1
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Wenbo L, Yewei Y, Hui Z, Zhongyu L. Hijacking host cell vesicular transport: New insights into the nutrient acquisition mechanism of Chlamydia. Virulence 2024; 15:2351234. [PMID: 38773735 PMCID: PMC11123459 DOI: 10.1080/21505594.2024.2351234] [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: 07/26/2023] [Accepted: 04/27/2024] [Indexed: 05/24/2024] Open
Abstract
Chlamydia infection is an important cause of public health diseases, and no effective vaccine is currently available. Owing to its unique intracellular lifestyle, Chlamydia requires a variety of nutrients and substrates from host cells, particularly sphingomyelin, cholesterol, iron, amino acids, and the mannose-6-phosphate receptor, which are essential for inclusion development. Here, we summarize the recent advances in Chlamydia nutrient acquisition mechanism by hijacking host cell vesicular transport, which plays an important role in chlamydial growth and development. Chlamydia obtains the components necessary to complete its intracellular developmental cycle by recruiting Rab proteins (major vesicular trafficking regulators) and Rab effector proteins to the inclusion, interfering with Rab-mediated multivesicular trafficking, reorienting the nutrition of host cells, and reconstructing the intracellular niche environment. Consequently, exploring the role of vesicular transport in nutrient acquisition offers a novel perspective on new approaches for preventing and treating Chlamydia infection.
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Affiliation(s)
- Lei Wenbo
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang Medical School, University of South China, Hengyang, Hunan, P.R. China
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, P.R. China
| | - Yang Yewei
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang Medical School, University of South China, Hengyang, Hunan, P.R. China
| | - Zhou Hui
- Department of Laboratory Medicine and Pathology, First Affiliated Hospital of Hunan University of Chinese Traditional Medicine, Changsha, Hunan, P.R. China
| | - Li Zhongyu
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang Medical School, University of South China, Hengyang, Hunan, P.R. China
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2
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Wee Y, Wang J, Wilson EC, Rich CP, Rogers A, Tong Z, DeGroot E, Gopal YNV, Davies MA, Ekiz HA, Tay JKH, Stubben C, Boucher KM, Oviedo JM, Fairfax KC, Williams MA, Holmen SL, Wolff RK, Grossmann AH. Tumour-intrinsic endomembrane trafficking by ARF6 shapes an immunosuppressive microenvironment that drives melanomagenesis and response to checkpoint blockade therapy. Nat Commun 2024; 15:6613. [PMID: 39098861 PMCID: PMC11298541 DOI: 10.1038/s41467-024-50881-1] [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: 01/04/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
Tumour-host immune interactions lead to complex changes in the tumour microenvironment (TME), impacting progression, metastasis and response to therapy. While it is clear that cancer cells can have the capacity to alter immune landscapes, our understanding of this process is incomplete. Herein we show that endocytic trafficking at the plasma membrane, mediated by the small GTPase ARF6, enables melanoma cells to impose an immunosuppressive TME that accelerates tumour development. This ARF6-dependent TME is vulnerable to immune checkpoint blockade therapy (ICB) but in murine melanoma, loss of Arf6 causes resistance to ICB. Likewise, downregulation of ARF6 in patient tumours correlates with inferior overall survival after ICB. Mechanistically, these phenotypes are at least partially explained by ARF6-dependent recycling, which controls plasma membrane density of the interferon-gamma receptor. Collectively, our findings reveal the importance of endomembrane trafficking in outfitting tumour cells with the ability to shape their immune microenvironment and respond to immunotherapy.
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Affiliation(s)
- Yinshen Wee
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- School of Dentistry, Taipei Medical University, Taipei, Taiwan
| | - Junhua Wang
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA
| | - Emily C Wilson
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Coulson P Rich
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Aaron Rogers
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Zongzhong Tong
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Evelyn DeGroot
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y N Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce, Urla, Izmir, Turkey
| | - Joshua K H Tay
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Kenneth M Boucher
- Cancer Biostatistics Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Juan M Oviedo
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Keke C Fairfax
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Matthew A Williams
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Sheri L Holmen
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA
- Department of Surgery, University of Utah, Salt Lake City, UT, USA
| | - Roger K Wolff
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Allie H Grossmann
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, Salt Lake City, UT, USA.
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA.
- Providence Cancer Institute of Oregon, Earle A. Chiles Research Institute, Portland, OR, USA.
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3
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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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4
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Zhang Y, Soubias O, Pant S, Heinrich F, Vogel A, Li J, Li Y, Clifton LA, Daum S, Bacia K, Huster D, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA. Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. Nat Commun 2023; 14:7570. [PMID: 37989735 PMCID: PMC10663523 DOI: 10.1038/s41467-023-43008-5] [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: 05/12/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
ADP-ribosylation factor 1 (Arf1) interacts with multiple cellular partners and membranes to regulate intracellular traffic, organelle structure and actin dynamics. Defining the dynamic conformational landscape of Arf1 in its active form, when bound to the membrane, is of high functional relevance and key to understanding how Arf1 can alter diverse cellular processes. Through concerted application of nuclear magnetic resonance (NMR), neutron reflectometry (NR) and molecular dynamics (MD) simulations, we show that, while Arf1 is anchored to the membrane through its N-terminal myristoylated amphipathic helix, the G domain explores a large conformational space, existing in a dynamic equilibrium between membrane-associated and membrane-distal conformations. These configurational dynamics expose different interfaces for interaction with effectors. Interaction with the Pleckstrin homology domain of ASAP1, an Arf-GTPase activating protein (ArfGAP), restricts motions of the G domain to lock it in what seems to be a conformation exposing functionally relevant regions.
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Affiliation(s)
- Yue Zhang
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Ring Therapeutics, Inc., Cambridge, MA, USA
| | - Olivier Soubias
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Loxo Oncology at Lilly, Louisville, CO, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- NIST Center for Neutron Research, Gaithersburg, MD, USA
| | - Alexander Vogel
- Institute of Medical Physics and Biophysics, University of Leipzig, 04107, Leipzig, Germany
| | - Jess Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Yifei Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Vonsun Pharmatech Co., Ltd., Suzhou, China
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK
| | - Sebastian Daum
- Institute for Chemistry, Department of Biophysical Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3A, 06120, Halle, Germany
| | - Kirsten Bacia
- Institute for Chemistry, Department of Biophysical Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3A, 06120, Halle, Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, 04107, Leipzig, Germany
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- NIST Center for Neutron Research, Gaithersburg, MD, USA
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - R Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA.
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5
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Wee Y, Wang J, Wilson EC, Rich CP, Rogers A, Tong Z, DeGroot E, Gopal YV, Davies MA, Ekiz HA, Tay JK, Stubben C, Boucher KM, Oviedo JM, Fairfax KC, Williams MA, Holmen SL, Wolff RK, Grossmann AH. ARF6-dependent endocytic trafficking of the Interferon-γ receptor drives adaptive immune resistance in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560199. [PMID: 37873189 PMCID: PMC10592860 DOI: 10.1101/2023.09.29.560199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Adaptive immune resistance (AIR) is a protective process used by cancer to escape elimination by CD8+ T cells. Inhibition of immune checkpoints PD-1 and CTLA-4 specifically target Interferon-gamma (IFNγ)-driven AIR. AIR begins at the plasma membrane where tumor cell-intrinsic cytokine signaling is initiated. Thus, plasma membrane remodeling by endomembrane trafficking could regulate AIR. Herein we report that the trafficking protein ADP-Ribosylation Factor 6 (ARF6) is critical for IFNγ-driven AIR. ARF6 prevents transport of the receptor to the lysosome, augmenting IFNγR expression, tumor intrinsic IFNγ signaling and downstream expression of immunosuppressive genes. In murine melanoma, loss of ARF6 causes resistance to immune checkpoint blockade (ICB). Likewise, low expression of ARF6 in patient tumors correlates with inferior outcomes with ICB. Our data provide new mechanistic insights into tumor immune escape, defined by ARF6-dependent AIR, and support that ARF6-dependent endomembrane trafficking of the IFNγ receptor influences outcomes of ICB.
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Affiliation(s)
- Yinshen Wee
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- These authors contributed equally
- current contact information: School of Dentistry, Taipei Medical University, Taiwan
| | - Junhua Wang
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- These authors contributed equally
| | - Emily C. Wilson
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Coulson P. Rich
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Aaron Rogers
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Zongzhong Tong
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Evelyn DeGroot
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y.N. Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - H. Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir institute of Technology, Gulbahce, Urla, 35430, Izmir, Turkey
| | - Joshua K.H. Tay
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Kenneth M. Boucher
- Cancer Biostatistics Shared Resource, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Juan M. Oviedo
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Keke C. Fairfax
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Matthew A. Williams
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Sheri L. Holmen
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Surgery, University of Utah, Salt Lake City, Utah
| | - Roger K. Wolff
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Allie H. Grossmann
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- Lead contact
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6
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Sabe H. KRAS, MYC, and ARF6: inseparable relationships cooperatively promote cancer malignancy and immune evasion. Cell Commun Signal 2023; 21:106. [PMID: 37158894 PMCID: PMC10165578 DOI: 10.1186/s12964-023-01130-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/15/2023] [Indexed: 05/10/2023] Open
Abstract
Mutations in the KRAS gene and overexpression of protein products of the MYC and ARF6 genes occur frequently in cancer. Here, the inseparable relationships and cooperation of the protein products of these three genes in cancer malignancy and immune evasion are discussed. mRNAs encoded by these genes share the common feature of a G-quadruplex structure, which directs them to be robustly expressed when cellular energy production is increased. These three proteins are also functionally inseparable from each other, as follows. 1) KRAS induces MYC gene expression, and may also promote eIF4A-dependent MYC and ARF6 mRNA translation, 2) MYC induces the expression of genes involved in mitochondrial biogenesis and oxidative phosphorylation, and 3) ARF6 protects mitochondria from oxidative injury. ARF6 may moreover promote cancer invasion and metastasis, and also acidosis and immune checkpoint. Therefore, the inseparable relationships and cooperation of KRAS, MYC, and ARF6 appear to result in the activation of mitochondria and the driving of ARF6-based malignancy and immune evasion. Such adverse associations are frequent in pancreatic cancer, and appear to be further enhanced by TP53 mutations. Video Abstract.
