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McHugh D, Sun B, Gutierrez-Muñoz C, Hernández-González F, Mellone M, Guiho R, Duran I, Pombo J, Pietrocola F, Birch J, Kallemeijn WW, Khadayate S, Dharmalingam G, Vernia S, Tate EW, Martínez-Barbera JP, Withers DJ, Thomas GJ, Serrano M, Gil J. COPI vesicle formation and N-myristoylation are targetable vulnerabilities of senescent cells. Nat Cell Biol 2023; 25:1804-1820. [PMID: 38012402 PMCID: PMC10709147 DOI: 10.1038/s41556-023-01287-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
Drugs that selectively kill senescent cells (senolytics) improve the outcomes of cancer, fibrosis and age-related diseases. Despite their potential, our knowledge of the molecular pathways that affect the survival of senescent cells is limited. To discover senolytic targets, we performed RNAi screens and identified coatomer complex I (COPI) vesicle formation as a liability of senescent cells. Genetic or pharmacological inhibition of COPI results in Golgi dispersal, dysfunctional autophagy, and unfolded protein response-dependent apoptosis of senescent cells, and knockdown of COPI subunits improves the outcomes of cancer and fibrosis in mouse models. Drugs targeting COPI have poor pharmacological properties, but we find that N-myristoyltransferase inhibitors (NMTi) phenocopy COPI inhibition and are potent senolytics. NMTi selectively eliminated senescent cells and improved outcomes in models of cancer and non-alcoholic steatohepatitis. Our results suggest that senescent cells rely on a hyperactive secretory apparatus and that inhibiting trafficking kills senescent cells with the potential to treat various senescence-associated diseases.
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Affiliation(s)
- Domhnall McHugh
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Bin Sun
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Carmen Gutierrez-Muñoz
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Fernanda Hernández-González
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Pulmonology, ICR, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
- Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Massimiliano Mellone
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- AstraZeneca, Immuno-Oncology Discovery, Oncology R&D, Cambridge, UK
| | - Romain Guiho
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Imanol Duran
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Joaquim Pombo
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Federico Pietrocola
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Jodie Birch
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Wouter W Kallemeijn
- Department of Chemistry, Molecular Sciences Research Hub, London, UK
- The Francis Crick Institute, London, UK
| | - Sanjay Khadayate
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Gopuraja Dharmalingam
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Santiago Vernia
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, London, UK
- The Francis Crick Institute, London, UK
| | - Juan Pedro Martínez-Barbera
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Dominic J Withers
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Gareth J Thomas
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Altos Labs, Cambridge Institute of Science, Granta Park, UK
| | - Jesús Gil
- MRC Laboratory of Medical Sciences (LMS), London, UK.
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.
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2
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Zhang YJ, Yang C, Wang W, Harafuji N, Stasiak P, Bell PD, Caldovic L, Sztul E, Guay-Woodford LM, Bebok Z. Cystin is required for maintaining fibrocystin (FPC) levels and safeguarding proteome integrity in mouse renal epithelial cells: A mechanistic connection between the kidney defects in cpk mice and human ARPKD. FASEB J 2023; 37:e23008. [PMID: 37318790 DOI: 10.1096/fj.202300100r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is caused primarily by mutations in PKHD1, encoding fibrocystin (FPC), but Pkhd1 mutant mice failed to reproduce the human phenotype. In contrast, the renal lesion in congenital polycystic kidney (cpk) mice, with a mutation in Cys1 and cystin protein loss, closely phenocopies ARPKD. Although the nonhomologous mutation diminished the translational relevance of the cpk model, recent identification of patients with CYS1 mutations and ARPKD prompted the investigations described herein. We examined cystin and FPC expression in mouse models (cpk, rescued-cpk (r-cpk), Pkhd1 mutants) and mouse cortical collecting duct (CCD) cell lines (wild type (wt), cpk). We found that cystin deficiency caused FPC loss in both cpk kidneys and CCD cells. FPC levels increased in r-cpk kidneys and siRNA of Cys1 in wt cells reduced FPC. However, FPC deficiency in Pkhd1 mutants did not affect cystin levels. Cystin deficiency and associated FPC loss impacted the architecture of the primary cilium, but not ciliogenesis. No reduction in Pkhd1 mRNA levels in cpk kidneys and CCD cells suggested posttranslational FPC loss. Studies of cellular protein degradation systems suggested selective autophagy as a mechanism. In support of the previously described function of FPC in E3 ubiquitin ligase complexes, we demonstrated reduced polyubiquitination and elevated levels of functional epithelial sodium channel in cpk cells. Therefore, our studies expand the function of cystin in mice to include inhibition of Myc expression via interaction with necdin and maintenance of FPC as functional component of the NEDD4 E3 ligase complexes. Loss of FPC from E3 ligases may alter the cellular proteome, contributing to cystogenesis through multiple, yet to be defined, mechanisms.
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Affiliation(s)
- Yiming J Zhang
- Department of Cell Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - Chaozhe Yang
- Center for Translational Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Wei Wang
- Cystic Fibrosis Research Center, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - Naoe Harafuji
- Center for Translational Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Piotr Stasiak
- Department of Cell Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - P Darwin Bell
- Department of Medicine, Division of Nephrology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ljubica Caldovic
- Center for Translational Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Elizabeth Sztul
- Department of Cell Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - Lisa M Guay-Woodford
- Center for Translational Research, Children's National Hospital, Washington, District of Columbia, USA
- Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Zsuzsanna Bebok
- Department of Cell Developmental and Integrative Biology (CDIB), University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
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3
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Van der Verren SE, Zanetti G. The small GTPase Sar1, control centre of COPII trafficking. FEBS Lett 2023; 597:865-882. [PMID: 36737236 DOI: 10.1002/1873-3468.14595] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Sar1 is a small GTPase of the ARF family. Upon exchange of GDP for GTP, Sar1 associates with the endoplasmic reticulum (ER) membrane and recruits COPII components, orchestrating cargo concentration and membrane deformation. Many aspects of the role of Sar1 and regulation of its GTP cycle remain unclear, especially as complexity increases in higher organisms that secrete a wider range of cargoes. This review focusses on the regulation of GTP hydrolysis and its role in coat assembly, as well as the mechanism of Sar1-induced membrane deformation and scission. Finally, we highlight the additional specialisation in higher eukaryotes and the outstanding questions on how Sar1 functions are orchestrated.
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Affiliation(s)
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College London, UK
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4
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Muccini AJ, Gustafson MA, Fromme JC. Structural basis for activation of Arf1 at the Golgi complex. Cell Rep 2022; 40:111282. [PMID: 36044848 PMCID: PMC9469209 DOI: 10.1016/j.celrep.2022.111282] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/11/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
The Golgi complex is the central sorting station of the eukaryotic secretory pathway. Traffic through the Golgi requires activation of Arf guanosine triphosphatases that orchestrate cargo sorting and vesicle formation by recruiting an array of effector proteins. Arf activation and Golgi membrane association is controlled by large guanine nucleotide exchange factors (GEFs) possessing multiple conserved regulatory domains. Here we present cryoelectron microscopy (cryoEM) structures of full-length Gea2, the yeast paralog of the human Arf-GEF GBF1, that reveal the organization of these regulatory domains and explain how Gea2 binds to the Golgi membrane surface. We find that the GEF domain adopts two different conformations compatible with different stages of the Arf activation reaction. The structure of a Gea2-Arf1 activation intermediate suggests that the movement of the GEF domain primes Arf1 for membrane insertion upon guanosine triphosphate binding. We propose that conformational switching of Gea2 during the nucleotide exchange reaction promotes membrane insertion of Arf1. Arf1 is a GTPase that regulates Golgi trafficking by recruiting many effector proteins. Muccini et al. report cryoEM structures of the Arf1 activator Gea2, capturing Gea2 in multiple conformational states including a Gea2-Arf1 activation intermediate. The structures help explain how Gea2 activates Arf1 on the Golgi membrane surface.
