1
|
Erol ÖD, Şenocak Ş, Aerts-Kaya F. The Role of Rab GTPases in the development of genetic and malignant diseases. Mol Cell Biochem 2024; 479:255-281. [PMID: 37060515 DOI: 10.1007/s11010-023-04727-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/01/2023] [Indexed: 04/16/2023]
Abstract
Small GTPases have been shown to play an important role in several cellular functions, including cytoskeletal remodeling, cell polarity, intracellular trafficking, cell-cycle, progression and lipid transformation. The Ras-associated binding (Rab) family of GTPases constitutes the largest family of GTPases and consists of almost 70 known members of small GTPases in humans, which are known to play an important role in the regulation of intracellular membrane trafficking, membrane identity, vesicle budding, uncoating, motility and fusion of membranes. Mutations in Rab genes can cause a wide range of inherited genetic diseases, ranging from neurodegenerative diseases, such as Parkinson's disease (PD) and Alzheimer's disease (AD) to immune dysregulation/deficiency syndromes, like Griscelli Syndrome Type II (GS-II) and hemophagocytic lymphohistiocytosis (HLH), as well as a variety of cancers. Here, we provide an extended overview of human Rabs, discussing their function and diseases related to Rabs and Rab effectors, as well as focusing on effects of (aberrant) Rab expression. We aim to underline their importance in health and the development of genetic and malignant diseases by assessing their role in cellular structure, regulation, function and biology and discuss the possible use of stem cell gene therapy, as well as targeting of Rabs in order to treat malignancies, but also to monitor recurrence of cancer and metastasis through the use of Rabs as biomarkers. Future research should shed further light on the roles of Rabs in the development of multifactorial diseases, such as diabetes and assess Rabs as a possible treatment target.
Collapse
Affiliation(s)
- Özgür Doğuş Erol
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey
| | - Şimal Şenocak
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey
| | - Fatima Aerts-Kaya
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey.
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey.
| |
Collapse
|
2
|
Putar D, Čizmar A, Chao X, Šimić M, Šoštar M, Ćutić T, Mijanović L, Smolko A, Tu H, Cosson P, Weber I, Cai H, Filić V. IqgC is a potent regulator of macropinocytosis in the presence of NF1 and its loading to macropinosomes is dependent on RasG. Open Biol 2024; 14:230372. [PMID: 38263885 PMCID: PMC10806400 DOI: 10.1098/rsob.230372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/26/2023] [Indexed: 01/25/2024] Open
Abstract
RasG is a major regulator of macropinocytosis in Dictyostelium discoideum. Its activity is under the control of an IQGAP-related protein, IqgC, which acts as a RasG-specific GAP (GTPase activating protein). IqgC colocalizes with the active Ras at the macropinosome membrane during its formation and for some time after the cup closure. However, the loss of IqgC induces only a minor enhancement of fluid uptake in axenic cells that already lack another RasGAP, NF1. Here, we show that IqgC plays an important role in the regulation of macropinocytosis in the presence of NF1 by restricting the size of macropinosomes. We further provide evidence that interaction with RasG is indispensable for the recruitment of IqgC to forming macropinocytic cups. We also demonstrate that IqgC interacts with another small GTPase from the Ras superfamily, Rab5A, but is not a GAP for Rab5A. Since mammalian Rab5 plays a key role in early endosome maturation, we hypothesized that IqgC could be involved in macropinosome maturation via its interaction with Rab5A. Although an excessive amount of Rab5A reduces the RasGAP activity of IqgC in vitro and correlates with IqgC dissociation from endosomes in vivo, the physiological significance of the Rab5A-IqgC interaction remains elusive.
Collapse
Affiliation(s)
- Darija Putar
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Anja Čizmar
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Xiaoting Chao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, People's Republic of China
| | - Marija Šimić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Marko Šoštar
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Tamara Ćutić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lucija Mijanović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ana Smolko
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Hui Tu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, People's Republic of China
| | - Pierre Cosson
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Igor Weber
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, People's Republic of China
| | - Vedrana Filić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| |
Collapse
|
3
|
Quentin D, Schuhmacher JS, Klink BU, Lauer J, Shaikh TR, Huis In 't Veld PJ, Welp LM, Urlaub H, Zerial M, Raunser S. Structural basis of mRNA binding by the human FERRY Rab5 effector complex. Mol Cell 2023; 83:1856-1871.e9. [PMID: 37267906 DOI: 10.1016/j.molcel.2023.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/05/2022] [Accepted: 05/05/2023] [Indexed: 06/04/2023]
Abstract
The pentameric FERRY Rab5 effector complex is a molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of human FERRY. It reveals a unique clamp-like architecture that bears no resemblance to any known structure of Rab effectors. A combination of functional and mutational studies reveals that while the Fy-2 C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils and Fy-5 concur to bind mRNA. Mutations causing truncations of Fy-2 in patients with neurological disorders impair Rab5 binding or FERRY complex assembly. Thus, Fy-2 serves as a binding hub connecting all five complex subunits and mediating the binding to mRNA and early endosomes via Rab5. Our study provides mechanistic insights into long-distance mRNA transport and demonstrates that the particular architecture of FERRY is closely linked to a previously undescribed mode of RNA binding, involving coiled-coil domains.
Collapse
Affiliation(s)
- Dennis Quentin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Jan S Schuhmacher
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Björn U Klink
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany; Center for Soft Nanoscience and Institute of Molecular Physics and Biophysics, 48149 Münster, Germany
| | - Jeni Lauer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tanvir R Shaikh
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Pim J Huis In 't Veld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Luisa M Welp
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.
| |
Collapse
|
4
|
Lee HK, Kwon DH, Aylor DL, Marchuk DA. A cross-species approach using an in vivo evaluation platform in mice demonstrates that sequence variation in human RABEP2 modulates ischemic stroke outcomes. Am J Hum Genet 2022; 109:1814-1827. [PMID: 36167069 PMCID: PMC9606478 DOI: 10.1016/j.ajhg.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/01/2022] [Indexed: 01/25/2023] Open
Abstract
Ischemic stroke, caused by vessel blockage, results in cerebral infarction, the death of brain tissue. Previously, quantitative trait locus (QTL) mapping of cerebral infarct volume and collateral vessel number identified a single, strong genetic locus regulating both phenotypes. Additional studies identified RAB GTPase-binding effector protein 2 (Rabep2) as the casual gene. However, there is yet no evidence that variation in the human ortholog of this gene plays any role in ischemic stroke outcomes. We established an in vivo evaluation platform in mice by using adeno-associated virus (AAV) gene replacement and verified that both mouse and human RABEP2 rescue the mouse Rabep2 knockout ischemic stroke volume and collateral vessel phenotypes. Importantly, this cross-species complementation enabled us to experimentally investigate the functional effects of coding sequence variation in human RABEP2. We chose four coding variants from the human population that are predicted by multiple in silico algorithms to be damaging to RABEP2 function. In vitro and in vivo analyses verify that all four led to decreased collateral vessel connections and increased infarct volume. Thus, there are naturally occurring loss-of-function alleles. This cross-species approach will expand the number of targets for therapeutics development for ischemic stroke.
Collapse
Affiliation(s)
- Han Kyu Lee
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Do Hoon Kwon
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - David L Aylor
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
5
|
Banworth MJ, Liang Z, Li G. A Novel Membrane Targeting Domain Mediates the Endosomal or Golgi Localization Specificity of Small GTPases Rab22 and Rab31. J Biol Chem 2022; 298:102281. [PMID: 35863437 PMCID: PMC9403361 DOI: 10.1016/j.jbc.2022.102281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Rab22 and Rab31 belong to the Rab5 subfamily of GTPases that regulates endocytic traffic and endosomal sorting. Rab22 and Rab31 (a.k.a. Rab22b) are closely related and share 87% amino acid sequence similarity, but they show distinct intracellular localization and function in the cell. Rab22 is localized to early endosomes and regulates early endosomal recycling, while Rab31 is mostly localized to the Golgi complex with only a small fraction in the endosomes at steady state. The specific determinants that affect this differential localization, however, are unclear. In this study, we identify a novel membrane targeting domain (MTD) consisting of the C-terminal hypervariable domain (HVD), inter-switch loop (ISL), and N-terminal domain as a major determinant of endosomal localization for Rab22 and Rab31, as well as Rab5. Rab22 and Rab31 share the same N-terminal domain, but we find Rab22 chimeras with Rab31 HVD exhibit phenotypic Rab31 localization to the Golgi complex while Rab31 chimeras with the Rab22 HVD localize to early endosomes, similar to wild type Rab22. We also find that the Rab22 HVD favors interaction with the early endosomal effector protein Rabenosyn-5, which may stabilize the Rab localization to the endosomes. The importance of effector interaction in endosomal localization is further demonstrated by the disruption of Rab22 endosomal localization in Rabenosyn-5 knockout cells and by the shift of Rab31 to the endosomes in Rabenosyn-5 overexpressing cells. Taken together, we have identified a novel MTD that mediates localization of Rab5 subfamily members to early endosomes via interaction with an effector such as Rabenosyn-5.
Collapse
Affiliation(s)
- Marcellus J Banworth
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Zhimin Liang
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Guangpu Li
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| |
Collapse
|
6
|
Poly(ADP-ribose) Polymerase 1 Mediates Rab5 Inactivation after DNA Damage. Int J Mol Sci 2022; 23:ijms23147827. [PMID: 35887176 PMCID: PMC9319841 DOI: 10.3390/ijms23147827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Parthanatos is programmed cell death mediated by poly(ADP-ribose) polymerase 1 (PARP1) after DNA damage. PARP1 acts by catalyzing the transfer of poly(ADP-ribose) (PAR) polymers to various nuclear proteins. PAR is subsequently cleaved, generating protein-free PAR polymers, which are translocated to the cytoplasm where they associate with cytoplasmic and mitochondrial proteins, altering their functions and leading to cell death. Proteomic studies revealed that several proteins involved in endocytosis bind PAR after PARP1 activation, suggesting endocytosis may be affected by the parthanatos process. Endocytosis is a mechanism for cellular uptake of membrane-impermeant nutrients. Rab5, a small G-protein, is associated with the plasma membrane and early endosomes. Once activated by binding GTP, Rab5 recruits its effectors to early endosomes and regulates their fusion. Here, we report that after DNA damage, PARP1-generated PAR binds to Rab5, suppressing its activity. As a result, Rab5 is dissociated from endosomal vesicles, inhibiting the uptake of membrane-impermeant nutrients. This PARP1-dependent inhibition of nutrient uptake leads to cell starvation and death. It thus appears that this mechanism may represent a novel parthanatos pathway.
