1
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Taylor RJ, Tagiltsev G, Briggs JAG. The structure of COPI vesicles and regulation of vesicle turnover. FEBS Lett 2023; 597:819-835. [PMID: 36513395 DOI: 10.1002/1873-3468.14560] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
COPI-coated vesicles mediate transport between Golgi stacks and retrograde transport from the Golgi to the endoplasmic reticulum. The COPI coat exists as a stable heptameric complex in the cytosol termed coatomer and is recruited en bloc to the membrane for vesicle formation. Recruitment of COPI onto membranes is mediated by the Arf family of small GTPases, which, in their GTP-bound state, bind both membrane and coatomer. Arf GTPases also influence cargo selection, vesicle scission and vesicle uncoating. Guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) regulate nucleotide binding by Arf GTPases. To understand the mechanism of COPI-coated vesicle trafficking, it is necessary to characterize the interplay between coatomer and Arf GTPases and their effectors. It is also necessary to understand interactions between coatomer and cargo, cargo adaptors/receptors and tethers facilitating binding to the target membrane. Here, we summarize current knowledge of COPI coat protein structure; we describe how structural and biochemical studies contributed to this knowledge; we review mechanistic insights into COPI vesicle biogenesis and disassembly; and we discuss the potential to answer open questions in the field.
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Affiliation(s)
- Rebecca J Taylor
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Grigory Tagiltsev
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - John A G Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
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2
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Mysore VP, Zhou ZW, Ambrogio C, Li L, Kapp JN, Lu C, Wang Q, Tucker MR, Okoro JJ, Nagy-Davidescu G, Bai X, Plückthun A, Jänne PA, Westover KD, Shan Y, Shaw DE. A structural model of a Ras-Raf signalosome. Nat Struct Mol Biol 2021; 28:847-857. [PMID: 34625747 PMCID: PMC8643099 DOI: 10.1038/s41594-021-00667-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/25/2021] [Indexed: 01/29/2023]
Abstract
The protein K-Ras functions as a molecular switch in signaling pathways regulating cell growth. In the human mitogen-activated protein kinase (MAPK) pathway, which is implicated in many cancers, multiple K-Ras proteins are thought to assemble at the cell membrane with Ras effector proteins from the Raf family. Here we propose an atomistic structural model for such an assembly. Our starting point was an asymmetric guanosine triphosphate-mediated K-Ras dimer model, which we generated using unbiased molecular dynamics simulations and verified with mutagenesis experiments. Adding further K-Ras monomers in a head-to-tail fashion led to a compact helical assembly, a model we validated using electron microscopy and cell-based experiments. This assembly stabilizes K-Ras in its active state and presents composite interfaces to facilitate Raf binding. Guided by existing experimental data, we then positioned C-Raf, the downstream kinase MEK1 and accessory proteins (Galectin-3 and 14-3-3σ) on and around the helical assembly. The resulting Ras-Raf signalosome model offers an explanation for a large body of data on MAPK signaling.
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Affiliation(s)
| | - Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin, Italy
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonas N Kapp
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Chunya Lu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi Wang
- D. E. Shaw Research, New York, NY, USA
| | | | - Jeffrey J Okoro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Xiaochen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - David E Shaw
- D. E. Shaw Research, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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3
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Nano PR, Johnson TK, Kudo T, Mooney NA, Ni J, Demeter J, Jackson PK, Chen JK. Structure-activity mapping of ARHGAP36 reveals regulatory roles for its GAP homology and C-terminal domains. PLoS One 2021; 16:e0251684. [PMID: 33999959 PMCID: PMC8128262 DOI: 10.1371/journal.pone.0251684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/01/2021] [Indexed: 11/24/2022] Open
Abstract
ARHGAP36 is an atypical Rho GTPase-activating protein (GAP) family member that drives both spinal cord development and tumorigenesis, acting in part through an N-terminal motif that suppresses protein kinase A and activates Gli transcription factors. ARHGAP36 also contains isoform-specific N-terminal sequences, a central GAP-like module, and a unique C-terminal domain, and the functions of these regions remain unknown. Here we have mapped the ARHGAP36 structure-activity landscape using a deep sequencing-based mutagenesis screen and truncation mutant analyses. Using this approach, we have discovered several residues in the GAP homology domain that are essential for Gli activation and a role for the C-terminal domain in counteracting an N-terminal autoinhibitory motif that is present in certain ARHGAP36 isoforms. In addition, each of these sites modulates ARHGAP36 recruitment to the plasma membrane or primary cilium. Through comparative proteomics, we also have identified proteins that preferentially interact with active ARHGAP36, and we demonstrate that one binding partner, prolyl oligopeptidase-like protein, is a novel ARHGAP36 antagonist. Our work reveals multiple modes of ARHGAP36 regulation and establishes an experimental framework that can be applied towards other signaling proteins.
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Affiliation(s)
- Patricia R. Nano
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Taylor K. Johnson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nancie A. Mooney
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jun Ni
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Janos Demeter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter K. Jackson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - James K. Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- * E-mail:
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4
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Wang J, Li L, Ming Z, Wu L, Yan L. Crystal Structure of the Epo1-Bem3 Complex for Bud Growth. Int J Mol Sci 2021; 22:ijms22083812. [PMID: 33917059 PMCID: PMC8067709 DOI: 10.3390/ijms22083812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 02/05/2023] Open
Abstract
Tubules of the endoplasmic reticulum (ER) spread into the buds of yeast by an actin-based mechanism and, upon entry, become attached to the polarisome, a proteinaceous micro-compartment below the tip of the bud. The minimal tether between polarisome and cortical ER is formed by a protein complex consisting of Epo1, a member of the polarisome, Scs2, a membrane protein of the ER and Cdc42 guanosine triphosphatase-activating protein Bem3. Here, we report the crystal structure of a complex between Epo1 and Bem3. In addition, we characterize through the hydrogen/deuterium (H/D) exchange assay the interface between Scs2 and Epo1. Our findings provide a first structural insight into the molecular architecture of the link between cortical ER and the polarisome.
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Affiliation(s)
- Jin Wang
- State Key Laboratory of Biotherapy, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu 610041, China; (J.W.); (L.L.)
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lei Li
- State Key Laboratory of Biotherapy, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu 610041, China; (J.W.); (L.L.)
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530000, China;
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China;
| | - Liming Yan
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China
- Correspondence:
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5
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Cheng N, Zhang H, Zhang S, Ma X, Meng G. Crystal structure of the GTP-binding protein-like domain of AGAP1. Acta Crystallogr F Struct Biol Commun 2021; 77:105-112. [PMID: 33830075 PMCID: PMC8034428 DOI: 10.1107/s2053230x21003150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 11/10/2022] Open
Abstract
AGAP1 is often considered to regulate membrane trafficking, protein transport and actin cytoskeleton dynamics. Recent studies have shown that aberrant expression of AGAP1 is associated with many diseases, including neurodevelopmental disorders and acute lymphoblastic leukemia. It has been proposed that the GTP-binding protein-like domain (GLD) is involved in the binding of cofactors and thus regulates the catalytic activity of AGAP1. To obtain a better understanding of the pathogenic mechanism underpinning AGAP1-related diseases, it is essential to obtain structural information. Here, the GLD (residues 70-235) of AGAP1 was overexpressed in Escherichia coli BL21 (DE3) cells. Affinity and gel-filtration chromatography were used to obtain AGAP1GLD with high purity for crystallization. Using the hanging-drop vapor-diffusion method with the protein at a final concentration of 20 mg ml-1, AGAP1GLD protein crystals of suitable size were obtained. The crystals were found to diffract to 3.0 Å resolution and belonged to space group I4, with unit-cell parameters a = 100.39, b = 100.39, c = 48.08 Å. The structure of AGAP1GLD exhibits the highly conserved functional G1-G5 loops and is generally similar to other characterized ADP-ribosylation factor (Arf) GTPase-activating proteins (GAPs), implying an analogous function to Arf GAPs. Additionally, this study indicates that AGAP1 could be classified as a type of NTPase, the activity of which might be regulated by protein partners or by its other domains. Taken together, these results provide insight into the regulatory mechanisms of AGAP1 in cell signaling.
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Affiliation(s)
- Nuo Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai 200025, People’s Republic of China
| | - Hao Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai 200025, People’s Republic of China
| | - Shiyan Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai 200025, People’s Republic of China
| | - Xiaodan Ma
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai 200025, People’s Republic of China
| | - Guoyu Meng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai 200025, People’s Republic of China
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6
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Hurd CA, Brear P, Revell J, Ross S, Mott HR, Owen D. Affinity maturation of the RLIP76 Ral binding domain to inform the design of stapled peptides targeting the Ral GTPases. J Biol Chem 2021; 296:100101. [PMID: 33214225 PMCID: PMC7949049 DOI: 10.1074/jbc.ra120.015735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/10/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Ral GTPases have been implicated as critical drivers of cell growth and metastasis in numerous Ras-driven cancers. We have previously reported stapled peptides, based on the Ral effector RLIP76, that can disrupt Ral signaling. Stapled peptides are short peptides that are locked into their bioactive form using a synthetic brace. Here, using an affinity maturation of the RLIP76 Ral-binding domain, we identified several sequence substitutions that together improve binding to Ral proteins by more than 20-fold. Hits from the selection were rigorously analyzed to determine the contributions of individual residues and two 1.5 Å cocrystal structures of the tightest-binding mutants in complex with RalB revealed key interactions. Insights gained from this maturation were used to design second-generation stapled peptides based on RLIP76 that exhibited vastly improved selectivity for Ral GTPases when compared with the first-generation lead peptide. The binding of second-generation peptides to Ral proteins was quantified and the binding site of the lead peptide on RalB was determined by NMR. Stapled peptides successfully competed with multiple Ral-effector interactions in cellular lysates. Our findings demonstrate how manipulation of a native binding partner can assist in the rational design of stapled peptide inhibitors targeting a protein-protein interaction.
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Affiliation(s)
- Catherine A Hurd
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jefferson Revell
- AstraZeneca, Sir Aaron Klug Building, Granta Park, Cambridge, UK
| | - Sarah Ross
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Helen R Mott
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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7
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Xie B, Jung C, Chandra M, Engel A, Kendall AK, Jackson LP. The Glo3 GAP crystal structure supports the molecular niche model for ArfGAPs in COPI coats. Adv Biol Regul 2021; 79:100781. [PMID: 33436318 PMCID: PMC7920988 DOI: 10.1016/j.jbior.2020.100781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 11/27/2022]
Abstract
Arf GTPase activating (ArfGAP) proteins are critical regulatory and effector proteins in membrane trafficking pathways. Budding yeast contain two ArfGAP proteins (Gcs1 and Glo3) implicated in COPI coat function at the Golgi, and yeast require Glo3 catalytic function for viability. A new X-ray crystal structure of the Glo3 GAP domain was determined at 2.1 Å resolution using molecular replacement methods. The structure reveals a Cys4-family zinc finger motif with an invariant residue (R59) positioned to act as an "arginine finger" during catalysis. Comparisons among eukaryotic GAP domains show a key difference between ArfGAP1 and ArfGAP2/3 family members in the final helix located within the domain. Conservation at both the sequence and structural levels suggest the Glo3 GAP domain interacts with yeast Arf1 switch I and II regions to promote catalysis. Together, the structural data presented here provide additional evidence for placing Glo3 near Arf1 triads within membrane-assembled COPI coats and further support the molecular niche model for COPI coat regulation by ArfGAPs.