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Affiliation(s)
- Hisataka Sabe
- Department of Molecular Biology, Graduate School of Medicine, and Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
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7
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Taylor RJ, Tagiltsev G, Briggs JAG. The structure of COPI vesicles and regulation of vesicle turnover. FEBS Lett 2023; 597:819-835. [PMID: 36513395 DOI: 10.1002/1873-3468.14560] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
COPI-coated vesicles mediate transport between Golgi stacks and retrograde transport from the Golgi to the endoplasmic reticulum. The COPI coat exists as a stable heptameric complex in the cytosol termed coatomer and is recruited en bloc to the membrane for vesicle formation. Recruitment of COPI onto membranes is mediated by the Arf family of small GTPases, which, in their GTP-bound state, bind both membrane and coatomer. Arf GTPases also influence cargo selection, vesicle scission and vesicle uncoating. Guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) regulate nucleotide binding by Arf GTPases. To understand the mechanism of COPI-coated vesicle trafficking, it is necessary to characterize the interplay between coatomer and Arf GTPases and their effectors. It is also necessary to understand interactions between coatomer and cargo, cargo adaptors/receptors and tethers facilitating binding to the target membrane. Here, we summarize current knowledge of COPI coat protein structure; we describe how structural and biochemical studies contributed to this knowledge; we review mechanistic insights into COPI vesicle biogenesis and disassembly; and we discuss the potential to answer open questions in the field.
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Affiliation(s)
- Rebecca J Taylor
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Grigory Tagiltsev
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - John A G Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
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8
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Adipose-specific deletion of the cation channel TRPM7 inhibits TAK1 kinase-dependent inflammation and obesity in male mice. Nat Commun 2023; 14:491. [PMID: 36717580 PMCID: PMC9887063 DOI: 10.1038/s41467-023-36154-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023] Open
Abstract
Chronic inflammation of white adipose tissue is a key link between obesity and the associated metabolic syndrome. Transient receptor potential melastatin-like 7 (TRPM7) is known to be related to inflammation; however, the role of TRPM7 in adipocyte phenotype and function in obesity remains unclear. Here, we observe that the activation of adipocyte TRPM7 plays an essential role in pro-inflammatory responses. Adult male mice are used in our experiments. Adipocyte-specific deficiency in TRPM7 attenuates the pro-inflammatory phenotype, improves glucose homeostasis, and suppresses weight gain in mice fed a high-fat diet. Mechanistically, the pro-inflammatory effect of TRPM7 is dependent on Ca2+ signaling. Ca2+ influx initiated by TRPM7 enhances transforming growth factor-β activated kinase 1 activation via the co-regulation of calcium/calmodulin-dependent protein kinase II and tumor necrosis factor receptor-associated factor 6, leading to exacerbated nuclear factor kappa B signaling. Additionally, obese mice treated with TRPM7 inhibitor are protected against obesity and insulin resistance. Our results demonstrate TRPM7 as a factor in the development of adipose inflammation that regulates insulin sensitivity in obesity.
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9
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Loose M, Auer A, Brognara G, Budiman HR, Kowalski L, Matijević I. In vitro
reconstitution of small
GTPase
regulation. FEBS Lett 2022; 597:762-777. [PMID: 36448231 DOI: 10.1002/1873-3468.14540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.
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Affiliation(s)
- Martin Loose
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Albert Auer
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Gabriel Brognara
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | | | - Lukasz Kowalski
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Ivana Matijević
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
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10
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Hashimoto A, Handa H, Hata S, Hashimoto S. Orchestration of mesenchymal plasticity and immune evasiveness via rewiring of the metabolic program in pancreatic ductal adenocarcinoma. Front Oncol 2022; 12:1005566. [PMID: 36408139 PMCID: PMC9669439 DOI: 10.3389/fonc.2022.1005566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most fatal cancer in humans, due to its difficulty of early detection and its high metastatic ability. The occurrence of epithelial to mesenchymal transition in preinvasive pancreatic lesions has been implicated in the early dissemination, drug resistance, and cancer stemness of PDAC. PDAC cells also have a reprogrammed metabolism, regulated by driver mutation-mediated pathways, a desmoplastic tumor microenvironment (TME), and interactions with stromal cells, including pancreatic stellate cells, fibroblasts, endothelial cells, and immune cells. Such metabolic reprogramming and its functional metabolites lead to enhanced mesenchymal plasticity, and creates an acidic and immunosuppressive TME, resulting in the augmentation of protumor immunity via cancer-associated inflammation. In this review, we summarize our recent understanding of how PDAC cells acquire and augment mesenchymal features via metabolic and immunological changes during tumor progression, and how mesenchymal malignancies induce metabolic network rewiring and facilitate an immune evasive TME. In addition, we also present our recent findings on the interesting relevance of the small G protein ADP-ribosylation factor 6-based signaling pathway driven by KRAS/TP53 mutations, inflammatory amplification signals mediated by the proinflammatory cytokine interleukin 6 and RNA-binding protein ARID5A on PDAC metabolic reprogramming and immune evasion, and finally discuss potential therapeutic strategies for the quasi-mesenchymal subtype of PDAC.
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Affiliation(s)
- Ari Hashimoto
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, Sapporo, Japan
- *Correspondence: Ari Hashimoto, ; Shigeru Hashimoto,
| | - Haruka Handa
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Soichiro Hata
- Department of Molecular Biology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shigeru Hashimoto
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
- *Correspondence: Ari Hashimoto, ; Shigeru Hashimoto,
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11
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Wang Y, Zhu G, Pei F, Wang Y, Liu J, Lu C, Zhao Z. RNA-Sequence Reveals the Regulatory Mechanism of miR-149 on Osteoblast Skeleton under Mechanical Tension. Stem Cells Int 2022; 2022:9640878. [PMID: 36193254 PMCID: PMC9525771 DOI: 10.1155/2022/9640878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Objective Based on RNA-sequencing (RNA-seq), the regulation of miRNAs differentially expressed in dental, periodontal, and alveolar bone tissue of orthodontic tree shrews on osteoblast skeleton under tension was investigated. Methods Tree shrews were used to construct orthodontic models. We used RNA-seq to identify differentially expressed miRNAs in periodontal tissues of the treatment group and control group tree shrews. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for enrichment analysis. Human osteoblast MG63 was treated with 5000 U mechanical tension. Real-time quantitative polymerase chain reaction (RT-qPCR) detected the expression of miR-149 and ARFGAP with SH3 domain, Ankyrin repeat, and Ph domain 3 (ASAP3) mRNA. Western blot detected the protein levels of ASAP3, F-actin, osteogenic markers bone morphogenetic protein 2 (BMP2), and runt-related transcription factor 2 (RUNX2). Rhodamine phalloidin was used to observe the fluorescence intensity of F-actin. Validation of the targeting relationship between miR-149 and ASAP3 by dual luciferase reporter gene assay. Results By performing miRNA-seq analysis on the dental and periodontal tissue of tree shrews in the treatment group and control group, we identified 51 upregulated miRNAs and 13 downregulated miRNAs. The expression of miR-149 in the dental and periodontal tissue of tree shrew and MG63 cells treated with mechanical tension was decreased, and miR-149 targeted ASAP3. Knockdown of ASAP3 inhibited the fluorescence intensity of F-actin in MG63 cells treated with 5000 U tension for 36 h, and overexpression of ASAP3 promoted the expression of F-actin and osteogenic markers BMP2 and RUNX2. Conclusions These findings revealed that miR-149 could modulate osteoblast differentiation under orthodontics mechanical tension through targeting ASAP3.
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Affiliation(s)
- Yifan Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041 Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Guanyin Zhu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041 Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fang Pei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041 Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yigan Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041 Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jun Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041 Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Caixia Lu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, 650106 Kunming, Yunnan, China
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, 3rd Section, South Renmin Road, Chengdu, 610041 Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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12
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Sakamoto M, Sasaki K, Sugie A, Nitta Y, Kimura T, Gürsoy S, Cinleti T, Iai M, Sengoku T, Ogata K, Suzuki A, Okamoto N, Iwama K, Tsuchida N, Uchiyama Y, Koshimizu E, Fujita A, Hamanaka K, Miyatake S, Mizuguchi T, Taguri M, Ito S, Takahashi H, Miyake N, Matsumoto N. De novo ARF3 variants cause neurodevelopmental disorder with brain abnormality. Hum Mol Genet 2021; 31:69-81. [PMID: 34346499 DOI: 10.1093/hmg/ddab224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
An optimal Golgi transport system is important for mammalian cells. The adenosine diphosphate (ADP) ribosylation factors (ARF) are key proteins for regulating cargo sorting at the Golgi network. In this family, ARF3 mainly works at the trans-Golgi network (TGN), and no ARF3-related phenotypes have yet been described in humans. We here report the clinical and genetic evaluations of two unrelated children with de novo pathogenic variants in the ARF3 gene: c.200A > T (p.Asp67Val) and c.296G > T (p.Arg99Leu). Although the affected individuals presented commonly with developmental delay, epilepsy, and brain abnormalities, there were differences in severity, clinical course, and brain lesions. In vitro subcellular localization assays revealed that the p.Arg99Leu mutant localized to Golgi apparatus, similar to the wild-type, whereas the p.Asp67Val mutant tended to show a disperse cytosolic pattern together with abnormally dispersed Golgi localization, similar to that observed in a known dominant negative variant (p.Thr31Asn). Pull-down assays revealed that the p.Asp67Val had a loss-of-function effect and the p.Arg99Leu variant had increased binding of the adaptor protein, Golgi-localized, γ-adaptin ear-containing, ARF-binding protein 1 (GGA1), supporting the gain of function. Furthermore, in vivo studies revealed that p.Asp67Val transfection led to lethality in flies. In contrast, flies expressing p.Arg99Leu had abnormal rough eye, as observed in the gain-of-function variant p.Gln71Leu. These data indicate that two ARF3 variants, the possibly loss-of-function p.Asp67Val and the gain-of-function p.Arg99Leu, both impair the Golgi transport system. Therefore, it may not be unreasonable that they showed different clinical features like diffuse brain atrophy (p.Asp67Val) and cerebellar hypoplasia (p.Arg99Leu).