Collapse
|
7
|
Martínez-Morales JC, Romero-Ávila MT, Reyes-Cruz G, García-Sáinz JA. Roles of receptor phosphorylation and Rab proteins in G protein-coupled receptor function and trafficking. Mol Pharmacol 2021; 101:144-153. [PMID: 34969830 DOI: 10.1124/molpharm.121.000429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/22/2021] [Indexed: 11/22/2022] Open
Abstract
The G Protein-Coupled Receptors form the most abundant family of membrane proteins and are crucial physiological players in the homeostatic equilibrium, which we define as health. They also participate in the pathogenesis of many diseases and are frequent targets of therapeutic intervention. Considering their importance, it is not surprising that different mechanisms regulate their function, including desensitization, resensitization, internalization, recycling to the plasma membrane, and degradation. These processes are modulated in a highly coordinated and specific way by protein kinases and phosphatases, ubiquitin ligases, protein adaptors, interaction with multifunctional complexes, molecular motors, phospholipid metabolism, and membrane distribution. This review describes significant advances in the study of the regulation of these receptors by phosphorylation and endosomal traffic (where signaling can take place); we revisited the bar code hypothesis and include two additional observations: a) that different phosphorylation patterns seem to be associated with internalization and endosome sorting for recycling or degradation, and b) that, surprisingly, phosphorylation of some G protein-coupled receptors appears to be required for proper receptor insertion into the plasma membrane. Significance Statement G protein-coupled receptor phosphorylation is an early event in desensitization/ signaling switching, endosomal traffic, and internalization. These events seem crucial for receptor responsiveness, cellular localization, and fate (recycling/ degradation) with important pharmacological/ therapeutic implications. Phosphorylation sites vary depending on the cells in which they are expressed and on the stimulus that leads to such covalent modification. Surprisingly, evidence suggests that phosphorylation also seems to be required for proper insertion into the plasma membrane for some receptors.
Collapse
|
8
|
Parkinson G, Roboti P, Zhang L, Taylor S, Woodman P. His domain protein tyrosine phosphatase and Rabaptin-5 couple endo-lysosomal sorting of EGFR with endosomal maturation. J Cell Sci 2021; 134:272512. [PMID: 34657963 PMCID: PMC8627557 DOI: 10.1242/jcs.259192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/13/2021] [Indexed: 01/20/2023] Open
Abstract
His domain protein tyrosine phosphatase (HD-PTP; also known as PTPN23) collaborates with endosomal sorting complexes required for transport (ESCRTs) to sort endosomal cargo into intralumenal vesicles, forming the multivesicular body (MVB). Completion of MVB sorting is accompanied by maturation of the endosome into a late endosome, an event that requires inactivation of the early endosomal GTPase Rab5 (herein referring to generically to all isoforms). Here, we show that HD-PTP links ESCRT function with endosomal maturation. HD-PTP depletion prevents MVB sorting, while also blocking cargo from exiting Rab5-rich endosomes. HD-PTP-depleted cells contain hyperphosphorylated Rabaptin-5 (also known as RABEP1), a cofactor for the Rab5 guanine nucleotide exchange factor Rabex-5 (also known as RABGEF1), although HD-PTP is unlikely to directly dephosphorylate Rabaptin-5. In addition, HD-PTP-depleted cells exhibit Rabaptin-5-dependent hyperactivation of Rab5. HD-PTP binds directly to Rabaptin-5, between its Rabex-5- and Rab5-binding domains. This binding reaction involves the ESCRT-0/ESCRT-III binding site in HD-PTP, which is competed for by an ESCRT-III peptide. Jointly, these findings indicate that HD-PTP may alternatively scaffold ESCRTs and modulate Rabex-5–Rabaptin-5 activity, thereby helping to coordinate the completion of MVB sorting with endosomal maturation. Summary: Sorting of endocytic cargo to the multivesicular body is accompanied by endosomal maturation. Here, we provide a potential mechanism by which these two processes are linked.
Collapse
Affiliation(s)
- Gabrielle Parkinson
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Peristera Roboti
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Ling Zhang
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Sandra Taylor
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Philip Woodman
- Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| |
Collapse
|
9
|
Probing the Peculiarity of EhRabX10, a pseudoRab GTPase, from the Enteric Parasite Entamoeba histolytica through In Silico Modeling and Docking Studies. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9913625. [PMID: 34660804 PMCID: PMC8514894 DOI: 10.1155/2021/9913625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/08/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022]
Abstract
Entamoeba histolytica (Eh) is a pathogenic eukaryote that often resides silently in humans under asymptomatic stages. Upon indeterminate stimulus, it develops into fulminant amoebiasis that causes severe hepatic abscesses with 50% mortality. This neglected tropical pathogen relies massively on membrane modulation to flourish and cause disease; these modulations range from the phagocytic mode for food acquisition to a complex trogocytosis mechanism for tissue invasion. Rab GTPases form the largest branch of the Ras-like small GTPases, with a diverse set of roles across the eukaryotic kingdom. Rab GTPases are vital for the orchestration of membrane transport and the secretory pathway responsible for transporting the pathogenic effectors, such as cysteine proteases (EhCPs) which help in tissue invasion. Rab GTPases thus play a crucial role in executing the cytolytic effect of E. histolytica. First, they interact with Gal/Nac lectins required for adhering to the host cells, and then, they assist in the secretion of EhCPs. Additionally, amoebic Rab GTPases are vital for encystation because substantial vesicular trafficking is required to create dormant amoebic cysts. These cysts are the infective agent and help to spread the disease. The absence of a "bonafide" vesicular transport machinery in Eh and the existence of a diverse repertoire of amoebic Rab GTPases (EhRab) hint at their contribution in supporting this atypical machinery. Here, we provide insights into a pseudoRab GTPase, EhRabX10, by performing physicochemical analysis, predictive 3D structure modeling, protein-protein interaction studies, and in silico molecular docking. Our group is the first one to classify EhRabX10 as a pseudoRab GTPase with four nonconserved G-motifs. It possesses the basic fold of the P-loop containing nucleotide hydrolases. Through this in silico study, we provide an introduction to the characterization of the atypical EhRabX10 and set the stage for future explorations into the mechanisms of nucleotide recognition, binding, and hydrolysis employed by the pseudoEhRab GTPase family.
Collapse
|
10
|
Structural basis of human PDZD8-Rab7 interaction for the ER-late endosome tethering. Sci Rep 2021; 11:18859. [PMID: 34552186 PMCID: PMC8458453 DOI: 10.1038/s41598-021-98419-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/31/2021] [Indexed: 02/02/2023] Open
Abstract
The membrane contact sites (MCSs) between the ER and late endosomes (LEs) are essential for the regulation of endosomal protein sorting, dynamics, and motility. PDZD8 is an ER transmembrane protein containing a Synaptotagmin-like Mitochondrial lipid-binding Proteins (SMP) domain. PDZD8 tethers the ER to late endosomes and lysosomes by associating its C-terminal coiled-coil (CC) with the LE Rab7. To identify the structural determinants for the PDZD8–Rab7 interaction, we determined the crystal structure of the human PDZD8 CC domain in complex with the GTP-bound form of Rab7. The PDZD8 CC contains one short helix and the two helices forming an antiparallel coiled-coil. Two Rab7 molecules bind to the opposite sides of the PDZD8 CC in a 2:1 ratio. The switch I/II and interswitch regions of the GTP-loaded Rab7 form the binding interfaces, which correlates with the GTP-dependent interaction of PDZD8 and Rab7. Analysis of the protein interaction by isothermal titration calorimetry confirms that two Rab7 molecules bind the PDZD8 CC in a GTP-dependent manner. The structural model of the PDZD8 CC–Rab7 complex correlates with the recruitment of PDZD8 at the LE–ER interface and its role in lipid transport and regulation.
Collapse
|
11
|
Baker MJ, Rubio I. Active GTPase Pulldown Protocol. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:117-135. [PMID: 33977474 DOI: 10.1007/978-1-0716-1190-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Ras and its related small GTPases are important signalling nodes that regulate a wide variety of cellular functions. The active form of these proteins exists in a transient GTP bound state that mediates downstream signalling events. The dysregulation of these GTPases has been associated with the progression of multiple diseases, most prominently cancer and developmental syndromes known as Rasopathies. Determining the activation state of Ras and its relatives has hence been of paramount importance for the investigation of the biochemical functions of small GTPases in the cellular signal transduction network. This chapter describes the most broadly employed approach for the rapid, label-free qualitative and semi-quantitative determination of the Ras GTPase activation state, which can readily be adapted to the analysis of other related GTPases. The method relies on the affinity-based isolation of the active GTP-bound fraction of Ras in cellular extracts, followed by its visualization via western blotting. Specifically, we describe the production of the recombinant affinity probes or baits that bind to the respective active GTPases and the pulldown method for isolating the active GTPase fraction from adherent or non-adherent cells. This method allows for the reproducible measurement of active Ras or Ras family GTPases in a wide variety of cellular contexts.
Collapse
Affiliation(s)
- Martin J Baker
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ignacio Rubio
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, University Hospital Jena, Jena, Germany. .,Clinic for Anaesthesiology and Intensive Care, University Hospital Jena, Jena, Germany.
| |
Collapse
|
12
|
Savitskiy S, Wachtel R, Pourjafar-Dehkordi D, Kang HS, Trauschke V, Lamb DC, Sattler M, Zacharias M, Itzen A. Proteolysis of Rab32 by Salmonella GtgE induces an inactive GTPase conformation. iScience 2020; 24:101940. [PMID: 33426511 PMCID: PMC7779776 DOI: 10.1016/j.isci.2020.101940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/18/2020] [Accepted: 12/10/2020] [Indexed: 12/26/2022] Open
Abstract
Rab GTPases are central regulators of intracellular vesicular trafficking. They are frequently targeted by bacterial pathogens through post-translational modifications. Salmonella typhimurium secretes the cysteine protease GtgE during infection, leading to a regioselective proteolytic cleavage of the regulatory switch I loop in the small GTPases of the Rab32 subfamily. Here, using a combination of biochemical methods, molecular dynamics simulations, NMR spectroscopy, and single-pair Förster resonance energy transfer, we demonstrate that the cleavage of Rab32 causes a local increase of conformational flexibility in both switch regions. Cleaved Rab32 maintains its ability to interact with the GDP dissociation inhibitor (GDI). Interestingly, the Rab32 cleavage enables GDI binding also with an active GTP-bound Rab32 in vitro. Furthermore, the Rab32 proteolysis provokes disturbance in the interaction with its downstream effector VARP. Thus, the proteolysis of Rab32 is not a globally degradative mechanism but affects various biochemical and structural properties of the GTPase in a diverse manner.
