1
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Marmorale LJ, Jin H, Reidy TG, Palomino-Alonso B, Zysnarski CJ, Jordan-Javed F, Lahiri S, Duncan MC. Fast-evolving cofactors regulate the role of HEATR5 complexes in intra-Golgi trafficking. J Cell Biol 2024; 223:e202309047. [PMID: 38240799 PMCID: PMC10798858 DOI: 10.1083/jcb.202309047] [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: 09/11/2023] [Revised: 11/22/2023] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
The highly conserved HEATR5 proteins are best known for their roles in membrane traffic mediated by the adaptor protein complex-1 (AP1). HEATR5 proteins rely on fast-evolving cofactors to bind to AP1. However, how HEATR5 proteins interact with these cofactors is unknown. Here, we report that the budding yeast HEATR5 protein, Laa1, functions in two biochemically distinct complexes. These complexes are defined by a pair of mutually exclusive Laa1-binding proteins, Laa2 and the previously uncharacterized Lft1/Yml037c. Despite limited sequence similarity, biochemical analysis and structure predictions indicate that Lft1 and Laa2 bind Laa1 via structurally similar mechanisms. Both Laa1 complexes function in intra-Golgi recycling. However, only the Laa2-Laa1 complex binds to AP1 and contributes to its localization. Finally, structure predictions indicate that human HEATR5 proteins bind to a pair of fast-evolving interacting partners via a mechanism similar to that observed in yeast. These results reveal mechanistic insight into how HEATR5 proteins bind their cofactors and indicate that Laa1 performs functions besides recruiting AP1.
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Affiliation(s)
- Lucas J Marmorale
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Huan Jin
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Thomas G Reidy
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Brandon Palomino-Alonso
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Christopher J Zysnarski
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Fatima Jordan-Javed
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Sagar Lahiri
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Ann Arbor, MI, USA
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2
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Clippinger AK, Naismith TV, Yoo W, Jansen S, Kast DJ, Hanson PI. IST1 regulates select recycling pathways. Traffic 2024; 25:e12921. [PMID: 37926552 PMCID: PMC11027954 DOI: 10.1111/tra.12921] [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: 12/09/2022] [Revised: 08/21/2023] [Accepted: 09/23/2023] [Indexed: 11/07/2023]
Abstract
ESCRTs (Endosomal Sorting Complex Required for Transports) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intraluminal vesicles (ILVs) to generate multivesicular endosomes. While most of the 12 ESCRT-III proteins are known to play roles in ILV formation, IST1 has been associated with a wider range of endosomal remodeling events. Here, we extend previous studies of IST1 function in endosomal trafficking and confirm that IST1, along with its binding partner CHMP1B, contributes to scission of early endosomal carriers. Functionally, depleting IST1 impaired delivery of transferrin receptor from early/sorting endosomes to the endocytic recycling compartment and instead increased its rapid recycling to the plasma membrane via peripheral endosomes enriched in the clathrin adaptor AP-1. IST1 is also important for export of mannose 6-phosphate receptor from early/sorting endosomes. Examination of IST1 binding partners on endosomes revealed that IST1 interacts with the MIT domain-containing sorting nexin SNX15, a protein previously reported to regulate endosomal recycling. Our kinetic and spatial analyses establish that SNX15 and IST1 occupy a clathrin-containing subdomain on the endosomal perimeter distinct from those previously implicated in cargo retrieval or degradation. Using live-cell microscopy, we see that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or the base of endosomal tubules. These findings indicate that IST1 contributes to a subset of recycling pathways from the early/sorting endosome.
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Affiliation(s)
- Amy K Clippinger
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Teresa V Naismith
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wonjin Yoo
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Silvia Jansen
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - David J Kast
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Phyllis I Hanson
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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3
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Rondón Ortiz AN, Zhang L, Ash PE, Basu A, Puri S, van der Spek SJ, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571324. [PMID: 38168279 PMCID: PMC10760047 DOI: 10.1101/2023.12.12.571324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network that are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Despite various attempts to unravel the complexity of the SQSTM1 protein network, our understanding of the relationship of various components in cellular physiology and disease states continues to evolve. To investigate the SQSTM1 protein interaction network, we performed proximity profile labeling by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including: production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners via defined functional SQSTM1 interacting domains and capture of novel SQSTM1 interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.
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Affiliation(s)
- Alejandro N. Rondón Ortiz
- Department of Biology, Boston University, Boston, MA 02215, USA
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Lushuang Zhang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Peter E.A. Ash
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Sambhavi Puri
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | | | - Luke Dorrian
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Benjamin Wolozin
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02115, USA
- Center for Neurophotonics, Boston University, Boston, MA 02115, USA
- Department of Neurology, Boston University, Boston, MA 02115, USA
- Department of Pharmacology, Physiology and Biophysics
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4
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Madan V, Albacete‐Albacete L, Jin L, Scaturro P, Watson JL, Muschalik N, Begum F, Boulanger J, Bauer K, Kiebler MA, Derivery E, Bullock SL. HEATR5B associates with dynein-dynactin and promotes motility of AP1-bound endosomal membranes. EMBO J 2023; 42:e114473. [PMID: 37872872 PMCID: PMC10690479 DOI: 10.15252/embj.2023114473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023] Open
Abstract
The microtubule motor dynein mediates polarised trafficking of a wide variety of organelles, vesicles and macromolecules. These functions are dependent on the dynactin complex, which helps recruit cargoes to dynein's tail and activates motor movement. How the dynein-dynactin complex orchestrates trafficking of diverse cargoes is unclear. Here, we identify HEATR5B, an interactor of the adaptor protein-1 (AP1) clathrin adaptor complex, as a novel player in dynein-dynactin function. HEATR5B was recovered in a biochemical screen for proteins whose association with the dynein tail is augmented by dynactin. We show that HEATR5B binds directly to the dynein tail and dynactin and stimulates motility of AP1-associated endosomal membranes in human cells. We also demonstrate that the Drosophila HEATR5B homologue is an essential gene that selectively promotes dynein-based transport of AP1-bound membranes to the Golgi apparatus. As HEATR5B lacks the coiled-coil architecture typical of dynein adaptors, our data point to a non-canonical process orchestrating motor function on a specific cargo. We additionally show that HEATR5B promotes association of AP1 with endosomal membranes independently of dynein. Thus, HEATR5B co-ordinates multiple events in AP1-based trafficking.
