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Rosenberg EM, Jian X, Soubias O, Jackson RA, Gladu E, Andersen E, Esser L, Sodt AJ, Xia D, Byrd RA, Randazzo PA. Point mutations in Arf1 reveal cooperative effects of the N-terminal extension and myristate for GTPase-activating protein catalytic activity. PLoS One 2024; 19:e0295103. [PMID: 38574162 PMCID: PMC10994351 DOI: 10.1371/journal.pone.0295103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/05/2024] [Indexed: 04/06/2024] Open
Abstract
The ADP-ribosylation factors (Arfs) constitute a family of small GTPases within the Ras superfamily, with a distinguishing structural feature of a hypervariable N-terminal extension of the G domain modified with myristate. Arf proteins, including Arf1, have roles in membrane trafficking and cytoskeletal dynamics. While screening for Arf1:small molecule co-crystals, we serendipitously solved the crystal structure of the non-myristoylated engineered mutation [L8K]Arf1 in complex with a GDP analogue. Like wild-type (WT) non-myristoylated Arf1•GDP, we observed that [L8K]Arf1 exhibited an N-terminal helix that occludes the hydrophobic cavity that is occupied by the myristoyl group in the GDP-bound state of the native protein. However, the helices were offset from one another due to the L8K mutation, with a significant change in position of the hinge region connecting the N-terminus to the G domain. Hypothesizing that the observed effects on behavior of the N-terminus affects interaction with regulatory proteins, we mutated two hydrophobic residues to examine the role of the N-terminal extension for interaction with guanine nucleotide exchange factors (GEFs) and GTPase Activating Proteins (GAPs. Different than previous studies, all mutations were examined in the context of myristoylated Arf. Mutations had little or no effect on spontaneous or GEF-catalyzed guanine nucleotide exchange but did affect interaction with GAPs. [F13A]myrArf1 was less than 1/2500, 1/1500, and 1/200 efficient as substrate for the GAPs ASAP1, ARAP1 and AGAP1; however, [L8A/F13A]myrArf1 was similar to WT myrArf1. Using molecular dynamics simulations, the effect of the mutations on forming alpha helices adjacent to a membrane surface was examined, yet no differences were detected. The results indicate that lipid modifications of GTPases and consequent anchoring to a membrane influences protein function beyond simple membrane localization. Hypothetical mechanisms are discussed.
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Affiliation(s)
- Eric M. Rosenberg
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States of America
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States of America
| | - Olivier Soubias
- Section of Macromolecular NMR, Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Rebekah A. Jackson
- Section of Macromolecular NMR, Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Erin Gladu
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States of America
| | - Emily Andersen
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States of America
| | - Lothar Esser
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Alexander J. Sodt
- Unit of Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States of America
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - R. Andrew Byrd
- Section of Macromolecular NMR, Center for Structural Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Paul A. Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States of America
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2
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Lübke S, Braukmann C, Rexer KH, Cigoja L, Rout P, Önel SF. The Abl-interactor Abi suppresses the function of the BRAG2 GEF family member Schizo. Biol Open 2024; 13:bio058666. [PMID: 34897417 PMCID: PMC10810563 DOI: 10.1242/bio.058666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 11/27/2021] [Indexed: 11/20/2022] Open
Abstract
Guanine nucleotide exchange factors (GEF) of the BRAG subfamily activate small Arf GTPases, which are pivotal regulators of intracellular membrane traffic and actin dynamics. Consequently, BRAG proteins have been implicated to regulate the surface levels of adhesive and signaling receptors. However, not much is known about the mechanism leading to the regulation of these surface proteins. In this study, we found that the Drosophila BRAG GEF Schizo interacts physically with the Abl-interactor (Abi). schizo mutants display severe defects in myoblast fusion during syncytial muscle formation and show increased amounts of the cell adhesion protein N-cadherin. We demonstrate that the schizo myoblast fusion phenotype can be rescued by the expression of the Schizo GEF (Sec7) and membrane-binding (pleckstrin homology) domain. Furthermore, the expression of the Sec7-PH domain in a wild-type background decreases the amounts of N-cadherin and impairs myoblast fusion. These findings support the notion that the Sec7-PH domain serves as a constitutive-active form of Schizo. Using a yeast-two hybrid assay, we show that the SH3 domain of Abi interacts with the N-terminal region of Schizo. This region is also able to bind to the cytodomain of the cell adhesion molecule N-cadherin. To shed light on the function of Schizo and Abi in N-cadherin removal, we employed epistasis experiments in different developmental contexts of Drosophila. These studies point towards a new model for the regulation of Schizo. We propose that the binding of Abi to the N-terminal part of Schizo antagonizes Schizo function to inhibit N-cadherin removal.
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Affiliation(s)
- Stefanie Lübke
- Fachbereich Medizin, Department for Molecular Cell Physiology, Institute for Physiology and Pathophysiology, Philipps-Universität Marburg, Emil-Mannkopff-Str. 2, 35037 Marburg, Germany
- Fachbereich Biologie, Department for Developmental Biology, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg, Germany
| | - Carina Braukmann
- Fachbereich Biologie, Department for Developmental Biology, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Karl-Heinz Rexer
- Fachbereich Biologie, Department for Biodiversity of Plants, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Lubjinka Cigoja
- Fachbereich Biologie, Department for Developmental Biology, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Pratiti Rout
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg, Germany
- Fachbereich Biologie, Department for Molecular Embryology, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Susanne F. Önel
- Fachbereich Medizin, Department for Molecular Cell Physiology, Institute for Physiology and Pathophysiology, Philipps-Universität Marburg, Emil-Mannkopff-Str. 2, 35037 Marburg, Germany
- Fachbereich Biologie, Department for Developmental Biology, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg, Germany
- Fachbereich Biologie, Department for Molecular Embryology, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
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3
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Jermusek FA, Webb LJ. Electrostatic Impact of Brefeldin A on Thiocyanate Probes Surrounding the Interface of Arf1-BFA-ARNO4M, a Protein-Drug-Protein Complex. Biochemistry 2024; 63:27-41. [PMID: 38078826 DOI: 10.1021/acs.biochem.3c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Protein-protein interactions regulate many cellular processes, making them ideal drug candidates. Design of such drugs, however, is hindered by a lack of understanding of the factors that contribute to the interaction specificity. Specific protein-protein complexes possess both structural and electrostatic complementarity, and while structural complementarity of protein complexes has been extensively investigated, fundamental understanding of the complicated networks of electrostatic interactions at these interfaces is lacking, thus hindering the rational design of orthosterically binding small molecules. To better understand the electrostatic interactions at protein interfaces and how a small molecule could contribute to and fit within that environment, we used a model protein-drug-protein system, Arf1-BFA-ARNO4M, to investigate how small molecule brefeldin A (BFA) perturbs the Arf1-ARNO4M interface. By using nitrile probe labeled Arf1 sites and measuring vibrational Stark effects as well as temperature dependent infrared shifts, we measured changes in the electric field and hydrogen bonding at this interface upon BFA binding. At all five probe locations of Arf1, we found that the vibrational shifts resulting from BFA binding corroborate trends found in Poisson-Boltzmann calculations of surface potentials of Arf1-ARNO4M and Arf1-BFA-ARNO4M, where BFA contributes negative electrostatic potential to the protein interface. The data also corroborate previous hypotheses about the mechanism of interfacial binding and confirm that alternating patches of hydrophobic and polar interactions lead to BFA binding specificity. These findings demonstrate the impact of BFA on this protein-protein interface and have implications for the design of other interfacial drug candidates.
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Affiliation(s)
- Frank A Jermusek
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
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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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Manzer KM, Fromme JC. The Arf-GAP Age2 localizes to the late-Golgi via a conserved amphipathic helix. Mol Biol Cell 2023; 34:ar119. [PMID: 37672345 PMCID: PMC10846627 DOI: 10.1091/mbc.e23-07-0283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023] Open
Abstract
Arf GTPases are central regulators of the Golgi complex, which serves as the nexus of membrane-trafficking pathways in eukaryotic cells. Arf proteins recruit dozens of effectors to modify membranes, sort cargos, and create and tether transport vesicles, and are therefore essential for orchestrating Golgi trafficking. The regulation of Arf activity is controlled by the action of Arf-GEFs which activate via nucleotide exchange, and Arf-GAPs which inactivate via nucleotide hydrolysis. The localization dynamics of Arf GTPases and their Arf-GAPs during Golgi maturation have not been reported. Here we use the budding yeast model to examine the temporal localization of the Golgi Arf-GAPs. We also determine the mechanisms used by the Arf-GAP Age2 to localize to the Golgi. We find that the catalytic activity of Age2 and a conserved sequence in the unstructured C-terminal domain of Age2 are both required for Golgi localization. This sequence is predicted to form an amphipathic helix and mediates direct binding of Age2 to membranes in vitro. We also report the development of a probe for sensing active Arf1 in living cells and use this probe to characterize the temporal dynamics of Arf1 during Golgi maturation.
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Affiliation(s)
- Kaitlyn M. Manzer
- Department of Molecular Biology & Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850
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6
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Manzer KM, Fromme JC. The Arf-GAP Age2 localizes to the late-Golgi via a conserved amphipathic helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550229. [PMID: 37546741 PMCID: PMC10402032 DOI: 10.1101/2023.07.23.550229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Arf GTPases are central regulators of the Golgi complex, which serves as the nexus of membrane trafficking pathways in eukaryotic cells. Arf proteins recruit dozens of effectors to modify membranes, sort cargos, and create and tether transport vesicles, and are therefore essential for orchestrating Golgi trafficking. The regulation of Arf activity is controlled by the action of Arf-GEFs, which activate via nucleotide exchange, and Arf-GAPs, which inactivate via nucleotide hydrolysis. The localization dynamics of Arf GTPases and their Arf-GAPs during Golgi maturation have not been reported. Here we use the budding yeast model to examine the temporal localization of the Golgi Arf-GAPs. We also determine the mechanisms used by the Arf-GAP Age2 to localize to the Golgi. We find that the catalytic activity of Age2 and a conserved sequence in the unstructured C-terminal domain of Age2 are both required for Golgi localization. This sequence is predicted to form an amphipathic helix and mediates direct binding of Age2 to membranes in vitro . We also report the development of a probe for sensing active Arf1 in living cells and use this probe to characterize the temporal dynamics of Arf1 during Golgi maturation.