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Affiliation(s)
- Arnold J Muccini
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Margaret A Gustafson
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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5
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Vargová R, Wideman JG, Derelle R, Klimeš V, Kahn RA, Dacks JB, Eliáš M. A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family. Genome Biol Evol 2021; 13:6319025. [PMID: 34247240 PMCID: PMC8358228 DOI: 10.1093/gbe/evab157] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.
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Affiliation(s)
- Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Romain Derelle
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, United Kingdom
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
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6
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Cross-Kingdom Activation of Vibrio Toxins by ADP-Ribosylation Factor Family GTPases. J Bacteriol 2020; 202:JB.00278-20. [PMID: 32900828 DOI: 10.1128/jb.00278-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic Vibrio species use many different approaches to subvert, attack, and undermine the host response. The toxins they produce are often responsible for the devastating effects associated with their diseases. These toxins target a variety of host proteins, which leads to deleterious effects, including dissolution of cell organelle integrity and inhibition of protein secretion. Becoming increasingly prevalent as cofactors for Vibrio toxins are proteins of the small GTPase families. ADP-ribosylation factor small GTPases (ARFs) in particular are emerging as a common host cofactor necessary for full activation of Vibrio toxins. While ARFs are not the direct target of Vibrio cholerae cholera toxin (CT), ARF binding is required for its optimal activity as an ADP-ribosyltransferase. The makes caterpillars floppy (MCF)-like and the domain X (DmX) effectors of the Vibrio vulnificus multifunctional autoprocessing repeats-in-toxin (MARTX) toxin also both require ARFs to initiate autoprocessing and activation as independent effectors. ARFs are ubiquitously expressed in eukaryotes and are key regulators of many cellular processes, and as such they are ideal cofactors for Vibrio pathogens that infect many host species. In this review, we cover in detail the known Vibrio toxins that use ARFs as cross-kingdom activators to both stimulate and optimize their activity. We further discuss how these contrast to toxins and effectors from other bacterial species that coactivate, stimulate, or directly modify host ARFs as their mechanisms of action.
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7
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Luo PM, Boyce M. Directing Traffic: Regulation of COPI Transport by Post-translational Modifications. Front Cell Dev Biol 2019; 7:190. [PMID: 31572722 PMCID: PMC6749011 DOI: 10.3389/fcell.2019.00190] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022] Open
Abstract
The coat protein complex I (COPI) is an essential, highly conserved pathway that traffics proteins and lipids between the endoplasmic reticulum (ER) and the Golgi. Many aspects of the COPI machinery are well understood at the structural, biochemical and genetic levels. However, we know much less about how cells dynamically modulate COPI trafficking in response to changing signals, metabolic state, stress or other stimuli. Recently, post-translational modifications (PTMs) have emerged as one common theme in the regulation of the COPI pathway. Here, we review a range of modifications and mechanisms that govern COPI activity in interphase cells and suggest potential future directions to address as-yet unanswered questions.
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Affiliation(s)
- Peter M Luo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
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8
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Francis JW, Goswami D, Novick SJ, Pascal BD, Weikum ER, Ortlund EA, Griffin PR, Kahn RA. Nucleotide Binding to ARL2 in the TBCD∙ARL2∙β-Tubulin Complex Drives Conformational Changes in β-Tubulin. J Mol Biol 2017; 429:3696-3716. [PMID: 28970104 DOI: 10.1016/j.jmb.2017.09.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/31/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022]
Abstract
Microtubules are highly dynamic tubulin polymers that are required for a variety of cellular functions. Despite the importance of a cellular population of tubulin dimers, we have incomplete information about the mechanisms involved in the biogenesis of αβ-tubulin heterodimers. In addition to prefoldin and the TCP-1 Ring Complex, five tubulin-specific chaperones, termed cofactors A-E (TBCA-E), and GTP are required for the folding of α- and β-tubulin subunits and assembly into heterodimers. We recently described the purification of a novel trimer, TBCD•ARL2•β-tubulin. Here, we employed hydrogen/deuterium exchange coupled with mass spectrometry to explore the dynamics of each of the proteins in the trimer. Addition of guanine nucleotides resulted in changes in the solvent accessibility of regions of each protein that led to predictions about each's role in tubulin folding. Initial testing of that model confirmed that it is ARL2, and not β-tubulin, that exchanges GTP in the trimer. Comparisons of the dynamics of ARL2 monomer to ARL2 in the trimer suggested that its protein interactions were comparable to those of a canonical GTPase with an effector. This was supported by the use of nucleotide-binding assays that revealed an increase in the affinity for GTP by ARL2 in the trimer. We conclude that the TBCD•ARL2•β-tubulin complex represents a functional intermediate in the β-tubulin folding pathway whose activity is regulated by the cycling of nucleotides on ARL2. The co-purification of guanine nucleotide on the β-tubulin in the trimer is also shown, with implications to modeling the pathway.
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Affiliation(s)
- Joshua W Francis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Devrishi Goswami
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States.
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9
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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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10
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Mariani LE, Bijlsma MF, Ivanova AA, Suciu SK, Kahn RA, Caspary T. Arl13b regulates Shh signaling from both inside and outside the cilium. Mol Biol Cell 2016; 27:mbc.E16-03-0189. [PMID: 27682584 PMCID: PMC5170560 DOI: 10.1091/mbc.e16-03-0189] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/16/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022] Open
Abstract
The regulatory GTPase Arl13b localizes to primary cilia, where it regulates Sonic hedgehog (Shh) signaling. Missense mutations in ARL13B can cause the ciliopathy Joubert syndrome, while the mouse null allele is embryonic lethal. We used mouse embryonic fibroblasts as a system to determine the effects of Arl13b mutations on Shh signaling. We tested a total of seven different mutants, three JS-causing variants, two point mutants predicted to alter guanine nucleotide handling, one that disrupts cilia localization, and one that prevents palmitoylation and thus membrane binding, in assays of transcriptional and non-transcriptional Shh signaling. We found that mutations disrupting Arl13b's palmitoylation site, cilia localization signal, or GTPase handling altered the Shh response in distinct assays of transcriptional or non-transcriptional signaling. In contrast, JS-causing mutations in Arl13b did not affect Shh signaling in these same assays, suggesting these mutations result in more subtle defects, likely affecting only a subset of signaling outputs. Finally, we show that restricting Arl13b from cilia interferes with its ability to regulate Shh-stimulated chemotaxis, despite previous evidence that cilia themselves are not required for this non-transcriptional Shh response. This points to a more complex relationship between the ciliary and non-ciliary roles of this regulatory GTPase than previously envisioned.
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Affiliation(s)
- Laura E Mariani
- *Department of Human Genetics, Emory University, Atlanta, GA, USA Neuroscience Graduate Program, Emory University, Atlanta, GA, USA
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Academic Medical Center and Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Anna A Ivanova
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Sarah K Suciu
- *Department of Human Genetics, Emory University, Atlanta, GA, USA Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Richard A Kahn
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Tamara Caspary
- *Department of Human Genetics, Emory University, Atlanta, GA, USA
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11
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Mishra AK, Lambright DG. Invited review: Small GTPases and their GAPs. Biopolymers 2016; 105:431-48. [PMID: 26972107 PMCID: PMC5439442 DOI: 10.1002/bip.22833] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 03/10/2016] [Indexed: 12/11/2022]
Abstract
Widespread utilization of small GTPases as major regulatory hubs in many different biological systems derives from a conserved conformational switch mechanism that facilitates cycling between GTP-bound active and GDP-bound inactive states under control of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which accelerate slow intrinsic rates of activation by nucleotide exchange and deactivation by GTP hydrolysis, respectively. Here we review developments leading to current understanding of intrinsic and GAP catalyzed GTP hydrolytic reactions in small GTPases from structural, molecular and chemical mechanistic perspectives. Despite the apparent simplicity of the GTPase cycle, the structural bases underlying the hallmark hydrolytic reaction and catalytic acceleration by GAPs are considerably more diverse than originally anticipated. Even the most fundamental aspects of the reaction mechanism have been challenging to decipher. Through a combination of experimental and in silico approaches, the outlines of a consensus view have begun to emerge for the best studied paradigms. Nevertheless, recent observations indicate that there is still much to be learned. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 431-448, 2016.