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Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazunori Sasaki
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Sugie
- Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Yohei Nitta
- Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Tetsuaki Kimura
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Semra Gürsoy
- Department of Pediatric Genetics, S.B.Ü. Dr. Behçet Uz Children's Education and Research Hospital, Izmir, 35210, Turkey
| | - Tayfun Cinleti
- Department of Pediatric Genetics, Dokuz Eylul University, Faculty of Medicine, Izumir, 35340, Turkey
| | - Mizue Iai
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, 232-8555, Japan
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Suzuki
- Molecular Cellular Biology Laboratory, Yokohama City University Graduate School of Medical Life Science, Yokohama, 230-0045, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, 594-1101, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Masataka Taguri
- Department of Data Science, Yokohama City University School of Data Science, Yokohama, 236-0027, Japan
| | - Shuuichi Ito
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
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13
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Su MY, Fromm SA, Remis J, Toso DB, Hurley JH. Structural basis for the ARF GAP activity and specificity of the C9orf72 complex. Nat Commun 2021; 12:3786. [PMID: 34145292 PMCID: PMC8213707 DOI: 10.1038/s41467-021-24081-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/27/2021] [Indexed: 02/05/2023] Open
Abstract
Mutation of C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 forms a complex with SMCR8 and WDR41, which was reported to have GTPase activating protein activity toward ARF proteins, RAB8A, and RAB11A. We determined the cryo-EM structure of ARF1-GDP-BeF3- bound to C9orf72:SMCR8:WDR41. The SMCR8longin and C9orf72longin domains form the binding pocket for ARF1. One face of the C9orf72longin domain holds ARF1 in place, while the SMCR8longin positions the catalytic finger Arg147 in the ARF1 active site. Mutations in interfacial residues of ARF1 and C9orf72 reduced or eliminated GAP activity. RAB8A GAP required ~10-fold higher concentrations of the C9orf72 complex than for ARF1. These data support a specific function for the C9orf72 complex as an ARF GAP. The structure also provides a model for the active forms of the longin domain GAPs of FLCN and NPRL2 that regulate the Rag GTPases of the mTORC1 pathway.
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Affiliation(s)
- Ming-Yuan Su
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Simon A Fromm
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonathan Remis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Daniel B Toso
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
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14
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In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proc Natl Acad Sci U S A 2021; 118:2010054118. [PMID: 33443153 PMCID: PMC7817218 DOI: 10.1073/pnas.2010054118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1's functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1's enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.
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15
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Xie B, Jung C, Chandra M, Engel A, Kendall AK, Jackson LP. The Glo3 GAP crystal structure supports the molecular niche model for ArfGAPs in COPI coats. Adv Biol Regul 2021; 79:100781. [PMID: 33436318 PMCID: PMC7920988 DOI: 10.1016/j.jbior.2020.100781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 11/27/2022]
Abstract
Arf GTPase activating (ArfGAP) proteins are critical regulatory and effector proteins in membrane trafficking pathways. Budding yeast contain two ArfGAP proteins (Gcs1 and Glo3) implicated in COPI coat function at the Golgi, and yeast require Glo3 catalytic function for viability. A new X-ray crystal structure of the Glo3 GAP domain was determined at 2.1 Å resolution using molecular replacement methods. The structure reveals a Cys4-family zinc finger motif with an invariant residue (R59) positioned to act as an "arginine finger" during catalysis. Comparisons among eukaryotic GAP domains show a key difference between ArfGAP1 and ArfGAP2/3 family members in the final helix located within the domain. Conservation at both the sequence and structural levels suggest the Glo3 GAP domain interacts with yeast Arf1 switch I and II regions to promote catalysis. Together, the structural data presented here provide additional evidence for placing Glo3 near Arf1 triads within membrane-assembled COPI coats and further support the molecular niche model for COPI coat regulation by ArfGAPs.
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Affiliation(s)
- Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Christian Jung
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Andrew Engel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Amy K Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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16
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Zhu J, Zhou Q, Xia Y, Lin L, Li J, Peng M, Zhang R, Zhang M. GIT/PIX Condensates Are Modular and Ideal for Distinct Compartmentalized Cell Signaling. Mol Cell 2020; 79:782-796.e6. [DOI: 10.1016/j.molcel.2020.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/02/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022]
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17
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Expression of ArfGAP3 in Vaginal Anterior Wall of Patients With Pelvic Floor Organ Prolapse in Pelvic Organ Prolapse and Non-Pelvic Organ Prolapse Patients. Female Pelvic Med Reconstr Surg 2020; 27:e64-e69. [PMID: 31868832 PMCID: PMC7774809 DOI: 10.1097/spv.0000000000000808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The purpose of this study was to study the expression of adenosine diphosphate ribosylation factor GTPase-activating protein 3 (ArfGAP3) in the anterior vaginal wall of patients with pelvic organ prolapse (POP).
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18
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Song X, Xu W, Xu G, Kong S, Ding L, Xiao J, Cao X, Wang F. ACAP4 interacts with CrkII to promote the recycling of integrin β1. Biochem Biophys Res Commun 2019; 516:8-14. [PMID: 31182282 DOI: 10.1016/j.bbrc.2019.05.173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
ACAP4, a GTPase-activating protein (GAP) for the ADP-ribosylation factor 6 (ARF6), plays import roles in cell migration, cell polarity, vesicle trafficking and tumorigenesis. Similarly, the ubiquitously expressed adaptor protein CrkII functions in a wide range of cellular activities, including cell proliferation, T cell adhesion and activation, tumorigenesis, and bacterial pathogenesis. Here, we demonstrate that ACAP4 physically interacts with CrkII. Biochemical experiments revealed that ACAP4550-660 and the SH3N domain of CrkII are responsible for the interaction. Functional characterization showed that the interaction is required for the recruitment of ACAP4 to the plasma membrane where ACAP4 functions to regulate the recycling of the signal transducer integrin β1. Thus, we suggest that the CrkII-ACAP4 complex may be involved in regulation of cell adhesion.
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Affiliation(s)
- Xueyan Song
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Wenjuan Xu
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Guangsheng Xu
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Shuai Kong
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Lu Ding
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Jin Xiao
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Xinwang Cao
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Fengsong Wang
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China.
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19
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Chao FA, Li Y, Zhang Y, Byrd RA. Probing the Broad Time Scale and Heterogeneous Conformational Dynamics in the Catalytic Core of the Arf-GAP ASAP1 via Methyl Adiabatic Relaxation Dispersion. J Am Chem Soc 2019; 141:11881-11891. [PMID: 31293161 PMCID: PMC7505415 DOI: 10.1021/jacs.9b02602] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Methyl-TROSY is one of the most powerful NMR spectroscopic tools for studying structures and conformational dynamics of large protein complexes in solution. In studying conformational dynamics, side chains usually display heterogeneous dynamics, including collective and local motions, that can be difficult to detect and analyze by conventional relaxation dispersion (RD) approaches. The combination of NH-based heteronuclear adiabatic relaxation dispersion (HARD) experiments and a geometric approximation (geoHARD) has been shown to have several advantages over conventional RD in revealing conformational dynamics over a broad time scale. Here, we demonstrate a new technique that has been developed to detect both heterogeneous and wide time scale conformational dynamics in the hydrophobic interior of large macromolecules utilizing methyl-geoHARD. It is shown that methyl-geoHARD will be feasible at ultrahigh magnetic fields (>1 GHz), when this technology becomes available. For the ZA domain of Arf-GAP ASAP1, with a global correlational time of 24 ns at 15 °C, a wide range of conformational dynamics (exhibiting chemical exchange rates (kex) between 102 and 105 s-1) are observed in the methyl groups of isoleucine, leucine, and valine. The dynamics include collective and independent local motions. Furthermore, portions of the collective motions have been confirmed by single-quantum Carr-Purcell-Meiboom-Gill (SQ-CPMG) RD experiments; however, motions outside of the detectable CPMG window (400-8000 s-1) cannot be accurately determined by SQ-CPMG experiments. The methyl-geoHARD experiment allows the dissection of heterogeneous conformational dynamics and pinpoints important motions that, potentially, can be correlated with important biological functions and recognition.