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Affiliation(s)
- Kaitlyn M Manzer
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - J Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
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7
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Palicharla VR, Hwang SH, Somatilaka BN, Legué E, Shimada IS, Familiari NE, Tran VM, Woodruff JB, Liem KF, Mukhopadhyay S. Interactions between TULP3 tubby domain and ARL13B amphipathic helix promote lipidated protein transport to cilia. Mol Biol Cell 2023; 34:ar18. [PMID: 36652335 PMCID: PMC10011728 DOI: 10.1091/mbc.e22-10-0473] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The primary cilium is a nexus for cell signaling and relies on specific protein trafficking for function. The tubby family protein TULP3 transports integral membrane proteins into cilia through interactions with the intraflagellar transport complex-A (IFT-A) and phosphoinositides. It was previously shown that short motifs called ciliary localization sequences (CLSs) are necessary and sufficient for TULP3-dependent ciliary trafficking of transmembrane cargoes. However, the mechanisms by which TULP3 regulates ciliary compartmentalization of nonintegral, membrane-associated proteins and whether such trafficking requires TULP3-dependent CLSs is unknown. Here we show that TULP3 is required for ciliary transport of the Joubert syndrome-linked palmitoylated GTPase ARL13B through a CLS. An N-terminal amphipathic helix, preceding the GTPase domain of ARL13B, couples with the TULP3 tubby domain for ciliary trafficking, irrespective of palmitoylation. ARL13B transport requires TULP3 binding to IFT-A but not to phosphoinositides, indicating strong membrane-proximate interactions, unlike transmembrane cargo transport requiring both properties of TULP3. TULP3-mediated trafficking of ARL13B also regulates ciliary enrichment of farnesylated and myristoylated downstream effectors of ARL13B. The lipidated cargoes show distinctive depletion kinetics from kidney epithelial cilia with relation to Tulp3 deletion-induced renal cystogenesis. Overall, these findings indicate an expanded role of the tubby domain in capturing analogous helical secondary structural motifs from diverse cargoes.
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Affiliation(s)
- Vivek Reddy Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | | | - Emilie Legué
- Vertebrate Developmental Biology Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520
| | - Issei S Shimada
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Nicole E Familiari
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Vanna M Tran
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jeffrey B Woodruff
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Karel F Liem
- Vertebrate Developmental Biology Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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8
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Jaimon E, Tripathi A, Khurana A, Ghosh D, Sugatha J, Datta S. Binding with heat shock cognate protein HSC70 fine-tunes the Golgi association of the small GTPase ARL5B. J Biol Chem 2021; 297:101422. [PMID: 34798070 PMCID: PMC8661063 DOI: 10.1016/j.jbc.2021.101422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022] Open
Abstract
ARL5B, an ARF-like small GTPase localized to the trans-Golgi, is known for regulating endosome-Golgi trafficking and promoting the migration and invasion of breast cancer cells. Although a few interacting partners have been identified, the mechanism of the shuttling of ARL5B between the Golgi membrane and the cytosol is still obscure. Here, using GFP-binding protein (GBP) pull-down followed by mass spectrometry, we identified heat shock cognate protein (HSC70) as an additional interacting partner of ARL5B. Our pull-down and isothermal titration calorimetry (ITC)-based studies suggested that HSC70 binds to ARL5B in an ADP-dependent manner. Additionally, we showed that the N-terminal helix and the nucleotide status of ARL5B contribute to its recognition by HSC70. The confocal microscopy and cell fractionation studies in MDA-MB-231 breast cancer cells revealed that the depletion of HSC70 reduces the localization of ARL5B to the Golgi. Using in vitro reconstitution approach, we provide evidence that HSC70 fine-tunes the association of ARL5B with Golgi membrane. Finally, we demonstrated that the interaction between ARL5B and HSC70 is important for the localization of cation independent mannose-6-phosphate receptor (CIMPR) at Golgi. Collectively, we propose a mechanism by which HSC70, a constitutively expressed chaperone, modulates the Golgi association of ARL5B, which in turn has implications for the Golgi-associated functions of this GTPase.
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Affiliation(s)
- Ebsy Jaimon
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Aashutosh Tripathi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Arohi Khurana
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Dipanjana Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Jini Sugatha
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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9
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Deretic D, Lorentzen E, Fresquez T. The ins and outs of the Arf4-based ciliary membrane-targeting complex. Small GTPases 2021; 12:1-12. [PMID: 31068062 PMCID: PMC7781591 DOI: 10.1080/21541248.2019.1616355] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/09/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022] Open
Abstract
The small GTPase Arf4-based ciliary membrane-targeting complex recognizes specific targeting signals within sensory receptors and regulates their directed movement to primary cilia. Activated Arf4 directly binds the VxPx ciliary-targeting signal (CTS) of the light-sensing receptor rhodopsin. Recent findings revealed that at the trans-Golgi, marked by the small GTPase Rab6, activated Arf4 forms a functional complex with rhodopsin and the Arf guanine nucleotide exchange factor (GEF) GBF1, providing positive feedback that drives further Arf4 activation in ciliary trafficking. Arf4 function is conserved across diverse cell types; however, it appears that not all its aspects are conserved across species, as mouse Arf4 is a natural mutant in the conserved α3 helix, which is essential for its interaction with rhodopsin. Generally, activated Arf4 regulates the assembly of the targeting nexus containing the Arf GAP ASAP1 and the Rab11a-FIP3-Rabin8 dual effector complex, which controls the assembly of the highly conserved Rab11a-Rabin8-Rab8 ciliary-targeting module. It was recently found that this module interacts with the R-SNARE VAMP7, likely in its activated, c-Src-phosphorylated form. Rab11 and Rab8 bind VAMP7 regulatory longin domain (LD), whereas Rabin8 interacts with the SNARE domain, capturing VAMP7 for delivery to the ciliary base and subsequent pairing with the cognate SNAREs syntaxin 3 and SNAP-25. This review will focus on the implications of these novel findings that further illuminate the role of well-ordered Arf and Rab interaction networks in targeting of sensory receptors to primary cilia. Abbreviations: CTS: Ciliary-Targeting Signal; GAP: GTPase Activating Protein; GEF: Guanine Nucleotide Exchange Factor; RTC(s), Rhodopsin Transport Carrier(s); SNARE: Soluble N-ethylmaleimide-sensitive Factor Attachment Protein Receptor; TGN: Trans-Golgi Network.
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Affiliation(s)
- Dusanka Deretic
- Departments of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA
- Cell Biology and Physiology, University of New Mexico, Albuquerque, NM, USA
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Theresa Fresquez
- Departments of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA
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10
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Kosciuk T, Lin H. N-Myristoyltransferase as a Glycine and Lysine Myristoyltransferase in Cancer, Immunity, and Infections. ACS Chem Biol 2020; 15:1747-1758. [PMID: 32453941 DOI: 10.1021/acschembio.0c00314] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein myristoylation, the addition of a 14-carbon saturated acyl group, is an abundant modification implicated in biological events as diverse as development, immunity, oncogenesis, and infections. N-Myristoyltransferase (NMT) is the enzyme that catalyzes this modification. Many elegant studies have established the rules guiding the catalysis including substrate amino acid sequence requirements with the indispensable N-terminal glycine, and a co-translational mode of action. Recent advances in technology such as the development of fatty acid analogs, small molecule inhibitors, and new proteomic strategies, allowed a deeper insight into the NMT activity and function. Here we focus on discussing recent work demonstrating that NMT is also a lysine myristoyltransferase, the enzyme's regulation by a previously unnoticed solvent channel, and the mechanism of NMT regulation by protein-protein interactions. We also summarize recent findings on NMT's role in cancer, immunity, and infections and the advances in pharmacological targeting of myristoylation. Our analyses highlight opportunities for further understanding and discoveries.
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Affiliation(s)
- Tatsiana Kosciuk
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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11
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Kosciuk T, Price IR, Zhang X, Zhu C, Johnson KN, Zhang S, Halaby SL, Komaniecki GP, Yang M, DeHart CJ, Thomas PM, Kelleher NL, Fromme JC, Lin H. NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle. Nat Commun 2020; 11:1067. [PMID: 32103017 PMCID: PMC7044312 DOI: 10.1038/s41467-020-14893-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 02/08/2023] Open
Abstract
Lysine fatty acylation in mammalian cells was discovered nearly three decades ago, yet the enzymes catalyzing it remain unknown. Unexpectedly, we find that human N-terminal glycine myristoyltransferases (NMT) 1 and 2 can efficiently myristoylate specific lysine residues. They modify ADP-ribosylation factor 6 (ARF6) on lysine 3 allowing it to remain on membranes during the GTPase cycle. We demonstrate that the NAD+-dependent deacylase SIRT2 removes the myristoyl group, and our evidence suggests that NMT prefers the GTP-bound while SIRT2 prefers the GDP-bound ARF6. This allows the lysine myrisotylation-demyristoylation cycle to couple to and promote the GTPase cycle of ARF6. Our study provides an explanation for the puzzling dissimilarity of ARF6 to other ARFs and suggests the existence of other substrates regulated by this previously unknown function of NMT. Furthermore, we identified a NMT/SIRT2-ARF6 regulatory axis, which may offer new ways to treat human diseases.