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Affiliation(s)
- Ashwini K Mishra
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - David G Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
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12
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Nawrotek A, Zeghouf M, Cherfils J. Allosteric regulation of Arf GTPases and their GEFs at the membrane interface. Small GTPases 2016; 7:283-296. [PMID: 27449855 DOI: 10.1080/21541248.2016.1215778] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Arf GTPases assemble protein complexes on membranes to carry out major functions in cellular traffic. An essential step is their activation by guanine nucleotide exchange factors (GEFs), whose Sec7 domain stimulates GDP/GTP exchange. ArfGEFs form 2 major families: ArfGEFs with DCB, HUS and HDS domains (GBF1 and BIG1/BIG2 in humans), which act at the Golgi; and ArfGEFs with a C-terminal PH domain (cytohesin, EFA6 and BRAG), which function at the plasma membrane and endosomes. In addition, pathogenic bacteria encode an ArfGEF with a unique membrane-binding domain. Here we review the allosteric regulation of Arf GTPases and their GEFs at the membrane interface. Membranes contribute several regulatory layers: at the GTPase level, where activation by GTP is coupled to membrane recruitment by a built-in structural device; at the Sec7 domain, which manipulates this device to ensure that Arf-GTP is attached to membranes; and at the level of non-catalytic ArfGEF domains, which form direct or GTPase-mediated interactions with membranes that enable a spectacular diversity of regulatory regimes. Notably, we show here that membranes increase the efficiency of a large ArfGEF (human BIG1) by 32-fold by interacting directly with its N-terminal DCB and HUS domains. The diversity of allosteric regulatory regimes suggests that ArfGEFs can function in cascades and circuits to modulate the shape, amplitude and duration of Arf signals in cells. Because Arf-like GTPases feature autoinhibitory elements similar to those of Arf GTPases, we propose that their activation also requires allosteric interactions of these elements with membranes or other proteins.
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Affiliation(s)
- Agata Nawrotek
- a Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure de Cachan and Université Paris-Saclay , Cachan , France
| | - Mahel Zeghouf
- a Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure de Cachan and Université Paris-Saclay , Cachan , France
| | - Jacqueline Cherfils
- a Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure de Cachan and Université Paris-Saclay , Cachan , France
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13
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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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14
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Regulating the large Sec7 ARF guanine nucleotide exchange factors: the when, where and how of activation. Cell Mol Life Sci 2014; 71:3419-38. [PMID: 24728583 DOI: 10.1007/s00018-014-1602-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/27/2014] [Accepted: 03/03/2014] [Indexed: 10/25/2022]
Abstract
Eukaryotic cells require selective sorting and transport of cargo between intracellular compartments. This is accomplished at least in part by vesicles that bud from a donor compartment, sequestering a subset of resident protein "cargos" destined for transport to an acceptor compartment. A key step in vesicle formation and targeting is the recruitment of specific proteins that form a coat on the outside of the vesicle in a process requiring the activation of regulatory GTPases of the ARF family. Like all such GTPases, ARFs cycle between inactive, GDP-bound, and membrane-associated active, GTP-bound, conformations. And like most regulatory GTPases the activating step is slow and thought to be rate limiting in cells, requiring the use of ARF guanine nucleotide exchange factor (GEFs). ARF GEFs are characterized by the presence of a conserved, catalytic Sec7 domain, though they also contain motifs or additional domains that confer specificity to localization and regulation of activity. These domains have been used to define and classify five different sub-families of ARF GEFs. One of these, the BIG/GBF1 family, includes three proteins that are each key regulators of the secretory pathway. GEF activity initiates the coating of nascent vesicles via the localized generation of activated ARFs and thus these GEFs are the upstream regulators that define the site and timing of vesicle production. Paradoxically, while we have detailed molecular knowledge of how GEFs activate ARFs, we know very little about how GEFs are recruited and/or activated at the right time and place to initiate transport. This review summarizes the current knowledge of GEF regulation and explores the still uncertain mechanisms that position GEFs at "budding ready" membrane sites to generate highly localized activated ARFs.
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15
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Yorimitsu T, Sato K, Takeuchi M. Molecular mechanisms of Sar/Arf GTPases in vesicular trafficking in yeast and plants. FRONTIERS IN PLANT SCIENCE 2014; 5:411. [PMID: 25191334 PMCID: PMC4140167 DOI: 10.3389/fpls.2014.00411] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/03/2014] [Indexed: 05/21/2023]
Abstract
Small GTPase proteins play essential roles in the regulation of vesicular trafficking systems in eukaryotic cells. Two types of small GTPases, secretion-associated Ras-related protein (Sar) and ADP-ribosylation factor (Arf), act in the biogenesis of transport vesicles. Sar/Arf GTPases function as molecular switches by cycling between active, GTP-bound and inactive, GDP-bound forms, catalyzed by guanine nucleotide exchange factors and GTPase-activating proteins, respectively. Activated Sar/Arf GTPases undergo a conformational change, exposing the N-terminal amphipathic α-helix for insertion into membranes. The process triggers the recruitment and assembly of coat proteins to the membranes, followed by coated vesicle formation and scission. In higher plants, Sar/Arf GTPases also play pivotal roles in maintaining the dynamic identity of organelles in the secretory pathway. Sar1 protein strictly controls anterograde transport from the endoplasmic reticulum (ER) through the recruitment of plant COPII coat components onto membranes. COPII vesicle transport is responsible for the organization of highly conserved polygonal ER networks. In contrast, Arf proteins contribute to the regulation of multiple trafficking routes, including transport through the Golgi complex and endocytic transport. These transport systems have diversified in the plant kingdom independently and exhibit several plant-specific features with respect to Golgi organization, endocytic cycling, cell polarity and cytokinesis. The functional diversification of vesicular trafficking systems ensures the multicellular development of higher plants. This review focuses on the current knowledge of Sar/Arf GTPases, highlighting the molecular details of GTPase regulation in vesicle formation in yeast and advances in knowledge of the characteristics of vesicle trafficking in plants.
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Affiliation(s)
- Tomohiro Yorimitsu
- Department of Life Sciences, Graduate School of Arts and Sciences, University of TokyoTokyo, Japan
| | - Ken Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, University of TokyoTokyo, Japan
| | - Masaki Takeuchi
- Department of Chemistry, Graduate School of Science, University of TokyoTokyo, Japan
- *Correspondence: Masaki Takeuchi, Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan e-mail:
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16
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Padovani D, Zeghouf M, Traverso JA, Giglione C, Cherfils J. High yield production of myristoylated Arf6 small GTPase by recombinant N-myristoyl transferase. Small GTPases 2013; 4:3-8. [PMID: 23319116 DOI: 10.4161/sgtp.22895] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Small GTP-binding proteins of the Arf family (Arf GTPases) interact with multiple cellular partners and with membranes to regulate intracellular traffic and organelle structure. Understanding the underlying molecular mechanisms requires in vitro biochemical assays to test for regulations and functions. Such assays should use proteins in their cellular form, which carry a myristoyl lipid attached in N-terminus. N-myristoylation of recombinant Arf GTPases can be achieved by co-expression in E. coli with a eukaryotic N-myristoyl transferase. However, purifying myristoylated Arf GTPases is difficult and has a poor overall yield. Here we show that human Arf6 can be N-myristoylated in vitro by recombinant N-myristoyl transferases from different eukaryotic species. The catalytic efficiency depended strongly on the guanine nucleotide state and was highest for Arf6-GTP. Large-scale production of highly pure N-myristoylated Arf6 could be achieved, which was fully functional for liposome-binding and EFA6-stimulated nucleotide exchange assays. This establishes in vitro myristoylation as a novel and simple method that could be used to produce other myristoylated Arf and Arf-like GTPases for biochemical assays.