Collapse
Affiliation(s)
- Sergey Savitskiy
- Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Rudolf Wachtel
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Danial Pourjafar-Dehkordi
- Physics Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, 85748 Garching, Germany
| | - Vanessa Trauschke
- Department of Chemistry, Center for Nanoscience (CeNS), NanoSystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians-Universität München, Munich Germany
| | - Don C Lamb
- Department of Chemistry, Center for Nanoscience (CeNS), NanoSystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians-Universität München, Munich Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Aymelt Itzen
- Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.,Centre for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| |
Collapse
|
13
|
Flores-Espinoza E, Meizoso-Huesca A, Villegas-Comonfort S, Reyes-Cruz G, García-Sáinz JA. Effect of docosahexaenoic acid, phorbol myristate acetate, and insulin on the interaction of the FFA4 (short isoform) receptor with Rab proteins. Eur J Pharmacol 2020; 889:173595. [PMID: 32986985 DOI: 10.1016/j.ejphar.2020.173595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/12/2020] [Accepted: 09/22/2020] [Indexed: 12/29/2022]
Abstract
Human embryonic kidney (HEK) 293 cells were co-transfected with plasmids for the expression of mCherry fluorescent protein-tagged FFA4 receptors and the enhanced green fluorescent protein-tagged Rab proteins involved in retrograde transport and recycling, to study their possible interaction through Förster Resonance Energy Transfer (FRET), under the action of agents that induce FFA4 receptor phosphorylation and internalization through different processes, i.e., the agonist, docosahexaenoic acid, the protein kinase C activator phorbol myristate acetate, and insulin. Data indicate that FFA4 receptor internalization varied depending on the agent that induced the process. Agonist activation (docosahexaenoic acid) induced an association with early endosomes (as suggested by interaction with Rab5) and rapid recycling to the plasma membrane (as indicated by receptor interaction with Rab4). More prolonged agonist stimulation also appears to allow the FFA4 receptors to interact with late endosomes (interaction with Rab9), slow recycling (interaction with Rab 11), and target to degradation (Rab7). Phorbol myristate acetate, triggered a rapid association with early endosomes (Rab5), slow recycling to the plasma membrane (Rab11), and some receptor degradation (Rab7). Insulin-induced FFA4 receptor internalization appears to be associated with interaction with early endosomes (Rab5) and late endosomes (Rab9) and fast and slow recycling to the plasma membrane (Rab4, Rab11). Additionally, we observed that agonist- and PMA-induced FFA4 internalization was markedly reduced by paroxetine, which suggests a possible role of G protein-coupled receptor kinase 2.
Collapse
Affiliation(s)
- Emmanuel Flores-Espinoza
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Aldo Meizoso-Huesca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sócrates Villegas-Comonfort
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guadalupe Reyes-Cruz
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-CINVESTAV, Av. Instituto Politécnico Nacional, 2508, Col. San Pedro Zacatenco, Mexico City, Mexico
| | - J Adolfo García-Sáinz
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| |
Collapse
|
14
|
Zohib M, Maheshwari D, Pal RK, Freitag-Pohl S, Biswal BK, Pohl E, Arora A. Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2020; 76:544-556. [PMID: 33135673 DOI: 10.1107/s2053230x20013722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/13/2020] [Indexed: 11/10/2022]
Abstract
Eukaryotic Rab5s are highly conserved small GTPase-family proteins that are involved in the regulation of early endocytosis. Leishmania donovani Rab5a regulates the sorting of early endosomes that are involved in the uptake of essential nutrients through fluid-phase endocytosis. Here, the 1.80 Å resolution crystal structure of the N-terminal GTPase domain of L. donovani Rab5a in complex with GDP is presented. The crystal structure determination was enabled by the design of specific single-site mutations and two deletions that were made to stabilize the protein for previous NMR studies. The structure of LdRab5a shows the canonical GTPase fold, with a six-stranded central mixed β-sheet surrounded by five α-helices. The positions of the Switch I and Switch II loops confirm an open conformation, as expected in the absence of the γ-phosphate. However, in comparison to other GTP-bound and GDP-bound homologous proteins, the Switch I region traces a unique disposition in LdRab5a. One magnesium ion is bound to the protein at the GTP-binding site. Molecular-dynamics simulations indicate that the GDP-bound structure exhibits higher stability than the apo structure. The GDP-bound LdRab5a structure presented here will aid in efforts to unravel its interactions with its regulators, including the guanine nucleotide-exchange factor, and will lay the foundation for a structure-based search for specific inhibitors.
Collapse
Affiliation(s)
- Muhammad Zohib
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226 031, India
| | - Diva Maheshwari
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226 031, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110 067, India
| | | | - Bichitra Kumar Biswal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110 067, India
| | - Ehmke Pohl
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Ashish Arora
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Lucknow 226 031, India
| |
Collapse
|
15
|
Waschbüsch D, Khan AR. Phosphorylation of Rab GTPases in the regulation of membrane trafficking. Traffic 2020; 21:712-719. [PMID: 32969543 PMCID: PMC7756361 DOI: 10.1111/tra.12765] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022]
Abstract
Rab GTPases are master regulators of membrane trafficking in eukaryotic cells. Phosphorylation of Rab GTPases was characterized in the 1990s and there have been intermittent reports of its relevance to Rab functions. Phosphorylation as a regulatory mechanism has gained prominence through the identification of Rabs as physiological substrates of leucine‐rich repeat kinase 2 (LRRK2). LRRK2 is a Ser/Thr kinase that is associated with inherited and sporadic forms of Parkinson disease. In recent years, numerous kinases and their associated signaling pathways have been identified that lead to phosphorylation of Rabs. These emerging studies suggest that serine/threonine and tyrosine phosphorylation of Rabs may be a widespread and under‐appreciated mechanism for controlling their membrane trafficking functions. Here we survey current knowledge of Rab phosphorylation and discuss models for how this post‐translational mechanism exerts control of membrane trafficking.
Collapse
Affiliation(s)
- Dieter Waschbüsch
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
16
|
Metje-Sprink J, Groffmann J, Neumann P, Barg-Kues B, Ficner R, Kühnel K, Schalk AM, Binotti B. Crystal structure of the Rab33B/Atg16L1 effector complex. Sci Rep 2020; 10:12956. [PMID: 32737358 PMCID: PMC7395093 DOI: 10.1038/s41598-020-69637-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 07/14/2020] [Indexed: 12/03/2022] Open
Abstract
The Atg12-Atg5/Atg16L1 complex is recruited by WIPI2b to the site of autophagosome formation. Atg16L1 is an effector of the Golgi resident GTPase Rab33B. Here we identified a minimal stable complex of murine Rab33B(30–202) Q92L and Atg16L1(153–210). Atg16L1(153–210) comprises the C-terminal part of the Atg16L1 coiled-coil domain. We have determined the crystal structure of the Rab33B Q92L/Atg16L1(153–210) effector complex at 3.47 Å resolution. This structure reveals that two Rab33B molecules bind to the diverging α-helices of the dimeric Atg16L1 coiled-coil domain. We mutated Atg16L1 and Rab33B interface residues and found that they disrupt complex formation in pull-down assays and cellular co-localization studies. The Rab33B binding site of Atg16L1 comprises 20 residues and immediately precedes the WIPI2b binding site. Rab33B mutations that abolish Atg16L binding also abrogate Rab33B association with the Golgi stacks. Atg16L1 mutants that are defective in Rab33B binding still co-localize with WIPI2b in vivo. The close proximity of the Rab33B and WIPI2b binding sites might facilitate the recruitment of Rab33B containing vesicles to provide a source of lipids during autophagosome biogenesis.
Collapse
Affiliation(s)
- Janina Metje-Sprink
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany. .,Institute for Biosafety in Plant Biotechnology, Julius Kuehn-Institute, 06484, Quedlinburg, Germany.
| | - Johannes Groffmann
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Brigitte Barg-Kues
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Karin Kühnel
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany. .,Nature Communications, 4 Crinan Street, London, N1 9XW, UK.
| | - Amanda M Schalk
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Beyenech Binotti
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany. .,Department of Biochemistry, University of Würzburg, 97074, Würzburg, Germany.
| |
Collapse
|
17
|
Cezanne A, Lauer J, Solomatina A, Sbalzarini IF, Zerial M. A non-linear system patterns Rab5 GTPase on the membrane. eLife 2020; 9:54434. [PMID: 32510320 PMCID: PMC7279886 DOI: 10.7554/elife.54434] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
Proteins can self-organize into spatial patterns via non-linear dynamic interactions on cellular membranes. Modelling and simulations have shown that small GTPases can generate patterns by coupling guanine nucleotide exchange factors (GEF) to effectors, generating a positive feedback of GTPase activation and membrane recruitment. Here, we reconstituted the patterning of the small GTPase Rab5 and its GEF/effector complex Rabex5/Rabaptin5 on supported lipid bilayers. We demonstrate a 'handover' of Rab5 from Rabex5 to Rabaptin5 upon nucleotide exchange. A minimal system consisting of Rab5, RabGDI and a complex of full length Rabex5/Rabaptin5 was necessary to pattern Rab5 into membrane domains. Rab5 patterning required a lipid membrane composition mimicking that of early endosomes, with PI(3)P enhancing membrane recruitment of Rab5 and acyl chain packing being critical for domain formation. The prevalence of GEF/effector coupling in nature suggests a possible universal system for small GTPase patterning involving both protein and lipid interactions.
Collapse
Affiliation(s)
- Alice Cezanne
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Janelle Lauer
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Anastasia Solomatina
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Chair of Scientific Computing for Systems Biology, Faculty of Computer Science, Dresden, Germany.,MOSAIC Group, Center for Systems Biology Dresden, Dresden, Germany
| | - Ivo F Sbalzarini
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Chair of Scientific Computing for Systems Biology, Faculty of Computer Science, Dresden, Germany.,MOSAIC Group, Center for Systems Biology Dresden, Dresden, Germany
| | - Marino Zerial
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
18
|
Liu D, Fu X, Wang Y, Wang X, Wang H, Wen J, Kang N. Protein diaphanous homolog 1 (Diaph1) promotes myofibroblastic activation of hepatic stellate cells by regulating Rab5a activity and TGFβ receptor endocytosis. FASEB J 2020; 34:7345-7359. [PMID: 32304339 PMCID: PMC7686927 DOI: 10.1096/fj.201903033r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 01/19/2023]
Abstract
TGFβ induces the differentiation of hepatic stellate cells (HSCs) into tumor-promoting myofibroblasts but underlying mechanisms remain incompletely understood. Because endocytosis of TGFβ receptor II (TβRII), in response to TGFβ stimulation, is a prerequisite for TGF signaling, we investigated the role of protein diaphanous homolog 1 (known as Diaph1 or mDia1) for the myofibroblastic activation of HSCs. Using shRNA to knockdown Diaph1 or SMIFH2 to target Diaph1 activity of HSCs, we found that the inactivation of Diaph1 blocked internalization and intracellular trafficking of TβRII and reduced SMAD3 phosphorylation induced by TGFβ1. Mechanistic studies revealed that the N-terminal portion of Diaph1 interacted with both TβRII and Rab5a directly and that Rab5a activity of HSCs was increased by Diaph1 overexpression and decreased by Diaph1 knockdown. Additionally, expression of Rab5aQ79L (active Rab5a mutant) increased whereas the expression of Rab5aS34N (inactive mutant) reduced the endosomal localization of TβRII in HSCs compared to the expression of wild-type Rab5a. Functionally, TGFβ stimulation promoted HSCs to express tumor-promoting factors, and α-smooth muscle actin, fibronection, and CTGF, markers of myofibroblastic activation of HSCs. Targeting Diaph1 or Rab5a suppressed HSC activation and limited tumor growth in a tumor implantation mouse model. Thus, Dipah1 and Rab5a represent targets for inhibiting HSC activation and the hepatic tumor microenvironment.