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Affiliation(s)
- Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Christian Jung
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Andrew Engel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Amy K Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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8
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Crawley-Snowdon H, Yang JC, Zaccai NR, Davis LJ, Wartosch L, Herman EK, Bright NA, Swarbrick JS, Collins BM, Jackson LP, Seaman MNJ, Luzio JP, Dacks JB, Neuhaus D, Owen DJ. Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29. Nat Commun 2020; 11:5031. [PMID: 33024112 PMCID: PMC7539009 DOI: 10.1038/s41467-020-18773-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/08/2020] [Indexed: 01/13/2023] Open
Abstract
VARP and TBC1D5 are accessory/regulatory proteins of retromer-mediated retrograde trafficking from endosomes. Using an NMR/X-ray approach, we determined the structure of the complex between retromer subunit VPS29 and a 12 residue, four-cysteine/Zn++ microdomain, which we term a Zn-fingernail, two of which are present in VARP. Mutations that abolish VPS29:VARP binding inhibit trafficking from endosomes to the cell surface. We show that VARP and TBC1D5 bind the same site on VPS29 and can compete for binding VPS29 in vivo. The relative disposition of VPS29s in hetero-hexameric, membrane-attached, retromer arches indicates that VARP will prefer binding to assembled retromer coats through simultaneous binding of two VPS29s. The TBC1D5:VPS29 interaction is over one billion years old but the Zn-fingernail appears only in VARP homologues in the lineage directly giving rise to animals at which point the retromer/VARP/TBC1D5 regulatory network became fully established.
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Affiliation(s)
- Harriet Crawley-Snowdon
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Nathan R Zaccai
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Luther J Davis
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Lena Wartosch
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Emily K Herman
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada, T6G 2G3
| | | | - James S Swarbrick
- Pharmacology and Therapeutics, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, QLD, 4072, Australia
| | - Lauren P Jackson
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | | | - J Paul Luzio
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada, T6G 2G3.
| | - David Neuhaus
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK.
| | - David J Owen
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK.
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9
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Liu D, Yang F, Liu Z, Wang J, Huang W, Meng W, Billadeau DD, Sun Q, Mo X, Jia D. Structure of TBC1D23 N-terminus reveals a novel role for rhodanese domain. PLoS Biol 2020; 18:e3000746. [PMID: 32453802 PMCID: PMC7274447 DOI: 10.1371/journal.pbio.3000746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 06/05/2020] [Accepted: 05/14/2020] [Indexed: 02/05/2023] Open
Abstract
Members of the Tre2-Bub2-Cdc16 (TBC) family often function to regulate membrane trafficking and to control signaling transductions pathways. As a member of the TBC family, TBC1D23 is critical for endosome-to-Golgi cargo trafficking by serving as a bridge between Golgi-bound golgin-97/245 and the WASH/FAM21 complex on endosomal vesicles. However, the exact mechanisms by which TBC1D23 regulates cargo transport are poorly understood. Here, we present the crystal structure of the N-terminus of TBC1D23 (D23N), which consists of both the TBC and rhodanese domains. We show that the rhodanese domain is unlikely to be an active sulfurtransferase or phosphatase, despite containing a putative catalytic site. Instead, it packs against the TBC domain and forms part of the platform to interact with golgin-97/245. Using the zebrafish model, we show that impacting golgin-97/245-binding, but not the putative catalytic site, impairs neuronal growth and brain development. Altogether, our studies provide structural and functional insights into an essential protein that is required for organelle-specific trafficking and brain development.
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Affiliation(s)
- Dingdong Liu
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Fan Yang
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Zhe Liu
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jinrui Wang
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wenjie Huang
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wentong Meng
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Daniel D. Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Qingxiang Sun
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- * E-mail: (DJ); (XM); (QS)
| | - Xianming Mo
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- * E-mail: (DJ); (XM); (QS)
| | - Da Jia
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- * E-mail: (DJ); (XM); (QS)
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10
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Liang C, Li A, Raza SHA, Khan R, Wang X, Wang S, Wang G, Zhang Y, Zan L. The Molecular Characteristics of the FAM13A Gene and the Role of Transcription Factors ACSL1 and ASCL2 in Its Core Promoter Region. Genes (Basel) 2019; 10:genes10120981. [PMID: 31795267 PMCID: PMC6947481 DOI: 10.3390/genes10120981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 12/16/2022] Open
Abstract
The gene family with sequence similarity 13 member A (FAM13A) has recently been identified as a marker gene in insulin sensitivity and lipolysis. In this study, we first analyzed the expression patterns of this gene in different tissues of adult cattle and then constructed a phylogenetic tree based on the FAM13A amino acid sequence. This showed that subcutaneous adipose tissue had the highest expression in all tissues except lung tissue. Then we summarized the gene structure. The promoter region sequence of the gene was successfully amplified, and the -241/+54 region has been identified as the core promoter region. The core promoter region was determined by the unidirectional deletion of the 5' flanking promoter region of the FAM13A gene. Based on the bioinformatics analysis, we examined the dual luciferase activity of the vector constructed by the mutation site, and the transcription factors ACSL1 and ASCL2 were found as transcriptional regulators of FAM13A. Moreover, electrophoretic mobility shift assay (EMSA) further validated the regulatory role of ACSL1 and ASCL2 in the regulation of FAM13A. ACSL1 and ASCL2 were finally identified as activating transcription factors. Our results provide a basis for the function of the FAM13A gene in bovine adipocytes in order to improve the deposition of fat deposition in beef cattle muscle.
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Affiliation(s)
- Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
| | - Xiaoyu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
| | - Sihu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
| | - Guohua Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
| | - Yu Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (C.L.); (A.L.); (S.H.A.R.); (R.K.); (X.W.); (S.W.); (G.W.); (Y.Z.)
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling 712100, Shaanxi, China
- Correspondence: ; Tel.: +86-2987-091-923
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11
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Chan C, Pang X, Zhang Y, Niu T, Yang S, Zhao D, Li J, Lu L, Hsu VW, Zhou J, Sun F, Fan J. ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages. PLoS Comput Biol 2019; 15:e1007081. [PMID: 31291238 PMCID: PMC6663034 DOI: 10.1371/journal.pcbi.1007081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/29/2019] [Accepted: 05/06/2019] [Indexed: 11/19/2022] Open
Abstract
Studies on the Bin-Amphiphysin-Rvs (BAR) domain have advanced a fundamental understanding of how proteins deform membrane. We previously showed that a BAR domain in tandem with a Pleckstrin Homology (PH domain) underlies the assembly of ACAP1 (Arfgap with Coil-coil, Ankryin repeat, and PH domain I) into an unusual lattice structure that also uncovers a new paradigm for how a BAR protein deforms membrane. Here, we initially pursued computation-based refinement of the ACAP1 lattice to identify its critical protein contacts. Simulation studies then revealed how ACAP1, which dimerizes into a symmetrical structure in solution, is recruited asymmetrically to the membrane through dynamic behavior. We also pursued electron microscopy (EM)-based structural studies, which shed further insight into the dynamic nature of the ACAP1 lattice assembly. As ACAP1 is an unconventional BAR protein, our findings broaden the understanding of the mechanistic spectrum by which proteins assemble into higher-ordered structures to achieve membrane deformation.
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Affiliation(s)
- Chun Chan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Xiaoyun Pang
- National Laboratory of Biomacromolecules, CAS Center for excellence in biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, CAS Center for excellence in biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tongxin Niu
- National Laboratory of Biomacromolecules, CAS Center for excellence in biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shengjiang Yang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Daohui Zhao
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Jian Li
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Victor W. Hsu
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, China
- * E-mail: (JZ); (FS); (JF)
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for excellence in biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (JZ); (FS); (JF)
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Hong Kong, China
- * E-mail: (JZ); (FS); (JF)
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12
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Tanna CE, Goss LB, Ludwig CG, Chen PW. Arf GAPs as Regulators of the Actin Cytoskeleton-An Update. Int J Mol Sci 2019; 20:ijms20020442. [PMID: 30669557 PMCID: PMC6358971 DOI: 10.3390/ijms20020442] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/25/2022] Open
Abstract
Arf GTPase-activating proteins (Arf GAPs) control the activity of ADP-ribosylation factors (Arfs) by inducing GTP hydrolysis and participate in a diverse array of cellular functions both through mechanisms that are dependent on and independent of their Arf GAP activity. A number of these functions hinge on the remodeling of actin filaments. Accordingly, some of the effects exerted by Arf GAPs involve proteins known to engage in regulation of the actin dynamics and architecture, such as Rho family proteins and nonmuscle myosin 2. Circular dorsal ruffles (CDRs), podosomes, invadopodia, lamellipodia, stress fibers and focal adhesions are among the actin-based structures regulated by Arf GAPs. Arf GAPs are thus important actors in broad functions like adhesion and motility, as well as the specialized functions of bone resorption, neurite outgrowth, and pathogen internalization by immune cells. Arf GAPs, with their multiple protein-protein interactions, membrane-binding domains and sites for post-translational modification, are good candidates for linking the changes in actin to the membrane. The findings discussed depict a family of proteins with a critical role in regulating actin dynamics to enable proper cell function.
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Affiliation(s)
- Christine E Tanna
- Department of Biology, Williams College, Williamstown, MA 01267, USA.
| | - Louisa B Goss
- Department of Biology, Williams College, Williamstown, MA 01267, USA.
| | - Calvin G Ludwig
- Department of Biology, Williams College, Williamstown, MA 01267, USA.
| | - Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, MA 01267, USA.
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13
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Ali I, Eu S, Koch D, Bleimling N, Goody RS, Müller MP. Structure of the tandem PX-PH domains of Bem3 from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2018; 74:315-321. [PMID: 29718000 PMCID: PMC5931145 DOI: 10.1107/s2053230x18005915] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/16/2018] [Indexed: 11/11/2022] Open
Abstract
The structure of the tandem lipid-binding PX and pleckstrin-homology (PH) domains of the Cdc42 GTPase-activating protein Bem3 from Saccharomyces cerevisiae (strain S288c) has been determined to a resolution of 2.2 Å (Rwork = 21.1%, Rfree = 23.4%). It shows that the domains adopt a relative orientation that enables them to simultaneously bind to a membrane and suggests possible cooperativity in membrane binding.
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Affiliation(s)
- Imtiaz Ali
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sungmin Eu
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Daniel Koch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Nathalie Bleimling
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Roger S. Goody
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Matthias P. Müller
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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14
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Shen K, Huang RK, Brignole EJ, Condon KJ, Valenstein ML, Chantranupong L, Bomaliyamu A, Choe A, Hong C, Yu Z, Sabatini DM. Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Nature 2018; 556:64-69. [PMID: 29590090 PMCID: PMC5975964 DOI: 10.1038/nature26158] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 02/16/2018] [Indexed: 12/22/2022]
Abstract
Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase.
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Affiliation(s)
- Kuang Shen
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rick K. Huang
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Edward J. Brignole
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kendall J. Condon
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Max L. Valenstein
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Lynne Chantranupong
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Aimaiti Bomaliyamu
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Abigail Choe
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Chuan Hong
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - David M. Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
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15
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Martinez D, Prouzet-Mauléon V, Hugues M, Doignon F, Odaert B. Assignment of 1H, 13C and 15N resonances and secondary structure of the Rgd1-RhoGAP domain. Biomol NMR Assign 2018; 12:129-132. [PMID: 29280056 DOI: 10.1007/s12104-017-9794-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
The protein Rgd1 is involved in the regulation of cytoskeleton formation and in signalling pathways that control cell polarity and growth in Saccharomyces cerevisiae. Rgd1p is composed of a F-BAR domain required for membrane binding and a RhoGAP domain responsible for activating Rho3p and Rho4p, two GTPases respectively involved in bud growth and cytokinesis. Rgd1p is recruited to the membrane through interactions with phosphoinositide lipids, which bind the two isolated domains and stimulate the RhoGAP activity on Rho4p. As previously shown by crystallography, the membrane-binding F-BAR domain contains a conserved inositol phosphate binding site, which explains the preferential binding of phosphoinositides. In contrast, RhoGAP domains are not expected to bind lipids. In order to unravel this puzzling feature, we solved the three-dimensional structure of the isolated protein and found a cryptic phosphoinositide binding site involving non conserved residues (Martinez et al. 2017). The assignment of the resonances and secondary structure of Rgd1-RhoGAP (aa 450-666) is presented here.