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Affiliation(s)
- Dominique Padovani
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif (CNRS), Gif-sur-Yvette, France
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17
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Someya A, Nagaoka I. Role of ARF-GEP100, a guanine nucleotide-exchange protein for ADP-ribosylation factor in macrophage phagocytosis. Inflamm Regen 2010. [DOI: 10.2492/inflammregen.30.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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18
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Rudnick DA, McWherter CA, Gokel GW, Gordon JI. MyristoylCoA:protein N-myristoyltransferase. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 67:375-430. [PMID: 8322618 DOI: 10.1002/9780470123133.ch5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- D A Rudnick
- Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis, MO
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19
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Wang ZX, Shi L, Liu JF, An XM, Chang WR, Liang DC. 2.0 A crystal structure of human ARL5-GDP3'P, a novel member of the small GTP-binding proteins. Biochem Biophys Res Commun 2005; 332:640-5. [PMID: 15896705 DOI: 10.1016/j.bbrc.2005.04.168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 04/29/2005] [Indexed: 10/25/2022]
Abstract
ARL5 is a member of ARLs, which is widespread in high eukaryotes and homologous between species. But no structure or biological function of this member is reported. We expressed, purified, and resolved the structure of human ARL5 with bound GDP3'P at 2.0 A resolution. A comparison with the known structures of ARFs shows that besides the typical features of ARFs, human ARL5 has specific features of its own. Bacterially expressed human ARL5 contains bound GDP3'P which is seldom seen in other structures. The hydrophobic tail of the introduced detergent Triton X-305 binds at the possible myristoylation site of Gly2, simulating the myristoylated state of N-terminal amphipathic helix in vivo. The structural features of the nucleotide binding motifs and the switch regions prove that ARL5 will undergo the typical GDP/GTP structural cycle as other members of ARLs, which is the basis of their biological functions.
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Affiliation(s)
- Zhan-Xin Wang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, PR China
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20
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Seidel RD, Amor JC, Kahn RA, Prestegard JH. Conformational changes in human Arf1 on nucleotide exchange and deletion of membrane-binding elements. J Biol Chem 2004; 279:48307-18. [PMID: 15308674 DOI: 10.1074/jbc.m402109200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conformational changes associated with nucleotide exchange or truncation of the N-terminal alpha-helix of human Arf1 have been investigated by using forms of easily acquired NMR data, including residual dipolar couplings and amide proton exchange rates. ADP-ribosylation factors (Arfs) are 21-kDa GTPases that regulate aspects of membrane traffic in all eukaryotic cells. An essential component of the biological actions of Arfs is their ability to reversibly bind to membranes, a process that involves exposure of the myristoylated N-terminal amphipathic alpha-helix upon activation and GTP binding. Deletion of this helix results in a protein, termed Delta17Arf1, that has a reduced affinity for GDP and the ability to bind GTP in the absence of lipids or detergents. Previous studies, comparing crystal structures for Arf1.GDP and Delta17Arf1.GTP, identified several regions of structural variation and suggested that these be associated with nucleotide exchange rather than removal of the N-terminal helix. However, separation of conformational changes because of nucleotide binding and N-terminal truncation cannot be addressed in comparing these structures, because both the bound nucleotide and the N terminus differ. Resolving the two effects is important as any structural changes involving the N terminus may represent membrane-mediated conformational adjustments that precede GTP binding. Results from NMR experiments presented here on Arf1.GDP and Delta17Arf1.GDP in solution reveal substantial structural differences that can only be associated with N-terminal truncation.
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Affiliation(s)
- Ronald D Seidel
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712, USA
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21
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Kim SW, Hayashi M, Lo JF, Yang Y, Yoo JS, Lee JD. ADP-ribosylation factor 4 small GTPase mediates epidermal growth factor receptor-dependent phospholipase D2 activation. J Biol Chem 2003; 278:2661-8. [PMID: 12446727 DOI: 10.1074/jbc.m205819200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) plays a critical role in the development, proliferation, and differentiation of cells of epithelial and mesenchymal origin. These EGFR-dependent cellular processes are mediated by a repertoire of intracellular signaling pathways triggered by the activation of the EGFR cytoplasmic domain, which originates from ligand binding of its extracellular domain. To understand the molecular mechanisms by which the intracellular domain of EGFR transmits mitogenic messages to the downstream signaling pathways, we used the cytoplasmic region of EGFR as bait in yeast two-hybrid screening. We found that ADP-ribosylation factor 4 (ARF4) interacts with the intracellular part of EGFR and mediates the EGF-dependent cellular activation of phospholipase D2 (PLD2) but does not mediate the activation of PLD1. In addition, ARF4-mediated PLD2 activation leads to dramatic activation of the transcription factor activator protein 1 (AP-1), and, importantly, ARF4 activity is required for EGF-induced activation of cellular AP-1. Our findings indicate that ARF4 is a critical molecule that directly regulates cellular PLD2 activity and that this ARF4-mediated PLD2 activation stimulates AP-1-dependent transcription in the EGF-induced cellular response.
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Affiliation(s)
- Sung-Woo Kim
- Department of Immunology, The Scripps Research Institute, La Jolla, California 92037, USA
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22
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Van Valkenburgh HA, Kahn RA. Coexpression of proteins with methionine aminopeptidase and/or N-myristoyltransferase in Escherichia coli to increase acylation and homogeneity of protein preparations. Methods Enzymol 2002; 344:186-93. [PMID: 11771383 DOI: 10.1016/s0076-6879(02)44715-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
New plasmid constructs described in this article allow the coexpression in bacteria of any protein with several different NMT proteins, including the recently cloned full-length human NMT1 and 2, and with increased expression of bacterial Met-AP. Through the use of these plasmids in different combinations it should be possible to improve the homogeneity of a large number of recombinant protein preparations by the complete removal of the initiating methionine and increased extent of N-myristoylation. The new reagents described in this article are available upon request.
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23
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Sharer JD, Shern JF, Van Valkenburgh H, Wallace DC, Kahn RA. ARL2 and BART enter mitochondria and bind the adenine nucleotide transporter. Mol Biol Cell 2002; 13:71-83. [PMID: 11809823 PMCID: PMC65073 DOI: 10.1091/mbc.01-05-0245] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The ADP-ribosylation factor-like 2 (ARL2) GTPase and its binding partner binder of ARL2 (BART) are ubiquitously expressed in rodent and human tissues and are most abundant in brain. Both ARL2 and BART are predominantly cytosolic, but a pool of each was found associated with mitochondria in a protease-resistant form. ARL2 was found to lack covalent N-myristoylation, present on all other members of the ARF family, thereby preserving the N-terminal amphipathic alpha-helix as a potential mitochondrial import sequence. An overlay assay was developed to identify binding partners for the BART.ARL2.GTP complex and revealed a specific interaction with a protein in bovine brain mitochondria. Purification and partial microsequencing identified the protein as an adenine nucleotide transporter (ANT). The overlay assay was performed on mitochondria isolated from five different tissues from either wild-type or transgenic mice deleted for ANT1. Results confirmed that ANT1 is the predominant binding partner for the BART.ARL2.GTP complex and that the structurally homologous ANT2 protein does not bind the complex. Cardiac and skeletal muscle mitochondria from ant1(-)/ant1(-) mice had increased levels of ARL2, relative to that seen in mitochondria from wild-type animals. We conclude that the amount of ARL2 in mitochondria is subject to regulation via an ANT1-sensitive pathway in muscle tissues.
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Affiliation(s)
- J Daniel Sharer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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24
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Okamura Y, Takeyama H, Matsunaga T. A magnetosome-specific GTPase from the magnetic bacterium Magnetospirillum magneticum AMB-1. J Biol Chem 2001; 276:48183-8. [PMID: 11557762 DOI: 10.1074/jbc.m106408200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Magnetic bacteria produce intracellular vesicles that envelope single domain magnetite crystals. Although many proteins are present in this intracellular vesicle membrane, five are specific to this membrane. A 16-kDa protein, designated Mms16, is the most abundant of the magnetosome-specific proteins, and to establish its function we cloned and sequenced its gene from Magnetospirillum magneticum AMB-1. This was achieved by determination of the N-terminal amino acid sequence of the protein following two dimensional polyacrylamide gel electrophoresis, and sequencing of the gene was performed by gene walking using anchored polymerase chain reaction. Mms16 contains a putative ATP/GTP binding motif (P-loop). Recombinant Mms16 with a hemagglutinin tag, was expressed in Escherichia coli and purified. Recombinant Mms16 protein could bind GTP and showed GTPase activity. GTP was the preferred substrate for Mms16-catalyzed nucleotide triphosphate hydrolysis. These results suggest that a novel protein specifically localized on the magnetic particle membrane, Mms16, is a GTPase. Mms16 protein showed similar characteristics to small GTPases involved in the formation of intracellular vesicles. Furthermore, addition of the GTPase inhibitor AlF(4)- also inhibited magnetic particle synthesis, suggesting that GTPase is required for magnetic particles synthesis.