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Affiliation(s)
- Vanesa Madan
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
AbcamCambridgeUK
| | - Lucas Albacete‐Albacete
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Li Jin
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | | | - Joseph L Watson
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Nadine Muschalik
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Farida Begum
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Jérôme Boulanger
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Karl Bauer
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Emmanuel Derivery
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Simon L Bullock
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
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5
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Marmorale LJ, Jin H, Reidy TG, Palomino-Alonso B, Zysnarski C, Jordan-Javed F, Lahiri S, Duncan MC. Two functionally distinct HEATR5 protein complexes are defined by fast-evolving co-factors in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554671. [PMID: 37662263 PMCID: PMC10473696 DOI: 10.1101/2023.08.24.554671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The highly conserved HEATR5 proteins are best known for their roles in membrane traffic mediated by the adaptor protein complex-1 (AP1). HEATR5 proteins rely on fast-evolving co-factors to bind to AP1. However, how HEATR5 proteins interact with these co-factors is unknown. Here, we report that the budding yeast HEATR5 protein, Laa1, functions in two biochemically distinct complexes. These complexes are defined by a pair of mutually exclusive Laa1-binding proteins, Laa2 and the previously uncharacterized Lft1/Yml037c. Despite limited sequence similarity, biochemical analysis and structure predictions indicate that Lft1 and Laa2 bind Laa1 via structurally similar mechanisms. Both Laa1 complexes function in intra-Golgi recycling. However, only the Laa2-Laa1 complex binds to AP1 and contributes to its localization. Finally, structure predictions indicate that human HEATR5 proteins bind to a pair of fast-evolving interacting partners via a mechanism similar to that observed in yeast. These results reveal mechanistic insight into how HEATR5 proteins bind their co-factors and indicate that Laa1 performs functions besides recruiting AP1.
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Affiliation(s)
- Lucas J. Marmorale
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
- Present address: Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
| | - Huan Jin
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
| | - Thomas G. Reidy
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
- Present address: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Fatima Jordan-Javed
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
| | - Sagar Lahiri
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor MI
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6
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Clippinger AK, Naismith TV, Yoo W, Jansen S, Kast D, Hanson PI. IST1 regulates select endosomal recycling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551359. [PMID: 37577466 PMCID: PMC10418098 DOI: 10.1101/2023.07.31.551359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
ESCRTs (Endosomal Sorting Complex Required for Transport) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intralumenal vesicles (ILVs) to generate multivesicular endosomes. While most of the 12 ESCRT-III proteins are known to play roles in ILV formation, IST1 has been associated with a wider range of endosomal remodeling events. Here, we extend previous studies of IST1 function in endosomal trafficking and confirm that IST1, along with its binding partner CHMP1B, contributes to scission of early endosomal carriers. Depleting IST1 impaired delivery of transferrin receptor from early/sorting endosomes to the endocytic recycling compartment and instead increased its rapid recycling to the plasma membrane via peripheral endosomes enriched in the clathrin adaptor AP-1. IST1 is also important for export of mannose 6-phosphate receptor from early/sorting endosomes. Examination of IST1 binding partners on endosomes revealed that IST1 interacts with the MIT domain-containing sorting nexin SNX15, a protein previously reported to regulate endosomal recycling. Our kinetic and spatial analyses establish that SNX15 and IST1 occupy a clathrin-containing subdomain on the endosomal perimeter distinct from those previously implicated in cargo retrieval or degradation. Using live-cell microscopy we see that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or the base of endosomal tubules. These findings indicate that IST1 contributes to a subset of recycling pathways from the early/sorting endosome.
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7
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Koss KM, Son T, Li C, Hao Y, Cao J, Churchward MA, Zhang ZJ, Wertheim JA, Derda R, Todd KG. Toward discovering a novel family of peptides targeting neuroinflammatory states of brain microglia and astrocytes. J Neurochem 2023:10.1111/jnc.15840. [PMID: 37171455 PMCID: PMC10640667 DOI: 10.1111/jnc.15840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Microglia are immune-derived cells critical to the development and healthy function of the brain and spinal cord, yet are implicated in the active pathology of many neuropsychiatric disorders. A range of functional phenotypes associated with the healthy brain or disease states has been suggested from in vivo work and were modeled in vitro as surveying, reactive, and primed sub-types of primary rat microglia and mixed microglia/astrocytes. It was hypothesized that the biomolecular profile of these cells undergoes a phenotypical change as well, and these functional phenotypes were explored for potential novel peptide binders using a custom 7 amino acid-presenting M13 phage library (SX7) to identify unique peptides that bind differentially to these respective cell types. Surveying glia were untreated, reactive were induced with a lipopolysaccharide treatment, recovery was modeled with a potent anti-inflammatory treatment dexamethasone, and priming was determined by subsequently challenging the cells with interferon gamma. Microglial function was profiled by determining the secretion of cytokines and nitric oxide, and expression of inducible nitric oxide synthase. After incubation with the SX7 phage library, populations of SX7-positive microglia and/or astrocytes were collected using fluorescence-activated cell sorting, SX7 phage was amplified in Escherichia coli culture, and phage DNA was sequenced via next-generation sequencing. Binding validation was done with synthesized peptides via in-cell westerns. Fifty-eight unique peptides were discovered, and their potential functions were assessed using a basic local alignment search tool. Peptides potentially originated from proteins ranging in function from a variety of supportive glial roles, including synapse support and pruning, to inflammatory incitement including cytokine and interleukin activation, and potential regulation in neurodegenerative and neuropsychiatric disorders.