Collapse
Affiliation(s)
- Donglian Liu
- Tumor Microenvironment and Metastasis Section, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Xinhui Fu
- Tumor Microenvironment and Metastasis Section, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Yuanguo Wang
- Tumor Microenvironment and Metastasis Section, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Xianghu Wang
- Tumor Microenvironment and Metastasis Section, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Hua Wang
- Tumor Microenvironment and Metastasis Section, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Jialing Wen
- Tumor Microenvironment and Metastasis Section, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Ningling Kang
- Tumor Microenvironment and Metastasis Section, The Hormel Institute, University of Minnesota, Austin, MN, USA
| |
Collapse
|
19
|
The Emerging Role of Rab5 in Membrane Receptor Trafficking and Signaling Pathways. Biochem Res Int 2020; 2020:4186308. [PMID: 32104603 PMCID: PMC7036122 DOI: 10.1155/2020/4186308] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/16/2019] [Accepted: 12/07/2019] [Indexed: 02/06/2023] Open
Abstract
Ras analog in brain (Rab) proteins are small guanosine triphosphatases (GTPases) that belong to the Ras-like GTPase superfamily, and they can regulate vesicle trafficking. Rab proteins alternate between an activated (GTP-bound) state and an inactivated (GDP-bound) state. Early endosome marker Rab5 GTPase, a key member of the Rab family, plays a crucial role in endocytosis and membrane transport. The activated-state Rab5 recruits its effectors and regulates the internalization and trafficking of membrane receptors by regulating vesicle fusion and receptor sorting in the early endosomes. In this review, we summarize the role of small Rab GTPases Rab5 in membrane receptor trafficking and the activation of signaling pathways, such as Ras/MAPK and PI3K/Akt, which ultimately affect cell growth, apoptosis, tumorigenesis, and tumor development. This review may provide some insights for our future research and novel therapeutic targets for diseases.
Collapse
|
20
|
Kumar AP, Verma CS, Lukman S. Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design. Brief Bioinform 2020; 22:270-287. [PMID: 31950981 DOI: 10.1093/bib/bbz161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/29/2019] [Accepted: 11/15/2019] [Indexed: 01/09/2023] Open
Abstract
Rab proteins represent the largest family of the Rab superfamily guanosine triphosphatase (GTPase). Aberrant human Rab proteins are associated with multiple diseases, including cancers and neurological disorders. Rab subfamily members display subtle conformational variations that render specificity in their physiological functions and can be targeted for subfamily-specific drug design. However, drug discovery efforts have not focused much on targeting Rab allosteric non-nucleotide binding sites which are subjected to less evolutionary pressures to be conserved, hence are likely to offer subfamily specificity and may be less prone to undesirable off-target interactions and side effects. To discover druggable allosteric binding sites, Rab structural dynamics need to be first incorporated using multiple experimentally and computationally obtained structures. The high-dimensional structural data may necessitate feature extraction methods to identify manageable representative structures for subsequent analyses. We have detailed state-of-the-art computational methods to (i) identify binding sites using data on sequence, shape, energy, etc., (ii) determine the allosteric nature of these binding sites based on structural ensembles, residue networks and correlated motions and (iii) identify small molecule binders through structure- and ligand-based virtual screening. To benefit future studies for targeting Rab allosteric sites, we herein detail a refined workflow comprising multiple available computational methods, which have been successfully used alone or in combinations. This workflow is also applicable for drug discovery efforts targeting other medically important proteins. Depending on the structural dynamics of proteins of interest, researchers can select suitable strategies for allosteric drug discovery and design, from the resources of computational methods and tools enlisted in the workflow.
Collapse
Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.,Research Unit in Bioinformatics, Department of Biochemistry and Microbiology, Rhodes University, South Africa
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| |
Collapse
|
21
|
Lauer J, Segeletz S, Cezanne A, Guaitoli G, Raimondi F, Gentzel M, Alva V, Habeck M, Kalaidzidis Y, Ueffing M, Lupas AN, Gloeckner CJ, Zerial M. Auto-regulation of Rab5 GEF activity in Rabex5 by allosteric structural changes, catalytic core dynamics and ubiquitin binding. eLife 2019; 8:46302. [PMID: 31718772 PMCID: PMC6855807 DOI: 10.7554/elife.46302] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Intracellular trafficking depends on the function of Rab GTPases, whose activation is regulated by guanine exchange factors (GEFs). The Rab5 GEF, Rabex5, was previously proposed to be auto-inhibited by its C-terminus. Here, we studied full-length Rabex5 and Rabaptin5 proteins as well as domain deletion Rabex5 mutants using hydrogen deuterium exchange mass spectrometry. We generated a structural model of Rabex5, using chemical cross-linking mass spectrometry and integrative modeling techniques. By correlating structural changes with nucleotide exchange activity for each construct, we uncovered new auto-regulatory roles for the ubiquitin binding domains and the Linker connecting those domains to the catalytic core of Rabex5. We further provide evidence that enhanced dynamics in the catalytic core are linked to catalysis. Our results suggest a more complex auto-regulation mechanism than previously thought and imply that ubiquitin binding serves not only to position Rabex5 but to also control its Rab5 GEF activity through allosteric structural alterations.
Collapse
Affiliation(s)
- Janelle Lauer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sandra Segeletz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alice Cezanne
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Francesco Raimondi
- Bioquant, Heidelberg University, Heidelberg, Germany.,Heidelberg University Biochemistry Centre (BZH), Heidelberg, Germany
| | - Marc Gentzel
- Molecular Analysis-Mass Spectrometry Center for Molecular and Cellular Bioengineering, Technical University Dresden, Dresden, Germany
| | - Vikram Alva
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Michael Habeck
- Statistical Inverse Problems in Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Göttingen, Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases, Tübingen, Germany.,Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
22
|
Fakhree MAA, Blum C, Claessens MMAE. Shaping membranes with disordered proteins. Arch Biochem Biophys 2019; 677:108163. [PMID: 31672499 DOI: 10.1016/j.abb.2019.108163] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/23/2019] [Accepted: 10/27/2019] [Indexed: 12/15/2022]
Abstract
Membrane proteins control and shape membrane trafficking processes. The role of protein structure in shaping cellular membranes is well established. However, a significant fraction of membrane proteins is disordered or contains long disordered regions. It becomes more and more clear that these disordered regions contribute to the function of membrane proteins. While the fold of a structured protein is essential for its function, being disordered seems to be a crucial feature of membrane bound intrinsically disordered proteins and protein regions. Here we outline the motifs that encode function in disordered proteins and discuss how these functional motifs enable disordered proteins to modulate membrane properties. These changes in membrane properties facilitate and regulate membrane trafficking processes which are highly abundant in eukaryotes.
Collapse
Affiliation(s)
| | - Christian Blum
- Nanobiophysics Group, University of Twente, 7522, NB, Enschede, the Netherlands
| | | |
Collapse
|
23
|
S1P 1 receptor phosphorylation, internalization, and interaction with Rab proteins: effects of sphingosine 1-phosphate, FTY720-P, phorbol esters, and paroxetine. Biosci Rep 2018; 38:BSR20181612. [PMID: 30366961 PMCID: PMC6294635 DOI: 10.1042/bsr20181612] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/19/2018] [Accepted: 10/26/2018] [Indexed: 01/04/2023] Open
Abstract
Sphingosine 1-phosphate (S1P) and FTY720-phosphate (FTYp) increased intracellular calcium in cells expressing S1P1 mCherry-tagged receptors; the synthetic agonist was considerably less potent. Activation of protein kinase C by phorbol myristate acetate (PMA) blocked these effects. The three agents induced receptor phosphorylation and internalization, with the action of FTYp being more intense. S1P1 receptor–Rab protein (GFP-tagged) interaction was studied using FRET. The three agents were able to induce S1P1 receptor–Rab5 interaction, although with different time courses. S1P1 receptor–Rab9 interaction was mainly increased by the phorbol ester, whereas S1P1 receptor–Rab7 interaction was only increased by FTYp and after a 30-min incubation. These actions were not observed using dominant negative (GDP-bound) Rab protein mutants. The data suggested that the three agents induce interaction with early endosomes, but that the natural agonist induced rapid receptor recycling, whereas activation of protein kinase C favored interaction with late endosome and slow recycling and FTYp triggered receptor interaction with vesicles associated with proteasomal/lysosomal degradation. The ability of bisindolylmaleimide I and paroxetine to block some of these actions suggested the activation of protein kinase C was associated mainly with the action of PMA, whereas G protein-coupled receptor kinase (GRK) 2 (GRK2) was involved in the action of the three agents.
Collapse
|
24
|
Maheshwari D, Yadav R, Rastogi R, Jain A, Tripathi S, Mukhopadhyay A, Arora A. Structural and Biophysical Characterization of Rab5a from Leishmania Donovani. Biophys J 2018; 115:1217-1230. [PMID: 30241678 PMCID: PMC6170798 DOI: 10.1016/j.bpj.2018.08.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/10/2018] [Accepted: 08/15/2018] [Indexed: 12/21/2022] Open
Abstract
Leishmania donovani possess two isoforms of Rab5 (Rab5a and Rab5b), which are involved in fluid phase and receptor-mediated endocytosis, respectively. We have characterized the solution structure and dynamics of a stabilized truncated LdRab5a mutant. For the purpose of NMR structure determination, protein stability was enhanced by systematically introducing various deletions and mutations. Deletion of hypervariable C-terminal and the 20 residues LdRab5a specific insert slightly enhanced the stability, which was further improved by C107S mutation. The final construct, truncated LdRab5a with C107S mutation, was found to be stable for longer durations at higher concentration, with an increase in melting temperature by 10°C. Solution structure of truncated LdRab5a shows the characteristic GTPase fold having nucleotide and effector binding sites. Orientation of switch I and switch II regions match well with that of guanosine 5'-(β, γ-imido)triphosphate (GppNHp)-bound human Rab5a, indicating that the truncated LdRab5a attains the canonical GTP bound state. However, the backbone dynamics of the P-loop, switch I, and switch II regions were slower than that observed for guanosine 5'-(β, γ-imido)triphosphate (GMPPNP)-bound H-Ras. This dynamic profile may further complement the residue-specific complementarity in determining the specificity of interaction with the effectors. In parallel, biophysical investigations revealed the urea induced unfolding of truncated LdRab5a to be a four-state process that involved two intermediates, I1 and I2. The maximal 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (Bis-ANS) binding was observed for I2 state, which was inferred to have molten globule like characteristics. Overall, the strategy presented would have significant impact for studying other Rab and small GTPase proteins by NMR spectroscopy.
