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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.
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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
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Khumukcham SS, Penugurti V, Bugide S, Dwivedi A, Kumari A, Kesavan PS, Kalali S, Mishra YG, Ramesh VA, Nagarajaram HA, Mazumder A, Manavathi B. HPIP and RUFY3 are noncanonical guanine nucleotide exchange factors of Rab5 to regulate endocytosis-coupled focal adhesion turnover. J Biol Chem 2023; 299:105311. [PMID: 37797694 PMCID: PMC10641178 DOI: 10.1016/j.jbc.2023.105311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023] Open
Abstract
While the role of endocytosis in focal adhesion turnover-coupled cell migration has been established in addition to its conventional role in cellular functions, the molecular regulators and precise molecular mechanisms that underlie this process remain largely unknown. In this study, we report that proto-oncoprotein hematopoietic PBX-interacting protein (HPIP) localizes to focal adhesions as well as endosomal compartments along with RUN FYVE domain-containing protein 3 (RUFY3) and Rab5, an early endosomal protein. HPIP contains two coiled-coil domains (CC1 and CC2) that are necessary for its association with Rab5 and RUFY3 as CC domain double mutant, that is, mtHPIPΔCC1-2 failed to support it. Furthermore, we show that HPIP and RUFY3 activate Rab5 by serving as noncanonical guanine nucleotide exchange factors of Rab5. In support of this, either deletion of coiled-coil domains or silencing of HPIP or RUFY3 impairs Rab5 activation and Rab5-dependent cell migration. Mechanistic studies further revealed that loss of HPIP or RUFY3 expression severely impairs Rab5-mediated focal adhesion disassembly, FAK activation, fibronectin-associated-β1 integrin trafficking, and thus cell migration. Together, this study underscores the importance of HPIP and RUFY3 as noncanonical guanine nucleotide exchange factors of Rab5 and in integrin trafficking and focal adhesion turnover, which implicates in cell migration.
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Affiliation(s)
| | - Vasudevarao Penugurti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Suresh Bugide
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Anju Dwivedi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Anita Kumari
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - P S Kesavan
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Hyderabad, Telangana, India
| | - Sruchytha Kalali
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Yasaswi Gayatri Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Vakkalagadda A Ramesh
- Laboratory of Computational Biology, Centre for DNA Finger Printing and Diagnostics (CDFD), Hyderabad, Telangana, India; Laboratory of Computational Biology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | - Aprotim Mazumder
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Hyderabad, Telangana, India
| | - Bramanandam Manavathi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
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Koop K, Yuan W, Tessadori F, Rodriguez-Polanco WR, Grubbs J, Zhang B, Osmond M, Graham G, Sawyer S, Conboy E, Vetrini F, Treat K, Płoski R, Pienkowski VM, Kłosowska A, Fieg E, Krier J, Mallebranche C, Alban Z, Aldinger KA, Ritter D, Macnamara E, Sullivan B, Herriges J, Alaimo JT, Helbig C, Ellis CA, van Eyk C, Gecz J, Farrugia D, Osei-Owusu I, Adès L, van den Boogaard MJ, Fuchs S, Bakker J, Duran K, Dawson ZD, Lindsey A, Huang H, Baldridge D, Silverman GA, Grant BD, Raizen D, van Haaften G, Pak SC, Rehmann H, Schedl T, van Hasselt P. Macrocephaly and developmental delay caused by missense variants in RAB5C. Hum Mol Genet 2023; 32:3063-3077. [PMID: 37552066 PMCID: PMC10586195 DOI: 10.1093/hmg/ddad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/06/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023] Open
Abstract
Rab GTPases are important regulators of intracellular vesicular trafficking. RAB5C is a member of the Rab GTPase family that plays an important role in the endocytic pathway, membrane protein recycling and signaling. Here we report on 12 individuals with nine different heterozygous de novo variants in RAB5C. All but one patient with missense variants (n = 9) exhibited macrocephaly, combined with mild-to-moderate developmental delay. Patients with loss of function variants (n = 2) had an apparently more severe clinical phenotype with refractory epilepsy and intellectual disability but a normal head circumference. Four missense variants were investigated experimentally. In vitro biochemical studies revealed that all four variants were damaging, resulting in increased nucleotide exchange rate, attenuated responsivity to guanine exchange factors and heterogeneous effects on interactions with effector proteins. Studies in C. elegans confirmed that all four variants were damaging in vivo and showed defects in endocytic pathway function. The variant heterozygotes displayed phenotypes that were not observed in null heterozygotes, with two shown to be through a dominant negative mechanism. Expression of the human RAB5C variants in zebrafish embryos resulted in defective development, further underscoring the damaging effects of the RAB5C variants. Our combined bioinformatic, in vitro and in vivo experimental studies and clinical data support the association of RAB5C missense variants with a neurodevelopmental disorder characterized by macrocephaly and mild-to-moderate developmental delay through disruption of the endocytic pathway.