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Affiliation(s)
- Tatsiana Kosciuk
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ian R Price
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Xiaoyu Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Chengliang Zhu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Kayla N Johnson
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Shuai Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Steve L Halaby
- Department of Molecular Biology and Genetics; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Garrison P Komaniecki
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Min Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, USA
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Departments of Chemistry and Molecular Biosciences and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
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12
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Li J, Zhang Y, Soubias O, Khago D, Chao FA, Li Y, Shaw K, Byrd RA. Optimization of sortase A ligation for flexible engineering of complex protein systems. J Biol Chem 2020; 295:2664-2675. [PMID: 31974162 DOI: 10.1074/jbc.ra119.012039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/22/2020] [Indexed: 01/06/2023] Open
Abstract
Engineering and bioconjugation of proteins is a critically valuable tool that can facilitate a wide range of biophysical and structural studies. The ability to orthogonally tag or label a domain within a multidomain protein may be complicated by undesirable side reactions to noninvolved domains. Furthermore, the advantages of segmental (or domain-specific) isotopic labeling for NMR, or deuteration for neutron scattering or diffraction, can be realized by an efficient ligation procedure. Common methods-expressed protein ligation, protein trans-splicing, and native chemical ligation-each have specific limitations. Here, we evaluated the use of different variants of Staphylococcus aureus sortase A for a range of ligation reactions and demonstrate that conditions can readily be optimized to yield high efficiency (i.e. completeness of ligation), ease of purification, and functionality in detergents. These properties may enable joining of single domains into multidomain proteins, lipidation to mimic posttranslational modifications, and formation of cyclic proteins to aid in the development of nanodisc membrane mimetics. We anticipate that the method for ligating separate domains into a single functional multidomain protein reported here may enable many applications in structural biology.
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Affiliation(s)
- Jess Li
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Yue Zhang
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Olivier Soubias
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Domarin Khago
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Fa-An Chao
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Yifei Li
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Katherine Shaw
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - R Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201.
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13
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Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes. Structure 2019; 27:1782-1797.e7. [PMID: 31601460 PMCID: PMC6948192 DOI: 10.1016/j.str.2019.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/03/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022]
Abstract
Membrane dynamic processes require Arf GTPase activation by guanine nucleotide exchange factors (GEFs) with a Sec7 domain. Cytohesin family Arf GEFs function in signaling and cell migration through Arf GTPase activation on the plasma membrane and endosomes. In this study, the structural organization of two cytohesins (Grp1 and ARNO) was investigated in solution by size exclusion-small angle X-ray scattering and negative stain-electron microscopy and on membranes by dynamic light scattering, hydrogen-deuterium exchange-mass spectrometry and guanosine diphosphate (GDP)/guanosine triphosphate (GTP) exchange assays. The results suggest that cytohesins form elongated dimers with a central coiled coil and membrane-binding pleckstrin-homology (PH) domains at opposite ends. The dimers display significant conformational heterogeneity, with a preference for compact to intermediate conformations. Phosphoinositide-dependent membrane recruitment is mediated by one PH domain at a time and alters the conformational dynamics to prime allosteric activation by Arf-GTP. A structural model for membrane targeting and allosteric activation of full-length cytohesin dimers is discussed.
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14
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Roy NS, Jian X, Soubias O, Zhai P, Hall JR, Dagher JN, Coussens NP, Jenkins LM, Luo R, Akpan IO, Hall MD, Byrd RA, Yohe ME, Randazzo PA. Interaction of the N terminus of ADP-ribosylation factor with the PH domain of the GTPase-activating protein ASAP1 requires phosphatidylinositol 4,5-bisphosphate. J Biol Chem 2019; 294:17354-17370. [PMID: 31591270 DOI: 10.1074/jbc.ra119.009269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/02/2019] [Indexed: 12/15/2022] Open
Abstract
Arf GAP with Src homology 3 domain, ankyrin repeat, and pleckstrin homology (PH) domain 1 (ASAP1) is a multidomain GTPase-activating protein (GAP) for ADP-ribosylation factor (ARF)-type GTPases. ASAP1 affects integrin adhesions, the actin cytoskeleton, and invasion and metastasis of cancer cells. ASAP1's cellular function depends on its highly-regulated and robust ARF GAP activity, requiring both the PH and the ARF GAP domains of ASAP1, and is modulated by phosphatidylinositol 4,5-bisphosphate (PIP2). The mechanistic basis of PIP2-stimulated GAP activity is incompletely understood. Here, we investigated whether PIP2 controls binding of the N-terminal extension of ARF1 to ASAP1's PH domain and thereby regulates its GAP activity. Using [Δ17]ARF1, lacking the N terminus, we found that PIP2 has little effect on ASAP1's activity. A soluble PIP2 analog, dioctanoyl-PIP2 (diC8PIP2), stimulated GAP activity on an N terminus-containing variant, [L8K]ARF1, but only marginally affected activity on [Δ17]ARF1. A peptide comprising residues 2-17 of ARF1 ([2-17]ARF1) inhibited GAP activity, and PIP2-dependently bound to a protein containing the PH domain and a 17-amino acid-long interdomain linker immediately N-terminal to the first β-strand of the PH domain. Point mutations in either the linker or the C-terminal α-helix of the PH domain decreased [2-17]ARF1 binding and GAP activity. Mutations that reduced ARF1 N-terminal binding to the PH domain also reduced the effect of ASAP1 on cellular actin remodeling. Mutations in the ARF N terminus that reduced binding also reduced GAP activity. We conclude that PIP2 regulates binding of ASAP1's PH domain to the ARF1 N terminus, which may partially regulate GAP activity.
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Affiliation(s)
- Neeladri Sekhar Roy
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Olivier Soubias
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702
| | - Peng Zhai
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Jessica R Hall
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Jessica N Dagher
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Ruibai Luo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Itoro O Akpan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Matthew D Hall
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - R Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702
| | - Marielle E Yohe
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892 .,Pediatric Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
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15
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Li Y, Soubias O, Li J, Sun S, Randazzo PA, Byrd RA. Functional Expression and Characterization of Human Myristoylated-Arf1 in Nanodisc Membrane Mimetics. Biochemistry 2019; 58:1423-1431. [PMID: 30735034 DOI: 10.1021/acs.biochem.8b01323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipidated small GTP-binding proteins of the Arf family interact with multiple cellular partners and with membranes to regulate intracellular traffic and organelle structure. Here, we focus on the ADP-ribosylation factor 1 (Arf1), which interacts with numerous proteins in the Arf pathway, such as the ArfGAP ASAP1 that is highly expressed and activated in several cancer cell lines and associated with enhanced migration, invasiveness, and poor prognosis. Understanding the molecular and mechanistic details of Arf1 regulation at the membrane via structural and biophysical studies requires large quantities of fully functional protein bound to lipid bilayers. Here, we report on the production of a functional human Arf1 membrane platform on nanodiscs for biophysical studies. Large scale bacterial production of highly pure, N-myristoylated human Arf1 has been achieved, including complex isotopic labeling for nuclear magnetic resonance (NMR) studies, and the myr-Arf1 can be readily assembled in small nanoscale lipid bilayers (nanodiscs, NDs). It is determined that myr-Arf1 requires a minimum binding surface in the NDs of ∼20 lipids. Fluorescence and NMR were used to establish nucleotide exchange and ArfGAP-stimulated GTP hydrolysis at the membrane, indicating that phophoinositide stimulation of the activity of the ArfGAP ASAP1 is ≥2000-fold. Differences in nonhydrolyzable GTP analogues are observed, and GMPPCP is found to be the most stable. Combined, these observations establish a functional environment for biophysical studies of Arf1 effectors and interactions at the membrane.
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Affiliation(s)
- Yifei Li
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - Olivier Soubias
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - Jess Li
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - Shangjin Sun
- Structural Biophysics Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , Maryland 21702-1201 , United States
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research , National Cancer Institute , Bethesda , Maryland 20892 , 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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16
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Pocognoni CA, Viktorova EG, Wright J, Meissner JM, Sager G, Lee E, Belov GA, Sztul E. Highly conserved motifs within the large Sec7 ARF guanine nucleotide exchange factor GBF1 target it to the Golgi and are critical for GBF1 activity. Am J Physiol Cell Physiol 2018; 314:C675-C689. [PMID: 29443553 DOI: 10.1152/ajpcell.00221.2017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cellular life requires the activation of the ADP-ribosylation factors (ARFs) by Golgi brefeldin A-resistant factor 1 (GBF1), a guanine nucleotide exchange factor (GEF) with a highly conserved catalytic Sec7 domain (Sec7d). In addition to the Sec7d, GBF1 contains other conserved domains whose functions remain unclear. Here, we focus on HDS2 (homology downstream of Sec7d 2) domain because the L1246R substitution within the HDS2 α-helix 5 of the zebrafish GBF1 ortholog causes vascular hemorrhaging and embryonic lethality (13). To dissect the structure/function relationships within HDS2, we generated six variants, in which the most conserved residues within α-helices 1, 2, 4, and 6 were mutated to alanines. Each HDS2 mutant was assessed in a cell-based "replacement" assay for its ability to support cellular functions normally supported by GBF1, such as maintaining Golgi homeostasis, facilitating COPI recruitment, supporting secretion, and sustaining cellular viability. We show that cells treated with the pharmacological GBF1 inhibitor brefeldin A (BFA) and expressing a BFA-resistant GBF1 variant with alanine substitutions of RDR1168 or LF1266 are compromised in Golgi homeostasis, impaired in ARF activation, unable to sustain secretion, and defective in maintaining cellular viability. To gain insight into the molecular mechanism of this dysfunction, we assessed the ability of each GBF1 mutant to target to Golgi membranes and found that mutations in RDR1168 and LF1266 significantly decrease targeting efficiency. Thus, these residues within α-helix 2 and α-helix 6 of the HDS2 domain in GBF1 are novel regulatory determinants that support GBF1 cellular function by impacting the Golgi-specific membrane association of GBF1.