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Affiliation(s)
- Fa-An Chao
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - Yifei Li
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - Yue Zhang
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - R Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
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20
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Sztul E, Chen PW, Casanova JE, Cherfils J, Dacks JB, Lambright DG, Lee FJS, Randazzo PA, Santy LC, Schürmann A, Wilhelmi I, Yohe ME, Kahn RA. ARF GTPases and their GEFs and GAPs: concepts and challenges. Mol Biol Cell 2019; 30:1249-1271. [PMID: 31084567 PMCID: PMC6724607 DOI: 10.1091/mbc.e18-12-0820] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 12/12/2022] Open
Abstract
Detailed structural, biochemical, cell biological, and genetic studies of any gene/protein are required to develop models of its actions in cells. Studying a protein family in the aggregate yields additional information, as one can include analyses of their coevolution, acquisition or loss of functionalities, structural pliability, and the emergence of shared or variations in molecular mechanisms. An even richer understanding of cell biology can be achieved through evaluating functionally linked protein families. In this review, we summarize current knowledge of three protein families: the ARF GTPases, the guanine nucleotide exchange factors (ARF GEFs) that activate them, and the GTPase-activating proteins (ARF GAPs) that have the ability to both propagate and terminate signaling. However, despite decades of scrutiny, our understanding of how these essential proteins function in cells remains fragmentary. We believe that the inherent complexity of ARF signaling and its regulation by GEFs and GAPs will require the concerted effort of many laboratories working together, ideally within a consortium to optimally pool information and resources. The collaborative study of these three functionally connected families (≥70 mammalian genes) will yield transformative insights into regulation of cell signaling.
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Affiliation(s)
- Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, MA 01267
| | - James E. Casanova
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS and Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France
| | - Joel B. Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - David G. Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Amherst, MA 01605
| | - Fang-Jen S. Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | | | - Lorraine C. Santy
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Annette Schürmann
- German Institute of Human Nutrition, 85764 Potsdam-Rehbrücke, Germany
| | - Ilka Wilhelmi
- German Institute of Human Nutrition, 85764 Potsdam-Rehbrücke, Germany
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322-3050
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21
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Song X, Liu W, Yuan X, Jiang J, Wang W, Mullen M, Zhao X, Zhang Y, Liu F, Du S, Rehman A, Tian R, Li J, Frost A, Song Z, Green HN, Henry C, Liu X, Ding X, Wang D, Yao X. Acetylation of ACAP4 regulates CCL18-elicited breast cancer cell migration and invasion. J Mol Cell Biol 2018; 10:559-572. [PMID: 30395269 PMCID: PMC6692856 DOI: 10.1093/jmcb/mjy058] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/03/2018] [Accepted: 08/20/2018] [Indexed: 01/03/2023] Open
Abstract
Tumor metastasis represents the main causes of cancer-related death. Our recent study showed that chemokine CCL18 secreted from tumor-associated macrophages regulates breast tumor metastasis, but the underlying mechanisms remain less clear. Here, we show that ARF6 GTPase-activating protein ACAP4 regulates CCL18-elicited breast cancer cell migration via the acetyltransferase PCAF-mediated acetylation. CCL18 stimulation elicited breast cancer cell migration and invasion via PCAF-dependent acetylation. ACAP4 physically interacts with PCAF and is a cognate substrate of PCAF during CCL18 stimulation. The acetylation site of ACAP4 by PCAF was mapped to Lys311 by mass spectrometric analyses. Importantly, dynamic acetylation of ACAP4 is essential for CCL18-induced breast cancer cell migration and invasion, as overexpression of the persistent acetylation-mimicking or non-acetylatable ACAP4 mutant blocked CCL18-elicited cell migration and invasion. Mechanistically, the acetylation of ACAP4 at Lys311 reduced the lipid-binding activity of ACAP4 to ensure a robust and dynamic cycling of ARF6-ACAP4 complex with plasma membrane in response to CCL18 stimulation. Thus, these results present a previously undefined mechanism by which CCL18-elicited acetylation of the PH domain controls dynamic interaction between ACAP4 and plasma membrane during breast cancer cell migration and invasion.
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Affiliation(s)
- Xiaoyu Song
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Wei Liu
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Xiao Yuan
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
- Department of Chemistry, Southern University of Science & Technology, Shenzhen, China
| | - Jiying Jiang
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Wanjuan Wang
- School of Basic Medical Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - McKay Mullen
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Xuannv Zhao
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
| | - Yin Zhang
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
- School of Basic Medical Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Fusheng Liu
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
- School of Basic Medical Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shihao Du
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
- School of Basic Medical Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Adeel Rehman
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
| | - Ruijun Tian
- Department of Chemistry, Southern University of Science & Technology, Shenzhen, China
| | - Jian Li
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Andra Frost
- Department of Pathology, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Zhenwei Song
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
| | - Hadiyah-Nicole Green
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Calmour Henry
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Xing Liu
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Xia Ding
- School of Basic Medical Sciences, Beijing University of Chinese Medicine, Beijing, China
- Keck Center for Cellular Dynamics & Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Dongmei Wang
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
| | - Xuebiao Yao
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei National Science Center for Physical Sciences at Nanoscale, CAS Center of Excellence in Molecular Cell Sciences, University of Science & Technology of China, Hefei, China
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22
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Kutscher LM, Keil W, Shaham S. RAB-35 and ARF-6 GTPases Mediate Engulfment and Clearance Following Linker Cell-Type Death. Dev Cell 2018; 47:222-238.e6. [PMID: 30220571 PMCID: PMC6200590 DOI: 10.1016/j.devcel.2018.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 07/18/2018] [Accepted: 08/17/2018] [Indexed: 12/11/2022]
Abstract
Clearance of dying cells is essential for development and homeostasis. Conserved genes mediate apoptotic cell removal, but whether these genes control non-apoptotic cell removal is a major open question. Linker cell-type death (LCD) is a prevalent non-apoptotic developmental cell death process with features conserved from C. elegans to vertebrates. Using microfluidics-based long-term in vivo imaging, we show that unlike apoptotic cells, the C. elegans linker cell, which dies by LCD, is competitively phagocytosed by two neighboring cells, resulting in cell splitting. Subsequent cell elimination does not require apoptotic engulfment genes. Rather, we find that RAB-35 GTPase is a key coordinator of competitive phagocytosis onset and cell degradation. RAB-35 binds CNT-1, an ARF-6 GTPase activating protein, and removes ARF-6, a degradation inhibitor, from phagosome membranes. This facilitates phosphatidylinositol-4,5-bisphosphate removal from phagosome membranes, promoting phagolysosome maturation. Our studies suggest that RAB-35 and ARF-6 drive a conserved program eliminating cells dying by LCD.
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Affiliation(s)
- Lena M Kutscher
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Wolfgang Keil
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY 10065, USA; Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY 10065, USA.
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23
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Singh V, Erady C, Balasubramanian N. Cell-matrix adhesion controls Golgi organization and function through Arf1 activation in anchorage-dependent cells. J Cell Sci 2018; 131:jcs.215855. [PMID: 30054383 PMCID: PMC6127727 DOI: 10.1242/jcs.215855] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/27/2018] [Indexed: 12/15/2022] Open
Abstract
Cell-matrix adhesion regulates membrane trafficking controlling anchorage-dependent signaling. While a dynamic Golgi complex can contribute to this pathway, its regulation by adhesion remains unclear. Here we report that loss of adhesion dramatically disorganized the Golgi in mouse and human fibroblast cells. Golgi integrity is restored rapidly upon integrin-mediated re-adhesion to FN and is disrupted by integrin blocking antibody. In suspended cells, the cis, cis-medial and trans-Golgi networks differentially disorganize along the microtubule network but show no overlap with the ER, making this disorganization distinct from known Golgi fragmentation. This pathway is regulated by an adhesion-dependent reduction and recovery of Arf1 activation. Constitutively active Arf1 disrupts this regulation and prevents Golgi disorganization due to loss of adhesion. Adhesion-dependent Arf1 activation regulates its binding to the microtubule minus-end motor protein dynein to control Golgi reorganization, which is blocked by ciliobrevin. Adhesion-dependent Golgi organization controls its function, regulating cell surface glycosylation due to loss of adhesion, which is blocked by constitutively active Arf1. This study, hence, identified integrin-dependent cell-matrix adhesion to be a novel regulator of Arf1 activation, controlling Golgi organization and function in anchorage-dependent cells.
This article has an associated First Person interview with the first author of the paper. Summary: Integrin-dependent cell-matrix adhesion activates Arf1, which then recruits dynein to regulate Golgi organization and function along the microtubule network.
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Affiliation(s)
- Vibha Singh
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Chaitanya Erady
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Nagaraj Balasubramanian
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
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24
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Abstract
In eukaryotes, distinct transport vesicles functionally connect various intracellular compartments. These carriers mediate transport of membranes for the biogenesis and maintenance of organelles, secretion of cargo proteins and peptides, and uptake of cargo into the cell. Transport vesicles have distinct protein coats that assemble on a donor membrane where they can select cargo and curve the membrane to form a bud. A multitude of structural elements of coat proteins have been solved by X-ray crystallography. More recently, the architectures of the COPI and COPII coats were elucidated in context with their membrane by cryo-electron tomography. Here, we describe insights gained from the structures of these two coat lattices and discuss the resulting functional implications.