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Affiliation(s)
- K M Koss
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Department of Surgery, University of Arizona College of Medicine, Arizona, Tucson, USA
| | - T Son
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
| | - C Li
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
| | - Y Hao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
| | - J Cao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
- 48Hour Discovery Inc, 11421 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada
| | - M A Churchward
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Alberta, Edmonton, Canada
- Department of Biology and Environmental Sciences, Concordia University of Edmonton, Alberta, Edmonton, Canada
| | - Z J Zhang
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
| | - J A Wertheim
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
- Department of Surgery, University of Arizona College of Medicine, Arizona, Tucson, USA
| | - R Derda
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
- 48Hour Discovery Inc, 11421 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada
| | - K G Todd
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Alberta, Edmonton, Canada
- Department of Biomedical Engineering, University of Alberta, Alberta, Edmonton, Canada
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8
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Roşianu F, Mihaylov SR, Eder N, Martiniuc A, Claxton S, Flynn HR, Jalal S, Domart MC, Collinson L, Skehel M, Snijders AP, Krause M, Tooze SA, Ultanir SK. Loss of NDR1/2 kinases impairs endomembrane trafficking and autophagy leading to neurodegeneration. Life Sci Alliance 2023; 6:6/2/e202201712. [PMID: 36446521 PMCID: PMC9711861 DOI: 10.26508/lsa.202201712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/30/2022] Open
Abstract
Autophagy is essential for neuronal development and its deregulation contributes to neurodegenerative diseases. NDR1 and NDR2 are highly conserved kinases, implicated in neuronal development, mitochondrial health and autophagy, but how they affect mammalian brain development in vivo is not known. Using single and double Ndr1/2 knockout mouse models, we show that only dual loss of Ndr1/2 in neurons causes neurodegeneration. This phenotype was present when NDR kinases were deleted both during embryonic development, as well as in adult mice. Proteomic and phosphoproteomic comparisons between Ndr1/2 knockout and control brains revealed novel kinase substrates and indicated that endocytosis is significantly affected in the absence of NDR1/2. We validated the endocytic protein Raph1/Lpd1, as a novel NDR1/2 substrate, and showed that both NDR1/2 and Raph1 are critical for endocytosis and membrane recycling. In NDR1/2 knockout brains, we observed prominent accumulation of transferrin receptor, p62 and ubiquitinated proteins, indicative of a major impairment of protein homeostasis. Furthermore, the levels of LC3-positive autophagosomes were reduced in knockout neurons, implying that reduced autophagy efficiency mediates p62 accumulation and neurotoxicity. Mechanistically, pronounced mislocalisation of the transmembrane autophagy protein ATG9A at the neuronal periphery, impaired axonal ATG9A trafficking and increased ATG9A surface levels further confirm defects in membrane trafficking, and could underlie the impairment in autophagy. We provide novel insight into the roles of NDR1/2 kinases in maintaining neuronal health.
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Affiliation(s)
- Flavia Roşianu
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Simeon R Mihaylov
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Noreen Eder
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Antonie Martiniuc
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Suzanne Claxton
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Shamsinar Jalal
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Marie-Charlotte Domart
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Mark Skehel
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Matthias Krause
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
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9
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Buser DP, Spang A. Protein sorting from endosomes to the TGN. Front Cell Dev Biol 2023; 11:1140605. [PMID: 36895788 PMCID: PMC9988951 DOI: 10.3389/fcell.2023.1140605] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/09/2023] [Indexed: 02/23/2023] Open
Abstract
Retrograde transport from endosomes to the trans-Golgi network is essential for recycling of protein and lipid cargoes to counterbalance anterograde membrane traffic. Protein cargo subjected to retrograde traffic include lysosomal acid-hydrolase receptors, SNARE proteins, processing enzymes, nutrient transporters, a variety of other transmembrane proteins, and some extracellular non-host proteins such as viral, plant, and bacterial toxins. Efficient delivery of these protein cargo molecules depends on sorting machineries selectively recognizing and concentrating them for their directed retrograde transport from endosomal compartments. In this review, we outline the different retrograde transport pathways governed by various sorting machineries involved in endosome-to-TGN transport. In addition, we discuss how this transport route can be analyzed experimentally.
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Affiliation(s)
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
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10
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YAP promotes cell-autonomous immune responses to tackle intracellular Staphylococcus aureus in vitro. Nat Commun 2022; 13:6995. [PMID: 36384856 PMCID: PMC9669043 DOI: 10.1038/s41467-022-34432-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Transcriptional cofactors YAP/TAZ have recently been found to support autophagy and inflammation, which are part of cell-autonomous immunity and are critical in antibacterial defense. Here, we studied the role of YAP against Staphylococcus aureus using CRISPR/Cas9-mutated HEK293 cells and a primary cell-based organoid model. We found that S. aureus infection increases YAP transcriptional activity, which is required to reduce intracellular S. aureus replication. A 770-gene targeted transcriptomic analysis revealed that YAP upregulates genes involved in autophagy/lysosome and inflammation pathways in both infected and uninfected conditions. The YAP-TEAD transcriptional activity promotes autophagic flux and lysosomal acidification, which are then important for defense against intracellular S. aureus. Furthermore, the staphylococcal toxin C3 exoenzyme EDIN-B was found effective in preventing YAP-mediated cell-autonomous immune response. This study provides key insights on the anti-S. aureus activity of YAP, which could be conserved for defense against other intracellular bacteria.
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11
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Song C, Li W, Wang Z. The Landscape of Liver Chromatin Accessibility and Conserved Non-coding Elements in Larimichthys crocea, Nibea albiflora, and Lateolabrax maculatus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:763-775. [PMID: 35895229 DOI: 10.1007/s10126-022-10142-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Large yellow croaker (Larimichthys crocea), yellow drum (Nibea albiflora), and Chinese seabass (Lateolabrax maculatus) are important economic marine fishes in China. The conserved non-coding elements (CNEs) in the liver tissues of the three kinds of fish are directly or indirectly involved in the regulation of gene expression and affect liver functions. However, the fishes' CNEs and even chromatin accessibility landscape have not been effectively investigated. Hence, this study established the landscapes of the fishes' genome-wide chromatin accessibility and CNEs by detecting regions of the open chromatin in their livers using an assay for transposase-accessible chromatin by high-throughput sequencing (ATAC-seq) and comparative genomics approach. The results showed that Smad1, Sp1, and Foxl1 transcription factor binding motifs were considerably enriched in the chromatin accessibility landscape in the liver of the three species, and the three transcription factors (TFs) had a wide range of common targets. The hypothetical gene set was targeted by one, two, or all three TFs, which was much higher than would be expected for an accidental outcome. The gene sets near the CNEs were mainly enriched through processes such as a macromolecule metabolic process and ribonucleoprotein complex biogenesis. The active CNEs were found in the promoter regions of genes such as ap1g1, hax1, and ndufs2. And 5 CNEs were predicted to be highly conserved active enhancers. These results demonstrated that Smad1, Sp1, and Foxl1 might be related to the liver function in the three fishes. In addition, we found a series of ATAC-seq-labeled CNEs located in the gene promoter regions, and highly conserved H3k27ac + -labeled CNEs located in the liver function genes. The highly conserved nature of these regulatory elements suggests that they play important roles in the liver in fish. This study mined the landscape of chromatin accessibility and CNEs of three important economic fishes to fill the knowledge gaps in this field. Moreover, the work provides useful data for the industrial application and theoretical research of these three fish species.