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Affiliation(s)
- Cristian A Pocognoni
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham , Birmingham, Alabama
| | - Ekaterina G Viktorova
- Department of Veterinary Medicine, Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland , College Park, Maryland
| | - John Wright
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham , Birmingham, Alabama
| | - Justyna M Meissner
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham , Birmingham, Alabama
| | - Garrett Sager
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham , Birmingham, Alabama
| | - Eunjoo Lee
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham , Birmingham, Alabama
| | - George A Belov
- Department of Veterinary Medicine, Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland , College Park, Maryland
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham , Birmingham, Alabama
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17
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Malaby AW, Das S, Chakravarthy S, Irving TC, Bilsel O, Lambright DG. Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors. Structure 2017; 26:106-117.e6. [PMID: 29276036 PMCID: PMC5752578 DOI: 10.1016/j.str.2017.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/22/2017] [Accepted: 11/27/2017] [Indexed: 11/16/2022]
Abstract
Membrane dynamic processes including vesicle biogenesis depend on Arf
GTPase activation by guanine nucleotide exchange factors (GEFs) containing a
catalytic Sec7 domain and a membrane targeting module such as a PH domain. The
catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory
interactions that impede accessibility of the exchange site in the Sec7 domain.
These restraints can be relieved through activator Arf-GTP binding to an
allosteric site comprising the PH domain and proximal autoinhibitory elements
(Sec7-PH linker and C-terminal helix). Small angle X-ray scattering and
negative-stain electron microscopy were used to investigate the structural
organization and conformational dynamics of Cytohesin-3 (Grp1) in autoinhibited
and active states. The results support a model in which hinge dynamics in the
autoinhibited state expose the activator site for Arf-GTP binding, while
subsequent C-terminal helix unlatching and repositioning unleash conformational
entropy in the Sec7-PH linker to drive exposure of the exchange site.
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Affiliation(s)
- Andrew W Malaby
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Sanchaita Das
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Thomas C Irving
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - David G Lambright
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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18
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Rafiullah R, Long AB, Ivanova AA, Ali H, Berkel S, Mustafa G, Paramasivam N, Schlesner M, Wiemann S, Wade RC, Bolthauser E, Blum M, Kahn RA, Caspary T, Rappold GA. A novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity. Eur J Hum Genet 2017; 25:1324-1334. [PMID: 29255182 PMCID: PMC5865152 DOI: 10.1038/s41431-017-0031-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/10/2017] [Indexed: 11/09/2022] Open
Abstract
ARL13B encodes for the ADP-ribosylation factor-like 13B GTPase, which is required for normal cilia structure and Sonic hedgehog (Shh) signaling. Disruptions in cilia structure or function lead to a class of human disorders called ciliopathies. Joubert syndrome is characterized by a wide spectrum of symptoms, including a variable degree of intellectual disability, ataxia, and ocular abnormalities. Here we report a novel homozygous missense variant c.[223G>A] (p.(Gly75Arg) in the ARL13B gene, which was identified by whole-exome sequencing of a trio from a consanguineous family with multiple-affected individuals suffering from intellectual disability, ataxia, ocular defects, and epilepsy. The same variant was also identified in a second family. We saw a striking difference in the severity of ataxia between affected male and female individuals in both families. Both ARL13B and ARL13B-c.[223G>A] (p.(Gly75Arg) expression rescued the cilia length and Shh defects displayed by Arl13b hennin (null) cells, indicating that the variant did not disrupt either ARL13B function. In contrast, ARL13B-c.[223G>A] (p.(Gly75Arg) displayed a marked loss of ARL3 guanine nucleotide-exchange factor activity, with retention of its GTPase activities, highlighting the correlation between its loss of function as an ARL3 guanine nucleotide-exchange factor and Joubert syndrome.
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Affiliation(s)
- Rafiullah Rafiullah
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Alyssa B Long
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Anna A Ivanova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Hazrat Ali
- Department of Psychiatry, Bolan Medical College, 87600, Quetta, Pakistan
| | - Simone Berkel
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Ghulam Mustafa
- Molecular and Cellular Modeling (MCM) Group, Heidelberg Institute for Theoretical Studies (HITS), 69118, Heidelberg, Germany
- Center for Molecular Biology, DKFZ-ZMBH Alliance, Heidelberg University, 69120, Heidelberg, Germany
| | - Nagarajan Paramasivam
- Computational Oncology Group, Theoretical Bioinformatics Division (B080), German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, 69120, Heidelberg, Germany
| | - Matthias Schlesner
- Computational Oncology Group, Theoretical Bioinformatics Division (B080), German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Stefan Wiemann
- Genomic and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling (MCM) Group, Heidelberg Institute for Theoretical Studies (HITS), 69118, Heidelberg, Germany
- Center for Molecular Biology, DKFZ-ZMBH Alliance, Heidelberg University, 69120, Heidelberg, Germany
| | - Eugen Bolthauser
- Division of Pediatric Neurology, University Children's Hospital, 8032, Zurich, Switzerland
| | - Martin Blum
- Institute of Zoology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany.
- Interdisciplinary Centre for Neurosciences (IZN), University of Heidelberg, 69120, Heidelberg, Germany.
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19
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Wang J, Fresquez T, Kandachar V, Deretic D. The Arf GEF GBF1 and Arf4 synergize with the sensory receptor cargo, rhodopsin, to regulate ciliary membrane trafficking. J Cell Sci 2017; 130:3975-3987. [PMID: 29025970 DOI: 10.1242/jcs.205492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/10/2017] [Indexed: 01/05/2023] Open
Abstract
The small GTPase Arf4 and the Arf GTPase-activating protein (GAP) ASAP1 cooperatively sequester sensory receptor cargo into transport carriers targeted to primary cilia, but the input that drives Arf4 activation in this process remains unknown. Here, we show, by using frog retinas and recombinant human proteins, that during the carrier biogenesis from the photoreceptor Golgi/trans-Golgi network (TGN) a functional complex is formed between Arf4, the Arf guanine nucleotide exchange factor (GEF) GBF1 and the light-sensing receptor, rhodopsin. Rhodopsin and Arf4 bind the regulatory N-terminal dimerization and cyclophillin-binding (DCB)-homology upstream of Sec7 (HUS) domain of GBF1. The complex is sensitive to Golgicide A (GCA), a selective inhibitor of GBF1 that accordingly blocks rhodopsin delivery to the cilia, without disrupting the photoreceptor Golgi. The emergence of newly synthesized rhodopsin in the endomembrane system is essential for GBF1-Arf4 complex formation in vivo Notably, GBF1 interacts with the Arf GAP ASAP1 in a GCA-resistant manner. Our findings indicate that converging signals on GBF1 from the influx of cargo into the Golgi/TGN and the feedback from Arf4, combined with input from ASAP1, control Arf4 activation during sensory membrane trafficking to primary cilia.
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Affiliation(s)
- Jing Wang
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Theresa Fresquez
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Vasundhara Kandachar
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Dusanka Deretic
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, New Mexico 87131, USA .,Cell Biology and Physiology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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20
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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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21
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Newman LE, Schiavon C, Kahn RA. Plasmids for variable expression of proteins targeted to the mitochondrial matrix or intermembrane space. CELLULAR LOGISTICS 2016; 6:e1247939. [PMID: 28042516 DOI: 10.1080/21592799.2016.1247939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 12/27/2022]
Abstract
We describe the construction and uses of a series of plasmids for directing expression to varied levels of exogenous proteins targeted to the mitochondrial matrix or intermembrane space. We found that the level of protein expression achieved, the kinetics of expression and mitochondrial import, and half-life after import can each vary with the protein examined. These factors should be considered when directing localization of an exogenous protein to mitochondria for rescue, proteomics, or other approaches. We describe the construction of a collection of plasmids for varied expression of proteins targeted to the mitochondrial matrix or intermembrane space, using previously defined targeting sequences and strength CMV promoters. The limited size of these compartments makes them particularly vulnerable to artifacts from over-expression. We found that different proteins display different kinetics of expression and import that should be considered when analyzing results from this approach. Finally, this collection of plasmids has been deposited in the Addgene plasmid repository to facilitate the ready access and use of these tools.
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Affiliation(s)
- Laura E Newman
- Department of Biochemistry, Emory University School of Medicine , Atlanta, GA, USA
| | - Cara Schiavon
- Department of Biochemistry, Emory University School of Medicine , Atlanta, GA, USA
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine , Atlanta, GA, USA
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22
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Kerr SC, Kahn RA. Tool box: Plasmids for the expression or knockdown of human ARF Family GTPases (ARF/ARL/SAR) and their co-expression in bacteria with N-myristoyltransferases. CELLULAR LOGISTICS 2016; 5:e1090523. [PMID: 27057421 PMCID: PMC4820815 DOI: 10.1080/21592799.2015.1090523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 10/30/2022]
Affiliation(s)
- Shana C Kerr
- School of Biology; Georgia Institute of Technology ; Atlanta, GA USA
| | - Richard A Kahn
- Department of Biochemistry; Emory University School of Medicine ; Atlanta, GA USA
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23
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Chavan TS, Jang H, Khavrutskii L, Abraham SJ, Banerjee A, Freed BC, Johannessen L, Tarasov SG, Gaponenko V, Nussinov R, Tarasova NI. High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site. Biophys J 2015; 109:2602-2613. [PMID: 26682817 PMCID: PMC4699860 DOI: 10.1016/j.bpj.2015.09.034] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/08/2015] [Accepted: 09/16/2015] [Indexed: 12/24/2022] Open
Abstract
Ras proteins are small GTPases that act as signal transducers between cell surface receptors and several intracellular signaling cascades. They contain highly homologous catalytic domains and flexible C-terminal hypervariable regions (HVRs) that differ across Ras isoforms. KRAS is among the most frequently mutated oncogenes in human tumors. Surprisingly, we found that the C-terminal HVR of K-Ras4B, thought to minimally impact the catalytic domain, directly interacts with the active site of the protein. The interaction is almost 100-fold tighter with the GDP-bound than the GTP-bound protein. HVR binding interferes with Ras-Raf interaction, modulates binding to phospholipids, and slightly slows down nucleotide exchange. The data indicate that contrary to previously suggested models of K-Ras4B signaling, HVR plays essential roles in regulation of signaling. High affinity binding of short peptide analogs of HVR to K-Ras active site suggests that targeting this surface with inhibitory synthetic molecules for the therapy of KRAS-dependent tumors is feasible.