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Affiliation(s)
- Julien Béthune
- Heidelberg University Biochemistry Centre, 69120 Heidelberg, Germany; ,
| | - Felix T Wieland
- Heidelberg University Biochemistry Centre, 69120 Heidelberg, Germany; ,
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25
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Mao X, Fan C, Yu X, Chen B, Jin F. DDEFL1 correlated with Rho GTPases activity in breast cancer. Oncotarget 2017; 8:112487-112497. [PMID: 29348842 PMCID: PMC5762527 DOI: 10.18632/oncotarget.22095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/22/2017] [Indexed: 01/13/2023] Open
Abstract
DDEFL1 is related to maintaining a limiting amount of ARF6 in GTP-loaded form by accelerating its GTP hydrolysis activity, which has been implicated in hepatocellular cancer pathogenesis and lung cancer development. We investigated DDEFL1 expression in breast cancer and paired normal breast tissues by immunohistochemistry and found that DDEFL1 expression was significantly associated with tumor size, lymph node metastasis, high content of elastosis and TNM stage but not with menopausal status or age. We detected the mRNA and protein expression of DDEFL1 in breast cancer cell lines by Western blotting and quantitative real-time PCR (qRT-PCR). DDEFL1 was obvious in MDA-MB-435s and MDA-MB-231 but very weak in ZR-75-1. Further experiments were conducted to evaluate the effect of DDEFL1 small interfering RNA (siRNA) transfection on the biological behavior of MDA-MB-231. After transfection, the effects of DDEFL1 inhibition on expression of mRNA and protein were also analyzed by Western blotting and qRT-PCR. Increased apoptosis and invasive ability, decreased cellular proliferation was found in MDA-MB-231 with successful DDEFL1 siRNA transient transfection (p < 0.05). Western blotting and qRT-PCR results showed that the DDEFL1 inhibition up-regulated Caspase-3, Apaf-1, cytochrome c, and Bax expression and down-regulated Bcl-2 expression. The DDEFL1 inhibition also down-regulated the mRNA and protein expression of Rho, CDC42 and Rac1. Our study provided a functional linkage through DDEFL1 with breast cancer biological behaviours by Rho GTPases. Possible implication of our main finding for the DDEFL1 role in breast cancer and the downstream signaling pathways for the treatment of breast cancer.
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Affiliation(s)
- Xiaoyun Mao
- Department of Breast Surgery, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Chuifeng Fan
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, Liaoning 110001, China
| | - Xinmiao Yu
- Department of Breast Surgery, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Bo Chen
- Department of Breast Surgery, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Feng Jin
- Department of Breast Surgery, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
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26
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Vetter IR. Interface analysis of small GTP binding protein complexes suggests preferred membrane orientations. Biol Chem 2017; 398:637-651. [PMID: 28002022 DOI: 10.1515/hsz-2016-0287] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/12/2016] [Indexed: 11/15/2022]
Abstract
Crystal structures of small GTP binding protein complexes with their effectors and regulators reveal that one particularly flat side of the G domain that contains helix α4 and the C-terminal helix α5 is practically devoid of contacts. Although this observation seems trivial as the main binding targets are the switch I and II regions opposite of this side, the fact that all interacting proteins, even the largest ones, seem to avoid occupying this area (except for Ran, that does not localize to membranes) is very striking. An orientation with this 'flat' side parallel to the membrane was proposed before and would allow simultaneous interaction of the lipidated C-terminus and positive charges in the α4 helix with the membrane while being bound to effector or regulator molecules. Furthermore, this 'flat' side might be involved in regulatory mechanisms: a Ras dimer that is found in different crystal forms interacts exactly at this side. Additional interface analysis of GTPase complexes nicely confirms the effect of different flexibilities of the GTP and GDP forms. Besides Ran proteins, guanine nucleotide exchange factors (GEFs) bury the largest surface areas to provide the binding energy to open up the switch regions for nucleotide exchange.
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Affiliation(s)
- Ingrid R Vetter
- Max Planck Institute of Molecular Physiology, Department of Mechanistic Cell Biology, Otto-Hahn-Str. 11, D-44227 Dortmund
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27
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Ivanova AA, Caspary T, Seyfried NT, Duong DM, West AB, Liu Z, Kahn RA. Biochemical characterization of purified mammalian ARL13B protein indicates that it is an atypical GTPase and ARL3 guanine nucleotide exchange factor (GEF). J Biol Chem 2017; 292:11091-11108. [PMID: 28487361 PMCID: PMC5491791 DOI: 10.1074/jbc.m117.784025] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/02/2017] [Indexed: 12/11/2022] Open
Abstract
Primary cilia play central roles in signaling during metazoan development. Several key regulators of ciliogenesis and ciliary signaling are mutated in humans, resulting in a number of ciliopathies, including Joubert syndrome (JS). ARL13B is a ciliary GTPase with at least three missense mutations identified in JS patients. ARL13B is a member of the ADP ribosylation factor family of regulatory GTPases, but is atypical in having a non-homologous, C-terminal domain of ∼20 kDa and at least one key residue difference in the consensus GTP-binding motifs. For these reasons, and to establish a solid biochemical basis on which to begin to model its actions in cells and animals, we developed preparations of purified, recombinant, murine Arl13b protein. We report results from assays for solution-based nucleotide binding, intrinsic and GTPase-activating protein-stimulated GTPase, and ARL3 guanine nucleotide exchange factor activities. Biochemical analyses of three human missense mutations found in JS and of two consensus GTPase motifs reinforce the atypical properties of this regulatory GTPase. We also discovered that murine Arl13b is a substrate for casein kinase 2, a contaminant in our preparation from human embryonic kidney cells. This activity, and the ability of casein kinase 2 to use GTP as a phosphate donor, may be a source of differences between our data and previously published results. These results provide a solid framework for further research into ARL13B on which to develop models for the actions of this clinically important cell regulator.
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Affiliation(s)
| | - Tamara Caspary
- Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | | | | | - Andrew B West
- the Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Zhiyong Liu
- the Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama 35294
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28
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Dodonova SO, Aderhold P, Kopp J, Ganeva I, Röhling S, Hagen WJH, Sinning I, Wieland F, Briggs JAG. 9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments. eLife 2017. [PMID: 28621666 PMCID: PMC5482573 DOI: 10.7554/elife.26691] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution. We also obtained a 2.57 Å resolution crystal structure of βδ-COP. By combining these structures we built a molecular model of the coat. We additionally determined the coat structure in the presence of ArfGAP proteins that regulate coat dissociation. We found that Arf1 occupies contrasting molecular environments within the coat, leading us to hypothesize that some Arf1 molecules may regulate vesicle assembly while others regulate coat disassembly. DOI:http://dx.doi.org/10.7554/eLife.26691.001
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Affiliation(s)
- Svetlana O Dodonova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Molecular Biology Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Aderhold
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Juergen Kopp
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Iva Ganeva
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Simone Röhling
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Felix Wieland
- Heidelberg University Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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29
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Functional analysis of rare variants found in schizophrenia implicates a critical role for GIT1-PAK3 signaling in neuroplasticity. Mol Psychiatry 2017; 22:417-429. [PMID: 27457813 PMCID: PMC6186433 DOI: 10.1038/mp.2016.98] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/21/2016] [Accepted: 05/02/2016] [Indexed: 01/21/2023]
Abstract
Although the pathogenesis of schizophrenia (SCZ) is proposed to involve alterations of neural circuits via synaptic dysfunction, the underlying molecular mechanisms remain poorly understood. Recent exome sequencing studies of SCZ have uncovered numerous single-nucleotide variants (SNVs); however, the majority of these SNVs have unknown functional consequences, leaving their disease relevance uncertain. Filling this knowledge gap requires systematic application of quantitative and scalable assays to assess known and novel biological functions of genes. Here we demonstrate loss-of-function effects of multiple rare coding SNVs found in SCZ subjects in the GIT1 (G protein-coupled receptor kinase interacting ArfGAP 1) gene using functional cell-based assays involving coexpression of GIT1 and PAK3 (p21 protein (Cdc42/Rac)-activated kinase 3). Most notably, a GIT1-R283W variant reported in four independent SCZ cases was defective in activating PAK3 as well as MAPK (mitogen-activated protein kinase). Similar functional deficits were found for a de novo SCZ variant GIT1-S601N. Additional assays revealed deficits in the capacity of GIT1-R283W to stimulate PAK phosphorylation in cultured hippocampal neurons. In addition, GIT1-R283W showed deficits in the induction of GAD1 (glutamate decarboxylase 1) protein expression. Extending these functional assays to 10 additional rare GIT1 variants revealed the existence of an allelic series with the majority of the SCZ case variants exhibiting loss of function toward MAPK activation in a manner correlated with loss of PAK3 activation. Taken together, we propose that rare variants in GIT1, along with other genetic and environmental factors, cause dysregulation of PAK3 leading to synaptic deficits in SCZ.
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30
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Qian J, Li Y, Yao H, Tian H, Wang H, Ai L, Xie Y, Bao Y, Liang L, Hu Y, Zhang Y, Wang J, Li C, Tang J, Chen Y, Xu J, Fang JY. ASAP3 regulates microvilli structure in parietal cells and presents intervention target for gastric acidity. Signal Transduct Target Ther 2017; 2:17003. [PMID: 29263912 PMCID: PMC5661632 DOI: 10.1038/sigtrans.2017.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 01/28/2023] Open
Abstract
Gastric acidity-associated disorders such as peptic ulcer and reflux diseases are widespread, and the reported resistance and side effects of currently used medicines suggest an urgent requirement for alternative therapeutic approaches. Here we demonstrate a critical role of ASAP3 in regulating the microvilli structure of parietal cells in vivo, and reveal the feasibility of controlling gastric acidity by targeting ASAP3. Conditional knockout of ASAP3 in mice caused elongation and stacking of microvilli in parietal cells, and substantially decreased gastric acid secretion. These were associated with active assembly of F-actin caused by a higher level of GTP-bound Arf6 GTPase. Consistently, a small molecular compound QS11 inhibited ASAP3 function and significantly reduced gastric acidity in vivo. Of note, the expression of ASAP3 was positively correlated with gastric acid secretion in 90 human cases, and high expression of ASAP3 was associated with reflux disease and peptic ulcer. These results reveal for the first time that ASAP3 regulates the microvilli structures in parietal cells. Our data also suggest ASAP3 as a feasible and drugable therapeutic target for gastric acidity-associated diseases.