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Affiliation(s)
- Chaowei Song
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, China.
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12
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Duncan MC. New directions for the clathrin adaptor AP-1 in cell biology and human disease. Curr Opin Cell Biol 2022; 76:102079. [DOI: 10.1016/j.ceb.2022.102079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/03/2022]
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13
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Buser DP, Bader G, Spiess M. Retrograde transport of CDMPR depends on several machineries as analyzed by sulfatable nanobodies. Life Sci Alliance 2022; 5:5/7/e202101269. [PMID: 35314489 PMCID: PMC8961009 DOI: 10.26508/lsa.202101269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
Nanobody toolkit enables the quantitative analysis of endosome-to-TGN transport of the mannose-6-phosphate receptor in cells depleted of retrograde transport machineries Retrograde protein transport from the cell surface and endosomes to the TGN is essential for membrane homeostasis in general and for the recycling of mannose-6-phosphate receptors (MPRs) for sorting of lysosomal hydrolases in particular. We used a nanobody-based sulfation tool to more directly determine transport kinetics from the plasma membrane to the TGN for the cation-dependent MPR (CDMPR) with and without rapid or gradual inactivation of candidate machinery proteins. Although knockdown of retromer (Vps26), epsinR, or Rab9a reduced CDMPR arrival to the TGN, no effect was observed upon silencing of TIP47. Strikingly, when retrograde transport was analyzed by rapamycin-induced rapid depletion (knocksideways) or long-term depletion by knockdown of the clathrin adaptor AP-1 or of the GGA machinery, distinct phenotypes in sulfation kinetics were observed, suggesting a potential role of GGA adaptors in retrograde and anterograde transport. Our study illustrates the usefulness of derivatized, sulfation-competent nanobodies, reveals novel insights into CDMPR trafficking biology, and further outlines that the selection of machinery inactivation is critical for phenotype analysis.
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Affiliation(s)
| | - Gaétan Bader
- Biozentrum, University of Basel, Basel, Switzerland
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14
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Zhu T, Chen Y, Liu Z, Leng Y, Tian Y. Expression profiles and prognostic significance of AFTPH in different tumors. FEBS Open Bio 2020; 10:2666-2677. [PMID: 33090728 PMCID: PMC7714068 DOI: 10.1002/2211-5463.13003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/24/2020] [Accepted: 09/23/2020] [Indexed: 01/16/2023] Open
Abstract
Aftiphilin (AFTPH) plays an important role in regulating intracellular trafficking, exocytosis, and the pro‐inflammatory response. However, the potential prognostic role of AFTPH in cancers remains unclear. Here, we examined the expression profiles and prognostic significance of AFTPH in breast invasive carcinoma (BRCA), diffuse large B‐cell lymphoma (DLBC), lung squamous cell carcinoma (LUSC), and pancreatic adenocarcinoma (PADD) using the GEPIA and UALCAN databases. AFTPH expression was observed to be higher in cancer tissues than in normal tissues, but expression did not differ significantly between tumor stages for the four cancer types. AFTPH expression in cancer cell lines was investigated using the CCLE database; AFTPH was found to be highly expressed in four cancer cell lines. The relationship between AFTPH expression and patient prognosis was analyzed using GEPIA, LinkedOmics, and Kaplan–Meier plotter databases. Low expression of AFTPH was associated with improved prognosis for BRCA, DLBC, LUSC, and PAAD. Genetic alterations of AFTPH in cancers were explored using the cBioPortal website, revealing that gene copy number gains and amplification are common in BRCA, DLBC, LUSC, and PAAD. Related genes and markers associated with AFTPH were discovered using the LinkedOmics database. Furthermore, transfection of cells with AFTPH siRNA demonstrated that AFTPH exerts positive effects on cell proliferation in BRCA, LUSC, and PAAD cells. In conclusion, AFTPH may be a potential therapeutic target and prognostic biomarker for BRCA, DLBC, LUSC, and/or PAAD.
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Affiliation(s)
- Tengjiao Zhu
- Third Hospital of Peking University, Beijing, China
| | | | - Zhongjun Liu
- Third Hospital of Peking University, Beijing, China
| | - Yuxin Leng
- Third Hospital of Peking University, Beijing, China
| | - Yun Tian
- Third Hospital of Peking University, Beijing, China
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15
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Uemura T, Waguri S. Emerging roles of Golgi/endosome-localizing monomeric clathrin adaptors GGAs. Anat Sci Int 2019; 95:12-21. [DOI: 10.1007/s12565-019-00505-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/10/2019] [Indexed: 01/13/2023]
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16
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Zysnarski CJ, Lahiri S, Javed FT, Martínez-Márquez JY, Trowbridge JW, Duncan MC. Adaptor protein complex-1 (AP-1) is recruited by the HEATR5 protein Laa1 and its co-factor Laa2 in yeast. J Biol Chem 2018; 294:1410-1419. [PMID: 30523155 DOI: 10.1074/jbc.ra118.005253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/03/2018] [Indexed: 11/06/2022] Open
Abstract
Cellular membrane trafficking mediated by the clathrin adaptor protein complex-1 (AP-1) is important for the proper composition and function of organelles of the endolysosomal system. Normal AP-1 function requires proteins of the HEAT repeat-containing 5 (HEATR5) family. Although HEATR5 proteins were first identified based on their ability to interact with AP-1, the functional significance of this interaction was unknown. We used bioinformatics-based phenotypic profiling and information from genome-wide fluorescence microscopy studies in the budding yeast Saccharomyces cerevisiae to identify a protein, Laa2, that mediates the interaction between AP-1 and the yeast HEATR5 protein Laa1. Further characterization of Laa2 revealed that it binds to both Laa1 and AP-1. Laa2 contains a motif similar to the characterized γ-ear-binding sites found in other AP-1-binding proteins. This motif in Laa2 is essential for the Laa1-AP-1 interaction. Moreover, mutation of this motif disrupted AP-1 localization and function and caused effects similar to mutations that remove the γ-ear of AP-1. These results indicate that Laa2 mediates the interaction between Laa1 and AP-1 and reveal that this interaction promotes the stable association of AP-1 with membranes in yeast.