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Affiliation(s)
- Tanmay S Chavan
- Medicinal Chemistry Department, University of Illinois at Chicago, Chicago, Illinois; Biochemistry and Molecular Genetics Department, University of Illinois at Chicago, Chicago, Illinois
| | - Hyunbum Jang
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland
| | - Lyuba Khavrutskii
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland
| | - Sherwin J Abraham
- Biochemistry and Molecular Genetics Department, University of Illinois at Chicago, Chicago, Illinois
| | - Avik Banerjee
- Chemistry Department, University of Illinois at Chicago, Chicago, Illinois; Structural Biophysics Laboratory, National Cancer Institute at Frederick, Frederick, Maryland
| | - Benjamin C Freed
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland
| | - Liv Johannessen
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland
| | - Sergey G Tarasov
- Chemistry Department, University of Illinois at Chicago, Chicago, Illinois; Structural Biophysics Laboratory, National Cancer Institute at Frederick, Frederick, Maryland
| | - Vadim Gaponenko
- Biochemistry and Molecular Genetics Department, University of Illinois at Chicago, Chicago, Illinois.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Nadya I Tarasova
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland.
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24
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Jian X, Tang WK, Zhai P, Roy NS, Luo R, Gruschus JM, Yohe ME, Chen PW, Li Y, Byrd RA, Xia D, Randazzo PA. Molecular Basis for Cooperative Binding of Anionic Phospholipids to the PH Domain of the Arf GAP ASAP1. Structure 2015; 23:1977-88. [PMID: 26365802 PMCID: PMC4788500 DOI: 10.1016/j.str.2015.08.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/12/2015] [Accepted: 08/14/2015] [Indexed: 11/18/2022]
Abstract
We have defined the molecular basis for association of the PH domain of the Arf GAP ASAP1 with phospholipid bilayers. Structures of the unliganded and dibutyryl PtdIns(4,5)P2-bound PH domain were solved. PtdIns(4,5)P2 made contact with both a canonical site (C site) and an atypical site (A site). We hypothesized cooperative binding of PtdIns(4,5)P2 to the C site and a nonspecific anionic phospholipid to the A site. PtdIns(4,5)P2 dependence of binding to large unilamellar vesicles and GAP activity was sigmoidal, consistent with cooperative sites. In contrast, PtdIns(4,5)P2 binding to the PH domain of PLC δ1 was hyperbolic. Mutation of amino acids in either the C or A site resulted in decreased PtdIns(4,5)P2-dependent binding to vesicles and decreased GAP activity. The results support the idea of cooperative phospholipid binding to the C and A sites of the PH domain of ASAP1. We propose that the mechanism underlies rapid switching between active and inactive ASAP1.
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Affiliation(s)
- Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wai-Kwan Tang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peng Zhai
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neeladri Sekhar Roy
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruibai Luo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James M Gruschus
- Laboratory of Structural Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marielle E Yohe
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pei-Wen Chen
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yifei Li
- Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - R Andrew Byrd
- Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Laboratory of Cell Biology, National Cancer Institute, Building 37, Room 2122, Bethesda, MD 20892, USA.
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Building 37, Room 2042, Bethesda, MD 20892, USA.
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25
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Knyphausen P, Kuhlmann N, de Boor S, Lammers M. Lysine-acetylation as a fundamental regulator of Ran function: Implications for signaling of proteins of the Ras-superfamily. Small GTPases 2015; 6:189-95. [PMID: 26507377 PMCID: PMC4905271 DOI: 10.1080/21541248.2015.1103399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The small GTP-binding protein Ran is involved in the regulation of essential cellular processes in interphase but also in mitotic cells: Ran controls the nucleocytoplasmic transport of proteins and RNA, it regulates mitotic spindle formation and nuclear envelope assembly. Deregulations in Ran dependent processes were implicated in the development of severe diseases such as cancer and neurodegenerative disorders. To understand how Ran-function is regulated is therefore of highest importance. Recently, several lysine-acetylation sites in Ran were identified by quantitative mass-spectrometry, some being located in highly important regions such as the P-loop, switch I, switch II and the G5/SAK motif. We recently reported that lysine-acetylation regulates nearly all aspects of Ran-function such as RCC1 catalyzed nucleotide exchange, intrinsic nucleotide hydrolysis, its interaction with NTF2 and the formation of import- and export-complexes. As a hint for its biological importance, we identified Ran-specific lysine-deacetylases (KDACs) and -acetyltransferases (KATs). Also for other small GTPases such as Ras, Rho, Cdc42, and for many effectors and regulators thereof, lysine-acetylation sites were discovered. However, the functional impact of lysine-acetylation as a regulator of protein function has only been marginally investigated so far. We will discuss recent findings of lysine-acetylation as a novel modification to regulate Ras-protein signaling.
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Affiliation(s)
- Philipp Knyphausen
- a Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD ); University of Cologne ; Cologne , Germany
| | - Nora Kuhlmann
- a Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD ); University of Cologne ; Cologne , Germany
| | - Susanne de Boor
- a Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD ); University of Cologne ; Cologne , Germany
| | - Michael Lammers
- a Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD ); University of Cologne ; Cologne , Germany
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26
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Abstract
Mutant genes that underlie Mendelian forms of amyotrophic lateral sclerosis (ALS) and biochemical investigations of genetic disease models point to potential driver pathophysiological events involving endoplasmic reticulum (ER) stress and autophagy. Several steps in these cell biological processes are known to be controlled physiologically by small ADP-ribosylation factor (ARF) signaling. Here, we investigated the role of ARF guanine nucleotide exchange factors (GEFs), cytohesins, in models of ALS. Genetic or pharmacological inhibition of cytohesins protects motor neurons in vitro from proteotoxic insults and rescues locomotor defects in a Caenorhabditis elegans model of disease. Cytohesins form a complex with mutant superoxide dismutase 1 (SOD1), a known cause of familial ALS, but this is not associated with a change in GEF activity or ARF activation. ER stress evoked by mutant SOD1 expression is alleviated by antagonism of cytohesin activity. In the setting of mutant SOD1 toxicity, inhibition of cytohesin activity enhances autophagic flux and reduces the burden of misfolded SOD1. These observations suggest that targeting cytohesins may have potential benefits for the treatment of ALS.
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27
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Chen PW, Jian X, Luo R, Randazzo PA. Simple in vitro assay of Arf GAPs and preparation of Arf proteins as substrates. Methods Cell Biol 2015; 130:69-80. [PMID: 26360029 DOI: 10.1016/bs.mcb.2015.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Defining the interaction of Arf GAPs with specific Arfs is important for understanding their functions in the endocytic system. Cell-based approaches have been valuable for identifying Arfs and Arf GAPs active in the endocytic compartment; however, the cell-based assays have some limitations in establishing relationships among the Arfs and ArfGAPs. Here we describe a simple in vitro assay that will provide a means for comparing Arfs as substrates and serve to complement cell-based studies.
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Affiliation(s)
- Pei-Wen Chen
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ruibai Luo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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28
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Davis CT, Zhu W, Gibson CC, Bowman-Kirigin JA, Sorensen L, Ling J, Sun H, Navankasattusas S, Li DY. ARF6 inhibition stabilizes the vasculature and enhances survival during endotoxic shock. THE JOURNAL OF IMMUNOLOGY 2014; 192:6045-52. [PMID: 24835390 DOI: 10.4049/jimmunol.1400309] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The vascular endothelium responds to infection by destabilizing endothelial cell-cell junctions to allow fluid and cells to pass into peripheral tissues, facilitating clearance of infection and tissue repair. During sepsis, endotoxin and other proinflammatory molecules induce excessive vascular leak, which can cause organ dysfunction, shock, and death. Current therapies for sepsis are limited to antibiotics and supportive care, which are often insufficient to reduce morbidity and prevent mortality. Previous attempts at blocking inflammatory cytokine responses in humans proved ineffective at reducing the pathologies associated with sepsis, highlighting the need for a new therapeutic strategy. The small GTPase ARF6 is activated by a MyD88-ARNO interaction to induce vascular leak through disruption of endothelial adherens junctions. In this study, we show that the MyD88-ARNO-ARF6-signaling axis is responsible for LPS-induced endothelial permeability and is a destabilizing convergence point used by multiple inflammatory cues. We also show that blocking ARF6 with a peptide construct of its N terminus is sufficient to reduce vascular leak and enhance survival during endotoxic shock, without inhibiting the host cytokine response. Our data highlight the therapeutic potential of blocking ARF6 and reducing vascular leak for the treatment of inflammatory conditions, such as endotoxemia.
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Affiliation(s)
- Chadwick T Davis
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112; Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112
| | - Weiquan Zhu
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112
| | - Christopher C Gibson
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112; Department of Bioengineering, University of Utah, Salt Lake City, UT 84112
| | - Jay A Bowman-Kirigin
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112
| | - Lise Sorensen
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112
| | - Jing Ling
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112
| | - Huiming Sun
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112; Department of Respiratory and Critical Care Medicine, Jinling Hospital, Clinical School of Nanjing University, Nanjing 210002, China
| | - Sutip Navankasattusas
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112
| | - Dean Y Li
- Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112; Department of Medicine, University of Utah, Salt Lake City, UT 84112; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112; Division of Cardiology, Department of Medicine, University of Utah, Salt Lake City, UT 84112; The Key Laboratory for Human Disease Gene Study of Sichuan Province, Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China; and Cardiology Section, VA Salt Lake City Health Care System, Salt Lake City, UT 84112
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29
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Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors. Proc Natl Acad Sci U S A 2013; 110:14213-8. [PMID: 23940353 PMCID: PMC3761562 DOI: 10.1073/pnas.1301883110] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Membrane recruitment of cytohesin family Arf guanine nucleotide exchange factors depends on interactions with phosphoinositides and active Arf GTPases that, in turn, relieve autoinhibition of the catalytic Sec7 domain through an unknown structural mechanism. Here, we show that Arf6-GTP relieves autoinhibition by binding to an allosteric site that includes the autoinhibitory elements in addition to the PH domain. The crystal structure of a cytohesin-3 construct encompassing the allosteric site in complex with the head group of phosphatidyl inositol 3,4,5-trisphosphate and N-terminally truncated Arf6-GTP reveals a large conformational rearrangement, whereby autoinhibition can be relieved by competitive sequestration of the autoinhibitory elements in grooves at the Arf6/PH domain interface. Disposition of the known membrane targeting determinants on a common surface is compatible with multivalent membrane docking and subsequent activation of Arf substrates, suggesting a plausible model through which membrane recruitment and allosteric activation could be structurally integrated.