Collapse
Affiliation(s)
- Diva Maheshwari
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Rahul Yadav
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ruchir Rastogi
- Cell Biology Lab, National Institute of Immunology, New Delhi, India
| | - Anupam Jain
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Sarita Tripathi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | | | - Ashish Arora
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.
| |
Collapse
|
25
|
Pylypenko O, Hammich H, Yu IM, Houdusse A. Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity. Small GTPases 2018. [PMID: 28632484 DOI: 10.1080/215412481336191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Rab molecular switches are key players in defining membrane identity and regulating intracellular trafficking events in eukaryotic cells. In spite of their global structural similarity, Rab-family members acquired particular features that allow them to perform specific cellular functions. The overall fold and local sequence conservations enable them to utilize a common machinery for prenylation and recycling; while individual Rab structural differences determine interactions with specific partners such as GEFs, GAPs and effector proteins. These interactions orchestrate the spatiotemporal regulation of Rab localization and their turning ON and OFF, leading to tightly controlled Rab-specific functionalities such as membrane composition modifications, recruitment of molecular motors for intracellular trafficking, or recruitment of scaffold proteins that mediate interactions with downstream partners, as well as actin cytoskeleton regulation. In this review we summarize structural information on Rab GTPases and their complexes with protein partners in the context of partner binding specificity and functional outcomes of their interactions in the cell.
Collapse
Affiliation(s)
- Olena Pylypenko
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Hussein Hammich
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
- b Sorbonne Universités , UPMC Univ Paris 06, Sorbonne Universités, IFD , Paris , France
| | - I-Mei Yu
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Anne Houdusse
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| |
Collapse
|
26
|
Whitecross DE, Anderson DH. Identification of the Binding Sites on Rab5 and p110beta Phosphatidylinositol 3-kinase. Sci Rep 2017; 7:16194. [PMID: 29170408 PMCID: PMC5700975 DOI: 10.1038/s41598-017-16029-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/06/2017] [Indexed: 12/19/2022] Open
Abstract
Rab5 is a small monomeric GTPase that mediates protein trafficking during endocytosis. Inactivation of Rab5 by GTP hydrolysis causes a conformational change that masks binding sites on its “switch regions” from downstream effectors. The p85 subunit of phosphatidylinositol 3-kinase (PI3K) is a GTPase activating protein (GAP) towards Rab5. Whereas p85 can bind with both Rab5-GTP and Rab5-GDP, the PI3K catalytic subunit p110β binds only Rab5-GTP, suggesting it interacts with the switch regions. Thus, the GAP functions of the catalytic arginine finger (from p85) and switch region stabilization (from p110β) may be provided by both proteins, acting together. To identify the Rab5 residues involved in binding p110β, residues in the Rab5 switch regions were mutated. A stabilized recombinant p110 protein, where the p85-iSH2 domain was fused to p110 (alpha or beta) was used in binding experiments. Eleven Rab5 mutants, including E80R and H83E, showed reduced p110β binding. The Rab5 binding site on p110β was also resolved through mutation of p110β in its Ras binding domain, and includes residues I234, E238 and Y244. This is a second region within p110β important for Rab5 binding. The Rab5-GTP:p110β interaction may be further elucidated through the characterization of these non-binding mutants in cells.
Collapse
Affiliation(s)
- Dielle E Whitecross
- Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Deborah H Anderson
- Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Departments of Oncology and Biochemistry, College of Medicine, 107 Wiggins Road, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada.
| |
Collapse
|
27
|
Porcine Hemagglutinating Encephalomyelitis Virus Enters Neuro-2a Cells via Clathrin-Mediated Endocytosis in a Rab5-, Cholesterol-, and pH-Dependent Manner. J Virol 2017; 91:JVI.01083-17. [PMID: 28956766 PMCID: PMC5686734 DOI: 10.1128/jvi.01083-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/07/2017] [Indexed: 12/24/2022] Open
Abstract
Porcine hemagglutinating encephalomyelitis virus (PHEV) is a highly neurovirulent coronavirus that invades the central nervous system (CNS) in piglets. Although important progress has been made toward understanding the biology of PHEV, many aspects of its life cycle remain obscure. Here we dissected the molecular mechanism underlying cellular entry and intracellular trafficking of PHEV in mouse neuroblastoma (Neuro-2a) cells. We first performed a thin-section transmission electron microscopy (TEM) assay to characterize the kinetics of PHEV, and we found that viral entry and transfer occur via membranous coating-mediated endo- and exocytosis. To verify the roles of distinct endocytic pathways, systematic approaches were used, including pharmacological inhibition, RNA interference, confocal microscopy analysis, use of fluorescently labeled virus particles, and overexpression of a dominant negative (DN) mutant. Quantification of infected cells showed that PHEV enters cells by clathrin-mediated endocytosis (CME) and that low pH, dynamin, cholesterol, and Eps15 are indispensably involved in this process. Intriguingly, PHEV invasion leads to rapid actin rearrangement, suggesting that the intactness and dynamics of the actin cytoskeleton are positively correlated with viral endocytosis. We next investigated the trafficking of internalized PHEV and found that Rab5- and Rab7-dependent pathways are required for the initiation of a productive infection. Furthermore, a GTPase activation assay suggested that endogenous Rab5 is activated by PHEV and is crucial for viral progression. Our findings demonstrate that PHEV hijacks the CME and endosomal system of the host to enter and traffic within neural cells, providing new insights into PHEV pathogenesis and guidance for antiviral drug design. IMPORTANCE Porcine hemagglutinating encephalomyelitis virus (PHEV), a nonsegmented, positive-sense, single-stranded RNA coronavirus, invades the central nervous system (CNS) and causes neurological dysfunction. Neural cells are its targets for viral progression. However, the detailed mechanism underlying PHEV entry and trafficking remains unknown. PHEV is the etiological agent of porcine hemagglutinating encephalomyelitis, which is an acute and highly contagious disease that causes numerous deaths in suckling piglets and enormous economic losses in China. Understanding the viral entry pathway will not only advance our knowledge of PHEV infection and pathogenesis but also open new approaches to the development of novel therapeutic strategies. Therefore, we employed systematic approaches to dissect the internalization and intracellular trafficking mechanism of PHEV in Neuro-2a cells. This is the first report to describe the process of PHEV entry into nerve cells via clathrin-mediated endocytosis in a dynamin-, cholesterol-, and pH-dependent manner that requires Rab5 and Rab7.
Collapse
|
28
|
Shin D, Na W, Lee JH, Kim G, Baek J, Park SH, Choi CY, Lee S. Site-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion. eLife 2017; 6. [PMID: 28968219 PMCID: PMC5624781 DOI: 10.7554/elife.29154] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/05/2017] [Indexed: 02/07/2023] Open
Abstract
Rab GTPases, which are involved in intracellular trafficking pathways, have recently been reported to be ubiquitinated. However, the functions of ubiquitinated Rab proteins remain unexplored. Here we show that Rab5 is monoubiquitinated on K116, K140, and K165. Upon co-transfection with ubiquitin, Rab5 exhibited abnormalities in endosomal localization and EGF-induced EGF receptor degradation. Rab5 K140R and K165R mutants restored these abnormalities, whereas K116R did not. We derived structural models of individual monoubiquitinated Rab5 proteins (mUbRab5s) by solution scattering and observed different conformational flexibilities in a site-specific manner. Structural analysis combined with biochemical data revealed that interactions with downstream effectors were impeded in mUbRab5K140, whereas GDP release and GTP loading activities were altered in mUbRab5K165. By contrast, mUbRab5K116 apparently had no effect. We propose a regulatory mechanism of Rab5 where monoubiquitination downregulates effector recruitment and GDP/GTP conversion in a site-specific manner.
Collapse
Affiliation(s)
- Donghyuk Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Wooju Na
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji-Hyung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Gyuhee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Jiseok Baek
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Seok Hee Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| |
Collapse
|
29
|
Ku B, You JA, Oh KJ, Yun HY, Lee HS, Shin HC, Jung J, Shin YB, Kim SJ. Crystal structures of two forms of the Acanthamoeba polyphaga mimivirus Rab GTPase. Arch Virol 2017; 162:3407-3416. [PMID: 28779233 DOI: 10.1007/s00705-017-3510-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/30/2017] [Indexed: 01/09/2023]
Abstract
Acanthamoeba polyphaga mimivirus (APMV) is a member of the family of giant viruses, harboring a 1,200 kbp genome within its 700 nm-diameter viral particle. The R214 gene of the APMV genome was recently shown to encode a homologue of the Rab GTPases, molecular switch proteins known to play a pivotal role in the regulation of membrane trafficking that were considered to exist only in eukaryotes. Herein, we report the first crystal structures of GDP- and GTP-bound forms of APMV Rab GTPase, both of which were determined at high resolution. An in-depth structural comparison of APMV Rab with each other and with mammalian Rab homologues led to an atomic-level elucidation of the inactive-active conformational change upon GDP/GTP exchange. APMV Rab GTPase exhibited considerable structural similarity to human Rab5, as previously predicted based on its amino acid sequence. However, it also contains unique structural features differentiating it from mammalian homologues, such as the functional substitution of a phenylalanine residue for the stabilization of the nucleotide's guanine base.
Collapse
Affiliation(s)
- Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea.
| | - Jin A You
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ho-Chul Shin
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Juyeon Jung
- Hazard Monitoring BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Yong-Beom Shin
- Hazard Monitoring BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
30
|
Pylypenko O, Hammich H, Yu IM, Houdusse A. Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity. Small GTPases 2017. [PMID: 28632484 PMCID: PMC5902227 DOI: 10.1080/21541248.2017.1336191] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rab molecular switches are key players in defining membrane identity and regulating intracellular trafficking events in eukaryotic cells. In spite of their global structural similarity, Rab-family members acquired particular features that allow them to perform specific cellular functions. The overall fold and local sequence conservations enable them to utilize a common machinery for prenylation and recycling; while individual Rab structural differences determine interactions with specific partners such as GEFs, GAPs and effector proteins. These interactions orchestrate the spatiotemporal regulation of Rab localization and their turning ON and OFF, leading to tightly controlled Rab-specific functionalities such as membrane composition modifications, recruitment of molecular motors for intracellular trafficking, or recruitment of scaffold proteins that mediate interactions with downstream partners, as well as actin cytoskeleton regulation. In this review we summarize structural information on Rab GTPases and their complexes with protein partners in the context of partner binding specificity and functional outcomes of their interactions in the cell.