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Affiliation(s)
| | - Sagar Lahiri
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Fatima T Javed
- Cell and Developmental Biology Department, Ann Arbor, Michigan 48109
| | | | | | - Mara C Duncan
- Cell and Developmental Biology Department, Ann Arbor, Michigan 48109.
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17
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UEMURA T, SAWADA N, SAKABA T, KAMETAKA S, YAMAMOTO M, WAGURI S. Intracellular localization of GGA accessory protein p56 in cell lines and central nervous system neurons . Biomed Res 2018; 39:179-187. [DOI: 10.2220/biomedres.39.179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Takefumi UEMURA
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine
| | - Naoki SAWADA
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine
| | - Takao SAKABA
- Department of Plastic and Reconstructive Surgery, Fukushima Medical University School of Medicine
| | - Satoshi KAMETAKA
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine
| | - Masaya YAMAMOTO
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine
| | - Satoshi WAGURI
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine
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The Role of Stress-Induced O-GlcNAc Protein Modification in the Regulation of Membrane Transport. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1308692. [PMID: 29456783 PMCID: PMC5804373 DOI: 10.1155/2017/1308692] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/03/2017] [Indexed: 02/06/2023]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is a posttranslational modification that is increasingly recognized as a signal transduction mechanism. Unlike other glycans, O-GlcNAc is a highly dynamic and reversible process that involves the addition and removal of a single N-acetylglucosamine molecule to Ser/Thr residues of proteins. UDP-GlcNAc—the direct substrate for O-GlcNAc modification—is controlled by the rate of cellular metabolism, and thus O-GlcNAc is dependent on substrate availability. Serving as a feedback mechanism, O-GlcNAc influences the regulation of insulin signaling and glucose transport. Besides nutrient sensing, O-GlcNAc was also implicated in the regulation of various physiological and pathophysiological processes. Due to improvements of mass spectrometry techniques, more than one thousand proteins were detected to carry the O-GlcNAc moiety; many of them are known to participate in the regulation of metabolites, ions, or protein transport across biological membranes. Recent studies also indicated that O-GlcNAc is involved in stress adaptation; overwhelming evidences suggest that O-GlcNAc levels increase upon stress. O-GlcNAc elevation is generally considered to be beneficial during stress, although the exact nature of its protective effect is not understood. In this review, we summarize the current data regarding the oxidative stress-related changes of O-GlcNAc levels and discuss the implications related to membrane trafficking.
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19
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Law IKM, Padua DM, Iliopoulos D, Pothoulakis C. Role of G protein-coupled receptors-microRNA interactions in gastrointestinal pathophysiology. Am J Physiol Gastrointest Liver Physiol 2017; 313:G361-G372. [PMID: 28774868 PMCID: PMC5792214 DOI: 10.1152/ajpgi.00144.2017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/13/2017] [Accepted: 07/24/2017] [Indexed: 01/31/2023]
Abstract
G protein-coupled receptors (GPCRs) make up the largest transmembrane receptor superfamily in the human genome and are expressed in nearly all gastrointestinal cell types. Coupling of GPCRs and their respective ligands activates various phosphotransferases in the cytoplasm, and, thus, activation of GPCR signaling in intestine regulates many cellular and physiological processes. Studies in microRNAs (miRNAs) demonstrate that they represent critical epigenetic regulators of different pathophysiological responses in different organs and cell types in humans and animals. Here, we reviewed recent research on GPCR-miRNA interactions related to gastrointestinal pathophysiology, such as inflammatory bowel diseases, irritable bowel syndrome, and gastrointestinal cancers. Given that the presence of different types of cells in the gastrointestinal tract suggests the importance of cell-cell interactions in maintaining gastrointestinal homeostasis, we also discuss how GPCR-miRNA interactions regulate gene expression at the cellular level and subsequently modulate gastrointestinal pathophysiology through molecular regulatory circuits and cell-cell interactions. These studies helped identify novel molecular pathways leading to the discovery of potential biomarkers for gastrointestinal diseases.
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Affiliation(s)
- Ivy Ka Man Law
- 1Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California; and
| | - David Miguel Padua
- 1Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California; and
| | - Dimitrios Iliopoulos
- 1Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California; and ,2Center for Systems Biomedicine, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Charalabos Pothoulakis
- Center for Inflammatory Bowel Diseases, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California; and
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20
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Law IKM, Jensen D, Bunnett NW, Pothoulakis C. Neurotensin-induced miR-133α expression regulates neurotensin receptor 1 recycling through its downstream target aftiphilin. Sci Rep 2016; 6:22195. [PMID: 26902265 PMCID: PMC4763298 DOI: 10.1038/srep22195] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/09/2016] [Indexed: 01/05/2023] Open
Abstract
Neurotensin (NT) triggers signaling in human colonic epithelial cells by activating the G protein-coupled receptor, the neurotensin receptor 1 (NTR1). Activated NTR1 traffics from the plasma membrane to early endosomes, and then recycles. Although sustained NT/NTR1 signaling requires efficient NTR1 recycling, little is known about the regulation of NTR1 recycling. We recently showed that NT/NTR1 signaling increases expression of miR-133α. Herein, we studied the mechanism of NT-regulated miR-133α expression and examined the role of miR-133α in intracellular NTR1 trafficking in human NCM460 colonocytes. We found that NT-induced miR-133α upregulation involves the negative transcription regulator, zinc finger E-box binding homeobox 1. Silencing of miR-133α or overexpression of aftiphilin (AFTPH), a binding target of miR-133α, attenuated NTR1 trafficking to plasma membrane in human colonocytes, without affecting NTR1 internalization. We localized AFTPH to early endosomes and the trans-Golgi network (TGN) in unstimulated human colonic epithelial cells. AFTPH overexpression reduced NTR1 localization in early endosomes and increased expression of proteins related to endosomes and the TGN trafficking pathway. AFTPH overexpression and de-acidification of intracellular vesicles increased NTR1 expression. Our results suggest a novel mechanism of GPCR trafficking in human colonic epithelial cells by which a microRNA, miR-133α regulates NTR1 trafficking through its downstream target AFTPH.