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Affiliation(s)
- Denis Martinez
- Chimie et Biologie des Membranes et des Nano-objets, Université de Bordeaux, CNRS UMR 5248, Allée Geoffroy Saint Hilaire, 33600, Pessac Cedex, France
| | - Valérie Prouzet-Mauléon
- Laboratoire d'Hématopoïèse Leucémique et Cibles Thérapeutiques, Université de Bordeaux, INSERM 1035, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France
| | - Michel Hugues
- Chimie et Biologie des Membranes et des Nano-objets, Université de Bordeaux, CNRS UMR 5248, Allée Geoffroy Saint Hilaire, 33600, Pessac Cedex, France
| | - François Doignon
- Laboratoire de Biogenèse Membranaire, Université de Bordeaux, CNRS UMR 5200, 71 Avenue Edouard Bourlaux, 33883, Villenave d'Ornon Cedex, France
| | - Benoît Odaert
- Chimie et Biologie des Membranes et des Nano-objets, Université de Bordeaux, CNRS UMR 5248, Allée Geoffroy Saint Hilaire, 33600, Pessac Cedex, France.
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16
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Arshad M, Bhatti A, John P. Identification and in silico analysis of functional SNPs of human TAGAP protein: A comprehensive study. PLoS One 2018; 13:e0188143. [PMID: 29329296 PMCID: PMC5766082 DOI: 10.1371/journal.pone.0188143] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/01/2017] [Indexed: 12/02/2022] Open
Abstract
Genetic polymorphisms in TAGAP gene have been associated with many diseases including rheumatoid arthritis, multiple sclerosis and other autoimmune disorders. Identifying functional SNPs in such disease associated genes is an uphill task hence before planning larger population study, it is better to scrutinize putative functional SNPs. In this study we used various computational approaches to identify nsSNPs which are deleterious to the structure and/or function of TAGAP protein that might be causing these diseases. Computational analysis was performed by five different in silico tools including SIFT, PROVEAN, PolyPhen-2, PhD-SNP and SNPs&GO. The study concludes that mutations of Glycine → Glutamic Acid at position 120, Glycine → Tryptophan at position 141 and Valine → Methionine at position 151 are major mutations in native TAGAP protein which might contribute to its malfunction and ultimately causing disease. The study also proposed 3D structures of native TAGAP protein and its three mutants. Future studies should consider these nsSNPs as main target mutations in various diseases involving TAGAP malfunction. This is the first comprehensive study, where TAGAP gene variants were analyzed using in silico tools hence will be of great help while considering large scale studies and also in developing precision medicines for cure of diseases related to these polymorphisms. Furthermore, animal models of various autoimmune diseases and having these mutations might be of help in exploring their precise roles.
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Affiliation(s)
- Maria Arshad
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Attya Bhatti
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Peter John
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
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17
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Bist P, Kim SSY, Pulloor NK, McCaffrey K, Nair SK, Liu Y, Lin R, Krishnan MN. ArfGAP Domain-Containing Protein 2 (ADAP2) Integrates Upstream and Downstream Modules of RIG-I Signaling and Facilitates Type I Interferon Production. Mol Cell Biol 2017; 37:e00537-16. [PMID: 27956705 PMCID: PMC5335504 DOI: 10.1128/mcb.00537-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/28/2016] [Accepted: 12/06/2016] [Indexed: 01/15/2023] Open
Abstract
Transcription of type I interferon genes during RNA virus infection requires signal communication between several pattern recognition receptor (PRR)-adaptor complexes located at distinct subcellular membranous compartments and a central cytoplasmic TBK1-interferon regulatory factor 3 (IRF3) kinase-transcription factor module. However, how the cell integrates signal transduction through spatially distinct modules of antiviral signaling pathways is less defined. RIG-I is a major cytosolic PRR involved in the control of several RNA viruses. Here we identify ArfGAP domain-containing protein 2 (ADAP2) as a key novel scaffolding protein that integrates different modules of the RIG-I pathway, located at distinct subcellular locations, and mediates cellular antiviral type I interferon production. ADAP2 served to bridge the mitochondrial membrane-bound upstream RIG-I adaptor MAVS and the downstream cytosolic complex of NEMO (regulatory subunit of TBK1), TBK1, and IRF3, leading to IRF3 phosphorylation. Furthermore, independently, ADAP2 also functioned as a major orchestrator of the interaction of TBK1 with NEMO and IRF3. Mutational and in vitro cell-free reconstituted RIG-I signaling assay-based analyses identified that the ArfGAP domain of ADAP2 mediates the interferon response. TRAF3 acted as a trigger for ADAP2 to recruit RIG-I pathway component proteins into a single macromolecular complex. This study provides important novel insights into the assembly and integration of different modules of antiviral signaling cascades.
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Affiliation(s)
- Pradeep Bist
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Susana Soo-Yeon Kim
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Niyas Kudukil Pulloor
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Kathleen McCaffrey
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Sajith Kumar Nair
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Yiliu Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Rongtuan Lin
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Manoj N Krishnan
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
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18
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Jia D, Zhang JS, Li F, Wang J, Deng Z, White MA, Osborne DG, Phillips-Krawczak C, Gomez TS, Li H, Singla A, Burstein E, Billadeau DD, Rosen MK. Structural and mechanistic insights into regulation of the retromer coat by TBC1d5. Nat Commun 2016; 7:13305. [PMID: 27827364 PMCID: PMC5105194 DOI: 10.1038/ncomms13305] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 09/19/2016] [Indexed: 01/09/2023] Open
Abstract
Retromer is a membrane coat complex that is recruited to endosomes by the small GTPase Rab7 and sorting nexin 3. The timing of this interaction and consequent endosomal dynamics are thought to be regulated by the guanine nucleotide cycle of Rab7. Here we demonstrate that TBC1d5, a GTPase-activating protein (GAP) for Rab7, is a high-affinity ligand of the retromer cargo selective complex VPS26/VPS29/VPS35. The crystal structure of the TBC1d5 GAP domain bound to VPS29 and complementary biochemical and cellular data show that a loop from TBC1d5 binds to a conserved hydrophobic pocket on VPS29 opposite the VPS29-VPS35 interface. Additional data suggest that a distinct loop of the GAP domain may contact VPS35. Loss of TBC1d5 causes defective retromer-dependent trafficking of receptors. Our findings illustrate how retromer recruits a GAP, which is likely to be involved in the timing of Rab7 inactivation leading to membrane uncoating, with important consequences for receptor trafficking.
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Affiliation(s)
- Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Paediatrics, West China Second University Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
- Department of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Jin-San Zhang
- Departments of Immunology, Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Key Laboratory of Biotechnology and Pharmaceutical Engineering, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Fang Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Paediatrics, West China Second University Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jing Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Paediatrics, West China Second University Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Zhihui Deng
- Departments of Immunology, Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Pathophysiology, Qiqihar Medical University, Qiqihar 161006, China
| | - Mark A. White
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Douglas G. Osborne
- Departments of Immunology, Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Christine Phillips-Krawczak
- Departments of Immunology, Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Timothy S. Gomez
- Departments of Immunology, Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Haiying Li
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Amika Singla
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ezra Burstein
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Daniel D. Billadeau
- Departments of Immunology, Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Michael K. Rosen
- Department of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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19
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Dümmer M, Michalski C, Essen LO, Rath M, Galland P, Forreiter C. EHB1 and AGD12, two calcium-dependent proteins affect gravitropism antagonistically in Arabidopsis thaliana. J Plant Physiol 2016; 206:114-124. [PMID: 27728837 DOI: 10.1016/j.jplph.2016.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Abstract
The ADP-RIBOSYLATION FACTOR GTPase-ACTIVATING PROTEIN (AGD) 12, a member of the ARF-GAP protein family, affects gravitropism in Arabidopsis thaliana. A loss-of-function mutant lacking AGD12 displayed diminished gravitropism in roots and hypocotyls indicating that both organs are affected by this regulator. AGD12 is structurally related to ENHANCED BENDING (EHB) 1, previously described as a negative effector of gravitropism. In contrast to agd12 mutants, ehb1 loss-of function seedlings displayed enhanced gravitropic bending. While EHB1 and AGD12 both possess a C-terminal C2/CaLB-domain, EHB1 lacks the N-terminal ARF-GAP domain present in AGD12. Subcellular localization analysis using Brefeldin A indicated that both proteins are elements of the trans Golgi network. Physiological analyses provided evidence that gravitropic signaling might operate via an antagonistic interaction of ARF-GAP (AGD12) and EHB1 in their Ca2+-activated states.
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Affiliation(s)
- Michaela Dümmer
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Christian Michalski
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Lars-Oliver Essen
- Fachbereich Chemie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Magnus Rath
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Paul Galland
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
| | - Christoph Forreiter
- Institut für Biologie, Universität Siegen, Adolf-Reichwein Str. 2, D-57068 Siegen, Germany.
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20
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Amin E, Jaiswal M, Derewenda U, Reis K, Nouri K, Koessmeier KT, Aspenström P, Somlyo AV, Dvorsky R, Ahmadian MR. Deciphering the Molecular and Functional Basis of RHOGAP Family Proteins: A SYSTEMATIC APPROACH TOWARD SELECTIVE INACTIVATION OF RHO FAMILY PROTEINS. J Biol Chem 2016; 291:20353-71. [PMID: 27481945 PMCID: PMC5034035 DOI: 10.1074/jbc.m116.736967] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Indexed: 12/30/2022] Open
Abstract
RHO GTPase-activating proteins (RHOGAPs) are one of the major classes of regulators of the RHO-related protein family that are crucial in many cellular processes, motility, contractility, growth, differentiation, and development. Using database searches, we extracted 66 distinct human RHOGAPs, from which 57 have a common catalytic domain capable of terminating RHO protein signaling by stimulating the slow intrinsic GTP hydrolysis (GTPase) reaction. The specificity of the majority of the members of RHOGAP family is largely uncharacterized. Here, we comprehensively investigated the sequence-structure-function relationship between RHOGAPs and RHO proteins by combining our in vitro data with in silico data. The activity of 14 representatives of the RHOGAP family toward 12 RHO family proteins was determined in real time. We identified and structurally verified hot spots in the interface between RHOGAPs and RHO proteins as critical determinants for binding and catalysis. We have found that the RHOGAP domain itself is nonselective and in some cases rather inefficient under cell-free conditions. Thus, we propose that other domains of RHOGAPs confer substrate specificity and fine-tune their catalytic efficiency in cells.
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Affiliation(s)
- Ehsan Amin
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Mamta Jaiswal
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Urszula Derewenda
- the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, and
| | - Katarina Reis
- the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Kazem Nouri
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Katja T Koessmeier
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Pontus Aspenström
- the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Avril V Somlyo
- the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, and
| | - Radovan Dvorsky
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany,
| | - Mohammad R Ahmadian
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany,
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21
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Zacharchenko T, Qian X, Goult BT, Jethwa D, Almeida TB, Ballestrem C, Critchley DR, Lowy DR, Barsukov IL. LD Motif Recognition by Talin: Structure of the Talin-DLC1 Complex. Structure 2016; 24:1130-41. [PMID: 27265849 PMCID: PMC4938799 DOI: 10.1016/j.str.2016.04.016] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/25/2022]
Abstract
Cell migration requires coordination between integrin-mediated cell adhesion to the extracellular matrix and force applied to adhesion sites. Talin plays a key role in coupling integrin receptors to the actomyosin contractile machinery, while deleted in liver cancer 1 (DLC1) is a Rho GAP that binds talin and regulates Rho, and therefore actomyosin contractility. We show that the LD motif of DLC1 forms a helix that binds to the four-helix bundle of the talin R8 domain in a canonical triple-helix arrangement. We demonstrate that the same R8 surface interacts with the paxillin LD1 and LD2 motifs. We identify key charged residues that stabilize the R8 interactions with LD motifs and demonstrate their importance in vitro and in cells. Our results suggest a network of competitive interactions in adhesion complexes that involve LD motifs, and identify mutations that can be used to analyze the biological roles of specific protein-protein interactions in cell migration.