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Affiliation(s)
- Y Okamura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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25
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Huang M, Weissman JT, Beraud-Dufour S, Luan P, Wang C, Chen W, Aridor M, Wilson IA, Balch WE. Crystal structure of Sar1-GDP at 1.7 A resolution and the role of the NH2 terminus in ER export. J Cell Biol 2001; 155:937-48. [PMID: 11739406 PMCID: PMC2150902 DOI: 10.1083/jcb.200106039] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2001] [Revised: 10/17/2001] [Accepted: 10/17/2001] [Indexed: 11/22/2022] Open
Abstract
The Sar1 GTPase is an essential component of COPII vesicle coats involved in export of cargo from the ER. We report the 1.7-A structure of Sar1 and find that consistent with the sequence divergence of Sar1 from Arf family GTPases, Sar1 is structurally distinct. In particular, we show that the Sar1 NH2 terminus contains two regions: an NH2-terminal extension containing an evolutionary conserved hydrophobic motif that facilitates membrane recruitment and activation by the mammalian Sec12 guanine nucleotide exchange factor, and an alpha1' amphipathic helix that contributes to interaction with the Sec23/24 complex that is responsible for cargo selection during ER export. We propose that the hydrophobic Sar1 NH2-terminal activation/recruitment motif, in conjunction with the alpha1' helix, mediates the initial steps in COPII coat assembly for export from the ER.
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Affiliation(s)
- M Huang
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92130, USA
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26
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Amor JC, Horton JR, Zhu X, Wang Y, Sullards C, Ringe D, Cheng X, Kahn RA. Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases. J Biol Chem 2001; 276:42477-84. [PMID: 11535602 DOI: 10.1074/jbc.m106660200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structures were determined by x-ray crystallography for two members of the ADP-ribosylation factor (ARF) family of regulatory GTPases, yeast ARF1 and ARL1, and were compared with previously determined structures of human ARF1 and ARF6. These analyses revealed an overall conserved fold but differences in primary sequence and length, particularly in an N-terminal loop, lead to differences in nucleotide and divalent metal binding. Packing of hydrophobic residues is central to the interplay between the N-terminal alpha-helix, switch I, and the interswitch region, which along with differences in surface electrostatics provide explanations for the different biophysical and biochemical properties of ARF and ARF-like proteins.
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Affiliation(s)
- J C Amor
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322-3050, USA
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27
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Kobayashi-Uehara A, Shimosaka E, Handa H. Cloning and expression analyses of cDNA encoding an ADP-ribosylation factor from wheat: tissue-specific expression of wheat ARF. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2001; 160:535-542. [PMID: 11166441 DOI: 10.1016/s0168-9452(00)00416-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We isolated and characterized a cDNA clone encoding a small GTP-binding protein, which has a high similarity to mammalian ADP-ribosylation factor (ARF), from a cDNA library prepared from immature spikes of wheat (Triticum aestivum L.). The cDNA contained an open reading frame that encodes a polypeptide of 181 amino acids with a calculated molecular mass of 20.7 kDa. The deduced amino acid sequence showed a quite high homology to known ARFs from other organisms. In particular, the wheat ARF was completely identical to the rice ARF1. Genomic Southern hybridization suggested that wheat ARF is encoded by at least two or three copies of ARF genes. Northern analyses showed that the accumulation of the ARF transcripts was nearly constant throughout various environmental stresses in both shoots and roots. However the RNA transcript was preferentially expressed in roots rather than in shoots. A similar expression pattern was also observed at the protein level by Western analysis. The relative abundance of the ARF proteins in root and flower tissues may indicate a high level of vesicular transporting activity in the roots and flowers of wheat plants.
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Affiliation(s)
- A Kobayashi-Uehara
- Laboratory of Plant Genecology, Hokkaido National Agricultural Experiment Station, 1, Hitsuji-ga-oka, Toyohira-ku, 062-8555, Sapporo, Japan
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28
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Partoens P, Slembrouck D, De Busser H, Vaughan PF, Van Dessel GA, De Potter WP, Lagrou AR. Neurons, chromaffin cells and membrane fusion. Subcell Biochem 2000; 34:323-78. [PMID: 10808338 DOI: 10.1007/0-306-46824-7_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- P Partoens
- Department of Medicine, UA-Faculty of Medicine and Pharmaceutical Sciences, University of Antwerp, Wilrijk-Antwerp, Belgium
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29
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Zhang C, Yu Y, Zhang S, Liu M, Xing G, Wei H, Bi J, Liu X, Zhou G, Dong C, Hu Z, Zhang Y, Luo L, Wu C, Zhao S, He F. Characterization, chromosomal assignment, and tissue expression of a novel human gene belonging to the ARF GAP family. Genomics 2000; 63:400-8. [PMID: 10704287 DOI: 10.1006/geno.1999.6095] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have identified and characterized a novel human ADP-ribosylation factor GTPase-activating protein (ARFGAP1) gene that is related to other members of the ARF GAP family. The full-length cDNA for human ARFGAP1 was cloned following the identification of an EST obtained by large-scale cDNA library sequencing through a Blast search of public databases. Structurally, ARFGAP1 encodes a polypeptide of 516 amino acids, which contained a typical GATA-1-type zinc finger motif (CXXCX(16)CXXC) with the four cysteine residues that are highly conserved among other members of the ARF GAP family. The conserved ARF GAP domain may emphasize the biological importance of this gene. The ARFGAP1 gene, which contained 16 exons ranging from 0.5 to 9.3 kb, was mapped to human chromosome 22q13.2-q13.3 using radiation hybridization and in silico analyses. ARFGAP1 is strongly expressed in endocrine glands and testis. Interestingly, the expression of ARFGAP1 in testis is about sixfold higher than that in ovary, indicating a possible role of ARFGAP1 in the physiological function of sperm. Expression of ARFGAP1 in four human fetal tissues and seven cancer cell lines was also detected.
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Affiliation(s)
- C Zhang
- Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Chinese National Human Genome Center at Beijing, 27 Taiping Road, Beijing, 100850, People's Republic of China
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30
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DeMar JC, Rundle DR, Wensel TG, Anderson RE. Heterogeneous N-terminal acylation of retinal proteins. Prog Lipid Res 1999; 38:49-90. [PMID: 10396602 DOI: 10.1016/s0163-7827(98)00020-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- J C DeMar
- Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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Hess DT, Smith DS, Patterson SI, Kahn RA, Skene JH, Norden JJ. Rapid arrest of axon elongation by brefeldin A: a role for the small GTP-binding protein ARF in neuronal growth cones. JOURNAL OF NEUROBIOLOGY 1999; 38:105-15. [PMID: 10027566 DOI: 10.1002/(sici)1097-4695(199901)38:1<105::aid-neu8>3.0.co;2-m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Members of the ADP-ribosylation factor (ARF) family of small guanosine triphosphate-binding proteins play an essential role in membrane trafficking which subserves constitutive protein transport along exocytic and endocytic pathways within eukaryotic cell bodies. In growing neurons, membrane trafficking within motile growth cones distant from the cell body underlies the rapid plasmalemmal expansion which subserves axon elongation. We report here that ARF is a constituent of axonal growth cones, and that application of brefeldin A to neurons in culture produces a rapid arrest of axon extension that can be ascribed to inhibition of ARF function in growth cones. Our findings demonstrate a role for ARF in growth cones that is coupled tightly to the rapid growth of neuronal processes characteristic of developmental and regenerative axon elongation, and indicate that ARF participates not only in constitutive membrane traffic within the cell body, but also in membrane dynamics within growing axon endings.