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Affiliation(s)
- Ivy Ka Man Law
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine, University of California at Los Angeles, California, USA
| | - Dane Jensen
- Monash Institute of Pharmaceutical Sciences, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology Parkville, Monash University, Australia
- Department of Anesthesia and Peri-operative Medicine, Monash University, Australia
| | - Nigel W. Bunnett
- Monash Institute of Pharmaceutical Sciences, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology Parkville, Monash University, Australia
- Department of Anesthesia and Peri-operative Medicine, Monash University, Australia
- Department of Pharmacology and Therapeutics, University of Melbourne, Australia
| | - Charalabos Pothoulakis
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine, University of California at Los Angeles, California, USA
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21
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Butler EC, Bradbury NA. Signal dependent ER export of lemur tyrosine kinase 2. BMC Cell Biol 2015; 16:26. [PMID: 26559041 PMCID: PMC4642647 DOI: 10.1186/s12860-015-0072-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The membrane anchored kinase, LMTK2, is a serine/threonine kinase predominantly localized to endosomal compartments. LMTK2 has been shown to be involved in the trafficking of the CFTR ion channel, the androgen receptor, as well as modulating neurodegeneration. As a membrane anchored protein, LMTK2 must be exported from the ER, yet the mechanisms whereby LMTK2 is sequestered within the ER for efficient export are unknown. METHODS Sequence analysis of the carboxyl tail of LMTK2 revealed a putative di-acidic ER export motif. Site-directed mutagenesis was utilized to ablate this potential motif. Subcellular fractionation, immunofluorescence microscopy, and transferrin recycling assays were used to determine the consequence of mutating LMTK2's export motif. RESULTS Mutation of the di-acidic export motif led to ER retention of LMTK2, and an increase in protein half-life and a concomitant loss of LMTK2 from its appropriate terminal destination. Loss of LMTK2 from endosomal compartments by preventing its release from the ER is linked to a reduction in transferrin recycling. CONCLUSIONS We have identified a di-acidic ER export motif within the carboxyl tail of the membrane anchored kinase LMTK2. This sequence is used by LMTK2 for its efficient export from the ER.
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Affiliation(s)
- E C Butler
- Department of Physiology and Biophysics, Chicago Medical School, 3333 Green Bay Rd, North Chicago, IL, 60064, USA.
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Chicago Medical School, 3333 Green Bay Rd, North Chicago, IL, 60064, USA.
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22
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Huo Q, Kayikci M, Odermatt P, Meyer K, Michels O, Saxena S, Ule J, Schümperli D. Splicing changes in SMA mouse motoneurons and SMN-depleted neuroblastoma cells: evidence for involvement of splicing regulatory proteins. RNA Biol 2015; 11:1430-46. [PMID: 25692239 PMCID: PMC4601534 DOI: 10.1080/15476286.2014.996494] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is caused by deletions or mutations in the Survival Motor Neuron 1 (SMN1) gene. The second gene copy, SMN2, produces some, but not enough, functional SMN protein. SMN is essential to assemble small nuclear ribonucleoproteins (snRNPs) that form the spliceosome. However, it is not clear whether SMA is caused by defects in this function that could lead to splicing changes in all tissues, or by the impairment of an additional, less well characterized, but motoneuron-specific SMN function. We addressed the first possibility by exon junction microarray analysis of motoneurons (MNs) isolated by laser capture microdissection from a severe SMA mouse model. This revealed changes in multiple U2-dependent splicing events. Moreover, splicing appeared to be more strongly affected in MNs than in other cells. By testing mutiple genes in a model of progressive SMN depletion in NB2a neuroblastoma cells, we obtained evidence that U2-dependent splicing changes occur earlier than U12-dependent ones. As several of these changes affect genes coding for splicing regulators, this may acerbate the splicing response induced by low SMN levels and induce secondary waves of splicing alterations.