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Affiliation(s)
- Thomas Zacharchenko
- Institute of Integrative Biology, University of Liverpool, BioSciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Xiaolan Qian
- Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin T Goult
- School of Biosciences, University of Kent, Kent, Canterbury, CT2 7NJ, UK
| | - Devina Jethwa
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Teresa B Almeida
- Institute of Integrative Biology, University of Liverpool, BioSciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Christoph Ballestrem
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David R Critchley
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Douglas R Lowy
- Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Igor L Barsukov
- Institute of Integrative Biology, University of Liverpool, BioSciences Building, Crown Street, Liverpool L69 7ZB, UK.
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22
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Ritterhoff T, Das H, Hofhaus G, Schröder RR, Flotho A, Melchior F. The RanBP2/RanGAP1*SUMO1/Ubc9 SUMO E3 ligase is a disassembly machine for Crm1-dependent nuclear export complexes. Nat Commun 2016; 7:11482. [PMID: 27160050 PMCID: PMC4866044 DOI: 10.1038/ncomms11482] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 03/31/2016] [Indexed: 02/07/2023] Open
Abstract
Continuous cycles of nucleocytoplasmic transport require disassembly of transport receptor/Ran-GTP complexes in the cytoplasm. A basic disassembly mechanism in all eukaryotes depends on soluble RanGAP and RanBP1. In vertebrates, a significant fraction of RanGAP1 stably interacts with the nucleoporin RanBP2 at a binding site that is flanked by FG-repeats and Ran-binding domains, and overlaps with RanBP2's SUMO E3 ligase region. Here, we show that the RanBP2/RanGAP1*SUMO1/Ubc9 complex functions as an autonomous disassembly machine with a preference for the export receptor Crm1. We describe three in vitro reconstituted disassembly intermediates, which show binding of a Crm1 export complex via two FG-repeat patches, cargo-release by RanBP2's Ran-binding domains and retention of free Crm1 at RanBP2 after Ran-GTP hydrolysis. Intriguingly, all intermediates are compatible with SUMO E3 ligase activity, suggesting that the RanBP2/RanGAP1*SUMO1/Ubc9 complex may link Crm1- and SUMO-dependent functions.
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Affiliation(s)
- Tobias Ritterhoff
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Hrishikesh Das
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany
- Cryo Electron Microscopy, CellNetworks, BioQuant, Universitätsklinikum Heidelberg, Heidelberg 69120, Germany
| | - Götz Hofhaus
- Cryo Electron Microscopy, CellNetworks, BioQuant, Universitätsklinikum Heidelberg, Heidelberg 69120, Germany
| | - Rasmus R. Schröder
- Cryo Electron Microscopy, CellNetworks, BioQuant, Universitätsklinikum Heidelberg, Heidelberg 69120, Germany
| | - Annette Flotho
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany
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23
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Boutaffala L, Bertrand MJM, Remouchamps C, Seleznik G, Reisinger F, Janas M, Bénézech C, Fernandes MT, Marchetti S, Mair F, Ganeff C, Hupalowska A, Ricci JE, Becher B, Piette J, Knolle P, Caamano J, Vandenabeele P, Heikenwalder M, Dejardin E. NIK promotes tissue destruction independently of the alternative NF-κB pathway through TNFR1/RIP1-induced apoptosis. Cell Death Differ 2015; 22:2020-33. [PMID: 26045047 PMCID: PMC4816116 DOI: 10.1038/cdd.2015.69] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 12/21/2022] Open
Abstract
NF-κB-inducing kinase (NIK) is well-known for its role in promoting p100/NF-κB2 processing into p52, a process defined as the alternative, or non-canonical, NF-κB pathway. Here we reveal an unexpected new role of NIK in TNFR1-mediated RIP1-dependent apoptosis, a consequence of TNFR1 activation observed in c-IAP1/2-depleted conditions. We show that NIK stabilization, obtained by activation of the non-death TNFRs Fn14 or LTβR, is required for TNFα-mediated apoptosis. These apoptotic stimuli trigger the depletion of c-IAP1/2, the phosphorylation of RIP1 and the RIP1 kinase-dependent assembly of the RIP1/FADD/caspase-8 complex. In the absence of NIK, the phosphorylation of RIP1 and the formation of RIP1/FADD/caspase-8 complex are compromised while c-IAP1/2 depletion is unaffected. In vitro kinase assays revealed that recombinant RIP1 is a bona fide substrate of NIK. In vivo, we demonstrated the requirement of NIK pro-death function, but not the processing of its substrate p100 into p52, in a mouse model of TNFR1/LTβR-induced thymus involution. In addition, we also highlight a role for NIK in hepatocyte apoptosis in a mouse model of virus-induced TNFR1/RIP1-dependent liver damage. We conclude that NIK not only contributes to lymphoid organogenesis, inflammation and cell survival but also to TNFR1/RIP1-dependent cell death independently of the alternative NF-κB pathway.
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Affiliation(s)
- L Boutaffala
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - M J M Bertrand
- The Inflammation Research Center IRC, VIB, DMBR, Ghent University, Ghent, Belgium
| | - C Remouchamps
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - G Seleznik
- Institute of Neuropathology, University Hospital Zürich, Zürich, Switzerland
| | | | - M Janas
- Institute of Molecular Immunology and Technische Universität München (TUM)/Helmholtz Zentrum München (HMGU), Munich, Germany
| | - C Bénézech
- School of Immunity and Infection, IBR-MRC, Centre for Immune Regulation, University of Birmingham, Birmingham, UK
| | - M T Fernandes
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - S Marchetti
- INSERM U1065, Centre Méditéranéen de Médecine Moléculaire, Nice, France
| | - F Mair
- Institute of Experimental Immunology, University of Zurich, Zürich, Switzerland
| | - C Ganeff
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - A Hupalowska
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
| | - J-E Ricci
- INSERM U1065, Centre Méditéranéen de Médecine Moléculaire, Nice, France
| | - B Becher
- Institute of Experimental Immunology, University of Zurich, Zürich, Switzerland
| | - J Piette
- Laboratory of Virology, GIGA-Research, University of Liège, Liège, Belgium
| | - P Knolle
- Institute of Molecular Immunology and Technische Universität München (TUM)/Helmholtz Zentrum München (HMGU), Munich, Germany
| | - J Caamano
- School of Immunity and Infection, IBR-MRC, Centre for Immune Regulation, University of Birmingham, Birmingham, UK
| | - P Vandenabeele
- The Inflammation Research Center IRC, VIB, DMBR, Ghent University, Ghent, Belgium
| | - M Heikenwalder
- Institute of Virology, Munich, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - E Dejardin
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Research, University of Liège, Liège, Belgium
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24
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Cha K, Sen P, Raghunayakula S, Zhang XD. The Cellular Distribution of RanGAP1 Is Regulated by CRM1-Mediated Nuclear Export in Mammalian Cells. PLoS One 2015; 10:e0141309. [PMID: 26506250 PMCID: PMC4624696 DOI: 10.1371/journal.pone.0141309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 10/07/2015] [Indexed: 11/19/2022] Open
Abstract
The Ran GTPase activating protein RanGAP1 plays an essential role in nuclear transport by stimulating RanGTP hydrolysis in the cytoplasmic compartment. In mammalian cells, unmodified RanGAP1 is predominantly cytoplasmic, whereas modification by small ubiquitin-related modifier protein (SUMO) targets RanGAP1 to the cytoplasmic filaments of nuclear pore complex (NPC). Although RanGAP1 contains nine putative nuclear export signals and a nuclear localization signal, little is known if RanGAP1 shuttles between the nuclear and cytoplasmic compartments and how its primary localization in the cytoplasm and at the NPC is regulated. Here we show that inhibition of CRM1-mediated nuclear export using RNAi-knockdown of CRM1 and inactivation of CRM1 by leptomycin B (LMB) results in nuclear accumulation of RanGAP1. LMB treatment induced a more robust redistribution of RanGAP1 from the cytoplasm to the nucleoplasm compared to CRM1 RNAi and also uniquely triggered a decrease or loss of RanGAP1 localization at the NPC, suggesting that LMB treatment is more effective in inhibiting CRM1-mediated nuclear export of RanGAP1. Our time-course analysis of LMB treatment reveals that the NPC-associated RanGAP1 is much more slowly redistributed to the nucleoplasm than the cytoplasmic RanGAP1. Furthermore, LMB-induced nuclear accumulation of RanGAP1 is positively correlated with an increase in levels of SUMO-modified RanGAP1, suggesting that SUMOylation of RanGAP1 may mainly take place in the nucleoplasm. Lastly, we demonstrate that the nuclear localization signal at the C-terminus of RanGAP1 is required for its nuclear accumulation in cells treated with LMB. Taken together, our results elucidate that RanGAP1 is actively transported between the nuclear and cytoplasmic compartments, and that the cytoplasmic and NPC localization of RanGAP1 is dependent on CRM1-mediated nuclear export.
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Affiliation(s)
- Keith Cha
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Progga Sen
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Sarita Raghunayakula
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Xiang-Dong Zhang
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
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25
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He F, Nie WC, Tong Z, Yuan SM, Gong T, Liao Y, Bi E, Gao XD. The GTPase-activating protein Rga1 interacts with Rho3 GTPase and may regulate its function in polarized growth in budding yeast. PLoS One 2015; 10:e0123326. [PMID: 25860339 PMCID: PMC4393305 DOI: 10.1371/journal.pone.0123326] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/03/2015] [Indexed: 12/02/2022] Open
Abstract
In budding yeast, Rga1 negatively regulates the Rho GTPase Cdc42 by acting as a GTPase-activating protein (GAP) for Cdc42. To gain insight into the function and regulation of Rga1, we overexpressed Rga1 and an N-terminally truncated Rga1-C538 (a.a. 538-1007) segment. Overexpression of Rga1-C538 but not full-length Rga1 severely impaired growth and cell morphology in wild-type cells. We show that Rga1 is phosphorylated during the cell cycle. The lack of phenotype for full-length Rga1 upon overexpression may result from a negative regulation by G1-specific Pho85, a cyclin-dependent kinase (CDK). From a high-copy suppressor screen, we isolated RHO3, SEC9, SEC1, SSO1, SSO2, and SRO7, genes involved in exocytosis, as suppressors of the growth defect caused by Rga1-C538 overexpression. Moreover, we detected that Rga1 interacts with Rho3 in two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Rga1 preferentially interacts with the GTP-bound form of Rho3 and the interaction requires the GAP domain and additional sequence upstream of the GAP domain. Our data suggest that the interaction of Rga1 with Rho3 may regulate Rho3’s function in polarized bud growth.
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Affiliation(s)
- Fei He
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen-Chao Nie
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zongtian Tong
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Si-Min Yuan
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ting Gong
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuan Liao
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Erfei Bi
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Xiang-Dong Gao
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, China
- * E-mail:
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26
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Moravcevic K, Alvarado D, Schmitz KR, Kenniston JA, Mendrola JM, Ferguson KM, Lemmon MA. Comparison of Saccharomyces cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site. Structure 2015; 23:352-63. [PMID: 25620000 DOI: 10.1016/j.str.2014.12.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 11/29/2014] [Accepted: 12/02/2014] [Indexed: 12/27/2022]
Abstract
F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although they are generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the Saccharomyces cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity and provide a basis for its prediction from sequence.
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Affiliation(s)
- Katarina Moravcevic
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Diego Alvarado
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Karl R Schmitz
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Jon A Kenniston
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Jeannine M Mendrola
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Kathryn M Ferguson
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Mark A Lemmon
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19014, USA.