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Affiliation(s)
- Jin Qian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yueyuan Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Han Yao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Haiying Tian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Huanbin Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Luoyan Ai
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yuanhong Xie
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yujie Bao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Lunxi Liang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ye Hu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yao Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jilin Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Chushu Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jiayin Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yingxuan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jie Xu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
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31
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Dümmer M, Michalski C, Essen LO, Rath M, Galland P, Forreiter C. EHB1 and AGD12, two calcium-dependent proteins affect gravitropism antagonistically in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2016; 206:114-124. [PMID: 27728837 DOI: 10.1016/j.jplph.2016.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Abstract
The ADP-RIBOSYLATION FACTOR GTPase-ACTIVATING PROTEIN (AGD) 12, a member of the ARF-GAP protein family, affects gravitropism in Arabidopsis thaliana. A loss-of-function mutant lacking AGD12 displayed diminished gravitropism in roots and hypocotyls indicating that both organs are affected by this regulator. AGD12 is structurally related to ENHANCED BENDING (EHB) 1, previously described as a negative effector of gravitropism. In contrast to agd12 mutants, ehb1 loss-of function seedlings displayed enhanced gravitropic bending. While EHB1 and AGD12 both possess a C-terminal C2/CaLB-domain, EHB1 lacks the N-terminal ARF-GAP domain present in AGD12. Subcellular localization analysis using Brefeldin A indicated that both proteins are elements of the trans Golgi network. Physiological analyses provided evidence that gravitropic signaling might operate via an antagonistic interaction of ARF-GAP (AGD12) and EHB1 in their Ca2+-activated states.
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Affiliation(s)
- Michaela Dümmer
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Christian Michalski
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Lars-Oliver Essen
- Fachbereich Chemie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Magnus Rath
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Paul Galland
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Christoph Forreiter
- Institut für Biologie, Universität Siegen, Adolf-Reichwein Str. 2, D-57068 Siegen, Germany.
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Classification of the treble clef zinc finger: noteworthy lessons for structure and function evolution. Sci Rep 2016; 6:32070. [PMID: 27562564 PMCID: PMC4999995 DOI: 10.1038/srep32070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/02/2016] [Indexed: 11/08/2022] Open
Abstract
Treble clef (TC) zinc fingers constitute a large fold-group of structural zinc-binding protein domains that mediate numerous cellular functions. We have analysed the sequence, structure, and function relationships among all TCs in the Protein Data Bank. This led to the identification of novel TCs, such as lsr2, YggX and TFIIIC τ 60 kDa subunit, and prediction of a nuclease-like function for the DUF1364 family. The structural malleability of TCs is evident from the many examples with variations to the core structural elements of the fold. We observe domains wherein the structural core of the TC fold is circularly permuted, and also some examples where the overall fold resembles both the TC motif and another unrelated fold. All extant TC families do not share a monophyletic origin, as several TC proteins are known to have been present in the last universal common ancestor and the last eukaryotic common ancestor. We identify several TCs where the zinc-chelating site and residues are not merely responsible for structure stabilization but also perform other functions, such as being redox active in C1B domain of protein kinase C, a nucleophilic acceptor in Ada and catalytic in organomercurial lyase, MerB.
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Mishra AK, Lambright DG. Invited review: Small GTPases and their GAPs. Biopolymers 2016; 105:431-48. [PMID: 26972107 PMCID: PMC5439442 DOI: 10.1002/bip.22833] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 03/10/2016] [Indexed: 12/11/2022]
Abstract
Widespread utilization of small GTPases as major regulatory hubs in many different biological systems derives from a conserved conformational switch mechanism that facilitates cycling between GTP-bound active and GDP-bound inactive states under control of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which accelerate slow intrinsic rates of activation by nucleotide exchange and deactivation by GTP hydrolysis, respectively. Here we review developments leading to current understanding of intrinsic and GAP catalyzed GTP hydrolytic reactions in small GTPases from structural, molecular and chemical mechanistic perspectives. Despite the apparent simplicity of the GTPase cycle, the structural bases underlying the hallmark hydrolytic reaction and catalytic acceleration by GAPs are considerably more diverse than originally anticipated. Even the most fundamental aspects of the reaction mechanism have been challenging to decipher. Through a combination of experimental and in silico approaches, the outlines of a consensus view have begun to emerge for the best studied paradigms. Nevertheless, recent observations indicate that there is still much to be learned. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 431-448, 2016.
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Affiliation(s)
- Ashwini K Mishra
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - David G Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
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Bao H, Li F, Wang C, Wang N, Jiang Y, Tang Y, Wu J, Shi Y. Structural Basis for the Specific Recognition of RhoA by the Dual GTPase-activating Protein ARAP3. J Biol Chem 2016; 291:16709-19. [PMID: 27311713 DOI: 10.1074/jbc.m116.736140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 02/04/2023] Open
Abstract
ARAP3 (Arf-GAP with Rho-GAP domain, ANK repeat, and PH domain-containing protein 3) is unique for its dual specificity GAPs (GTPase-activating protein) activity for Arf6 (ADP-ribosylation factor 6) and RhoA (Ras homolog gene family member A) regulated by phosphatidylinositol 3,4,5-trisphosphate and a small GTPase Rap1-GTP and is involved in regulation of cell shape and adhesion. However, the molecular interface between the ARAP3-RhoGAP domain and RhoA is unknown, as is the substrates specificity of the RhoGAP domain. In this study, we solved the crystal structure of RhoA in complex with the RhoGAP domain of ARAP3. The structure of the complex presented a clear interface between the RhoGAP domain and RhoA. By analyzing the crystal structure and in combination with in vitro GTPase activity assays and isothermal titration calorimetry experiments, we identified the crucial residues affecting RhoGAP activity and substrates specificity among RhoA, Rac1 (Ras-related C3 botulinum toxin substrate 1), and Cdc42 (cell division control protein 42 homolog).
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Affiliation(s)
- Hongyu Bao
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Fudong Li
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Chongyuan Wang
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Na Wang
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Yiyang Jiang
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Yajun Tang
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jihui Wu
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Yunyu Shi
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
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35
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Zhou Q, Lai Y, Bacaj T, Zhao M, Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Sauter NK, Cohen AE, Soltis SM, Alonso-Mori R, Chollet M, Lemke HT, Pfuetzner RA, Choi UB, Weis WI, Diao J, Südhof TC, Brunger AT. Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Nature 2015; 525:62-7. [PMID: 26280336 PMCID: PMC4607316 DOI: 10.1038/nature14975] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/27/2015] [Indexed: 02/07/2023]
Abstract
Synaptotagmin-1 and neuronal SNARE proteins have central roles in evoked synchronous neurotransmitter release; however, it is unknown how they cooperate to trigger synaptic vesicle fusion. Here we report atomic-resolution crystal structures of Ca(2+)- and Mg(2+)-bound complexes between synaptotagmin-1 and the neuronal SNARE complex, one of which was determined with diffraction data from an X-ray free-electron laser, leading to an atomic-resolution structure with accurate rotamer assignments for many side chains. The structures reveal several interfaces, including a large, specific, Ca(2+)-independent and conserved interface. Tests of this interface by mutagenesis suggest that it is essential for Ca(2+)-triggered neurotransmitter release in mouse hippocampal neuronal synapses and for Ca(2+)-triggered vesicle fusion in a reconstituted system. We propose that this interface forms before Ca(2+) triggering, moves en bloc as Ca(2+) influx promotes the interactions between synaptotagmin-1 and the plasma membrane, and consequently remodels the membrane to promote fusion, possibly in conjunction with other interfaces.
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Affiliation(s)
- Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Ying Lai
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Taulant Bacaj
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Oliver B Zeldin
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Aina E Cohen
- SLAC National Accelerator Laboratory, Stanford, California 94305, USA
| | - S Michael Soltis
- SLAC National Accelerator Laboratory, Stanford, California 94305, USA
| | | | - Matthieu Chollet
- SLAC National Accelerator Laboratory, Stanford, California 94305, USA
| | - Henrik T Lemke
- SLAC National Accelerator Laboratory, Stanford, California 94305, USA
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Ucheor B Choi
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - William I Weis
- Departments of Structural Biology, Molecular and Cellular Physiology, and Photon Science, Stanford University, Stanford, California 94305, USA
| | - Jiajie Diao
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
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36
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Dodonova SO, Diestelkoetter-Bachert P, von Appen A, Hagen WJH, Beck R, Beck M, Wieland F, Briggs JAG. VESICULAR TRANSPORT. A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly. Science 2015; 349:195-8. [PMID: 26160949 DOI: 10.1126/science.aab1121] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Transport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats that localize cargo and polymerize into cages to bend the membrane. Although extensive structural information is available for components of these coats, the heterogeneity of trafficking vesicles has prevented an understanding of how complete membrane coats assemble on the membrane. We combined cryo-electron tomography, subtomogram averaging, and cross-linking mass spectrometry to derive a complete model of the assembled coat protein complex I (COPI) coat involved in traffic between the Golgi and the endoplasmic reticulum. The highly interconnected COPI coat structure contradicted the current "adaptor-and-cage" understanding of coated vesicle formation.
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Affiliation(s)
- S O Dodonova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - P Diestelkoetter-Bachert
- Heidelberg University Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - A von Appen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - W J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - R Beck
- Heidelberg University Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - M Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - F Wieland
- Heidelberg University Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - J A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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37
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Arf GTPases and their effectors: assembling multivalent membrane-binding platforms. Curr Opin Struct Biol 2014; 29:67-76. [PMID: 25460270 DOI: 10.1016/j.sbi.2014.09.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 11/20/2022]
Abstract
Arf GTPases are major regulators of membrane traffic and organelle structure in eukaryotes where they recruit many different effectors, including components of vesicular coats, proteins that tether membranes, sort lipids or have diverse other functions in vesicular traffic, and bacterial proteins that divert Arf functions in host cells. A dozen of structures of unrelated effectors bound to Arf1, Arf6 or their close relative Arl1 are available, revealing that Arf GTPases do not recognize preferred structures in their effectors. In contrast, a trait common to many Arf/effector complexes is that they are juxtaposed to membranes by multiple protein/membrane contacts, yet of diverse sizes, shapes and physicochemistry. The common function of Arf GTPases thus appears to be their ability to assemble versatile, multivalent membrane-binding platforms, resulting in optimal orientation and allosteric regulation of their effectors leading to a plethora of membrane-localized functions.