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Affiliation(s)
- D T Hess
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina 27710, USA
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32
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Monier S, Chardin P, Robineau S, Goud B. Overexpression of the ARF1 exchange factor ARNO inhibits the early secretory pathway and causes the disassembly of the Golgi complex. J Cell Sci 1998; 111 ( Pt 22):3427-36. [PMID: 9788883 DOI: 10.1242/jcs.111.22.3427] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The small GTPase ARF1 is a key regulator of intracellular membrane traffic. In its active, GTP-bound form, ARF1 is associated with Golgi membranes and promotes the recruitment of the cytosolic coat protein complex, which will result in membrane budding and vesicle formation. ARNO (ARF nucleotide site opener) has been shown to act in vitro as a GTP exchange factor for ARF1. Here, we have investigated the function of ARNO in vivo. By immunofluorescence and cell fractionation, ARNO was found to be mostly cytosolic in HeLa cells. Its overexpression led to a strong inhibition of the secretion of SEAP (secreted form of alkaline phosphatase). Newly synthesized SEAP failed to acquire endoglycosidase H resistance, indicating a block in the early secretory pathway. This effect on secretion was accompanied by a disassembly of the Golgi complex and a redistribution of Golgi resident proteins into the endoplasmic reticulum (ER). On the other hand, ARNO overexpression did not affect the early endocytic pathway. These results show that ARNO functions in vivo in Golgi to ER transport. Its behavior is then consistent with ARNO being an exchange factor for ARF1.
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Affiliation(s)
- S Monier
- Institut Curie, CNRS UMR 144, 75248 Paris Cedex 5, France.
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33
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Sturm NR, Van Valkenburgh H, Kahn RA, Campbell DA. Characterization of a GTP-binding protein in the ADP-ribosylation factor subfamily from Leishmania tarentolae. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1442:347-52. [PMID: 9804987 DOI: 10.1016/s0167-4781(98)00150-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We report the cloning and characterization of a gene, LtARL, which encodes a small GTP-binding protein, from the protozoan Leishmania tarentolae. Hybridization analysis of genomic DNA under high stringency conditions indicates the single-copy nature of LtARL. LtARL is transcribed and yields a approximately 0.9 kb mRNA that is processed at the 5' end by trans-splicing. When expressed in Escherichia coli, LtArl binds GTP with a low stoichiometry and in a phospholipid-independent manner. Based on the greatest sequence identity with Homo sapiens Arl3 and lipid-independent binding of guanine nucleotides we designate this gene LtARL and the encoded protein LtArl.
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Affiliation(s)
- N R Sturm
- Department of Microbiology and Immunology, UCLA School of Medicine, 10833 Le Conte Avenue, Los Angeles, CA 90095-1747, USA
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34
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Aunis D. Exocytosis in chromaffin cells of the adrenal medulla. INTERNATIONAL REVIEW OF CYTOLOGY 1998; 181:213-320. [PMID: 9522458 DOI: 10.1016/s0074-7696(08)60419-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The chromaffin cell has been used as a model to characterize releasable components present in secretory granules and to understand the cellular mechanisms involved in catecholamine release. Recent physiological and biochemical developments have revealed that molecular mechanisms implicated in granule trafficking are conserved in all eukaryotic species: a rise in intracellular calcium triggers regulated exocytosis, and highly conserved proteins are essential elements which interact with each other to form a molecular scaffolding, ensuring the docking of granules at the plasma membrane, and perhaps membrane fusion. However, the mechanisms regulating secretion are multiple and cell specific. They operate at different steps along the life of a granule, from the time of granule biosynthesis up to the last step of exocytosis. With regard to cell specificity, noradrenaline and adrenaline chromaffin cells display different receptor and signaling characteristics that may be important to exocytosis. Characterization of regulated exocytosis in chromaffin cells provides not only fundamental knowledge of neurosecretion but is of additional importance as these cells are used for therapeutic purposes.
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Affiliation(s)
- D Aunis
- Biologie de la Communication Cellulaire, Unité INSERM U-338, Strasbourg, France
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35
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Lee FJ, Huang CF, Yu WL, Buu LM, Lin CY, Huang MC, Moss J, Vaughan M. Characterization of an ADP-ribosylation factor-like 1 protein in Saccharomyces cerevisiae. J Biol Chem 1997; 272:30998-1005. [PMID: 9388248 DOI: 10.1074/jbc.272.49.30998] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
ADP-ribosylation factors (ARFs) are highly conserved approximately 20-kDa guanine nucleotide-binding proteins that enhance the ADP-ribosyltransferase activity of cholera toxin and are believed to participate in vesicular transport in both exocytic and endocytic pathways. Several ARF-like proteins (ARLs) have been cloned from Drosophila, rat, and human; however, the biological functions of ARLs are unknown. We have identified a yeast gene (ARL1) encoding a protein that is structurally related (>60% identical) to human, rat, and Drosophila ARL1. Biochemical analyses of purified recombinant yeast ARL1 (yARL1) protein revealed properties similar to those ARF and ARL1 proteins, including the ability to bind and hydrolyze GTP. Like other ARLs, recombinant yARL1 protein did not stimulate cholera toxin-catalyzed auto-ADP-ribosylation. yARL1 was not recognized by antibodies against mammalian ARLs or yeast ARFs. Anti-yARL1 antibodies did not cross-react with yeast ARFs, but did react with human ARLs. On subcellular fractionation, yARL1, similar to yARF1, was localized to the soluble fraction. The amino terminus of yARL1, like that of ARF, was myristoylated. Unlike Drosophila Arl1, yeast ARL1 was not essential for cell viability. Like rat ARL1, yARL1 might be associated in part with the Golgi complex. However, yARL1 was not required for endoplasmic reticulum-to-Golgi protein transport, and it may offer an opportunity to define an ARL function in another kind of vesicular trafficking, such as the regulated secretory pathway.
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Affiliation(s)
- F J Lee
- Institute of Molecular Medicine, School of Medicine, National Taiwan University, Taipei, Taiwan, Republic of China.
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36
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Faúndez V, Horng JT, Kelly RB. ADP ribosylation factor 1 is required for synaptic vesicle budding in PC12 cells. J Cell Biol 1997; 138:505-15. [PMID: 9245782 PMCID: PMC2141633 DOI: 10.1083/jcb.138.3.505] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/1997] [Revised: 06/11/1997] [Indexed: 02/04/2023] Open
Abstract
Carrier vesicle generation from donor membranes typically progresses through a GTP-dependent recruitment of coats to membranes. Here we explore the role of ADP ribosylation factor (ARF) 1, one of the GTP-binding proteins that recruit coats, in the production of neuroendocrine synaptic vesicles (SVs) from PC12 cell membranes. Brefeldin A (BFA) strongly and reversibly inhibited SV formation in vivo in three different PC12 cell lines expressing vesicle-associated membrane protein-T Antigen derivatives. Other membrane traffic events remained unaffected by the drug, and the BFA effects were not mimicked by drugs known to interfere with formation of other classes of vesicles. The involvement of ARF proteins in the budding of SVs was addressed in a cell-free reconstitution system (Desnos, C., L. Clift-O'Grady, and R.B. Kelly. 1995. J. Cell Biol. 130:1041-1049). A peptide spanning the effector domain of human ARF1 (2-17) and recombinant ARF1 mutated in its GTPase activity, both inhibited the formation of SVs of the correct size. During in vitro incubation in the presence of the mutant ARFs, the labeled precursor membranes acquired different densities, suggesting that the two ARF mutations block at different biosynthetic steps. Cell-free SV formation in the presence of a high molecular weight, ARF-depleted fraction from brain cytosol was significantly enhanced by the addition of recombinant myristoylated native ARF1. Thus, the generation of SVs from PC12 cell membranes requires ARF and uses its GTPase activity, probably to regulate coating phenomena.