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Affiliation(s)
- Klaas Koop
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
| | - Weimin Yuan
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Wilmer R Rodriguez-Polanco
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jeremy Grubbs
- Department of Neurology and the Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bo Zhang
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Matt Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Gail Graham
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Sarah Sawyer
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Erin Conboy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kayla Treat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Rafal Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, 02-106, Poland
| | - Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, 02-106, Poland
- Marseille Medical Genetics U1251, Aix Marseille University, Marseille, 13005, France
| | - Anna Kłosowska
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdańsk, Gdańsk, 80-210, Poland
| | - Elizabeth Fieg
- Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Joel Krier
- Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Coralie Mallebranche
- Unité d'Onco-Hémato-Immunologie pédiatrique, CHU d’Angers, Angers, 49933, France
| | - Ziegler Alban
- Service de génétique, CHU d’Angers, Angers, 49933, France
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Deborah Ritter
- Department of Pediatrics, Oncology Section, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ellen Macnamara
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bonnie Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - John Herriges
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - Catherine Helbig
- The Epilepsy Neurogenetics Initiative, Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Colin A Ellis
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, 19104, USA
| | - Clare van Eyk
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5006, Australia
| | - Jozef Gecz
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5006, Australia
| | | | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lesley Adès
- Department of Clinical Genetics, The Children’s Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, 2145, Australia
| | - Marie-Jose van den Boogaard
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3584EA, The Netherlands
| | - Sabine Fuchs
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
| | - Jeroen Bakker
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Karen Duran
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Zachary D Dawson
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Anika Lindsey
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Huiyan Huang
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Dustin Baldridge
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Gary A Silverman
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - David Raizen
- Department of Neurology and the Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3584EA, The Netherlands
| | - Stephen C Pak
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Holger Rehmann
- Department of Energy and Biotechnology, Flensburg University of Applied Sciences, 24943, Flensburg, Germany
| | - Tim Schedl
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Peter van Hasselt
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
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Nakada-Tsukui K, Watanabe N, Maehama T, Nozaki T. Phosphatidylinositol Kinases and Phosphatases in Entamoeba histolytica. Front Cell Infect Microbiol 2019; 9:150. [PMID: 31245297 PMCID: PMC6563779 DOI: 10.3389/fcimb.2019.00150] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Phosphatidylinositol (PtdIns) metabolism is indispensable in eukaryotes. Phosphoinositides (PIs) are phosphorylated derivatives of PtdIns and consist of seven species generated by reversible phosphorylation of the inositol moieties at the positions 3, 4, and 5. Each of the seven PIs has a unique subcellular and membrane domain distribution. In the enteric protozoan parasite Entamoeba histolytica, it has been previously shown that the PIs phosphatidylinositol 3-phosphate (PtdIns3P), PtdIns(4,5)P2, and PtdIns(3,4,5)P3 are localized to phagosomes/phagocytic cups, plasma membrane, and phagocytic cups, respectively. The localization of these PIs in E. histolytica is similar to that in mammalian cells, suggesting that PIs have orthologous functions in E. histolytica. In contrast, the conservation of the enzymes that metabolize PIs in this organism has not been well-documented. In this review, we summarized the full repertoire of the PI kinases and PI phosphatases found in E. histolytica via a genome-wide survey of the current genomic information. E. histolytica appears to have 10 PI kinases and 23 PI phosphatases. It has a panel of evolutionarily conserved enzymes that generate all the seven PI species. However, class II PI 3-kinases, type II PI 4-kinases, type III PI 5-phosphatases, and PI 4P-specific phosphatases are not present. Additionally, regulatory subunits of class I PI 3-kinases and type III PI 4-kinases have not been identified. Instead, homologs of class I PI 3-kinases and PTEN, a PI 3-phosphatase, exist as multiple isoforms, which likely reflects that elaborate signaling cascades mediated by PtdIns(3,4,5)P3 are present in this organism. There are several enzymes that have the nuclear localization signal: one phosphatidylinositol phosphate (PIP) kinase, two PI 3-phosphatases, and one PI 5-phosphatase; this suggests that PI metabolism also has conserved roles related to nuclear functions in E. histolytica, as it does in model organisms.
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Affiliation(s)
- Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Natsuki Watanabe
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tomohiko Maehama
- Division of Molecular and Cellular Biology, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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