Collapse
Affiliation(s)
- Olena Pylypenko
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Hussein Hammich
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France.,b Sorbonne Universités , UPMC Univ Paris 06, Sorbonne Universités, IFD , Paris , France
| | - I-Mei Yu
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Anne Houdusse
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| |
Collapse
|
31
|
Edler E, Stein M. Probing the druggability of membrane-bound Rab5 by molecular dynamics simulations. J Enzyme Inhib Med Chem 2017; 32:434-443. [PMID: 28090783 PMCID: PMC6010109 DOI: 10.1080/14756366.2016.1260564] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Rab5 is a small GTPase and a key regulator in early endosomal trafficking. Rab5 and its effectors are involved in a large number of infectious diseases and certain types of cancer. We performed µs atomistic molecular dynamics simulations of inactive and active full-length Rab5 anchored to a complex model bilayer with composition of the early endosome membrane. Direct interactions between the Rab5 G domain and the bilayer were observed. We found two dominant nucleotide-dependent orientations characterised by a different accessibility of the switch regions. The “buried switch” orientation was mainly associated with inactive Rab5 accompanied with a rather extended structure of the hypervariable C-terminal region. Active Rab5 preferred an orientation in which the switch regions are accessible to effector proteins. These structural differences may provide an opportunity to selectively target one Rab5 state and lead to new approaches in the development of Rab5-specific therapies.
Collapse
Affiliation(s)
- Eileen Edler
- a Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical Systems , Magdeburg , Germany
| | - Matthias Stein
- a Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical Systems , Magdeburg , Germany
| |
Collapse
|
32
|
Abstract
Rab proteins regulate vesicular transport in eukaryotic cells and establish connections to various cellular structures and processes by interacting with so-called effector molecules. Several of these effectors are known to not only bind a single Rab protein, but to be able to bind multiple different Rabs simultaneously. In this review we will give a short overview of effectors in general and (putative) functions of the aforementioned multivalent Rab:effector interactions.
Collapse
Affiliation(s)
- Amrita Rai
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Roger S Goody
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Matthias P Müller
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| |
Collapse
|
33
|
Alfonzo-Méndez MA, Hernández-Espinosa DA, Carmona-Rosas G, Romero-Ávila MT, Reyes-Cruz G, García-Sáinz JA. Protein Kinase C Activation Promotes α 1B-Adrenoceptor Internalization and Late Endosome Trafficking through Rab9 Interaction. Role in Heterologous Desensitization. Mol Pharmacol 2017; 91:296-306. [PMID: 28082304 DOI: 10.1124/mol.116.106583] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/09/2017] [Indexed: 12/25/2022] Open
Abstract
Upon agonist stimulation, α1B-adrenergic receptors couple to Gq proteins, calcium signaling and protein kinase C activation; subsequently, the receptors are phosphorylated, desensitized, and internalized. Internalization seems to involve scaffolding proteins, such as β-arrestin and clathrin. However, the fine mechanisms that participate remain unsolved. The roles of protein kinase C and the small GTPase, Rab9, in α1B-AR vesicular traffic were investigated by studying α1B-adrenergic receptor-Rab protein interactions, using Förster resonance energy transfer (FRET), confocal microscopy, and intracellular calcium quantitation. In human embryonic kidney 293 cells overexpressing Discosoma spp. red fluorescent protein (DsRed)-tagged α1B-ARs and enhanced green fluorescent protein--tagged Rab proteins, pharmacological protein kinase C activation mimicked α1B-AR traffic elicited by nonrelated agents, such as sphingosine 1-phosphate (i.e., transient α1B-AR-Rab5 FRET signal followed by a sustained α1B-AR-Rab9 interaction), suggesting brief receptor localization in early endosomes and transfer to late endosomes. This latter interaction was abrogated by blocking protein kinase C activity, resulting in receptor retention at the plasma membrane. Similar effects were observed when a dominant-negative Rab9 mutant (Rab9-GDP) was employed. When α1B-adrenergic receptors that had been mutated at protein kinase C phosphorylation sites (S396A, S402A) were used, phorbol ester-induced desensitization of the calcium response was markedly decreased; however, interaction with Rab9 was only partially decreased and internalization was observed in response to phorbol esters and sphingosine 1-phosphate. Finally, Rab9-GDP expression did not affect adrenergic-mediated calcium response but abolished receptor traffic and altered desensitization. Data suggest that protein kinase C modulates α1B-adrenergic receptor transfer to late endosomes and that Rab9 regulates this process and participates in G protein-mediated signaling turn-off.
Collapse
Affiliation(s)
- Marco A Alfonzo-Méndez
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México (M.A.A.-M., D.A.H.-E., G.C.-R., M.T.R.-A., J.A.G.-S.) and Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-CINVESTAV, Col. San Pedro Zacatenco, Ciudad de México (G.R.-C.)
| | - David A Hernández-Espinosa
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México (M.A.A.-M., D.A.H.-E., G.C.-R., M.T.R.-A., J.A.G.-S.) and Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-CINVESTAV, Col. San Pedro Zacatenco, Ciudad de México (G.R.-C.)
| | - Gabriel Carmona-Rosas
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México (M.A.A.-M., D.A.H.-E., G.C.-R., M.T.R.-A., J.A.G.-S.) and Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-CINVESTAV, Col. San Pedro Zacatenco, Ciudad de México (G.R.-C.)
| | - M Teresa Romero-Ávila
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México (M.A.A.-M., D.A.H.-E., G.C.-R., M.T.R.-A., J.A.G.-S.) and Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-CINVESTAV, Col. San Pedro Zacatenco, Ciudad de México (G.R.-C.)
| | - Guadalupe Reyes-Cruz
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México (M.A.A.-M., D.A.H.-E., G.C.-R., M.T.R.-A., J.A.G.-S.) and Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-CINVESTAV, Col. San Pedro Zacatenco, Ciudad de México (G.R.-C.)
| | - J Adolfo García-Sáinz
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México (M.A.A.-M., D.A.H.-E., G.C.-R., M.T.R.-A., J.A.G.-S.) and Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-CINVESTAV, Col. San Pedro Zacatenco, Ciudad de México (G.R.-C.)
| |
Collapse
|
34
|
Abstract
Rab GTPases act as organizers of protein networks defining identities and functions of organelles of the endocytic and secretory pathways. Various modes of coordination between different Rabs drive the timely maturation and conversion of membranes. Endosomal Rab5 has been known as the prime example for self-activation via a feedback loop recruiting Rabaptin5, which is complexed with the Rab5 exchange factor Rabex5, and couples to Rab4-GTP. Among other effectors, Rab5 also recruits the Mon1/SAND1-Ccz1 complex that both activates Rab7 and dissociates Rabex5 for Rab5-to-Rab7 conversion of early-to-late endosomes. A detailed deletion analysis now revealed 2 separate binding sites each for Rab4-GTP and Rab5-GTP and indicates a feedforward mechanism of Rab5 activation. Rabaptin5/Rabex5 is recruited to endosomal membranes positive for Rab4-GTP and ubiquitinated cargo (binding to the ubiquitin binding site of Rabex5). This mechanism also suggests additional criteria for Rab5 inactivation concomitant with increasing Rab7-GTP levels. The disappearance of ubiquitinated cargo upon ESCRT-mediated formation of intraluminal vesicles and inactivation of Rab4 may also contribute to loss of Rab5 activation. Rabaptin5/Rabex5 thus may integrate several cues of maturation to perform Rab conversion. Furthermore Rab5 binding to Rabaptin5 appears to prevent uncontrolled progression to late endosomes.
Collapse
Affiliation(s)
- Simone Kälin
- a Biozentrum, University of Basel , Basel, Switzerland
| | | | - Martin Spiess
- a Biozentrum, University of Basel , Basel, Switzerland
| |
Collapse
|
35
|
da Silva SD, Marchi FA, Xu B, Bijian K, Alobaid F, Mlynarek A, Rogatto SR, Hier M, Kowalski LP, Alaoui-Jamali MA. Predominant Rab-GTPase amplicons contributing to oral squamous cell carcinoma progression to metastasis. Oncotarget 2016; 6:21950-63. [PMID: 26110570 PMCID: PMC4673138 DOI: 10.18632/oncotarget.4277] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/03/2015] [Indexed: 11/25/2022] Open
Abstract
Metastatic oral squamous cell carcinoma (OSCC) is frequently associated with recurrent gene abnormalities at specific chromosomal loci. Here, we utilized array comparative genomic hybridization and genome-wide screening of metastatic and non-metastatic tongue tumors to investigate genes potentially contributing to OSCC progression to metastasis. We identified predominant amplifications of chromosomal regions that encompass the RAB5, RAB7 and RAB11 genes (3p24-p22, 3q21.3 and 8p11-12, respectively) in metastatic OSCC. The expression of these Rab GTPases was confirmed by immunohistochemistry in OSCC tissues from a cohort of patients with a follow-up of 10 years. A significant overexpression of Rab5, Rab7 and Rab11 was observed in advanced OSCC cases and co-overexpression of these Rabs was predictive of poor survival (log-rank test, P = 0.006). We generated a Rab interaction network and identified central Rab interactions of relevance to metastasis signaling, including focal adhesion proteins. In preclinical models, mRNA and protein expression levels of these Rab members were elevated in a panel of invasive OSCC cell lines, and their down-regulation prevented cell invasion at least in part via inhibition of focal adhesion disassembly. In summary, our results provide insights into the cooperative role of Rab gene amplifications in OSCC progression and support their potential utility as prognostic markers and therapeutic approach for advanced OSCC.
Collapse
Affiliation(s)
- Sabrina Daniela da Silva
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Canada.,Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Canada.,Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), Brazil
| | - Fabio Albuquerque Marchi
- NeoGene Laboratory, Department of Urology, Faculty of Medicine, UNESP, and International Research Center (CIPE), AC Camargo Cancer Center, Brazil.,Inter-Institutional Grad Program on Bioinformatics, University of São Paulo, Brazil
| | - Bin Xu
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Canada
| | - Krikor Bijian
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Canada
| | - Faisal Alobaid
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Canada
| | - Alex Mlynarek
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Canada
| | - Silvia Regina Rogatto
- NeoGene Laboratory, Department of Urology, Faculty of Medicine, UNESP, and International Research Center (CIPE), AC Camargo Cancer Center, Brazil
| | - Michael Hier
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Canada
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), Brazil
| | - Moulay A Alaoui-Jamali
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Canada
| |
Collapse
|
36
|
Qi Y, Liang Z, Wang Z, Lu G, Li G. Determination of Rab5 activity in the cell by effector pull-down assay. Methods Mol Biol 2016; 1298:259-70. [PMID: 25800849 DOI: 10.1007/978-1-4939-2569-8_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Rab5 targets to early endosomes and is a master regulator of early endosome fusion and endocytosis in all eukaryotic cells. Like other GTPases, Rab5 functions as a molecular switch by alternating between GTP-bound and GDP-bound forms, with the former being biologically active via interactions with multiple effector proteins. Thus the Rab5-GTP level in the cell reflects Rab5 activity in promoting endosome fusion and endocytosis and is indicative of cellular endocytic activity. In this chapter, we describe a Rab5 activity assay by using GST fusion proteins with the Rab5 effectors such as Rabaptin-5, Rabenosyn-5, and EEA1 that specifically bind to GTP-bound Rab5. We compare the efficiencies of the three GST fusion proteins in the pull-down of mammalian and fungal Rab5 proteins.
