, we address both issues by performing two-color fluorescence correlation spectroscopy directly on the monolayer. With a fraction of the protein being fluorescently labeled, the number of inserted proteins is determined in situ without resorting to invasive techniques such as collecting the monolayer by aspiration. The second color channel is exploited to monitor a small fraction of labeled lipids to determine the total area increase. Here, we use this method to determine the insertion area per molecule of Sar1, a protein of the COPII complex, which is involved in transport vesicle formation. Sar1 has an N-terminal amphipathic helix, which is responsible for membrane binding and curvature generation. An insertion area of (3.4 ± 0.8) nm2 was obtained for Sar1 in monolayers from a lipid mixture typically used in COPII reconstitution experiments, in good agreement with the expected insertion area of the Sar1 amphipathic helix. By using the two-color approach, determining insertion areas relies only on local fluorescence measurements. No macroscopic area measurements are needed, giving the method the potential to also be applied to laterally heterogeneous monolayers and bilayers.
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50
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Li J, Lambright DG, Hsu VW. Coordination of Grp1 recruitment mechanisms by its phosphorylation. Mol Biol Cell 2020; 31:2816-2825. [PMID: 33026967 PMCID: PMC7851867 DOI: 10.1091/mbc.e20-03-0173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The action of guanine nucleotide exchange factors (GEFs) on the ADP-ribosylation factor (ARF) family of small GTPases initiates intracellular transport pathways. This role requires ARF GEFs to be recruited from the cytosol to intracellular membrane compartments. An ARF GEF known as General receptor for 3-phosphoinositides 1 (Grp1) is recruited to the plasma membrane through its pleckstrin homology (PH) domain that recognizes phosphatidylinositol 3,4,5-trisphosphate (PIP3). Here, we find that the phosphorylation of Grp1 induces its PH domain to recognize instead phosphatidylinositol 4-phosphate (PI4P). This phosphorylation also releases an autoinhibitory mechanism that results in the coil–coil (CC) domain of Grp1 engaging two peripheral membrane proteins of the recycling endosome. Because the combination of these actions results in Grp1 being recruited preferentially to the recycling endosome rather than to the plasma membrane, our findings reveal the complexity of recruitment mechanisms that need to be coordinated in localizing an ARF GEF to an intracellular compartment to initiate a transport pathway. Our elucidation is also remarkable for having revealed that phosphoinositide recognition by a PH domain can be switched through its phosphorylation.
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Affiliation(s)
- Jian Li
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - David G Lambright
- Program in Molecular Medicine, Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Victor W Hsu
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA 02115
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