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30
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Adolf F, Herrmann A, Hellwig A, Beck R, Brügger B, Wieland FT. Scission of COPI and COPII vesicles is independent of GTP hydrolysis. Traffic 2013; 14:922-32. [PMID: 23691917 DOI: 10.1111/tra.12084] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 05/15/2013] [Accepted: 05/20/2013] [Indexed: 12/29/2022]
Abstract
Intracellular transport and maintenance of the endomembrane system in eukaryotes depends on formation and fusion of vesicular carriers. A seeming discrepancy exists in the literature about the basic mechanism in the scission of transport vesicles that depend on GTP-binding proteins. Some reports describe that the scission of COP-coated vesicles is dependent on GTP hydrolysis, whereas others found that GTP hydrolysis is not required. In order to investigate this pivotal mechanism in vesicle formation, we analyzed formation of COPI- and COPII-coated vesicles utilizing semi-intact cells. The small GTPases Sar1 and Arf1 together with their corresponding coat proteins, the Sec23/24 and Sec13/31 complexes for COPII and coatomer for COPI vesicles were required and sufficient to drive vesicle formation. Both types of vesicles were efficiently generated when GTP hydrolysis was blocked either by utilizing the poorly hydrolyzable GTP analogs GTPγS and GMP-PNP, or with constitutively active mutants of the small GTPases. Thus, GTP hydrolysis is not required for the formation and release of COP vesicles.
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Affiliation(s)
- Frank Adolf
- Heidelberg University Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, D-69120, Heidelberg, Germany
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31
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Chen PW, Jian X, Yoon HY, Randazzo PA. ARAP2 signals through Arf6 and Rac1 to control focal adhesion morphology. J Biol Chem 2013; 288:5849-60. [PMID: 23295182 DOI: 10.1074/jbc.m112.415778] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Focal adhesions (FAs) are dynamic structures that connect the actin cytoskeleton with the extracellular matrix. At least six ADP-ribosylation factor (Arf) GTPase-activating proteins (GAPs), including ARAP2 (an Arf6 GAP), are implicated in regulation of FAs but the mechanisms for most are not well defined. Although Rac1 has been reported to function downstream of Arf6 to control membrane ruffling and cell migration, this pathway has not been directly examined as a regulator of FAs. Here we test the hypothesis that ARAP2 promotes the growth of FAs by converting Arf6·GTP to Arf6·GDP thereby preventing the activation of the Rho family GTP-binding protein Rac1. Reduced expression of ARAP2 decreased the number and size of FAs in cells and increased cellular Arf6·GTP and Rac1·GTP levels. Overexpression of ARAP2 had the opposite effects. The effects of ARAP2 on FAs and Rac1 were dependent on a functional ArfGAP domain. Constitutively active Arf6 affected FAs in the same way as did reduced ARAP2 expression and dominant negative mutants of Arf6 and Rac1 reversed the effect of reduced ARAP2 expression. However, neither dominant negative Arf6 nor Rac1 had the same effect as ARAP2 overexpression. We conclude that changes in Arf6 and Rac1 activities are necessary but not sufficient for ARAP2 to promote the growth of FAs and we speculate that ARAP2 has additional functions that are effector in nature to promote or stabilize FAs.
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Affiliation(s)
- Pei-Wen Chen
- Laboratory of Cellular and Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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32
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Shiba Y, Randazzo PA. ArfGAP1 function in COPI mediated membrane traffic: currently debated models and comparison to other coat-binding ArfGAPs. Histol Histopathol 2012; 27:1143-53. [PMID: 22806901 DOI: 10.14670/hh-27.1143] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ArfGAPs are a family of proteins containing an ArfGAP catalytic domain that induces the hydrolysis of GTP bound to the small guanine nucleotide binding-protein ADP-ribosylation factor (Arf). Functional models for Arfs, which are regulators of membrane traffic, are based on the idea that guanine nucleotide-binding proteins function as switches: Arf with GTP bound is active and binds to effector proteins; the conversion of GTP to GDP inactivates Arf. The cellular activities of ArfGAPs have been examined primarily as regulatory proteins that inactivate Arf; however, Arf function in membrane traffic does not strictly adhere to the concept of a simple switch, adding complexity to models explaining the role of ArfGAPs. Here, we review the literature addressing the function Arf and ArfGAP1 in COPI mediated transport, focusing on two critical and integrated functions of membrane traffic, cargo sorting and vesicle coat polymerization. We briefly discuss other ArfGAPs that may have similar function in Arf-dependent membrane traffic outside the ER-Golgi.
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Affiliation(s)
- Yoko Shiba
- National Cancer Institute, Laboratory of Cellular and Molecular Biology, Bethesda, MD 20892, USA
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33
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Northup JK, Jian X, Randazzo PA. Nucleotide exchange factors: Kinetic analyses and the rationale for studying kinetics of GEFs. CELLULAR LOGISTICS 2012. [PMID: 23181196 PMCID: PMC3498072 DOI: 10.4161/cl.21627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Exchange factors are enzymes that catalyze the exchange of GTP for GDP on guanine nucleotide binding proteins. Progress in understanding the molecular basis of action and the cellular functions of these enzymes has largely come from structural determinations (e.g., crystal structures) and studying effects on cells when expression levels of the exchange factors are perturbed or mutated exchange factors are expressed. Proportionally little effort has been expended on studying the kinetics of exchange; however, reaction rates are central to understanding enzymes. Here, we discuss the importance of kinetic analysis of exchange factors for guanine nucleotide binding proteins, with a focus on ADP-ribosylation factor (Arf) and heterotrimeric G proteins, for providing unique insights into molecular mechanisms and regulation as well as how kinetic analyses are used to complement other approaches.
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Affiliation(s)
- John K Northup
- Laboratory of Cellular Biology; National Institute of Deafness and Other Communication Disorders; Rockville, MD USA
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34
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Jian X, Gruschus JM, Sztul E, Randazzo PA. The pleckstrin homology (PH) domain of the Arf exchange factor Brag2 is an allosteric binding site. J Biol Chem 2012; 287:24273-83. [PMID: 22613714 DOI: 10.1074/jbc.m112.368084] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Brag2, a Sec7 domain (sec7d)-containing guanine nucleotide exchange factor, regulates cell adhesion and tumor cell invasion. Brag2 catalyzes nucleotide exchange, converting Arf·GDP to Arf·GTP. Brag2 contains a pleckstrin homology (PH) domain, and its nucleotide exchange activity is stimulated by phosphatidylinositol 4,5-bisphosphate (PIP(2)). Here we determined kinetic parameters for Brag2 and examined the basis for regulation by phosphoinositides. Using myristoylated Arf1·GDP as a substrate, the k(cat) was 1.8 ± 0.1/s as determined by single turnover kinetics, and the K(m) was 0.20 ± 0.07 μm as determined by substrate saturation kinetics. PIP(2) decreased the K(m) and increased the k(cat) of the reaction. The effect of PIP(2) required the PH domain of Brag2 and the N terminus of Arf and was largely independent of Arf myristoylation. Structural analysis indicated that the linker between the sec7d and the PH domain in Brag2 may directly contact Arf. In support, we found that a Brag2 fragment containing the sec7d and the linker was more active than sec7d alone. We conclude that Brag2 is allosterically regulated by PIP(2) binding to the PH domain and that activity depends on the interdomain linker. Thus, the PH domain and the interdomain linker of Brag2 may be targets for selectively regulating the activity of Brag2.
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Affiliation(s)
- Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NHLBI, National Institutes of Health Bethesda, Maryland 20892, USA
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Okamura H, Nishikiori M, Xiang H, Ishikawa M, Katoh E. Interconversion of two GDP-bound conformations and their selection in an Arf-family small G protein. Structure 2011; 19:988-98. [PMID: 21742265 DOI: 10.1016/j.str.2011.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 03/25/2011] [Accepted: 04/01/2011] [Indexed: 01/06/2023]
Abstract
ADP-ribosylation factor (Arf) and other Arf-family small G proteins participate in many cellular functions via their characteristic GTP/GDP conformational cycles, during which a nucleotide(∗)Mg(2+)-binding site communicates with a remote N-terminal helix. However, the conformational interplay between the nucleotides, the helix, the protein core, and Mg(2+) has not been fully delineated. Herein, we report a study of the dynamics of an Arf-family protein, Arl8, under various conditions by means of NMR relaxation spectroscopy. The data indicated that, when GDP is bound, the protein core, which does not include the N-terminal helix, reversibly transition between an Arf-family GDP form and another conformation that resembles the Arf-family GTP form. Additionally, we found that the N-terminal helix and Mg(2+), respectively, stabilize the aforementioned former and latter conformations in a population-shift manner. Given the dynamics of the conformational changes, we can describe the Arl8 GTP/GDP cycle in terms of an energy diagram.