Collapse
Affiliation(s)
- Yaoyao Qi
- Key Laboratory of Biopesticides and Chemical Biology, Ministry of Education, Fujian Agriculture & Forestry University, 350002, Fuzhou, China
| | | | | | | | | |
Collapse
|
37
|
Kälin S, Hirschmann DT, Buser DP, Spiess M. Rabaptin5 is recruited to endosomes by Rab4 and Rabex5 to regulate endosome maturation. J Cell Sci 2015; 128:4126-37. [PMID: 26430212 DOI: 10.1242/jcs.174664] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022] Open
Abstract
Rab GTPases control membrane identity, fusion and transport by interaction with effector proteins. Effectors that influence the activation-inactivation cycle of their own or other Rab proteins contribute to the timely conversion of Rab membrane identities. Rab5 and its effector rabaptin5 (Rbpt5, also known as RABEP1) are generally considered the prime example for a positive-feedback loop in which Rab5-GTP recruits Rbpt5 in complex with Rabex5 (also known as RABGEF1), the GDP/GTP exchange factor of Rab5, to early endosomes, thus maintaining the Rab5 membrane identity. By deletion analysis, we found that the membrane recruitment of Rabaptin5 required binding to Rab4 and Rabex5, but not Rab5. Deletion of either one of the two Rab5-binding domains or silencing of Rab5 expression did not affect Rabaptin5 recruitment, but produced giant endosomes with early and late endosomal characteristics. The results contradict the model of feedback activation of Rab5 and instead indicate that Rbpt5 is recruited by both Rabex5 recognizing ubiquitylated cargo and by Rab4 to activate Rab5 in a feed-forward manner.
Collapse
Affiliation(s)
- Simone Kälin
- Biozentrum, University of Basel, Klingelbergstrasse 70, Basel CH-4056, Switzerland
| | - David T Hirschmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, Basel CH-4056, Switzerland
| | - Dominik P Buser
- Biozentrum, University of Basel, Klingelbergstrasse 70, Basel CH-4056, Switzerland
| | - Martin Spiess
- Biozentrum, University of Basel, Klingelbergstrasse 70, Basel CH-4056, Switzerland
| |
Collapse
|
38
|
Abstract
Rab GTPases control intracellular membrane traffic by recruiting specific effector proteins to restricted membranes in a GTP-dependent manner. In this Cell Science at a Glance and the accompanying poster, we highlight the regulation of Rab GTPases by proteins that control their membrane association and activation state, and provide an overview of the cellular processes that are regulated by Rab GTPases and their effectors, including protein sorting, vesicle motility and vesicle tethering. We also discuss the physiological importance of Rab GTPases and provide examples of diseases caused by their dysfunctions.
Collapse
Affiliation(s)
- Yan Zhen
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Montebello, Oslo N-0379, Norway Department for Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Oslo N-0379, Norway
| | - Harald Stenmark
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Montebello, Oslo N-0379, Norway Department for Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Oslo N-0379, Norway
| |
Collapse
|
39
|
Mott HR, Owen D. Structures of Ras superfamily effector complexes: What have we learnt in two decades? Crit Rev Biochem Mol Biol 2015; 50:85-133. [PMID: 25830673 DOI: 10.3109/10409238.2014.999191] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Ras superfamily small G proteins are master regulators of a diverse range of cellular processes and act via downstream effector molecules. The first structure of a small G protein-effector complex, that of Rap1A with c-Raf1, was published 20 years ago. Since then, the structures of more than 60 small G proteins in complex with their effectors have been published. These effectors utilize a diverse array of structural motifs to interact with the G protein fold, which we have divided into four structural classes: intermolecular β-sheets, helical pairs, other interactions, and pleckstrin homology (PH) domains. These classes and their representative structures are discussed and a contact analysis of the interactions is presented, which highlights the common effector-binding regions between and within the small G protein families.
Collapse
Affiliation(s)
- Helen R Mott
- Department of Biochemistry, University of Cambridge , Cambridge , UK
| | | |
Collapse
|
40
|
Priya A, Kalaidzidis IV, Kalaidzidis Y, Lambright D, Datta S. Molecular Insights into Rab7-Mediated Endosomal Recruitment of Core Retromer: Deciphering the Role of Vps26 and Vps35. Traffic 2014; 16:68-84. [DOI: 10.1111/tra.12237] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Amulya Priya
- Department of Biological Sciences; Indian Institute of Science Education and Research Bhopal; ITI Gas Rahat Building Bhopal 462023 India
| | - Inna V Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics; 108 Pfotenhauerstrasse Dresden 01307 Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics; 108 Pfotenhauerstrasse Dresden 01307 Germany
- Faculty of Bioengineering and Bioinformatics; Moscow State University; Moscow 119991 Russia
| | - David Lambright
- Program in Molecular Medicine; University of Massachusetts Medical School; 373 Plantation Street Worcester MA 01605 USA
| | - Sunando Datta
- Department of Biological Sciences; Indian Institute of Science Education and Research Bhopal; ITI Gas Rahat Building Bhopal 462023 India
| |
Collapse
|
41
|
Zhang Z, Wang S, Shen T, Chen J, Ding J. Crystal structure of the Rab9A-RUTBC2 RBD complex reveals the molecular basis for the binding specificity of Rab9A with RUTBC2. Structure 2014; 22:1408-20. [PMID: 25220469 DOI: 10.1016/j.str.2014.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/09/2014] [Accepted: 08/13/2014] [Indexed: 10/24/2022]
Abstract
Rab9 plays a vital role in regulating the transport of mannose 6-phosphate receptors from late endosomes to the trans-Golgi network through interactions with various effectors. Here, we report the crystal structure of GTP-bound Rab9A in complex with the Rab-binding domain (RBD) of the effector RUTBC2. RUTBC2 RBD assumes a pleckstrin homology domain fold that uses a binding site consisting of mainly β1 and the η1 insertion to interact with the switch and interswitch regions of Rab9A. The C-terminal hypervariable region of Rab9A is disordered and thus not required for RUTBC2 binding. The conformational plasticity of the switch and interswitch regions of Rab9A primarily determines the specificity for RUTBC2. Our biochemical and biological data confirm these findings and further show that Rab9B can bind to RUTBC2 probably in a similar manner as Rab9A. These results together reveal the molecular basis for the binding specificity of Rab9A with RUTBC2.
Collapse
Affiliation(s)
- Zhe Zhang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Shanshan Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Tong Shen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Jiangye Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.
| |
Collapse
|
42
|
Korobko EV, Kiselev SL, Korobko IV. Characterization of Rabaptin-5 γ isoform. BIOCHEMISTRY. BIOKHIMIIA 2014; 79:856-64. [PMID: 25385014 DOI: 10.1134/s000629791409003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rab GTPases are key regulators of intracellular membrane traffic acting through their effector molecules. Rabaptin-5 is a Rab5 effector in early endosome fusion and connects Rab5- and Rab4-positive membrane compartments owing to its ability to interact with Rab4 GTPase. Recent studies showed that Rabaptin-5 transcript is subjected to extensive alternative splicing, thus resulting in expression of Rabaptin-5 isoforms mostly bearing short deletions in the polypeptide chain. As interactions of a Rab GTPase with different effectors lead to different responses, functional characterization of Rabaptin-5 isoforms becomes an attractive issue. Indeed, it was shown that Rab GTPase effector properties of Rabaptin-5 and its α and δ isoforms are different. This work focused on another Rabaptin-5 isoform, Rabaptin-5γ. Despite its ability to interact with Rab5, endogenously produced Rabaptin-5γ was absent from early endosomes. Rather, it was found to be tightly associated with trans-Golgi network and partially localized to a Rab4-positive membrane compartment. The revealed intracellular localization of Rabaptin-5γ indicates that it is not involved in Rab5-driven events; rather, it functions in other membrane transport steps. Our study signifies the role of alternative splicing in determination of functional activities of Rab effector molecules.
Collapse
Affiliation(s)
- E V Korobko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | | | | |
Collapse
|
43
|
Lucas M, Gaspar AH, Pallara C, Rojas AL, Fernández-Recio J, Machner MP, Hierro A. Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5. Proc Natl Acad Sci U S A 2014; 111:E3514-23. [PMID: 25114243 PMCID: PMC4151760 DOI: 10.1073/pnas.1405391111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A challenge for microbial pathogens is to assure that their translocated effector proteins target only the correct host cell compartment during infection. The Legionella pneumophila effector vacuolar protein sorting inhibitor protein D (VipD) localizes to early endosomal membranes and alters their lipid and protein composition, thereby protecting the pathogen from endosomal fusion. This process requires the phospholipase A1 (PLA1) activity of VipD that is triggered specifically on VipD binding to the host cell GTPase Rab5, a key regulator of endosomes. Here, we present the crystal structure of VipD in complex with constitutively active Rab5 and reveal the molecular mechanism underlying PLA1 activation. An active site-obstructing loop that originates from the C-terminal domain of VipD is repositioned on Rab5 binding, thereby exposing the catalytic pocket within the N-terminal PLA1 domain. Substitution of amino acid residues located within the VipD-Rab5 interface prevented Rab5 binding and PLA1 activation and caused a failure of VipD mutant proteins to target to Rab5-enriched endosomal structures within cells. Experimental and computational analyses confirmed an extended VipD-binding interface on Rab5, explaining why this L. pneumophila effector can compete with cellular ligands for Rab5 binding. Together, our data explain how the catalytic activity of a microbial effector can be precisely linked to its subcellular localization.