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Key Words
- ESE, exonic splicing enhancer
- FCS, fetal calf serum
- MN, motoneuron
- NMD, nonsense-mediated mRNA decay
- NMJ, neuromuscular junction, PCR
- RT, reverse transcription
- SMA, Spinal Muscular Atrophy
- SMN, Survival Motor Neuron
- Spinal Muscular Atrophy
- TcRβ, T-cell receptor β chain
- exon junction microarray
- hz, heterozygote, LCM
- laser capture microdissection
- major spliceosome
- minor spliceosome
- motoneurons
- neurodegerative disease
- polymerase chain reaction, qPCR
- real-time (quantitative) PCR
- sh, short hairpin
- snRNA, small nuclear ribonucleic acid
- snRNP assembly
- snRNP, small nuclear ribonucleoprotein
- splicing
- splicing regulators
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Affiliation(s)
- Qing Huo
- a Institute of Cell Biology ; University of Bern ; Bern , Switzerland
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Law IKM, Bakirtzi K, Polytarchou C, Oikonomopoulos A, Hommes D, Iliopoulos D, Pothoulakis C. Neurotensin--regulated miR-133α is involved in proinflammatory signalling in human colonic epithelial cells and in experimental colitis. Gut 2015; 64:1095-104. [PMID: 25112884 PMCID: PMC4422787 DOI: 10.1136/gutjnl-2014-307329] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 07/22/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Neurotensin (NT) mediates colonic inflammation through its receptor neurotensin receptor 1 (NTR1). NT stimulates miR-133α expression in colonic epithelial cells. We investigated the role of miR-133α in NT-associated colonic inflammation in vitro and in vivo. DESIGN miR-133α and aftiphilin (AFTPH) levels were measured by quantitative PCR. Antisense (as)-miR-133α was administrated intracolonicaly prior to induction of 2, 4, 6-trinitrobenzene sulfonic acid (TNBS)-induced colitis and dextran sodium sulfate (DSS)-induced colitis. The effect of AFTPH was examined by gene silencing in vitro. RESULTS NT increased miR-133α levels in NCM-460 overexpressing NTR1 (NCM460-NTR1) and HCT-116 cells. NT-induced p38, ERK1/2, c-Jun, and NF-κB activation, as well as IL-6, IL-8 and IL-1β messenger RNA (mRNA) expression in NCM-460-NTR1 cells were reduced in miR-133α-silenced cells, while overexpression of miR-133α reversed these effects. MiR-133α levels were increased in TNBS (2 day) and DSS (5 day) colitis, while NTR1 deficient DSS-exposed mice had reduced miR-133α levels, compared to wild-type colitic mice. Intracolonic as-miR-133α attenuated several parameters of colitis as well expression of proinflammatory mediators in the colonic mucosa. In silico search coupled with qPCR identified AFTPH as a downstream target of miR-133α, while NT decreased AFTPH expression in NCM-460-NTR1 colonocytes. Gene silencing of AFTPH enhanced NT-induced proinflammatory responses and AFTPH levels were downregulated in experimental colitis. Levels of miR-133α were significantly upregulated, while AFTPH levels were downregulated in colonic biopsies of patients with ulcerative colitis compared to controls. CONCLUSIONS NT-associated colitis and inflammatory signalling are regulated by miR-133α-AFTPH interactions. Targeting of miR-133α or AFTPH may represent a novel therapeutic approach in inflammatory bowel disease.
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Affiliation(s)
- Ivy Ka Man Law
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Kyriaki Bakirtzi
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Christos Polytarchou
- Center for Systems Biomedicine, Division of Digestive Diseases, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Angelos Oikonomopoulos
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Daniel Hommes
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Dimitrios Iliopoulos
- Center for Systems Biomedicine, Division of Digestive Diseases, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Charalabos Pothoulakis
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
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Law IKM, Pothoulakis C. MicroRNA-133α regulates neurotensin-associated colonic inflammation in colonic epithelial cells and experimental colitis. RNA & DISEASE 2015; 2. [PMID: 26005712 DOI: 10.14800/rd.472] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ulcerative colitis (UC) and Crohn's Disease (CD) are the two most common forms of Inflammatory Bowel Diseases (IBD) marked by chronic and persistent inflammation. Neurotensin (NT), together with its receptor, NT receptor 1 (NTR1), are important mediators in intestinal inflammation and their expression is upregulated in the intestine of experimental colitis models and UC colonic biopsies. MicroRNAs (miRNAs) are short, non-coding RNA molecules which act as transcription repressors. We have previously shown that NT exposure upregulates miR-133α expression in human colonocytes NCM460 cells overexpressing NTR1 (NCM460-NTR1). Recently, miR-133α was further examined forits role in NT-associated proinflammatory signaling cascades and acute colitis in vivo. Our study shows that NT-induced miR-133α upregulation modulates NF-κB phosphorylation and promotes proinflammatory cytokine production. In addition, intracolonicinjection of antisense-miR-133α before colitis induction improves histological scores and proinflammatory cytokine transcription. More importantly, dysregulation of miR-133α levels and aftiphilin (AFTPH), a newly-identified miR-133α downstream target, is found only in UC patients, but not in patients with CD. Taken together, we identified NTR1/miR-133α/aftiphilin as a novel regulatory axis involved in NT-associated colonic inflammation in human colonocytes, acute colitis mouse model and in colonic biopsies from UC patients. Our results also provide evidence that colonic levels of NTR1, miR-133α and aftiphilin may also serve as potential biomarkers in UC.
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Affiliation(s)
- Ivy Ka Man Law
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Charalabos Pothoulakis
- Inflammatory Bowel Disease Center, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Ong YS, Tran THT, Gounko NV, Hong W. TMEM115 is an integral membrane protein of the Golgi complex involved in retrograde transport. J Cell Sci 2014; 127:2825-39. [PMID: 24806965 PMCID: PMC4077589 DOI: 10.1242/jcs.136754] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Searching and evaluating the Human Protein Atlas for transmembrane proteins enabled us to identify an integral membrane protein, TMEM115, that is enriched in the Golgi complex. Biochemical and cell biological analysis suggested that TMEM115 has four candidate transmembrane domains located in the N-terminal region. Both the N- and C-terminal domains are oriented towards the cytoplasm. Immunofluorescence analysis supports that TMEM115 is enriched in the Golgi cisternae. Functionally, TMEM115 knockdown or overexpression delays Brefeldin-A-induced Golgi-to-ER retrograde transport, phenocopying cells with mutations or silencing of the conserved oligomeric Golgi (COG) complex. Co-immunoprecipitation and in vitro binding experiments reveals that TMEM115 interacts with the COG complex, and might self-interact to form dimers or oligomers. A short region (residues 206–229) immediately to the C-terminal side of the fourth transmembrane domain is both necessary and sufficient for Golgi targeting. Knockdown of TMEM115 also reduces the binding of the lectins peanut agglutinin (PNA) and Helix pomatia agglutinin (HPA), suggesting an altered O-linked glycosylation profile. These results establish that TMEM115 is an integral membrane protein of the Golgi stack regulating Golgi-to-ER retrograde transport and is likely to be part of the machinery of the COG complex.