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Affiliation(s)
- V Faúndez
- Department of Biochemistry and Biophysics, The Hormone Research Institute, University of California, San Francisco, California 94143-0534, USA
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37
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Kanoh H, Williger BT, Exton JH. Arfaptin 1, a putative cytosolic target protein of ADP-ribosylation factor, is recruited to Golgi membranes. J Biol Chem 1997; 272:5421-9. [PMID: 9038142 DOI: 10.1074/jbc.272.9.5421] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
ADP-ribosylation factors (ARFs) have been implicated in vesicle transport in the Golgi complex. Employing yeast two-hybrid screening of an HL60 cDNA library using a constitutively active mutant of ARF3 (ARF3.Q71L), as a probe, we have identified a cDNA encoding a novel protein with a calculated molecular mass of 38.6 kDa, which we have named arfaptin 1. The mRNA of arfaptin 1 was ubiquitously expressed, and recombinant arfaptin 1 bound preferentially to class I ARFs, especially ARF1, but only in the GTP-bound form. The interactions were independent of myristoylation of ARF. Arfaptin 1 in cytosol was recruited to Golgi membranes by ARF in a guanosine 5'-O-(3-thiotriphosphate)-dependent and brefeldin A-sensitive manner. When expressed in COS cells, arfaptin 1 was localized to the Golgi complex. The yeast two-hybrid system yielded another clone, which encoded a putative protein, which we have named arfaptin 2. This consisted of the same number of amino acids as arfaptin 1 and was 60% identical to it. Arfaptin 2 was also ubiquitously expressed and bound to the GTP-, but not GDP-liganded form of class I ARFs, especially ARF1. These results suggest that arfaptins 1 and 2 may be direct target proteins of class 1 ARFs. Arfaptin 1 may be involved in Golgi function along with ARF1.
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Affiliation(s)
- H Kanoh
- Howard Hughes Medical Institute and the Department of Molecular Physiology and Biophysics and Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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38
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Galas MC, Helms JB, Vitale N, Thiersé D, Aunis D, Bader MF. Regulated exocytosis in chromaffin cells. A potential role for a secretory granule-associated ARF6 protein. J Biol Chem 1997; 272:2788-93. [PMID: 9006918 DOI: 10.1074/jbc.272.5.2788] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The ADP-ribosylation factor (ARF) GTP-binding proteins are believed to function as regulators of vesicular budding and fusion along the secretory pathway. To investigate the role of ARF in regulated exocytosis, we have examined its intracellular distribution in cultured chromaffin cells by subcellular fractionation and immunoreplica analysis. We found that ARF6 is specifically associated with the membrane of purified secretory chromaffin granules. Chemical cross-linking and immunoprecipitation experiments suggested that ARF6 may be part of a complex with betagamma subunits of trimeric G proteins. Stimulation of intact chromaffin cells or direct elevation of cytosolic calcium in permeabilized cells triggered the rapid dissociation of ARF6 from secretory granules. This effect could be inhibited by AlF4- which selectively activates trimeric G proteins. Furthermore, a synthetic myristoylated peptide corresponding to the N-terminal domain of ARF6 strongly inhibited calcium-evoked secretion in streptolysin-O-permeabilized chromaffin cells. The possibility that ARF6 plays a role in the effector pathway by which trimeric G proteins control exocytosis in chromaffin cells is discussed.
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Affiliation(s)
- M C Galas
- Institut National de la Santé et de la Recherche Médicale, U-338 Biologie de la Communication Cellulaire, 5 rue Blaise Pascal, 67084 Strasbourg Cedex, France
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39
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Stafford WH, Stockley RW, Ludbrook SB, Holder AA. Isolation, expression and characterization of the gene for an ADP-ribosylation factor from the human malaria parasite, Plasmodium falciparum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:104-13. [PMID: 8954160 DOI: 10.1111/j.1432-1033.1996.0104r.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have isolated an ADP-ribosylation factor (ARF) gene from the human malarial parasite, Plasmodium falciparum. The gene (P. falciparum arf1) has four introns and the exons encode a protein of 181 amino acids with high similarity to the mammalian class I ARF proteins 1-3 (> or = 74% amino acid identity). Southern hybridization suggests there is at least one additional arf in the P. falciparum genome. Northern analysis identified a single P. falciparum arf1 mRNA of 1.8 kb in the asexual blood stage form of the parasite. The P. falciparum arf1 mRNA levels are developmentally regulated, reaching a maximum during nuclear division towards the end of the intraerythrocytic cycle. P. falciparum arf1 cDNA was isolated by reverse-transcriptase polymerase chain reaction and used to express a recombinant protein in Escherichia coli. Recombinant P. falciparum ARF1 protein was purified with stoichiometric amounts of bound GDP, although intrinsic guanose triphosphatase activity of the protein could not be detected. The protein stimulated cholera-toxin-catalyzed ADP-ribosyltransferase activity in a reaction that was dependent upon the addition of both dimyristoylglycerophosphocholine and cholate. The protein bound GTP with first-order kinetics with an apparent rate constant, k', of 0.0145 (+/- 0.0019) min-1. These results suggest that P. falciparum ARF1 is a member of the class 1 ARF family and provide additional evidence for the existence of a classical secretory pathway in P. falciparum.
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Affiliation(s)
- W H Stafford
- Division of Parasitology, National Institute for Medical Research, Mill Hill, London, UK
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40
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Cavenagh MM, Whitney JA, Carroll K, Zhang CJ, Boman AL, Rosenwald AG, Mellman I, Kahn RA. Intracellular distribution of Arf proteins in mammalian cells. Arf6 is uniquely localized to the plasma membrane. J Biol Chem 1996; 271:21767-74. [PMID: 8702973 DOI: 10.1074/jbc.271.36.21767] [Citation(s) in RCA: 195] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Subcellular distributions of the five human Arf proteins were examined, using a set of isoform-specific polyclonal and a pan-Arf monoclonal antibodies. Subcellular fractionation of cultured mammalian cells allowed the demonstration that Arf6 is uniquely localized to the plasma membranes of Chinese hamster ovary cells. The plasma membrane distrubution was unaffected by either GTPgammaS (guanosine 5'-O-(3-thio)triphosphate) or brefeldin A, an activator and inhibitor of Arf activities, respectively. In contrast, Arf proteins 1, 3, 4, and 5 were predominantly cytosolic but could be recruited to a variety of intracellular membranes, but not plasma membranes, upon incubation in the presence of GTPgammaS. The GTPgammaS-promoted binding of the cytosolic Arf proteins to membranes was blocked by brefeldin A. The stable association of Arf6 with plasma membranes and the insensitivity of its localization to either GTPgammaS or brefeldin A revealed a clear distinction between Arf6 and the other Arf isoforms. Localization of Arf6 to the plasma membrane suggests a unique cellular role for this isoform at the plasma membrane, but failure to find endogenous Arf6 on endocytic structures, including clathrin-coated vesicles, appears inconsistent with the proposed role of Arf6 in assembly of coat structures or endosomes in transfected fibroblasts (1,2).
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Affiliation(s)
- M M Cavenagh
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322-3050, USA
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41
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Harter C, Wieland F. The secretory pathway: mechanisms of protein sorting and transport. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1286:75-93. [PMID: 8652612 DOI: 10.1016/0304-4157(96)00003-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- C Harter
- Institut für Biochemie I, Universität Heidelberg, Germany
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42
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Abstract
A general protein machinery that buds and fuses transport vesicles is harnessed to generate the complex web of intracellular transport pathways critical for such diverse processes as cell growth, endocytosis, hormone release, and neurotransmission. With this appreciation, the challenge of understanding the precise molecular mechanisms of these many facets of cell biology has been reduced to a series of problems in protein structure and chemistry.