Collapse
Affiliation(s)
- María Lucas
- Structural Biology Unit, Center for Cooperative Research in Biosciences, 48160 Derio, Spain
| | - Andrew H Gaspar
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Chiara Pallara
- Joint Barcelona Supercomputing Center-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain; and
| | - Adriana Lucely Rojas
- Structural Biology Unit, Center for Cooperative Research in Biosciences, 48160 Derio, Spain
| | - Juan Fernández-Recio
- Joint Barcelona Supercomputing Center-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain; and
| | - Matthias P Machner
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892;
| | - Aitor Hierro
- Structural Biology Unit, Center for Cooperative Research in Biosciences, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| |
Collapse
|
44
|
Wu KY, He M, Hou QQ, Sheng AL, Yuan L, Liu F, Liu WW, Li G, Jiang XY, Luo ZG. Semaphorin 3A activates the guanosine triphosphatase Rab5 to promote growth cone collapse and organize callosal axon projections. Sci Signal 2014; 7:ra81. [PMID: 25161316 DOI: 10.1126/scisignal.2005334] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Axon guidance (pathfinding) wires the brain during development and is regulated by various attractive and repulsive cues. Semaphorin 3A (Sema3A) is a repulsive cue, inducing the collapse of axon growth cones. In the mammalian forebrain, the corpus callosum is the major commissure that transmits information flow between the two hemispheres, and contralateral axons assemble into well-defined tracts. We found that the patterning of callosal axon projections in rodent layer II and III (L2/3) cortical neurons in response to Sema3A was mediated by the activation of Rab5, a small guanosine triphosphatase (GTPase) that mediates endocytosis, through the membrane fusion protein Rabaptin-5 and the Rab5 guanine nucleotide exchange factor (GEF) Rabex-5. Rabaptin-5 bound directly to Plexin-A1 in the Sema3A receptor complex [an obligate heterodimer formed by Plexin-A1 and neuropilin 1 (NP1)]; Sema3A enhanced this interaction in cultured neurons. Rabaptin-5 bridged the interaction between Rab5 and Plexin-A1. Sema3A stimulated endocytosis from the cell surface of callosal axon growth cones. In utero electroporation to reduce Rab5 or Rabaptin-5 impaired axon fasciculation or caused mistargeting of L2/3 callosal projections in rats. Overexpression of Rabaptin-5 or Rab5 rescued the defective callosal axon fasciculation or mistargeting of callosal axons caused by the loss of Sema3A-Plexin-A1 signaling in rats expressing dominant-negative Plexin-A1 or in NP1-deficient mice. Thus, our findings suggest that Rab5, its effector Rabaptin-5, and its regulator Rabex-5 mediate Sema3A-induced axon guidance during brain development.
Collapse
Affiliation(s)
- Kong-Yan Wu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Miao He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qiong-Qiong Hou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Ai-Li Sheng
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Lei Yuan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Fei Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Wen-Wen Liu
- Chinese Academy of Sciences Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 11 Beiyitiao, Zhong Guan Cun, Beijing 100190, China
| | - Guangpu Li
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Xing-Yu Jiang
- Chinese Academy of Sciences Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 11 Beiyitiao, Zhong Guan Cun, Beijing 100190, China
| | - Zhen-Ge Luo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.
| |
Collapse
|
45
|
Zhang Z, Zhang T, Wang S, Gong Z, Tang C, Chen J, Ding J. Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5. eLife 2014; 3. [PMID: 24957337 PMCID: PMC4102244 DOI: 10.7554/elife.02687] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 06/20/2014] [Indexed: 01/30/2023] Open
Abstract
Rabex-5 and Rabaptin-5 function together to activate Rab5 and further promote early endosomal fusion in endocytosis. The Rabex-5 GEF activity is autoinhibited by the Rabex-5 CC domain (Rabex-5CC) and activated by the Rabaptin-5 C2-1 domain (Rabaptin-5C21) with yet unknown mechanism. We report here the crystal structures of Rabex-5 in complex with the dimeric Rabaptin-5C21 (Rabaptin-5C212) and in complex with Rabaptin-5C212 and Rab5, along with biophysical and biochemical analyses. We show that Rabex-5CC assumes an amphipathic α-helix which binds weakly to the substrate-binding site of the GEF domain, leading to weak autoinhibition of the GEF activity. Binding of Rabaptin-5C21 to Rabex-5 displaces Rabex-5CC to yield a largely exposed substrate-binding site, leading to release of the GEF activity. In the ternary complex the substrate-binding site of Rabex-5 is completely exposed to bind and activate Rab5. Our results reveal the molecular mechanism for the regulation of the Rabex-5 GEF activity. DOI:http://dx.doi.org/10.7554/eLife.02687.001 Cells need to allow various molecules to pass through the plasma membrane on their surface. Some molecules have to enter the cell, whereas others have to leave. Cells rely on a process called endocytosis to move large molecules into the cell. This involves part of the membrane engulfing the molecule to form a ‘bubble’ around it. This bubble, which is called an endosome, then moves the molecule to final destination inside the cell. A protein called Rab5 controls how a new endosome is produced. However, before this can happen, various other molecules—including two proteins called Rabex-5 and Rabaptin-5—must activate the Rab5 protein. Exactly how these three proteins interact with each other was unknown. Zhang et al. used X-ray crystallography to examine the structures of the complexes formed when Rabex-5 and Rabaptin-5 bind to each other, both when Rab5 is present, and also when it is absent. Biochemical and biophysical experiments confirmed that the Rabex-5/Rabaptin-5 complex is able to activate Rab5. Zhang et al. also found that Rabex-5, on its own, folds so that the site that normally binds to Rab5 instead binds to a different part of Rabex-5, thus preventing endocytosis. However, when Rabaptin-5 forms a complex with Rabex-5, the Rab5 binding site is freed up. The Rabex-5/Rabaptin-5 complex can switch between a V shape and a linear structure. Binding to Rab5 stabilizes the linear form of the complex, which then helps activate Rab5, and subsequently the activated Rab5 can interact with other downstream molecules, triggering endocytosis. DOI:http://dx.doi.org/10.7554/eLife.02687.002
Collapse
Affiliation(s)
- Zhe Zhang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tianlong Zhang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shanshan Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Chun Tang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Jiangye Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
46
|
Kümmel D, Ungermann C. Principles of membrane tethering and fusion in endosome and lysosome biogenesis. Curr Opin Cell Biol 2014; 29:61-6. [PMID: 24813801 DOI: 10.1016/j.ceb.2014.04.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/15/2014] [Accepted: 04/23/2014] [Indexed: 11/29/2022]
Abstract
Endosomes and lysosomes receive cargo via vesicular carriers that arrive along multiple trafficking routes. On both organelles, tethering proteins have been identified that interact specifically with Rab5 on endosomes and Rab7 on late endosomes/lysosomes and that facilitate the SNARE-driven membrane fusion. Even though the structure and stoichiometry of the involved proteins and protein complexes differ strongly, they may operate by similar principles. Within this review, we will provide insights into their common functions and discuss the open questions in the field.
Collapse
Affiliation(s)
- Daniel Kümmel
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry Section, Barbarastrasse 13, Osnabrück 49076, Germany.
| | - Christian Ungermann
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry Section, Barbarastrasse 13, Osnabrück 49076, Germany.
| |
Collapse
|
47
|
Khan AR, Ménétrey J. Structural biology of Arf and Rab GTPases' effector recruitment and specificity. Structure 2014; 21:1284-97. [PMID: 23931141 DOI: 10.1016/j.str.2013.06.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/30/2013] [Accepted: 06/05/2013] [Indexed: 11/15/2022]
Abstract
Arf and Rab proteins, members of small GTPases superfamily, localize to specific subcellular compartments and regulate intracellular trafficking. To carry out their cellular functions, Arfs/Rabs interact with numerous and structurally diverse effector proteins. Over the years, a number of Arf/Rab:effector complexes have been crystallized and their structures reveal shared binding modes including α-helical packing, β-β complementation, and heterotetrameric assemblies. We review available structural information and provide a framework for in-depth analysis of complexes. The unifying features that we identify are organized into a classification scheme for different modes of Arf/Rab:effector interactions, which includes "all-α-helical," "mixed α-helical," "β-β zipping," and "bivalent" modes of binding. Additionally, we highlight structural determinants that are the basis of effector specificity. We conclude by expanding on functional implications that are emerging from available structural information under our proposed classification scheme.
Collapse
Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
| | | |
Collapse
|
48
|
Exoenzyme S ADP-ribosylates Rab5 effector sites to uncouple intracellular trafficking. Infect Immun 2013; 82:21-8. [PMID: 24101692 DOI: 10.1128/iai.01059-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Pseudomonas aeruginosa exoenzyme S (ExoS) ADP-ribosylates multiple eukaryotic targets to promote cytopathology and bacterial colonization. ADP-ribosylation of the small GTPase Rab5 has previously been shown to block fluid-phase endocytosis and trafficking of plasma membrane receptors to the early endosomes as well as inhibit phagocytosis of the bacterium. In this study, ExoS is shown to be capable of ADP-ribosylating 6 candidate arginine residues that are located in the effector binding region or in the C terminus of Rab5. Two Rab5 derivatives were engineered, which contained Arg→Ala mutations at four Arg residues within the effector binding region (EF) or two Arg residues within the C-terminal tail (TL). Expression of Rab5(TL) does not affect the ability of ExoS to modify intracellular trafficking, while expression of Rab5(EF) rescued the ability of ExoS to inhibit intracellular trafficking. ADP-ribosylation of effector arginines likely uncouples Rab5 signaling to downstream effectors. This is a different mechanism for inhibition than observed for the ADP-ribosylation of Ras by ExoS, where ADP-ribosylated Ras loses the ability to bind guanine nucleotide exchange factor (GEF). Other experiments showed that expression of dominant negative Rab5(Ser34Asn) does not inhibit ExoS trafficking to the perinuclear region of intoxicated cells. This study provides insight into a mechanism for how ExoS ADP-ribosylation of Rab5 inhibits Rab5 function.
Collapse
|
49
|
DFT Studies of Trans and Cis Influences in the Homolysis of the Co–C Bond in Models of the Alkylcobalamins. J Phys Chem A 2013; 117:3057-68. [DOI: 10.1021/jp311788t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
50
|
Khan AR. Oligomerization of rab/effector complexes in the regulation of vesicle trafficking. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:579-614. [PMID: 23663983 DOI: 10.1016/b978-0-12-386931-9.00021-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rabs comprise the largest member of the Ras superfamily of small GTPases with over 60 proteins in mammals and 11 proteins in yeast. Like all small GTPases, Rabs oscillate between an inactive GDP-bound conformation and an active GTP-bound state that is tethered to lipid membranes via a C-terminal prenylation site on conserved cysteine residues. In their active state, Rabs regulate various aspects of membrane trafficking, including vesicle formation, transport, docking, and fusion. The critical element of biological activity is the recruitment of cytosolic effector proteins to specific endomembranes by active Rabs. The importance of Rabs in cellular processes is apparent from their links to genetic disorders, immunodeficiency, cancer, and pathogen invasion. During the last decade, numerous structures of complexes have shed light on the molecular basis for Rab/effector specificity and their topological organization on subcellular membranes. Here, I review the known structures of Rab/effector complexes and their modes of oligomerization. This is followed by a brief discussion on the thermodynamics of effector recruitment, which has not been documented sufficiently in previous reviews. A summary of diseases associated with Rab/effector trafficking pathways concludes this chapter.
Collapse
Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| |
Collapse
|