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27
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Koyama M, Shirai N, Matsuura Y. Structural insights into how Yrb2p accelerates the assembly of the Xpo1p nuclear export complex. Cell Rep 2014; 9:983-95. [PMID: 25437554 DOI: 10.1016/j.celrep.2014.09.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 01/25/2014] [Accepted: 09/28/2014] [Indexed: 11/29/2022] Open
Abstract
Proteins and ribonucleoproteins containing a nuclear export signal (NES) assemble with the exportin Xpo1p (yeast CRM1) and Gsp1p-GTP (yeast Ran-GTP) in the nucleus and exit through the nuclear pore complex. In the cytoplasm, Yrb1p (yeast RanBP1) displaces NES from Xpo1p. Efficient export of NES-cargoes requires Yrb2p (yeast RanBP3), a primarily nuclear protein containing nucleoporin-like phenylalanine-glycine (FG) repeats and a low-affinity Gsp1p-binding domain (RanBD). Here, we show that Yrb2p strikingly accelerates the association of Gsp1p-GTP and NES to Xpo1p. We have solved the crystal structure of the Xpo1p-Yrb2p-Gsp1p-GTP complex, a key assembly intermediate that can bind cargo rapidly. Although the NES-binding cleft of Xpo1p is closed in this intermediate, our data suggest that preloading of Gsp1p-GTP onto Xpo1p by Yrb2p, conformational flexibility of Xpo1p, and the low affinity of RanBD enable active displacement of Yrb2p RanBD by NES to occur effectively. The structure also reveals the major binding sites for FG repeats on Xpo1p.
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Affiliation(s)
- Masako Koyama
- Division of Biological Science, Graduate School of Science, Nagoya University, 464-8602 Furo-cho, Chikusa-ku, Nagoya City, Japan
| | - Natsuki Shirai
- Division of Biological Science, Graduate School of Science, Nagoya University, 464-8602 Furo-cho, Chikusa-ku, Nagoya City, Japan
| | - Yoshiyuki Matsuura
- Division of Biological Science, Graduate School of Science, Nagoya University, 464-8602 Furo-cho, Chikusa-ku, Nagoya City, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, 464-8602 Furo-cho, Chikusa-ku, Nagoya City, Japan.
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28
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Wang D, Zhang P, Gao K, Tang Y, Jin X, Zhang Y, Yi Q, Wang C, Yu L. PLK1 and β-TrCP-dependent ubiquitination and degradation of Rap1GAP controls cell proliferation. PLoS One 2014; 9:e110296. [PMID: 25329897 PMCID: PMC4201484 DOI: 10.1371/journal.pone.0110296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 09/11/2014] [Indexed: 01/31/2023] Open
Abstract
Rap1GAP is a GTPase-activating protein (GAP) that specifically stimulates the GTP hydrolysis of Rap1 GTPase. Although Rap1GAP is recognized as a tumor suppressor gene and downregulated in various cancers, little is known regarding the regulation of Rap1GAP ubiquitination and degradation under physiological conditions. Here, we demonstrated that Rap1GAP is ubiquitinated and degraded through proteasome pathway in mitosis. Proteolysis of Rap1GAP requires the PLK1 kinase and β-TrCP ubiquitin ligase complex. We revealed that PLK1 interacts with Rap1GAP in vivo through recognition of an SSP motif within Rap1GAP. PLK1 phosphorylates Ser525 in conserved 524DSGHVS529 degron of Rap1GAP and promotes its interaction with β-TrCP. We also showed that Rap1GAP was a cell cycle regulator and that tight regulation of the Rap1GAP degradation in mitosis is required for cell proliferation.
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Affiliation(s)
- Dejie Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Department of Gastroenterology, Jiangxi Institute of Gastroenterology & Hepatology, the First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, P. R. China
| | - Pingzhao Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P.R. China
| | - Kun Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Yan Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Xiaofeng Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Yuanyuan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Qing Yi
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Long Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, P.R. China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P.R. China
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Pang X, Fan J, Zhang Y, Zhang K, Gao B, Ma J, Li J, Deng Y, Zhou Q, Egelman EH, Hsu VW, Sun F. A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature. Dev Cell 2014; 31:73-86. [PMID: 25284369 PMCID: PMC4198613 DOI: 10.1016/j.devcel.2014.08.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/12/2014] [Accepted: 08/21/2014] [Indexed: 11/29/2022]
Abstract
The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane curvature. In some cases, a BAR domain also possesses an amphipathic helix that inserts into the membrane to induce curvature. ACAP1 (Arfgap with Coil coil, Ankyrin repeat, and PH domain protein 1) contains a BAR domain. Here, we show that this BAR domain can neither bind membrane nor impart curvature, but instead requires a neighboring PH (Pleckstrin Homology) domain to achieve these functions. Specific residues within the PH domain are responsible for both membrane binding and curvature generation. The BAR domain adjacent to the PH domain instead interacts with the BAR domains of neighboring ACAP1 proteins to enable clustering at the membrane. Thus, we have uncovered the molecular basis for an unexpected and unconventional collaboration between PH and BAR domains in membrane bending.
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Affiliation(s)
- Xiaoyun Pang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Fan
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong 999077, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kai Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bingquan Gao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Ma
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Li
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Yuchen Deng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiangjun Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Victor W Hsu
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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30
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Kim H, Guo F, Brahma S, Xing Y, Burkard ME. Centralspindlin assembly and 2 phosphorylations on MgcRacGAP by Polo-like kinase 1 initiate Ect2 binding in early cytokinesis. Cell Cycle 2014; 13:2952-61. [PMID: 25486482 PMCID: PMC4614826 DOI: 10.4161/15384101.2014.947201] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 01/08/2023] Open
Abstract
Cytokinesis is the final step of cell division which partitions genetic and cytosolic content into daughter cells. Failed cytokinesis causes polyploidy, genetic instability, and cancer. Kinases use phosphorylation to regulate the timing and location of the cytokinetic furrow. Polo-like kinase 1 (Plk1) is an essential mitotic kinase that triggers cytokinesis by phosphorylating MgcRacGAP to create a docking site for Ect2 at the central spindle. Ect2 binds to MgcRacGAP via its N-terminal BRCT domain (BRCA1 C-terminal), which docks at specific phosphorylated residues. Here we investigate the minimal Plk1-dependent phosphorylation sites required for cytokinesis onset. We demonstrate that phosphorylation of the major MgcRacGAP site, S157, is necessary but not sufficient to bind the Ect2 BRCT domain. Phosphorylation of an additional residue on MgcRacGAP at S164 is also required to elicit efficient binding. Surprisingly, BRCT binding additionally requires MKLP1 and its cognate interacting N-terminal domain of MgcRacGAP. Our findings indicate that central spindle assembly and 2 Plk1-dependent phosphorylations are required to establish efficient binding of the Ect2 BRCT in early cytokinesis. We propose that these requirements establish a high threshold to restrain premature or ectopic cytokinesis.
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Affiliation(s)
- Hyunjung Kim
- Hematology/Oncology Division; Department of Medicine; University of Wisconsin Carbone Cancer Center; Madison, WI USA
| | - Feng Guo
- McArdle Laboratory; Department of Oncology; School of Medicine and Public Health; University of Wisconsin; Madison, WI USA
- Current Affiliation: School of Medicine; Stanford University; Stanford, CA USA
| | - Sarang Brahma
- Hematology/Oncology Division; Department of Medicine; University of Wisconsin Carbone Cancer Center; Madison, WI USA
| | - Yongna Xing
- McArdle Laboratory; Department of Oncology; School of Medicine and Public Health; University of Wisconsin; Madison, WI USA
| | - Mark E Burkard
- Hematology/Oncology Division; Department of Medicine; University of Wisconsin Carbone Cancer Center; Madison, WI USA
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31
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Roman N, Christie M, Swarbrick CMD, Kobe B, Forwood JK. Structural characterisation of the nuclear import receptor importin alpha in complex with the bipartite NLS of Prp20. PLoS One 2013; 8:e82038. [PMID: 24339986 PMCID: PMC3858281 DOI: 10.1371/journal.pone.0082038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/20/2013] [Indexed: 11/30/2022] Open
Abstract
The translocation of macromolecules into the nucleus is a fundamental eukaryotic process, regulating gene expression, cell division and differentiation, but which is impaired in a range of significant diseases including cancer and viral infection. The import of proteins into the nucleus is generally initiated by a specific, high affinity interaction between nuclear localisation signals (NLSs) and nuclear import receptors in the cytoplasm, and terminated through the disassembly of these complexes in the nucleus. For classical NLSs (cNLSs), this import is mediated by the importin-α (IMPα) adaptor protein, which in turn binds to IMPβ to mediate translocation of nuclear cargo across the nuclear envelope. The interaction and disassembly of import receptor:cargo complexes is reliant on the differential localisation of nucleotide bound Ran across the envelope, maintained in its low affinity, GDP-bound form in the cytoplasm, and its high affinity, GTP-bound form in the nucleus. This in turn is maintained by the differential localisation of Ran regulating proteins, with RanGAP in the cytoplasm maintaining Ran in its GDP-bound form, and RanGEF (Prp20 in yeast) in the nucleus maintaining Ran in its GTP-bound form. Here, we describe the 2.1 Å resolution x-ray crystal structure of IMPα in complex with the NLS of Prp20. We observe 1,091 Å2 of buried surface area mediated by an extensive array of contacts involving residues on armadillo repeats 2-7, utilising both the major and minor NLS binding sites of IMPα to contact bipartite NLS clusters 17RAKKMSK23 and 3KR4, respectively. One notable feature of the major site is the insertion of Prp20NLS Ala18 between the P0 and P1 NLS sites, noted in only a few classical bipartite NLSs. This study provides a detailed account of the binding mechanism enabling Prp20 interaction with the nuclear import receptor, and additional new information for the interaction between IMPα and cargo.
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Affiliation(s)
- Noelia Roman
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Mary Christie
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Crystall M. D. Swarbrick
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- * E-mail:
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32
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Rajasekar K, Campbell L, Nietlispach D, Owen D, Mott H. The structure of the RLIP76 RhoGAP-Ral binding domain dyad: fixed position of the domains leads to dual engagement of small G proteins at the membrane. Structure 2013; 21:2131-42. [PMID: 24207123 PMCID: PMC3852207 DOI: 10.1016/j.str.2013.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 01/15/2023]
Abstract
RLIP76 is an effector for Ral small GTPases, which in turn lie downstream of the master regulator Ras. Evidence is growing that Ral and RLIP76 play a role in tumorigenesis, invasion, and metastasis. RLIP76 contains both a RhoGAP domain and a Ral binding domain (GBD) and is, therefore, a node between Ras and Rho family signaling. The structure of the RhoGAP-GBD dyad reveals that the RLIP76 RhoGAP domain adopts a canonical RhoGAP domain structure and that the linker between the two RLIP76 domains is structured, fixing the orientation of the two domains and allowing RLIP76 to interact with Rho-family GTPases and Ral simultaneously. However, the juxtaposed domains do not influence each other functionally, suggesting that the RLIP76-Ral interaction controls cellular localization and that the fixed orientation of the two domains orientates the RhoGAP domain with respect to the membrane, allowing it to be perfectly poised to engage its target G proteins.
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Affiliation(s)
- Karthik V. Rajasekar
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Louise J. Campbell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Helen R. Mott
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Abstract
Cell migration is regulated by a number of small GTPases, including members of the Arf family. Cytohesins, a family of Arf-activating proteins, have been extensively implicated in the regulation of Arfs during migration and cell shape change. Membrane association of both the Arf and its activating protein is a prerequisite for Arf activation. Therefore regulating the extent of cytohesin membrane association is a mechanism for controlling the initiation of cell movement. We have discovered a novel intramolecular interaction that controls the association of cytohesins with membranes. The presence of the coiled-coil domain reduces the association of cytohesin 2 with membranes. We demonstrate that this domain interacts with more C-terminal regions of the protein. This interaction is independent of another previously identified autoinhibitory conformation. A threonine residue (T276) in the cytohesin 2 PH domain is a target for phosphorylation by Akt. Mutation of this threonine to aspartic acid, to mimic phosphorylation, disrupts the binding of the coiled-coil domain to c-terminal regions and promotes membrane association of cytohesin 2. The presence of a second autoinhibitory interaction in the cytohesins suggests that these proteins can act a signal integrators that stimulate migration only after receive multiple pro-migratory signals.