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Affiliation(s)
- Hideyasu Okamura
- Division of Plant Sciences, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
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Sakurai A, Jian X, Lee CJ, Manavski Y, Chavakis E, Donaldson J, Randazzo PA, Gutkind JS. Phosphatidylinositol-4-phosphate 5-kinase and GEP100/Brag2 protein mediate antiangiogenic signaling by semaphorin 3E-plexin-D1 through Arf6 protein. J Biol Chem 2011; 286:34335-45. [PMID: 21795701 DOI: 10.1074/jbc.m111.259499] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The semaphorins are a family of secreted or membrane-bound proteins that are known to guide axons in the developing nervous system. Genetic evidence revealed that a class III semaphorin, semaphorin 3E (Sema3E), and its receptor Plexin-D1 also control the vascular patterning during development. At the molecular level, we have recently shown that Sema3E acts on Plexin-D1 expressed in endothelial cells, thus initiating a novel antiangiogenic signaling pathway that results in the retraction of filopodia in endothelial tip cells. Sema3E induces the rapid disassembly of integrin-mediated adhesive structures, thereby inhibiting endothelial cell adhesion to the extracellular matrix. This process requires the activation of small GTPase Arf6 (ADP-ribosylation factor 6), which regulates intracellular trafficking of β1 integrin. However, the molecular mechanisms by which Sema3E-Plexin-D1 activates Arf6 remained to be identified. Here we show that GEP100 (guanine nucleotide exchange protein 100)/Brag2, a guanine nucleotide exchange factor for Arf6, mediates Sema3E-induced Arf6 activation in endothelial cells. We provide evidence that upon activation by Sema3E, Plexin-D1 recruits phosphatidylinositol-4-phosphate 5-kinase, and its enzymatic lipid product, phosphatidylinositol 4,5-bisphosphate, binds to the pleckstrin homology domain of GEP100. Phosphatidylinositol 4,5-bisphosphate binding to GEP100 enhances its guanine nucleotide exchange factor activity toward Arf6, thus resulting in the disassembly of integrin-mediated focal adhesions and endothelial cell collapse. Our present study reveals a novel phospholipid-regulated antiangiogenic signaling pathway whereby Sema3E activates Arf6 through Plexin-D1 and consequently controls integrin-mediated endothelial cell attachment to the extracellular matrix and migration.
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Affiliation(s)
- Atsuko Sakurai
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
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Meierhofer T, Eberhardt M, Spoerner M. Conformational states of ADP ribosylation factor 1 complexed with different guanosine triphosphates as studied by 31P NMR spectroscopy. Biochemistry 2011; 50:6316-27. [PMID: 21702511 DOI: 10.1021/bi101573j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Guanine nucleotide binding proteins (GNB-proteins) play an essential role in cellular signaling, acting as molecular switches, cycling between the inactive, GDP-bound form and the active, GTP-bound form. It has been shown that conformational equilibria also exist within the active form of GNB-proteins between conformational states with different functional properties. Here we present (31)P NMR data on ADP ribosylation factor 1 (Arf1), a GNB-protein involved in Golgi traffic, promoting the coating of secretory vesicles. To investigate conformational equilibria in active Arf1, the wild type and switch I mutants complexed with GTP and a variety of commonly used GTP analogues, namely, GppCH(2)p, GppNHp, and GTPγS, were analyzed. To gain deeper insight into the conformational state of active Arf1, we titrated with Cu(2+)-cyclen and GdmCl and formed the complex with the Sec7 domain of nucleotide exchange factor ARNO and an effector GAT domain. In contrast to the related proteins Ras, Ral, Cdc42, and Ran, from (31)P NMR spectroscopic view, Arf1 exists predominantly in a single conformation independent of the GTP analogue used. This state seems to correspond to the so-called state 2(T) conformation, according to Ras nomenclature, which is interacting with the effector domain. The exchange of the highly conserved threonine in position 48 with alanine led to a shift of the equilibrium toward a conformational state with typical properties obtained for state 1(T) in Ras, such as interaction with guanine nucleotide exchange factors, a lower affinity for nucleoside triphosphates, and greater sensitivity to chaotropic agents. In active Arf1(wt), the effector interacting conformation is strongly favored. These intrinsic conformational equilibria of active GNB-proteins could be a fine-tuning mechanism of regulation and thereby an interesting target for the modulation of protein activity.
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Affiliation(s)
- Tanja Meierhofer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Universitätsstrasse 31, D-93053 Regensburg, Germany
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Nangue TJ, Womeni HM, Mbiapo FT, Fanni J, Michel L. Irvingia gabonensis fat: nutritional properties and effect of increasing amounts on the growth and lipid metabolism of young rats wistar sp. Lipids Health Dis 2011; 10:43. [PMID: 21375740 PMCID: PMC3060135 DOI: 10.1186/1476-511x-10-43] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 03/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dietary saturated fatty acids (SFAs) are generally considered to increase plasma cholesterol. It has also been claimed that they increase cardio-vascular disease, although the claim that some of SFAs can increase HDL-cholesterol is poorly documented. Irvingia gabonensis kernels after being dried and crushed they are generally used to prepare a sticky and aromatic soup very much consumed in Cameroun and West Africa countries. This study was therefore aimed at evaluating the effects of dika nut fat on the growing and lipids metabolism of young rats. METHOD For The nutritional evaluation related to the performances of growth and the analysis of increasing amounts of dika nut fat (0; 5.1; 7.34 and 13.48%) in young rats of wistar sp. The animals were taken individually out of metabolic cage for each ration 5 repetitions per sex (males and females) were carried out. RESULTS The results obtained during the 3 weeks of treatment shows that the performances of consumption were positive. A highly significant increase (P<0.01) of serum cholesterol and triglycerides in the high dose fat groups (13.48%) of dika fat were observed compared to control groups. However, this rise of cholesterol is due to that of HDL-cholesterol without any change in the quantity of LDL-Receptor. In parallel, the weight of the vital organ did not vary much compared to control, except for males where we observed a significantly reduction (P<0.01) in the weight of the liver for the three diet tests. CONCLUSION This study shows that the increasing amount of dika nut fat alter significantly cholesterol and triglyceride at high dose diet, but also increase HDL-cholesterol.
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Affiliation(s)
- Thierry Joël Nangue
- Laboratory of Food Sciences Nutrition and Medicinal Plant, Department of Biochemistry, Faculty of Science, University of Dschang, P.O. BOX: 67, Cameroon.
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Energetics and mechanisms of folding and flipping the myristoyl switch in the {beta}-trefoil protein, hisactophilin. Proc Natl Acad Sci U S A 2010; 107:20952-7. [PMID: 21097705 DOI: 10.1073/pnas.1008026107] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Myristoylation, the covalent linkage of a saturated, C(14) fatty acyl chain to the N-terminal glycine in a protein, plays a vital role in reversible membrane binding and signaling by the modified proteins. Currently, little is known about the effects of myristoylation on protein folding and stability, or about the energetics and molecular mechanisms of switching involving states with sequestered versus accessible myristoyl group. Our analysis of these effects in hisactophilin, a histidine-rich protein that binds cell membranes and actin in a pH-dependent manner, shows that myristoylation significantly increases hisactophilin stability, while also markedly increasing global protein folding and unfolding rates. The switching between sequestered and accessible states is pH dependent, with an apparent pK(switch) of 6.95, and an apparent free energy change of 2.0 kcal·mol(-1). The myristoyl switch is linked to the reversible uptake of ∼1.5 protons, likely by histidine residues. This pH dependence of switching appears to be the physical basis of the sensitive, pH-dependent regulation of membrane binding observed in vivo. We conclude that an increase in protein stability upon modification and burial of the attached group is likely to occur in numerous proteins modified with fatty acyl or other hydrophobic groups, and that the biophysical effects of such modification are likely to play an important role in their functional switches. In addition, the increased global dynamics caused by myristoylation of hisactophilin reveals a general mechanism whereby hydrophobic moieties can make nonnative interactions or relieve strain in transition states, thereby increasing the rates of interconversion between different states.
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Spang A, Shiba Y, Randazzo PA. Arf GAPs: gatekeepers of vesicle generation. FEBS Lett 2010; 584:2646-51. [PMID: 20394747 DOI: 10.1016/j.febslet.2010.04.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 03/26/2010] [Accepted: 04/03/2010] [Indexed: 11/17/2022]
Abstract
Arf GAP proteins are a versatile and diverse group of proteins. They control the activity of the GTP-binding proteins of the ARF family by inducing the hydrolysis of GTP that is bound to Arf proteins. The best-studied role of Arf GAPs is in intracellular traffic. In this review, we will focus mainly on the Arf GAPs that play a role in vesicle formation, Arf GAP1, Arf GAP2 and Arf GAP3 and their yeast homologues, Gcs1p and Glo3p. We discuss the roles of Arf GAPs as regulators and effectors for Arf GTP-binding proteins.
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Affiliation(s)
- Anne Spang
- University of Basel, Growth and Development, Biozentrum, Switzerland.
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41
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Jian X, Cavenagh M, Gruschus JM, Randazzo PA, Kahn RA. Modifications to the C-terminus of Arf1 alter cell functions and protein interactions. Traffic 2010; 11:732-42. [PMID: 20214751 DOI: 10.1111/j.1600-0854.2010.01054.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Arf family proteins are approximately 21-kDa GTP-binding proteins that are critical regulators of membrane traffic and the actin cytoskeleton. Studies examining the complex signaling pathways underlying Arf action have relied on recombinant proteins comprised of Arf fused to epitope tags or proteins, such as glutathione S-transferase or green fluorescent protein, for both cell-based mammalian cell studies and bacterially expressed recombinant proteins for biochemical assays. However, the effects of such protein fusions on the biochemical properties relevant to the cellular function have been only incompletely studied at best. Here, we have characterized the effect of C-terminal tagging of Arf1 on (i) function in Saccharomyces cerevisiae, (ii) in vitro nucleotide exchange and (iii) interaction with guanine nucleotide exchange factors and GTPase-activating proteins. We found that the tagged Arfs were substantially impaired or altered in each assay, compared with the wild-type protein, and these changes are certain to alter actions in cells. We discuss the results related to the interpretation of experiments using these reagents and we propose that authors and editors consistently adopt a few simple rules for describing and discussing results obtained with Arf family members that can be readily applied to other proteins.