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Affiliation(s)
- J E Rothman
- Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
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43
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Memon AR, Hwang S, Deshpande N, Thompson GA, Herrin DL. Novel aspects of the regulation of a cDNA (Arf1) from Chlamydomonas with high sequence identity to animal ADP-ribosylation factor 1. PLANT MOLECULAR BIOLOGY 1995; 29:567-577. [PMID: 8534853 DOI: 10.1007/bf00020985] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
ADP-ribosylation factor (ARF) is a highly conserved, low molecular mass (ca. 21 kDa) GTP-binding protein that has been implicated in vesicle trafficking and signal transduction in yeast and mammalian cells. However, little is known of ARF in plant systems. A putative ARF polypeptide was identified in subcellular fractions of the green alga Chlamydomonas reinhardtii, based on [32P]GTP binding and immunoblot assays. A cDNA clone was isolated from Chlamydomonas (Arf1), which encodes a 20.7 kDa protein with 90% identity to human ARF1. Northern blot analyses showed that levels of Arf1 mRNA are highly regulated during 12 h/12 h light/dark (LD) cycles. A biphasic pattern of expression was observed: a transient peak of Arf1 mRNA occurred at the onset of the light period, which was followed ca. 12 h later by a more prominent peak in the early to mid-dark period. When LD-synchronized cells were shifted to continuous darkness, the dark-specific peak of Arf1 mRNA persisted, indicative of a circadian rhythm. The increase in Arf1 mRNA at the beginning of the light period, however, was shown to be light-dependent, and, moreover, dependent on photosynthesis, since it was prevented by DCMU. We conclude that the biphasic pattern of Arf1 mRNA accumulation during LD cycles is due to regulation by two different factors, light (which requires photosynthesis) and the circadian clock. Thus, these studies identify a novel pattern of expression for a GTP-binding protein gene.
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Affiliation(s)
- A R Memon
- Department of Botany, University of Texas, Austin 78713-7640
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44
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Abstract
COP-coated vesicles have originally been implicated in vesicular transport between subcompartments of the Golgi complex in mammals in a cis to trans direction. More recently, a role for COP-coated vesicles in transport between the endoplasmic reticulum (ER) and Golgi in mammalian cells has been proposed. Under certain conditions COP-coats have been localized to special domains of the transitional ER and to the cis side of the Golgi complex. This led to the assumption that COP-coated vesicles are involved in export of proteins from the ER. In addition, new findings point to a function of COP-coated vesicles in back transport of proteins from the Golgi to the ER. At present it is not known whether COP-coated vesicles move only in one or in both directions between ER and Golgi.
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Affiliation(s)
- C Harter
- Institut für Biochemie I, Universität Heidelberg, Germany
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45
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Randazzo PA, Terui T, Sturch S, Fales HM, Ferrige AG, Kahn RA. The myristoylated amino terminus of ADP-ribosylation factor 1 is a phospholipid- and GTP-sensitive switch. J Biol Chem 1995; 270:14809-15. [PMID: 7782347 DOI: 10.1074/jbc.270.24.14809] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
ADP-ribosylation factor 1 (Arf1) is an essential N-myristoylated 21-kDa GTP-binding protein with activities that include the regulation of membrane traffic and phospholipase D activity. Both the N terminus of the protein and the N-myristate bound to glycine 2 have previously been shown to be essential to the function of Arf in cells. We show that the bound nucleotide affects the conformation of either the N terminus or residues of Arf1 that are in direct contact with the N terminus. This was demonstrated by examining the effects of mutations in this N-terminal domain on guanosine 5'-O-(3-thio)triphosphate (GTP gamma S) and GDP binding and dissociation kinetics. Arf1 mutants, lacking 13 or 17 residues from the N terminus or mutated at residues 3-7, had a greater affinity for GTP gamma S and a lower affinity for GDP than did the wild-type protein. As the N terminus is required for interactions with target proteins, we conclude that the N terminus of Arf1 is a GTP-sensitive effector domain. When Arf1 was acylated, the GTP-dependent conformational changes were codependent on added phospholipids. In the absence of phospholipids, myristoylated Arf1 has a lower affinity for GTP gamma S than for GDP, and in the presence of phospholipids, the myristoylated protein has a greater affinity for GTP gamma S than for GDP. Thus, N-myristoylation is a critical component in the construction of this phospholipid- and GTP-dependent switch.
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Affiliation(s)
- P A Randazzo
- Laboratory of Biological Chemistry, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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46
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Makler V, Cukierman E, Rotman M, Admon A, Cassel D. ADP-ribosylation factor-directed GTPase-activating protein. Purification and partial characterization. J Biol Chem 1995; 270:5232-7. [PMID: 7890632 DOI: 10.1074/jbc.270.10.5232] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The small GTP-binding protein ARF plays an established role in the control of vesicular traffic and in the regulation of phospholipase D activity. Like other GTP binding proteins, ARF becomes activated upon the binding of GTP, whereas GTP hydrolysis acts as a turn-off signal. The fact that purified ARF proteins have negligible GTPase activity has suggested that GTP hydrolysis by ARFs is dependent on a GTPase-activating protein (GAP). Here we report the complete purification of an ARF GAP from rat liver cytosol. Advanced stages in the purification were carried out in the presence of denaturing agents, making use of an unusual conformational stability, or refolding capacity, of the GAP. The GAP was purified about 15,000-fold and was identified as a protein of 49 kDa. Partial amino acid sequence analysis showed that the GAP is a previously uncharacterized protein. Both crude and purified GAP migrated on a Superdex 200 column as a 200-kDa complex, suggesting a tetrameric structure. The purified ARF GAP was stimulated by phosphoinositides and was inhibited by phosphatidylcholine, similar to the results previously reported for a preparation from brain (Randazzo, P. A., and Kahn, R. A. (1994) J. Biol. Chem. 269, 10758). The availability of the ARF GAP molecule will advance the understanding of the regulation of the cellular processes in which ARF proteins participate.
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Affiliation(s)
- V Makler
- Department of Biology, Technion-Israel Institute of Technology, Haifa
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47
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Affiliation(s)
- P A Randazzo
- Laboratory of Biological Chemistry, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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48
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Affiliation(s)
- H A Brown
- Department of Pharmacology, Southwestern Medical Center, University of Texas, Dallas 75235, USA
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49
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Amor JC, Harrison DH, Kahn RA, Ringe D. Structure of the human ADP-ribosylation factor 1 complexed with GDP. Nature 1994; 372:704-8. [PMID: 7990966 DOI: 10.1038/372704a0] [Citation(s) in RCA: 232] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
ADP-ribosylation factors (ARFs) are essential and ubiquitous in eukaryotes, being involved in vesicular transport and functioning as an activator of phospholipase D (refs 1, 2) and cholera toxin. The functions of ARF proteins in membrane traffic and organelle integrity are intimately tied to its reversible association with membranes and specific interactions with membrane phospholipids. One common feature of these functions is their regulation by the binding and hydrolysis of GTP. Here we report the three-dimensional structure of full-length human ARF1 (M(r) 21,000) in its GDP-bound non-myristoylated form. The presence of a unique amino-terminal alpha-helix and loop, together with differences in Mg2+ ligation and the existence of a non-crystallographic dimer, set this structure apart from other GTP-binding proteins. These features provide a structural basis for the GTP-dependent modulation of membrane affinity, the lack of intrinsic GTPase activity, and the nature of effector binding surfaces.
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Affiliation(s)
- J C Amor
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254
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50
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Ma H. GTP-binding proteins in plants: new members of an old family. PLANT MOLECULAR BIOLOGY 1994; 26:1611-1636. [PMID: 7858207 DOI: 10.1007/bf00016493] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Regulatory guanine nucleotide-binding proteins (G proteins) have been studied extensively in animal and microbial organisms, and they are divided into the heterotrimeric and the small (monomeric) classes. Heterotrimeric G proteins are known to mediate signal responses in a variety of pathways in animals and simple eukaryotes, while small G proteins perform diverse functions including signal transduction, secretion, and regulation of cytoskeleton. In recent years, biochemical analyses have produced a large amount of information on the presence and possible functions of G proteins in plants. Further, molecular cloning has clearly demonstrated that plants have both heterotrimeric and small G proteins. Although the functions of the plant heterotrimeric G proteins are yet to be determined, expression analysis of an Arabidopsis G alpha protein suggests that it may be involved in the regulation of cell division and differentiation. In contrast to the very few genes cloned thus far that encode heterotrimeric G proteins in plants, a large number of small G proteins have been identified by molecular cloning from various plants. In addition, several plant small G proteins have been shown to be functional homologues of their counterparts in animals and yeasts. Future studies using a number of approaches are likely to yield insights into the role plant G proteins play.
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Affiliation(s)
- H Ma
- Cold Spring Harbor Laboratory, NY 11724
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