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Affiliation(s)
- Kevin G. Hiester
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lorraine C. Santy
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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34
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Fiebig JE, Weidauer SE, Qiu LY, Bauer M, Schmieder P, Beerbaum M, Zhang JL, Oschkinat H, Sebald W, Mueller TD. The clip-segment of the von Willebrand domain 1 of the BMP modulator protein Crossveinless 2 is preformed. Molecules 2013; 18:11658-82. [PMID: 24071977 PMCID: PMC6270503 DOI: 10.3390/molecules181011658] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 11/19/2022] Open
Abstract
Bone Morphogenetic Proteins (BMPs) are secreted protein hormones that act as morphogens and exert essential roles during embryonic development of tissues and organs. Signaling by BMPs occurs via hetero-oligomerization of two types of serine/threonine kinase transmembrane receptors. Due to the small number of available receptors for a large number of BMP ligands ligand-receptor promiscuity presents an evident problem requiring additional regulatory mechanisms for ligand-specific signaling. Such additional regulation is achieved through a plethora of extracellular antagonists, among them members of the Chordin superfamily, that modulate BMP signaling activity by binding. The key-element in Chordin-related antagonists for interacting with BMPs is the von Willebrand type C (VWC) module, which is a small domain of about 50 to 60 residues occurring in many different proteins. Although a structure of the VWC domain of the Chordin-member Crossveinless 2 (CV2) bound to BMP-2 has been determined by X-ray crystallography, the molecular mechanism by which the VWC domain binds BMPs has remained unclear. Here we present the NMR structure of the Danio rerio CV2 VWC1 domain in its unbound state showing that the key features for high affinity binding to BMP-2 is a pre-oriented peptide loop.
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Affiliation(s)
- Juliane E. Fiebig
- Julius-von-Sachs Institut für Biowissenschaften der Universität Würzburg, Julius-von-Sachs Platz 2, Würzburg D-97082, Germany; E-Mails: (J.E.F.); (S.E.W.); (M.B.)
| | - Stella E. Weidauer
- Julius-von-Sachs Institut für Biowissenschaften der Universität Würzburg, Julius-von-Sachs Platz 2, Würzburg D-97082, Germany; E-Mails: (J.E.F.); (S.E.W.); (M.B.)
| | - Li-Yan Qiu
- Lehrstuhl für Physiologische Chemie II, Biozentrum der Universität Würzburg, Am Hubland, Würzburg D-97074, Germany; E-Mails: (L.-Y.Q.); (J.-L.Z.); (W.S.)
| | - Markus Bauer
- Julius-von-Sachs Institut für Biowissenschaften der Universität Würzburg, Julius-von-Sachs Platz 2, Würzburg D-97082, Germany; E-Mails: (J.E.F.); (S.E.W.); (M.B.)
| | - Peter Schmieder
- Leibnizinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle Str. 10, Berlin D-13125, Germany; E-Mails: (P.S.); (M.B.); (H.O.)
| | - Monika Beerbaum
- Leibnizinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle Str. 10, Berlin D-13125, Germany; E-Mails: (P.S.); (M.B.); (H.O.)
| | - Jin-Li Zhang
- Lehrstuhl für Physiologische Chemie II, Biozentrum der Universität Würzburg, Am Hubland, Würzburg D-97074, Germany; E-Mails: (L.-Y.Q.); (J.-L.Z.); (W.S.)
| | - Hartmut Oschkinat
- Leibnizinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle Str. 10, Berlin D-13125, Germany; E-Mails: (P.S.); (M.B.); (H.O.)
| | - Walter Sebald
- Lehrstuhl für Physiologische Chemie II, Biozentrum der Universität Würzburg, Am Hubland, Würzburg D-97074, Germany; E-Mails: (L.-Y.Q.); (J.-L.Z.); (W.S.)
| | - Thomas D. Mueller
- Julius-von-Sachs Institut für Biowissenschaften der Universität Würzburg, Julius-von-Sachs Platz 2, Würzburg D-97082, Germany; E-Mails: (J.E.F.); (S.E.W.); (M.B.)
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Vanni S, Vamparys L, Gautier R, Drin G, Etchebest C, Fuchs PFJ, Antonny B. Amphipathic lipid packing sensor motifs: probing bilayer defects with hydrophobic residues. Biophys J 2013; 104:575-84. [PMID: 23442908 DOI: 10.1016/j.bpj.2012.11.3837] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 10/15/2012] [Accepted: 11/16/2012] [Indexed: 11/18/2022] Open
Abstract
Sensing membrane curvature allows fine-tuning of complex reactions that occur at the surface of membrane-bound organelles. One of the most sensitive membrane curvature sensors, the Amphipathic Lipid Packing Sensor (ALPS) motif, does not seem to recognize the curved surface geometry of membranes per se; rather, it recognizes defects in lipid packing that arise from membrane bending. In a companion paper, we show that these defects can be mimicked by introducing conical lipids in a flat lipid bilayer, in agreement with experimental observations. Here, we use molecular-dynamics (MD) simulations to characterize ALPS binding to such lipid bilayers. The ALPS motif recognizes lipid-packing defects by a conserved mechanism: peptide partitioning is driven by the insertion of hydrophobic residues into large packing defects that are preformed in the bilayer. This insertion induces only minor modifications in the statistical distribution of the free packing defects. ALPS insertion is severely hampered when monounsaturated lipids are replaced by saturated lipids, leading to a decrease in packing defects. We propose that the hypersensitivity of ALPS motifs to lipid packing defects results from the repetitive use of hydrophobic insertions along the monotonous ALPS sequence.
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Affiliation(s)
- Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7275, Valbonne, France
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36
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Lee MJ, Jang S, Nahm M, Yoon JH, Lee S. Tbc1d15-17 regulates synaptic development at the Drosophila neuromuscular junction. Mol Cells 2013; 36:163-8. [PMID: 23812537 PMCID: PMC3887947 DOI: 10.1007/s10059-013-0147-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 05/23/2013] [Indexed: 11/25/2022] Open
Abstract
Members of the Tre-2/Bub2/Cdc16 (TBC) family of proteins are believed to function as GTPase-activating proteins (GAPs) for Rab GTPases, which play pivotal roles in intracellular membrane trafficking. Although membrane trafficking is fundamental to neuronal morphogenesis and function, the roles of TBC-family Rab GAPs have been poorly characterized in the nervous system. In this paper, we provide genetic evidence that Tbc1d15-17, the Drosophila homolog of mammalian Rab7-GAP TBC1d15, is required for normal presynaptic growth and postsynaptic organization at the neuromuscular junction (NMJ). A loss-of-function mutation in Tbc1d15-17 or its presynaptic knockdown leads to an increase in synaptic bouton number and NMJ length. Tbc1d15-17 mutants are also defective in the distribution of the postsynaptic scaffold Discs-large (Dlg) and in the level of the postsynaptic glutamate subunit GluRIIA. These postsynaptic phenotypes are recapitulated by postsynaptic knockdown of Tbc1d15-17. We also show that presynaptic overexpression of a constitutively active Rab7 mutant in a wild-type background causes a synaptic overgrowth phenotype resembling that of Tbc1d15-17 mutants, while a dominant-negative form of Rab7 has the opposite effect. Together, our findings establish a novel role for Tbc1d15-17 and its potential substrate Rab7 in regulating synaptic development.
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Affiliation(s)
- Min-Jung Lee
- Department of Cell and Developmental Biology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul 110-749,
Korea
| | | | - Minyeop Nahm
- Department of Cell and Developmental Biology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul 110-749,
Korea
| | | | - Seungbok Lee
- Department of Cell and Developmental Biology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul 110-749,
Korea
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Richardson TG, Thomas EC, Sessions RB, Lawlor DA, Tavaré JM, Day INM. Structural and population-based evaluations of TBC1D1 p.Arg125Trp. PLoS One 2013; 8:e63897. [PMID: 23667688 PMCID: PMC3646766 DOI: 10.1371/journal.pone.0063897] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 04/09/2013] [Indexed: 12/04/2022] Open
Abstract
Obesity is now a leading cause of preventable death in the industrialised world. Understanding its genetic influences can enhance insight into molecular pathogenesis and potential therapeutic targets. A non-synonymous polymorphism (rs35859249, p.Arg125Trp) in the N-terminal TBC1D1 phosphotyrosine-binding (PTB) domain has shown a replicated association with familial obesity in women. We investigated these findings in the Avon Longitudinal Study of Parents and Children (ALSPAC), a large European birth cohort of mothers and offspring, and by generating a predicted model of the structure of this domain. Structural prediction involved the use of three separate algorithms; Robetta, HHpred/MODELLER and I-TASSER. We used the transmission disequilibrium test (TDT) to investigate familial association in the ALSPAC study cohort (N = 2,292 mother-offspring pairs). Linear regression models were used to examine the association of genotype with mean measurements of adiposity (Body Mass Index (BMI), waist circumference and Dual-energy X-ray absorptiometry (DXA) assessed fat mass), and logistic regression was used to examine the association with odds of obesity. Modelling showed that the R125W mutation occurs in a location of the TBC1D1 PTB domain that is predicted to have a function in a putative protein:protein interaction. We did not detect an association between R125W and BMI (mean per allele difference 0.27 kg/m2 (95% Confidence Interval: 0.00, 0.53) P = 0.05) or obesity (odds ratio 1.01 (95% Confidence Interval: 0.77, 1.31, P = 0.96) in offspring after adjusting for multiple comparisons. Furthermore, there was no evidence to suggest that there was familial association between R125W and obesity (χ2 = 0.06, P = 0.80). Our analysis suggests that R125W in TBC1D1 plays a role in the binding of an effector protein, but we find no evidence that the R125W variant is related to mean BMI or odds of obesity in a general population sample.
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Affiliation(s)
- Tom G Richardson
- Bristol Genetic Epidemiology Laboratories, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, United Kingdom.
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He H, Bronisz A, Liyanarachchi S, Nagy R, Li W, Huang Y, Akagi K, Saji M, Kula D, Wojcicka A, Sebastian N, Wen B, Puch Z, Kalemba M, Stachlewska E, Czetwertynska M, Dlugosinska J, Dymecka K, Ploski R, Krawczyk M, Morrison PJ, Ringel MD, Kloos RT, Jazdzewski K, Symer DE, Vieland VJ, Ostrowski M, Jarząb B, de la Chapelle A. SRGAP1 is a candidate gene for papillary thyroid carcinoma susceptibility. J Clin Endocrinol Metab 2013; 98:E973-80. [PMID: 23539728 PMCID: PMC3644596 DOI: 10.1210/jc.2012-3823] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/04/2013] [Indexed: 01/27/2023]
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) shows high heritability, yet efforts to find predisposing genes have been largely negative. OBJECTIVES The objective of this study was to identify susceptibility genes for PTC. METHODS A genome-wide linkage analysis was performed in 38 families. Targeted association study and screening were performed in 2 large cohorts of PTC patients and controls. Candidate DNA variants were tested in functional studies. RESULTS Linkage analysis and association studies identified the Slit-Robo Rho GTPase activating protein 1 gene (SRGAP1) in the linkage peak as a candidate gene. Two missense variants, Q149H and A275T, localized in the Fes/CIP4 homology domain segregated with the disease in 1 family each. One missense variant, R617C, located in the RhoGAP domain occurred in 1 family. Biochemical assays demonstrated that the ability to inactivate CDC42, a key function of SRGAP1, was severely impaired by the Q149H and R617C variants. CONCLUSIONS Our findings suggest that SRGAP1 is a candidate gene in PTC susceptibility. SRGAP1 is likely a low-penetrant gene, possibly of a modifier type.
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Affiliation(s)
- Huiling He
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Comprehensive Cancer Center, the Ohio State University, Columbus, Ohio 43210, USA
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Lévay M, Bartos B, Ligeti E. p190RhoGAP has cellular RacGAP activity regulated by a polybasic region. Cell Signal 2013; 25:1388-94. [PMID: 23499677 DOI: 10.1016/j.cellsig.2013.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 02/19/2013] [Accepted: 03/06/2013] [Indexed: 01/09/2023]
Abstract
p190RhoGAP is a GTPase-activating protein (GAP) known to regulate actin cytoskeleton dynamics by decreasing RhoGTP levels through activation of the intrinsic GTPase activity of Rho. Although the GAP domain of p190RhoGAP stimulates the intrinsic' GTPase activity of several Rho family members (Rho, Rac, Cdc42) under in vitro conditions, p190RhoGAP is generally regarded as a GAP for RhoA in the cell. The cellular RacGAP activity of the protein has not been proven directly. We have previously shown that the in vitro RacGAP and RhoGAP activity of p190RhoGAP was inversely regulated through a polybasic region of the protein. Here we provide evidence that p190RhoGAP shows remarkable GAP activity toward Rac also in the cell. The cellular RacGAP activity of p190RhoGAP requires an intact polybasic region adjacent to the GAP domain whereas the RhoGAP activity is inhibited by the same domain. Our data indicate that through its alternating RacGAP and RhoGAP activity, p190RhoGAP plays a more complex role in the Rac-Rho antagonism than it was realized earlier.