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Affiliation(s)
- Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, Bldg 37 Room 2042, Bethesda, MD 20892, USA
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42
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Chen PW, Randazzo PA, Parent CA. ACAP-A/B are ArfGAP homologs in dictyostelium involved in sporulation but not in chemotaxis. PLoS One 2010; 5:e8624. [PMID: 20062541 PMCID: PMC2797641 DOI: 10.1371/journal.pone.0008624] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 12/14/2009] [Indexed: 11/29/2022] Open
Abstract
Arfs and Arf GTPase-activating proteins (ArfGAPs) are regulators of membrane trafficking and actin dynamics in mammalian cells. In this study, we identified a primordial Arf, ArfA, and two ArfGAPs (ACAP-A/B) containing BAR, PH, ArfGAP and Ankyrin repeat domains in the eukaryote Dictyostelium discoideum. In vitro, ArfA has similar nucleotide binding properties as mammalian Arfs and, with GTP bound, is a substrate for ACAP-A and B. We also investigated the physiological functions of ACAP-A/B by characterizing cells lacking both ACAP-A and B. Although ACAP-A/B knockout cells showed no defects in cell growth, migration or chemotaxis, they exhibited abnormal actin protrusions and ∼50% reduction in spore yield. We conclude that while ACAP-A/B have a conserved biochemical mechanism and effect on actin organization, their role in migration is not conserved. The absence of an effect on Dictyostelium migration may be due to a specific requirement for ACAPs in mesenchymal migration, which is observed in epithelial cancer cells where most studies of mammalian ArfGAPs were performed.
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Affiliation(s)
- Pei-Wen Chen
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Paul A. Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
| | - Carole A. Parent
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, Bethesda, Maryland, United States of America
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Liu Y, Kahn RA, Prestegard JH. Structure and membrane interaction of myristoylated ARF1. Structure 2009; 17:79-87. [PMID: 19141284 PMCID: PMC2659477 DOI: 10.1016/j.str.2008.10.020] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 10/25/2008] [Accepted: 10/29/2008] [Indexed: 11/22/2022]
Abstract
ADP-ribosylation factors (ARFs) are small (21 kDa), monomeric GTPases that are important regulators of membrane traffic. When membrane bound, they recruit soluble adaptors to membranes and trigger the assembly of coating complexes involved in cargo selection and vesicular budding. N-myristoylation is a conserved feature of all ARF proteins that is required for its biological functions, although the mechanism(s) by which the myristate acts in ARF functions is not fully understood. Here we present the structure of a myristoylated ARF1 protein, determined by solution NMR methods, and an assessment of the influence of myristoylation on association of ARF1.GDP and ARF1.GTP with lipid bilayers. A model in which myristoylation contributes to both the regulation of guanine nucleotide exchange and stable membrane association is supported.
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Affiliation(s)
- Yizhou Liu
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602-4712
| | - Richard A. Kahn
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Rd., Atlanta, GA 30322-3050
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602-4712
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Pincetic A, Leis J. The Mechanism of Budding of Retroviruses From Cell Membranes. Adv Virol 2009; 2009:6239691-6239699. [PMID: 19865606 PMCID: PMC2768365 DOI: 10.1155/2009/623969] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 12/18/2008] [Indexed: 11/17/2022] Open
Abstract
Retroviruses have evolved a mechanism for the release of particles from the cell membrane that appropriates cellular protein complexes, referred to as ESCRT-I, -II, -III, normally involved in the biogenesis of multivesicular bodies. Three different classes of late assembly (L) domains encoded in Gag, with core sequences of PPXY, PTAP, and YPXL, recruit different components of the ESCRT machinery to form a budding complex for virus release. Here, we highlight recent progress in identifying the role of different ESCRT complexes in facilitating budding, ubiquitination, and membrane targeting of avian sarcoma and leukosis virus (ASLV) and human immunodeficiency virus, type 1 (HIV-1). These findings show that retroviruses adopt parallel budding pathways by recruiting different host factors from common cellular machinery for particle release.
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Affiliation(s)
- Andrew Pincetic
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jonathan Leis
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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45
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Abstract
Small G-proteins belonging to the Arf (ADP-ribosylation factor) family serve as regulatory proteins for numerous cellular processes through GTP-dependent recruitment of effector molecules. In the present study we demonstrate that proteins in this family regulate, and are regulated by, membrane curvature. Arf1 and Arf6 were shown to load GTP in a membrane-curvature-dependent manner and stabilize, or further facilitate, changes in membrane curvature through the insertion of an amphipathic helix.
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Abstract
Arf family GTP-binding proteins function in the regulation of membrane-trafficking events and in the maintenance of organelle structure. They act at membrane surfaces to modify lipid composition and to recruit coat proteins for the generation of transport vesicles. Arfs associate with membranes through insertion of an N-terminal myristoyl moiety in conjunction with an adjacent amphipathic alpha-helix, which embeds in the lipid bilayer when Arf1 is GTP-bound. In this issue of the Biochemical Journal, Lundmark et al. report that myristoylated Arfs in the presence of GTP bind to and cause tubulation of liposomes, and that GTP exchange on to Arfs is more efficient in the presence of liposomes of smaller diameter (increased curvature). These findings suggest that Arf protein activation and membrane interaction may initiate membrane curvature that will be enhanced further by coat proteins during vesicle formation.
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47
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Clark CG, Alsmark UCM, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N. Structure and content of the Entamoeba histolytica genome. ADVANCES IN PARASITOLOGY 2008; 65:51-190. [PMID: 18063096 DOI: 10.1016/s0065-308x(07)65002-7] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The intestinal parasite Entamoeba histolytica is one of the first protists for which a draft genome sequence has been published. Although the genome is still incomplete, it is unlikely that many genes are missing from the list of those already identified. In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes.
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Affiliation(s)
- C G Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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DiNitto JP, Delprato A, Gabe Lee MT, Cronin TC, Huang S, Guilherme A, Czech MP, Lambright DG. Structural basis and mechanism of autoregulation in 3-phosphoinositide-dependent Grp1 family Arf GTPase exchange factors. Mol Cell 2008; 28:569-83. [PMID: 18042453 DOI: 10.1016/j.molcel.2007.09.017] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 07/30/2007] [Accepted: 09/07/2007] [Indexed: 10/22/2022]
Abstract
Arf GTPases regulate membrane trafficking and actin dynamics. Grp1, ARNO, and Cytohesin-1 comprise a family of phosphoinositide-dependent Arf GTPase exchange factors with a Sec7-pleckstrin homology (PH) domain tandem. Here, we report that the exchange activity of the Sec7 domain is potently autoinhibited by conserved elements proximal to the PH domain. The crystal structure of the Grp1 Sec7-PH tandem reveals a pseudosubstrate mechanism of autoinhibition in which the linker region between domains and a C-terminal amphipathic helix physically block the docking sites for the switch regions of Arf GTPases. Mutations within either element result in partial or complete activation. Critical determinants of autoinhibition also contribute to insulin-stimulated plasma membrane recruitment. Autoinhibition can be largely reversed by binding of active Arf6 to Grp1 and by phosphorylation of tandem PKC sites in Cytohesin-1. These observations suggest that Grp1 family GEFs are autoregulated by mechanisms that depend on plasma membrane recruitment for activation.
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Affiliation(s)
- Jonathan P DiNitto
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Lay D, Gorgas K, Just WW. Peroxisome biogenesis: Where Arf and coatomer might be involved. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1678-87. [PMID: 17023067 DOI: 10.1016/j.bbamcr.2006.08.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 08/12/2006] [Accepted: 08/23/2006] [Indexed: 11/24/2022]
Abstract
The present review summarizes recent observations on binding of Arf and COPI coat to isolated rat liver peroxisomes. The general structural and functional features of both Arf and coatomer were considered along with the requirements and dependencies of peroxisomal Arf and coatomer recruitment. Studies on the expression of mammalian Pex11 proteins, mainly Pex11alpha and Pex11beta, intimately related to the process of peroxisome proliferation, revealed a sequence of individual steps including organelle elongation/tubulation, formation of membrane and matrix protein patches segregating distinct proteins from each other, development of membrane constrictions and final membrane fission. Based on the similarities of the processes leading to cargo selection and concentration on Golgi membranes on the one hand and to the formation of peroxisomal protein patches on the other hand, an implication of Arf and COPI in distinct processes of peroxisomal proliferation is hypothesized. Alternatively, peroxisomal Arf/COPI might facilitate the formation of COPI-coated peroxisomal vesicles functioning in cargo transport and retrieval from peroxisomes to the ER. Recent observations suggesting transport of Pex3 and Pex19 during early steps of peroxisome biogenesis from the ER to peroxisomes inevitably propose such a retrieval mechanism, provided the ER to peroxisome pathway is based on transporting vesicles.
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Affiliation(s)
- Dorothee Lay
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328D-69120 Heidelberg, Germany
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50
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Dawe S, Corcoran JA, Clancy EK, Salsman J, Duncan R. Unusual topological arrangement of structural motifs in the baboon reovirus fusion-associated small transmembrane protein. J Virol 2005; 79:6216-26. [PMID: 15858006 PMCID: PMC1091723 DOI: 10.1128/jvi.79.10.6216-6226.2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Select members of the Reoviridae are the only nonenveloped viruses known to induce syncytium formation. The fusogenic orthoreoviruses accomplish cell-cell fusion through a distinct class of membrane fusion-inducing proteins referred to as the fusion-associated small transmembrane (FAST) proteins. The p15 membrane fusion protein of baboon reovirus is unique among the FAST proteins in that it contains two hydrophobic regions (H1 and H2) recognized as potential transmembrane (TM) domains, suggesting a polytopic topology. However, detailed topological analysis of p15 indicated only the H1 domain is membrane spanning. In the absence of an N-terminal signal peptide, the H1 TM domain serves as a reverse signal-anchor to direct p15 membrane insertion and a bitopic N(exoplasmic)/C(cytoplasmic) topology. This topology results in the translocation of the smallest ectodomain ( approximately 20 residues) of any known viral fusion protein, with the majority of p15 positioned on the cytosolic side of the membrane. Mutagenic analysis indicated the unusual presence of an N-terminal myristic acid on the small p15 ectodomain is essential to the fusion process. Furthermore, the only other hydrophobic region (H2) present in p15, aside from the TM domain, is located within the endodomain. Consequently, the p15 ectodomain is devoid of a fusion peptide motif, a hallmark feature of membrane fusion proteins. The exceedingly small, myristoylated ectodomain and the unusual topological distribution of structural motifs in this nonenveloped virus membrane fusion protein necessitate alternate models of protein-mediated membrane fusion.
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Affiliation(s)
- Sandra Dawe
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.
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