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38
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Structural basis for membrane binding and remodeling by the exomer secretory vesicle cargo adaptor. Dev Cell 2014; 30:610-24. [PMID: 25203211 DOI: 10.1016/j.devcel.2014.07.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/29/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
Abstract
Cargo adaptor subunits of vesicle coat protein complexes sort transmembrane proteins to distinct membrane compartments in eukaryotic cells. The exomer complex is the only cargo adaptor known to sort proteins at the trans-Golgi network into secretory vesicles. Exomer function is regulated by the Arf1 GTPase, a master regulator of trafficking at the Golgi. We report the structure of exomer bound to two copies of Arf1. Exomer interacts with each Arf1 molecule via two surfaces, one of which is a noncanonical interface that regulates GTP hydrolysis. The structure uncovers an unexpected membrane-proximal hydrophobic element that exomer uses in cooperation with Arf1 to remodel membranes. Given the constrained motion of the exomer hinge region, we envision that exomer dynamically positions multiple membrane insertion elements to drive membrane fission. In contrast to other known cargo adaptors, exomer therefore couples two functions, cargo sorting and membrane fission, into a single complex.
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39
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Gasper R, Sot B, Wittinghofer A. GTPase activity of Di-Ras proteins is stimulated by Rap1GAP proteins. Small GTPases 2014; 1:133-141. [PMID: 21686267 DOI: 10.4161/sgtp.1.3.14742] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 01/06/2011] [Accepted: 01/06/2011] [Indexed: 11/19/2022] Open
Abstract
The Ras family is the largest and most diverse sub-group of Ras-like G proteins. This complexity is further increased by the high number of regulatory Guanine nucleotide Exchange Factors (GEFs) and GTPase Activating Proteins (GAPs) that target specific members of this subfamily. Di-Ras1 and Di-Ras2 are little characterized members of the Ras-like sub-group with still unidentified regulatory and effector proteins. Here we determined the nucleotide binding properties of Di-Ras1/Di-Ras2. The above nanomolar affinity and the inability to react with members of the Cdc25 RasGEF family might suggest that activation does not require a GEF. We identified Rap1GAP1 and Rap1GAP2 as specific GTPase activating proteins of the Di-Ras family. Dual-specificity GAPs of the GAP1(m) family could not activate Di-Ras proteins, despite the presence of the required catalytic residue. Although Di-Ras proteins share GAPs with Rap G proteins, no common effectors could be identified in vitro.
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Affiliation(s)
- Raphael Gasper
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Strukturelle Biologie; Dortmund, Germany
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40
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Fan C, Tian Y, Miao Y, Lin X, Zhang X, Jiang G, Luan L, Wang E. ASAP3 expression in non-small cell lung cancer: association with cancer development and patients' clinical outcome. Tumour Biol 2014; 35:1489-94. [PMID: 24078447 DOI: 10.1007/s13277-013-1205-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/16/2013] [Indexed: 01/15/2023] Open
Abstract
ASAP3 belongs to Arf-specific GTPase-activating proteins which regulate Arfs by stimulating their intrinsic GTP hydrolysis. ASAP3 expression and the clinical significance in malignant tumors are largely unknown. In this study, we examined ASAP3 expression in non-small cell lung cancer (NSCLC) to find out its clinicopathological significance. Immunohistochemistry shows elevated expression of ASAP3 in cancer tissues (54.8 % (57/104)) compared to normal lung tissues (18.0 % (9/50)) (p < 0.05). Increased ASAP3 expression was associated with poor differentiation, lymph node metastasis, and advanced TNM stages in NSCLC (p < 0.05). Survival analysis reveals that ASAP3 expression contributes to patients' poor clinical outcome (p < 0.05). We also examined ASAP3 expression in several lung cancer cell lines using Western blotting. We downregulated ASAP3 expression in LTE cell which has a relative high level of ASAP3 expression using siRNA and found that reduced ASAP3 leads to significant inhibition of cancer cell invasion (p < 0.05). These data indicate that ASAP3 is elevated in NSCLC and may contribute to cancer development and patients' poor clinical outcome, which is possibly due to its critical roles in regulating cancer invasion.
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41
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Koromyslova AD, Chugunov AO, Efremov RG. Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method. J Chem Inf Model 2014; 54:1189-99. [PMID: 24689707 DOI: 10.1021/ci500158y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.
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Affiliation(s)
- Anna D Koromyslova
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , 117997, Moscow, Russia
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42
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Putative RhoGAP proteins orchestrate vegetative growth, conidiogenesis and pathogenicity of the rice blast fungus Magnaporthe oryzae. Fungal Genet Biol 2014; 67:37-50. [PMID: 24731806 DOI: 10.1016/j.fgb.2014.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 03/02/2014] [Accepted: 03/31/2014] [Indexed: 11/21/2022]
Abstract
Rho GTPases, acting as molecular switches, are involved in the regulation of diverse cellular functions. Rho GTPase activating proteins (Rho GAPs) function as negative regulators of Rho GTPases and are required for a variety of signaling processes in cell development. But the mechanisms underlying Rho GAPs in Rho-mediated signaling pathways in fungi are still elusive. There are eight RhoGAP domain-containing genes annotated in the Magnaporthe oryzae genome. To understand the function of these RhoGAP genes, we generated knockout mutants of each of the RhoGAP genes through a homologous recombination-based method. Phenotypic analysis showed that growth rate of aerial hyphae of the Molrg1 deletion mutant decreased dramatically. The ΔMolrg1 mutant showed significantly reduced conidiation and appressorium formation by germ tubes. Moreover, it lost pathogenicity completely. Deletion of another Rho GAP (MoRga1) resulted in high percentage of larger or gherkin-shaped conidia and slight decrease in conidiation. Appressorial formation of the ΔMoRga1 mutant was delayed significantly on hydrophobic surface, while the development of mycelial growth and pathogenicity in plants was not affected. Confocal fluorescence microscopy imaging showed that MoRga1-GFP localizes to septal pore of the conidium, and this localization pattern requires both LIM and RhoGAP domains. Furthermore, either deleting the LIM or RhoGAP domain or introducing an inactivating R1032A mutation in the RhoGAP domain of MoRga1 caused similar defects as the Morga1 deletion mutant in terms of conidial morphology and appressorial formation, suggesting that MoRga1 is a stage-specific regulator of conidial differentiation by regulating some specific Rho GTPases. In this regard, MoRga1 and MoLrg1 physically interacted with both MoRac1-CA and MoCdc42-CA in the yeast two-hybrid and pull-down assays, suggesting that the actions of these two GAPs are involved in MoRac1 and MoCdc42 pathways. On the other hand, six other putative Rho GAPs (MoRga2 to MoRga7) were dispensable for conidiation, vegetative growth, appressorial formation and pathogenicity, suggesting that these Rho GAPs function redundantly during fungal development. Taking together, Rho GAP genes play important roles in M. oryzae development and infectious processes through coordination and modulation of Rho GTPases.
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43
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Miertzschke M, Koerner C, Spoerner M, Wittinghofer A. Structural insights into the small G-protein Arl13B and implications for Joubert syndrome. Biochem J 2014; 457:301-11. [PMID: 24168557 DOI: 10.1042/bj20131097] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ciliopathies are human diseases arising from defects in primary or motile cilia. The small G-protein Arl13B (ADP-ribosylation factor-like 13B) localizes to microtubule doublets of the ciliary axoneme and is mutated in Joubert syndrome. Its GDP/GTP mechanistic cycle and the effect of its mutations in patients with Joubert syndrome remain elusive. In the present study we applied high resolution structural and biochemical approaches to study Arl13B. The crystal structure of Chlamydomonas rheinhardtii Arl13B, comprising the G-domain and part of its unique C-terminus, revealed an incomplete active site, and together with biochemical data the present study accounts for the absence of intrinsic GTP hydrolysis by this protein. The structure shows that the residues representing patient mutations R79Q and R200C are involved in stabilizing important intramolecular interactions. Our studies suggest that Arg79 is crucial for the GDP/GTP conformational change by stabilizing the large two-residue register shift typical for Arf (ADP-ribosylation factor) and Arl subfamily proteins. A corresponding mutation in Arl3 induces considerable defects in effector and GAP (GTPase-activating protein) binding, suggesting a loss of Arl13B function in patients with Joubert syndrome.
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Affiliation(s)
- Mandy Miertzschke
- *Emeritus group A. Wittinghofer, Max-Planck-Institute for Molecular Physiology, BMZ, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Carolin Koerner
- *Emeritus group A. Wittinghofer, Max-Planck-Institute for Molecular Physiology, BMZ, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Michael Spoerner
- †Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Alfred Wittinghofer
- *Emeritus group A. Wittinghofer, Max-Planck-Institute for Molecular Physiology, BMZ, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
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44
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Luo Y, Kong F, Wang Z, Chen D, Liu Q, Wang T, Xu R, Wang X, Yang JY. Loss of ASAP3 destabilizes cytoskeletal protein ACTG1 to suppress cancer cell migration. Mol Med Rep 2013; 9:387-94. [PMID: 24284654 DOI: 10.3892/mmr.2013.1831] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 10/31/2013] [Indexed: 11/06/2022] Open
Abstract
ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 (ASAP3), previously known as ACAP4, DDEFL1 and UPLC1, is considered to be an important regulator in cancer cell migration/invasion and actin-based cytoskeletal remodeling. However, the underlying mechanisms through which ASAP3 mediates these processes are not well-elucidated. This study reported that in certain types of cancer cells, loss of ASAP3 suppressed cell migration/invasion, in part by destabilizing γ-actin-1 (ACTG1), a cytoskeletal protein considered to be an integral component of the cell migratory machinery, essential for the rearrangement of the dynamic cytoskeletal networks and important in diseases, such as brain malformation, hearing loss and cancer development. The data, for the first time, link ASAP3 with ACTG1 in the regulation of cytoskeletal maintenance and cell motility.