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Affiliation(s)
- Magdolna Lévay
- Department of Physiology, Semmelweis University, Budapest, Hungary
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40
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Ma Y, Mi YJ, Dai YK, Fu HL, Cui DX, Jin WL. The inverse F-BAR domain protein srGAP2 acts through srGAP3 to modulate neuronal differentiation and neurite outgrowth of mouse neuroblastoma cells. PLoS One 2013; 8:e57865. [PMID: 23505444 PMCID: PMC3591447 DOI: 10.1371/journal.pone.0057865] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022] Open
Abstract
The inverse F-BAR (IF-BAR) domain proteins srGAP1, srGAP2 and srGAP3 are implicated in neuronal development and may be linked to mental retardation, schizophrenia and seizure. A partially overlapping expression pattern and highly similar protein structures indicate a functional redundancy of srGAPs in neuronal development. Our previous study suggests that srGAP3 negatively regulates neuronal differentiation in a Rac1-dependent manner in mouse Neuro2a cells. Here we show that exogenously expressed srGAP1 and srGAP2 are sufficient to inhibit valporic acid (VPA)-induced neurite initiation and growth in the mouse Neuro2a cells. While ectopic- or over-expression of RhoGAP-defective mutants, srGAP1R542A and srGAP2R527A exert a visible inhibitory effect on neuronal differentiation. Unexpectedly, knockdown of endogenous srGAP2 fails to facilitate the neuronal differentiation induced by VPA, but promotes neurite outgrowth of differentiated cells. All three IF-BAR domains from srGAP1-3 can induce filopodia formation in Neuro2a, but the isolated IF-BAR domain from srGAP2, not from srGAP1 and srGAP3, can promote VPA-induced neurite initiation and neuronal differentiation. We identify biochemical and functional interactions of the three srGAPs family members. We propose that srGAP3-Rac1 signaling may be required for the effect of srGAP1 and srGAP2 on attenuating neuronal differentiation. Furthermore, inhibition of Slit-Robo interaction can phenocopy a loss-of-function of srGAP3, indicating that srGAP3 may be dedicated to the Slit-Robo pathway. Our results demonstrate the interplay between srGAP1, srGAP2 and srGAP3 regulates neuronal differentiation and neurite outgrowth. These findings may provide us new insights into the possible roles of srGAPs in neuronal development and a potential mechanism for neurodevelopmental diseases.
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Affiliation(s)
- Yue Ma
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Department of Bio-Nano-Science and Engineering, Institute of Micro-Nano Science and Technology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ya-Jing Mi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Lab of Cell Biology & Translational Medicine, Xi'an Medical University, Xi'an, People's Republic of China
| | - Yun-Kai Dai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hua-Lin Fu
- Department of Bio-Nano-Science and Engineering, Institute of Micro-Nano Science and Technology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Da-Xiang Cui
- Department of Bio-Nano-Science and Engineering, Institute of Micro-Nano Science and Technology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Wei-Lin Jin
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Department of Bio-Nano-Science and Engineering, Institute of Micro-Nano Science and Technology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- * E-mail:
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41
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Serva A, Knapp B, Tsai YT, Claas C, Lisauskas T, Matula P, Harder N, Kaderali L, Rohr K, Erfle H, Eils R, Braga V, Starkuviene V. miR-17-5p regulates endocytic trafficking through targeting TBC1D2/Armus. PLoS One 2012; 7:e52555. [PMID: 23285084 PMCID: PMC3527550 DOI: 10.1371/journal.pone.0052555] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/15/2012] [Indexed: 01/07/2023] Open
Abstract
miRNA cluster miR-17-92 is known as oncomir-1 due to its potent oncogenic function. miR-17-92 is a polycistronic cluster that encodes 6 miRNAs, and can both facilitate and inhibit cell proliferation. Known targets of miRNAs encoded by this cluster are largely regulators of cell cycle progression and apoptosis. Here, we show that miRNAs encoded by this cluster and sharing the seed sequence of miR-17 exert their influence on one of the most essential cellular processes – endocytic trafficking. By mRNA expression analysis we identified that regulation of endocytic trafficking by miR-17 can potentially be achieved by targeting of a number of trafficking regulators. We have thoroughly validated TBC1D2/Armus, a GAP of Rab7 GTPase, as a novel target of miR-17. Our study reveals regulation of endocytic trafficking as a novel function of miR-17, which might act cooperatively with other functions of miR-17 and related miRNAs in health and disease.
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Affiliation(s)
- Andrius Serva
- BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Bettina Knapp
- BioQuant, University of Heidelberg, Heidelberg, Germany
- Institute for Medical Informatics and Biometry, University of Technology Dresden, Dresden, Germany
| | - Yueh-Tso Tsai
- BioQuant, University of Heidelberg, Heidelberg, Germany
| | | | | | - Petr Matula
- Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
- Center for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Nathalie Harder
- Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Lars Kaderali
- BioQuant, University of Heidelberg, Heidelberg, Germany
- Institute for Medical Informatics and Biometry, University of Technology Dresden, Dresden, Germany
| | - Karl Rohr
- Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Holger Erfle
- BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Roland Eils
- Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Vania Braga
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Mercurio FA, Marasco D, Pirone L, Scognamiglio PL, Pedone EM, Pellecchia M, Leone M. Heterotypic Sam-Sam association between Odin-Sam1 and Arap3-Sam: binding affinity and structural insights. Chembiochem 2012; 14:100-6. [PMID: 23239578 DOI: 10.1002/cbic.201200592] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Indexed: 11/07/2022]
Abstract
Arap3 is a phosphatidylinositol 3 kinase effector protein that plays a role as GTPase activator (GAP) for Arf6 and RhoA. Arap3 contains a sterile alpha motif (Sam) domain that has high sequence homology with the Sam domain of the EphA2-receptor (EphA2-Sam). Both Arap3-Sam and EphA2-Sam are able to associate with the Sam domain of the lipid phosphatase Ship2 (Ship2-Sam). Recently, we reported a novel interaction between the first Sam domain of Odin (Odin-Sam1), a protein belonging to the ANKS (ANKyrin repeat and Sam domain containing) family, and EphA2-Sam. In our latest work, we applied NMR spectroscopy, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) to characterize the association between Arap3-Sam and Odin-Sam1. We show that these two Sam domains interact with low micromolar affinity. Moreover, by means of molecular docking techniques, supported by NMR data, we demonstrate that Odin-Sam1 and Arap3-Sam might bind with a topology that is common to several Sam-Sam complexes. The revealed structural details form the basis for the design of potential peptide antagonists that could be used as chemical tools to investigate functional aspects related to heterotypic Arap3-Sam associations.
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Affiliation(s)
- Flavia A Mercurio
- Department of Biological Sciences, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
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43
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Rajasekar KV, Campbell LJ, Nietlispach D, Owen D, Mott HR. 1H, 13C and 15N resonance assignments of the GTPase-activating (GAP) and Ral binding domains (GBD) of RLIP76 (RalBP1). Biomol NMR Assign 2012; 6:119-122. [PMID: 21915608 DOI: 10.1007/s12104-011-9337-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/25/2011] [Indexed: 05/31/2023]
Abstract
RLIP76 (also known as RalBP1) is an effector for Ral small G proteins. RLIP76 is a multifunctional, multi-domain protein that includes a GTPase activating domain for the Rho family (RhoGAP domain) and a GTPase binding domain (GBD) for the Ral small G proteins. The juxtaposition of these two domains (GAP and GBD) may be a strategy employed to co-ordinate regulation of Rho family and Ral-controlled signalling pathways at a crossover node. Here we present the (1)H, (15)N and (13)C NMR backbone and sidechain resonance assignments of the GAP and GBD di-domain (31 kDa).
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Affiliation(s)
- Karthik V Rajasekar
- Department of Biochemistry, University of Cambridge, 80, Tennis Court Road, Cambridge CB2 1GA, UK
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44
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Hu SH, Whitten AE, King GJ, Jones A, Rowland AF, James DE, Martin JL. The weak complex between RhoGAP protein ARHGAP22 and signal regulatory protein 14-3-3 has 1:2 stoichiometry and a single peptide binding mode. PLoS One 2012; 7:e41731. [PMID: 22952583 PMCID: PMC3429473 DOI: 10.1371/journal.pone.0041731] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/25/2012] [Indexed: 12/17/2022] Open
Abstract
ARHGAP22 is a RhoGAP protein comprising an N-terminal PH domain, a RhoGAP domain and a C-terminal coiled-coil domain. It has recently been identified as an Akt substrate that binds 14-3-3 proteins in response to treatment with growth factors involved in cell migration. We used a range of biophysical techniques to investigate the weak interaction between 14-3-3 and a truncated form of ARHGAP22 lacking the coiled-coil domain. This weak interaction could be stabilized by chemical cross-linking which we used to show that: a monomer of ARHGAP22 binds a dimer of 14-3-3; the ARHGAP22 PH domain is required for the 14-3-3 interaction; the RhoGAP domain is unlikely to participate in the interaction; Ser16 is the more important of two predicted 14-3-3 binding sites; and, phosphorylation of Ser16 may not be necessary for 14-3-3 interaction under the conditions we used. Small angle X-ray scattering and cross-link information were used to generate solution structures of the isolated proteins and of the cross-linked ARHGAP22:14-3-3 complex, showing that no major rearrangement occurs in either protein upon binding, and supporting a role for the PH domain and N-terminal peptide of ARHGAP22 in the 14-3-3 interaction. Small-angle X-ray scattering measurements of mixtures of ARHGAP22 and 14-3-3 were used to establish that the affinity of the interaction is ∼30 µM.
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Affiliation(s)
- Shu-Hong Hu
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew E. Whitten
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Gordon J. King
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland, Australia
| | - Alexander F. Rowland
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
| | - David E. James
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
| | - Jennifer L. Martin
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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45
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Rudack T, Xia F, Schlitter J, Kötting C, Gerwert K. The role of magnesium for geometry and charge in GTP hydrolysis, revealed by quantum mechanics/molecular mechanics simulations. Biophys J 2012; 103:293-302. [PMID: 22853907 PMCID: PMC3400779 DOI: 10.1016/j.bpj.2012.06.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 06/13/2012] [Accepted: 06/13/2012] [Indexed: 11/25/2022] Open
Abstract
The coordination of the magnesium ion in proteins by triphosphates plays an important role in catalytic hydrolysis of GTP or ATP, either in signal transduction or energy conversion. For example, in Ras the magnesium ion contributes to the catalysis of GTP hydrolysis. The cleavage of GTP to GDP and P(i) in Ras switches off cellular signaling. We analyzed GTP hydrolysis in water, Ras, and Ras·Ras-GTPase-activating protein using quantum mechanics/molecular mechanics simulations. By comparison of the theoretical IR-difference spectra for magnesium ion coordinated triphosphate to experimental ones, the simulations are validated. We elucidated thereby how the magnesium ion contributes to catalysis. It provides a temporary storage for the electrons taken from the triphosphate and it returns them after bond cleavage and P(i) release back to the diphosphate. Furthermore, the Ras·Mg(2+) complex forces the triphosphate into a stretched conformation in which the β- and γ-phosphates are coordinated in a bidentate manner. In this conformation, the triphosphate elongates the bond, which has to be cleaved during hydrolysis. Furthermore, the γ-phosphate adopts a more planar structure, driving the conformation of the molecule closer to the hydrolysis transition state. GTPase-activating protein enhances these changes in GTP conformation and charge distribution via the intruding arginine finger.
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Affiliation(s)
- Till Rudack
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
| | - Fei Xia
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China
| | - Jürgen Schlitter
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
| | - Carsten Kötting
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China
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Lachmann J, Barr FA, Ungermann C. The Msb3/Gyp3 GAP controls the activity of the Rab GTPases Vps21 and Ypt7 at endosomes and vacuoles. Mol Biol Cell 2012; 23:2516-26. [PMID: 22593206 PMCID: PMC3386215 DOI: 10.1091/mbc.e11-12-1030] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/23/2012] [Accepted: 05/08/2012] [Indexed: 12/04/2022] Open
Abstract
Fusion of organelles in the endomembrane system depends on Rab GTPases that interact with tethering factors before lipid bilayer mixing. In yeast, the Rab5 GTPase Vps21 controls fusion and membrane dynamics between early and late endosomes. Here we identify Msb3/Gyp3 as a specific Vps21 GTPase-activating protein (GAP). Loss of Msb3 results in an accumulation of Vps21 and one of its effectors Vps8, a subunit of the CORVET complex, at the vacuole membrane in vivo. In agreement, Msb3 forms a specific transition complex with Vps21, has the highest activity of all recombinant GAPs for Vps21 in vitro, and is found at vacuoles despite its predominant localization to bud tips and bud necks at the plasma membrane. Surprisingly, Msb3 also inhibits vacuole fusion, which can be rescued by the Ypt7 GDP-GTP exchange factor (GEF), the Mon1-Ccz1 complex. Consistently, msb3 vacuoles fuse more efficiently than wild-type vacuoles in vitro, suggesting that GAP can also act on Ypt7. Our data indicate that GAPs such as Msb3 can act on multiple substrates in vivo at both ends of a trafficking pathway. This ensures specificity of the subsequent GEF-mediated activation of the Rab that initiates the next transport event.
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Affiliation(s)
- Jens Lachmann
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Francis A. Barr
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Christian Ungermann
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
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Dixon MJ, Gray A, Schenning M, Agacan M, Tempel W, Tong Y, Nedyalkova L, Park HW, Leslie NR, van Aalten DMF, Downes CP, Batty IH. IQGAP proteins reveal an atypical phosphoinositide (aPI) binding domain with a pseudo C2 domain fold. J Biol Chem 2012; 287:22483-96. [PMID: 22493426 PMCID: PMC3391087 DOI: 10.1074/jbc.m112.352773] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/26/2012] [Indexed: 01/22/2023] Open
Abstract
Class I phosphoinositide (PI) 3-kinases act through effector proteins whose 3-PI selectivity is mediated by a limited repertoire of structurally defined, lipid recognition domains. We describe here the lipid preferences and crystal structure of a new class of PI binding modules exemplified by select IQGAPs (IQ motif containing GTPase-activating proteins) known to coordinate cellular signaling events and cytoskeletal dynamics. This module is defined by a C-terminal 105-107 amino acid region of which IQGAP1 and -2, but not IQGAP3, binds preferentially to phosphatidylinositol 3,4,5-trisphosphate (PtdInsP(3)). The binding affinity for PtdInsP(3), together with other, secondary target-recognition characteristics, are comparable with those of the pleckstrin homology domain of cytohesin-3 (general receptor for phosphoinositides 1), an established PtdInsP(3) effector protein. Importantly, the IQGAP1 C-terminal domain and the cytohesin-3 pleckstrin homology domain, each tagged with enhanced green fluorescent protein, were both re-localized from the cytosol to the cell periphery following the activation of PI 3-kinase in Swiss 3T3 fibroblasts, consistent with their common, selective recognition of endogenous 3-PI(s). The crystal structure of the C-terminal IQGAP2 PI binding module reveals unexpected topological similarity to an integral fold of C2 domains, including a putative basic binding pocket. We propose that this module integrates select IQGAP proteins with PI 3-kinase signaling and constitutes a novel, atypical phosphoinositide binding domain that may represent the first of a larger group, each perhaps structurally unique but collectively dissimilar from the known PI recognition modules.
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Affiliation(s)
| | | | | | - Mark Agacan
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow St., Dundee DD1 5EH, Scotland, United Kingdom and
| | | | | | | | - Hee-Won Park
- the Structural Genomics Consortium and
- Department of Pharmacology, University of Toronto, Toronto, Ontario M5G 1L5, Canada
| | | | | | | | - Ian H. Batty
- From the Division of Cell Signalling and Immunology and
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Longatti A, Lamb CA, Razi M, Yoshimura SI, Barr FA, Tooze SA. TBC1D14 regulates autophagosome formation via Rab11- and ULK1-positive recycling endosomes. J Cell Biol 2012; 197:659-75. [PMID: 22613832 PMCID: PMC3365497 DOI: 10.1083/jcb.201111079] [Citation(s) in RCA: 291] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 04/25/2012] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a bulk degradation process characterized by the formation of double membrane vesicles called autophagosomes. The exact molecular mechanism of autophagosome formation and the origin of the autophagosomal membrane remain unclear. We screened 38 human Tre-2/Bub2/Cdc16 domain-containing Rab guanosine triphosphatase-activating proteins (GAPs) and identified 11 negative regulators of starvation-induced autophagy. One of these putative RabGAPs, TBC1D14, colocalizes and interacts with the autophagy kinase ULK1. Overexpressed TBC1D14 tubulates ULK1-positive recycling endosomes (REs), impairing their function and inhibiting autophagosome formation. TBC1D14 binds activated Rab11 but is not a GAP for Rab11, and loss of Rab11 prevents TBC1D14-induced tubulation of REs. Furthermore, Rab11 is required for autophagosome formation. ULK1 and Atg9 are found on Rab11- and transferrin (Tfn) receptor (TfnR)-positive recycling endosomes. Amino acid starvation causes TBC1D14 to relocalize from REs to the Golgi complex, whereas TfnR and Tfn localize to forming autophagosomes, which are ULK1 and LC3 positive. Thus, TBC1D14- and Rab11-dependent vesicular transport from REs contributes to and regulates starvation-induced autophagy.
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Affiliation(s)
- Andrea Longatti
- Cancer Research UK London Research Institute, WC2A 3PF London, England, UK
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037
| | | | - Minoo Razi
- Cancer Research UK London Research Institute, WC2A 3PF London, England, UK
| | - Shin-ichiro Yoshimura
- Department of Cell Biology, Graduate School of Medicine, Osaka University, 565-0871 Osaka, Japan
| | - Francis A. Barr
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, England, UK
| | - Sharon A. Tooze
- Cancer Research UK London Research Institute, WC2A 3PF London, England, UK
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Gupta AB, Wee LE, Zhou YT, Hortsch M, Low BC. Cross-species analyses identify the BNIP-2 and Cdc42GAP homology (BCH) domain as a distinct functional subclass of the CRAL_TRIO/Sec14 superfamily. PLoS One 2012; 7:e33863. [PMID: 22479462 PMCID: PMC3313917 DOI: 10.1371/journal.pone.0033863] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 02/18/2012] [Indexed: 11/19/2022] Open
Abstract
The CRAL_TRIO protein domain, which is unique to the Sec14 protein superfamily, binds to a diverse set of small lipophilic ligands. Similar domains are found in a range of different proteins including neurofibromatosis type-1, a Ras GTPase-activating Protein (RasGAP) and Rho guanine nucleotide exchange factors (RhoGEFs). Proteins containing this structural protein domain exhibit a low sequence similarity and ligand specificity while maintaining an overall characteristic three-dimensional structure. We have previously demonstrated that the BNIP-2 and Cdc42GAP Homology (BCH) protein domain, which shares a low sequence homology with the CRAL_TRIO domain, can serve as a regulatory scaffold that binds to Rho, RhoGEFs and RhoGAPs to control various cell signalling processes. In this work, we investigate 175 BCH domain-containing proteins from a wide range of different organisms. A phylogenetic analysis with ∼100 CRAL_TRIO and similar domains from eight representative species indicates a clear distinction of BCH-containing proteins as a novel subclass within the CRAL_TRIO/Sec14 superfamily. BCH-containing proteins contain a hallmark sequence motif R(R/K)h(R/K)(R/K)NL(R/K)xhhhhHPs (‘h’ is large and hydrophobic residue and ‘s’ is small and weekly polar residue) and can be further subdivided into three unique subtypes associated with BNIP-2-N, macro- and RhoGAP-type protein domains. A previously unknown group of genes encoding ‘BCH-only’ domains is also identified in plants and arthropod species. Based on an analysis of their gene-structure and their protein domain context we hypothesize that BCH domain-containing genes evolved through gene duplication, intron insertions and domain swapping events. Furthermore, we explore the point of divergence between BCH and CRAL-TRIO proteins in relation to their ability to bind small GTPases, GAPs and GEFs and lipid ligands. Our study suggests a need for a more extensive analysis of previously uncharacterized BCH, ‘BCH-like’ and CRAL_TRIO-containing proteins and their significance in regulating signaling events involving small GTPases.
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Affiliation(s)
- Anjali Bansal Gupta
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Liang En Wee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yi Ting Zhou
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Michael Hortsch
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Boon Chuan Low
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- * E-mail:
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Zhang JL, Patterson LJ, Qiu LY, Graziussi D, Sebald W, Hammerschmidt M. Binding between Crossveinless-2 and Chordin von Willebrand factor type C domains promotes BMP signaling by blocking Chordin activity. PLoS One 2010; 5:e12846. [PMID: 20886103 PMCID: PMC2944808 DOI: 10.1371/journal.pone.0012846] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 08/24/2010] [Indexed: 12/04/2022] Open
Abstract
Background Crossveinless-2 (CV2) is an extracellular BMP modulator protein of the Chordin family, which can either enhance or inhibit BMP activity. CV2 binds to BMP2 via subdomain 1 of the first of its five N-terminal von Willebrand factor type C domains (VWC1). Previous studies showed that this BMP binding is required for the anti-, but not for the pro-BMP effect of CV2. More recently, it was shown that CV2 can also bind to the BMP inhibitor Chordin. However, it remained unclear which domains mediate this binding, and whether it accounts for an anti- or pro-BMP effect. Principal Findings Here we report that a composite interface of CV2 consisting of subdomain 2 of VWC1 and of VWC2-4, which are dispensable for BMP binding, binds to the VWC2 domain of Chordin. Functional data obtained in zebrafish embryos indicate that this binding of Chordin is required for CV2's pro-BMP effect, which actually is an anti-Chordin effect and, at least to a large extent, independent of Tolloid-mediated Chordin degradation. We further demonstrate that CV2 mutant versions that per se are incapable of BMP binding can attenuate the Chordin/BMP interaction. Conclusions We have physically dissected the anti- and pro-BMP effects of CV2. Its anti-BMP effect is obtained by binding to BMP via subdomain1 of the VWC1 domain, a binding that occurs in competition with Chordin. In contrast, its pro-BMP effect is achieved by direct binding to Chordin via subdomain 2 of VWC1 and VWC2-4. This binding seems to induce conformational changes within the Chordin protein that weaken Chordin's affinity to BMP. We propose that in ternary Chordin-CV2-BMP complexes, both BMP and Chordin are directly associated with CV2, whereas Chordin is pushed away from BMP, ensuring that BMPs can be more easily delivered to their receptors.
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Affiliation(s)
- Jin-Li Zhang
- Institute for Developmental Biology, Cologne Biocenter, University of Cologne, Cologne, Germany
- Department of Physiological Chemistry II, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- * E-mail: (MH); (JLZ)
| | - Lucy J. Patterson
- Institute for Developmental Biology, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Li-Yan Qiu
- Department of Physiological Chemistry II, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Daria Graziussi
- Institute for Developmental Biology, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Walter Sebald
- Department of Physiological Chemistry II, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Matthias Hammerschmidt
- Institute for Developmental Biology, Cologne Biocenter, University of Cologne, Cologne, Germany
- Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CEDAD), University of Cologne, Cologne, Germany
- * E-mail: (MH); (JLZ)
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