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Affiliation(s)
- Yu Luo
- School of Nursing, The Third Military Medical University, Chongqing 400038, P.R. China
| | - Fang Kong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, Fujian 361102, P.R. China
| | - Zhen Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, Fujian 361102, P.R. China
| | - Dahan Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, Fujian 361102, P.R. China
| | - Qiuyan Liu
- School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, P.R. China
| | - Tao Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, Fujian 361102, P.R. China
| | - Ruian Xu
- School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, P.R. China
| | - Xianyuan Wang
- School of Nursing, The Third Military Medical University, Chongqing 400038, P.R. China
| | - James Y Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, Fujian 361102, P.R. China
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Quilty D, Gray F, Summerfeldt N, Cassel D, Melançon P. Arf activation at the Golgi is modulated by feed-forward stimulation of the exchange factor GBF1. J Cell Sci 2013; 127:354-64. [PMID: 24213530 DOI: 10.1242/jcs.130591] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
ADP-ribosylation factors (Arfs) play central roles in the regulation of vesicular trafficking through the Golgi. Arfs are activated at the Golgi membrane by guanine-nucleotide-exchange factors (GEFs) that are recruited from cytosol. Here, we describe a novel mechanism for the regulation of recruitment and activity of the ArfGEF Golgi-specific BFA resistance factor 1 (GBF1). Conditions that alter the cellular Arf-GDP:Arf-GTP ratio result in GBF1 recruitment. This recruitment of GBF1 occurs selectively on cis-Golgi membranes in direct response to increased Arf-GDP. GBF1 recruitment requires Arf-GDP myristoylation-dependent interactions suggesting regulation of a membrane-bound factor. Once recruited, GBF1 causes increased Arf-GTP production at the Golgi, consistent with a feed-forward self-limiting mechanism of Arf activation. This mechanism is proposed to maintain steady-state levels of Arf-GTP at the cis-Golgi during cycles of Arf-dependent trafficking events.
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Affiliation(s)
- Douglas Quilty
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Wang J, Deretic D. Molecular complexes that direct rhodopsin transport to primary cilia. Prog Retin Eye Res 2013; 38:1-19. [PMID: 24135424 DOI: 10.1016/j.preteyeres.2013.08.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/13/2013] [Accepted: 08/19/2013] [Indexed: 11/27/2022]
Abstract
Rhodopsin is a key molecular constituent of photoreceptor cells, yet understanding of how it regulates photoreceptor membrane trafficking and biogenesis of light-sensing organelles, the rod outer segments (ROS) is only beginning to emerge. Recently identified sequence of well-orchestrated molecular interactions of rhodopsin with the functional networks of Arf and Rab GTPases at multiple stages of intracellular targeting fits well into the complex framework of the biogenesis and maintenance of primary cilia, of which the ROS is one example. This review will discuss the latest progress in dissecting the molecular complexes that coordinate rhodopsin incorporation into ciliary-targeted carriers with the recruitment and activation of membrane tethering complexes and regulators of fusion with the periciliary plasma membrane. In addition to revealing the fundamental principals of ciliary membrane renewal, recent advances also provide molecular insight into the ways by which disruptions of the exquisitely orchestrated interactions lead to cilia dysfunction and result in human retinal dystrophies and syndromic diseases that affect multiple organs, including the eyes.
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Affiliation(s)
- Jing Wang
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Dusanka Deretic
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM 87131, USA; Department of Cell Biology and Physiology, University of New Mexico, Albuquerque, NM 87131, USA.
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Phosphorylation of the Bin, Amphiphysin, and RSV161/167 (BAR) domain of ACAP4 regulates membrane tubulation. Proc Natl Acad Sci U S A 2013; 110:11023-8. [PMID: 23776207 DOI: 10.1073/pnas.1217727110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ArfGAP With Coiled-Coil, Ankyrin Repeat And PH Domains 4 (ACAP4) is an ADP-ribosylation factor 6 (ARF6) GTPase-activating protein essential for EGF-elicited cell migration. However, how ACAP4 regulates membrane dynamics and curvature in response to EGF stimulation is unknown. Here, we show that phosphorylation of the N-terminal region of ACAP4, named the Bin, Amphiphysin, and RSV161/167 (BAR) domain, at Tyr34 is necessary for EGF-elicited membrane remodeling. Domain structure analysis demonstrates that the BAR domain regulates membrane curvature. EGF stimulation of cells causes phosphorylation of ACAP4 at Tyr34, which subsequently promotes ACAP4 homodimer curvature. The phospho-mimicking mutant of ACAP4 demonstrates lipid-binding activity and tubulation in vitro, and ARF6 enrichment at the membrane is associated with ruffles of EGF-stimulated cells. Expression of the phospho-mimicking ACAP4 mutant promotes ARF6-dependent cell migration. Thus, the results present a previously undefined mechanism by which EGF-elicited phosphorylation of the BAR domain controls ACAP4 molecular plasticity and plasma membrane dynamics during cell migration.
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Abstract
Small GTPases are versatile temporal and spatial regulators of virtually all cellular processes including signal transduction, cytoskeleton dynamics and membrane trafficking. They function as molecular switches, aided by a multitude of regulatory and effector proteins that link them into functional networks. A picture is beginning to emerge whereupon scaffold proteins with many functional domains perform the regulatory and effector functions, thus allowing the ordered recruitment and activation of small GTPases. This leads to the formation of scaffolding patches that coordinate cargo concentration and capture, with the recruitment and activation of the membrane tethering complexes and fusion regulators. This review will focus on the crosstalk of Arf and Rab GTPases at the Golgi complex and the scaffolds that facilitate their activation during trafficking of sensory receptors to primary cilia. The evolutionary conservation of the GTPase cascades in ciliogenesis and yeast budding will be discussed.
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Affiliation(s)
- Dusanka Deretic
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA.
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Schlacht A, Mowbrey K, Elias M, Kahn RA, Dacks JB. Ancient complexity, opisthokont plasticity, and discovery of the 11th subfamily of Arf GAP proteins. Traffic 2013; 14:636-49. [PMID: 23433073 DOI: 10.1111/tra.12063] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 02/20/2013] [Accepted: 02/22/2013] [Indexed: 12/14/2022]
Abstract
The organelle paralogy hypothesis is one model for the acquisition of nonendosymbiotic organelles, generated from molecular evolutionary analyses of proteins encoding specificity in the membrane traffic system. GTPase activating proteins (GAPs) for the ADP-ribosylation factor (Arfs) GTPases are additional regulators of the kinetics and fidelity of membrane traffic. Here we describe molecular evolutionary analyses of the Arf GAP protein family. Of the 10 subfamilies previously defined in humans, we find that 5 were likely present in the last eukaryotic common ancestor. Of the 3 most recently derived subfamilies, 1 was likely present in the ancestor of opisthokonts (animals and fungi) and apusomonads (flagellates classified as the sister lineage to opisthokonts), while 2 arose in the holozoan lineage. We also propose to have identified a novel ancient subfamily (ArfGAPC2), present in diverse eukaryotes but which is lost frequently, including in the opisthokonts. Surprisingly few ancient domains accompanying the ArfGAP domain were identified, in marked contrast to the extensively decorated human Arf GAPs. Phylogenetic analyses of the subfamilies reveal patterns of single and multiple gene duplications specific to the Holozoa, to some degree mirroring evolution of Arf GAP targets, the Arfs. Conservation, and lack thereof, of various residues in the ArfGAP structure provide contextualization of previously identified functional amino acids and their application to Arf GAP biology in general. Overall, our results yield insights into current Arf GAP biology, reveal complexity in the ancient eukaryotic ancestor and integrate the Arf GAP family into a proposed mechanism for the evolution of nonendosymbiotic organelles.
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Affiliation(s)
- Alexander Schlacht
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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Abstract
Small GTPases use GDP/GTP alternation to actuate a variety of functional switches that are pivotal for cell dynamics. The GTPase switch is turned on by GEFs, which stimulate dissociation of the tightly bound GDP, and turned off by GAPs, which accelerate the intrinsically sluggish hydrolysis of GTP. For Ras, Rho, and Rab GTPases, this switch incorporates a membrane/cytosol alternation regulated by GDIs and GDI-like proteins. The structures and core mechanisms of representative members of small GTPase regulators from most families have now been elucidated, illuminating their general traits combined with scores of unique features. Recent studies reveal that small GTPase regulators have themselves unexpectedly sophisticated regulatory mechanisms, by which they process cellular signals and build up specific cell responses. These mechanisms include multilayered autoinhibition with stepwise release, feedback loops mediated by the activated GTPase, feed-forward signaling flow between regulators and effectors, and a phosphorylation code for RhoGDIs. The flipside of these highly integrated functions is that they make small GTPase regulators susceptible to biochemical abnormalities that are directly correlated with diseases, notably a striking number of missense mutations in congenital diseases, and susceptible to bacterial mimics of GEFs, GAPs, and GDIs that take command of small GTPases in infections. This review presents an overview of the current knowledge of these many facets of small GTPase regulation.
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Affiliation(s)
- Jacqueline Cherfils
- Laboratoire d’Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Centre deRecherche de Gif, Gif-sur-Yvette, France
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