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Affiliation(s)
- Yan Shan Ong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Ton Hoai Thi Tran
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Natalia V Gounko
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore IMB-IMCB Joint Electron Microscopy Suite, 20 Biopolis Street, Singapore 138671, Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore Department of Biochemistry, National University of Singapore, Singapore 117599, Singapore
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Yu Y, Li C, Kita A, Katayama Y, Kubouchi K, Udo M, Imanaka Y, Ueda S, Masuko T, Sugiura R. Sip1, an AP-1 accessory protein in fission yeast, is required for localization of Rho3 GTPase. PLoS One 2013; 8:e68488. [PMID: 23840894 PMCID: PMC3698097 DOI: 10.1371/journal.pone.0068488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/29/2013] [Indexed: 11/18/2022] Open
Abstract
Rho family GTPases act as molecular switches to regulate a range of physiological functions, including the regulation of the actin-based cytoskeleton, membrane trafficking, cell morphology, nuclear gene expression, and cell growth. Rho function is regulated by its ability to bind GTP and by its localization. We previously demonstrated functional and physical interactions between Rho3 and the clathrin-associated adaptor protein-1 (AP-1) complex, which revealed a role of Rho3 in regulating Golgi/endosomal trafficking in fission yeast. Sip1, a conserved AP-1 accessory protein, recruits the AP-1 complex to the Golgi/endosomes through physical interaction. In this study, we showed that Sip1 is required for Rho3 localization. First, overexpression of rho3⁺ suppressed defective membrane trafficking associated with sip1-i4 mutant cells, including defects in vacuolar fusion, Golgi/endosomal trafficking and secretion. Notably, Sip1 interacted with Rho3, and GFP-Rho3, similar to Apm1-GFP, did not properly localize to the Golgi/endosomes in sip1-i4 mutant cells at 27°C. Interestingly, the C-terminal region of Sip1 is required for its localization to the Golgi/endosomes, because Sip1-i4-GFP protein failed to properly localize to Golgi/endosomes, whereas the fluorescence of Sip1ΔN mutant protein co-localized with that of FM4-64. Consistently, in the sip1-i4 mutant cells, which lack the C-terminal region of Sip1, binding between Apm1 and Rho3 was greatly impaired, presumably due to mislocalization of these proteins in the sip1-i4 mutant cells. Furthermore, the interaction between Apm1 and Rho3 as well as Rho3 localization to the Golgi/endosomes were significantly rescued in sip1-i4 mutant cells by the expression of Sip1ΔN. Taken together, these results suggest that Sip1 recruits Rho3 to the Golgi/endosomes through physical interaction and enhances the formation of the Golgi/endosome AP-1/Rho3 complex, thereby promoting crosstalk between AP-1 and Rho3 in the regulation of Golgi/endosomal trafficking in fission yeast.
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Affiliation(s)
- Yang Yu
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
| | - Cuifang Li
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Ayako Kita
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
| | - Yuta Katayama
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
| | - Koji Kubouchi
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
| | - Masako Udo
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
| | - Yukako Imanaka
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
| | - Shiho Ueda
- Laboratory of Molecular Cell Biology, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
| | - Takashi Masuko
- Laboratory of Molecular Cell Biology, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Kowakae, Higashi-Osaka, Japan
- * E-mail:
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Sip1, a conserved AP-1 accessory protein, is important for Golgi/endosome trafficking in fission yeast. PLoS One 2012; 7:e45324. [PMID: 23028933 PMCID: PMC3444471 DOI: 10.1371/journal.pone.0045324] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/15/2012] [Indexed: 01/20/2023] Open
Abstract
We had previously identified the mutant allele of apm1+ that encodes a homolog of the mammalian μ 1A subunit of the clathrin-associated adaptor protein-1 (AP-1) complex and demonstrated that the AP-1 complex plays a role in Golgi/endosome trafficking, secretion, and vacuole fusion in fission yeast. Here, we isolated a mutant allele of its4+/sip1+, which encodes a conserved AP-1 accessory protein. The its4-1/sip1-i4 mutants and apm1-deletion cells exhibited similar phenotypes, including sensitivity to the calcineurin inhibitor FK506, Cl− and valproic acid as well as various defects in Golgi/endosomal trafficking and cytokinesis. Electron micrographs of sip1-i4 mutants revealed vacuole fragmentation and accumulation of abnormal Golgi-like structures and secretory vesicles. Overexpression of Apm1 suppressed defective membrane trafficking in sip1-i4 mutants. The Sip1-green fluorescent protein (GFP) co-localized with Apm1-mCherry at Golgi/endosomes, and Sip1 physically interacted with each subunit of the AP-1 complex. We found that Sip1 was a Golgi/endosomal protein and the sip1-i4 mutation affected AP-1 localization at Golgi/endosomes, thus indicating that Sip1 recruited the AP-1 complex to endosomal membranes by physically interacting with each subunit of this complex. Furthermore, Sip1 is required for the correct localization of Bgs1/Cps1, 1,3-β-D-glucan synthase to polarized growth sites. Consistently, the sip1-i4 mutants displayed a severe sensitivity to micafungin, a potent inhibitor of 1,3-β-D-glucan synthase. Taken together, our findings reveal a role for Sip1 in the regulation of Golgi/endosome trafficking in coordination with the AP-1 complex, and identified Bgs1, required for cell wall synthesis, as the new cargo of AP-1-dependent trafficking.
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Kametaka S, Kametaka A, Yonekura S, Haruta M, Takenoshita S, Goto S, Waguri S. AP-1 clathrin adaptor and CG8538/Aftiphilin are involved in Notch signaling during eye development in Drosophila melanogaster. J Cell Sci 2012; 125:634-48. [PMID: 22389401 DOI: 10.1242/jcs.090167] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Clathrin adaptor protein complex-1 (AP-1) and its accessory proteins play a role in the sorting of integral membrane proteins at the trans-Golgi network and endosomes. Their physiological functions in complex organisms, however, are not fully understood. In this study, we found that CG8538p, an uncharacterized Drosophila protein, shares significant structural and functional characteristics with Aftiphilin, a mammalian AP-1 accessory protein. The Drosophila Aftiphilin was shown to interact directly with the ear domain of γ-adaptin of Drosophila AP-1, but not with the GAE domain of Drosophila GGA. In S2 cells, Drosophila Aftiphilin and AP-1 formed a complex and colocalized at the Golgi compartment. Moreover, tissue-specific depletion of AP-1 or Aftiphilin in the developing eyes resulted in a disordered alignment of photoreceptor neurons in larval stage and roughened eyes with aberrant ommatidia in adult flies. Furthermore, AP-1-depleted photoreceptor neurons showed an intracellular accumulation of a Notch regulator, Scabrous, and downregulation of Notch by promoting its degradation in the lysosomes. These results suggest that AP-1 and Aftiphilin are cooperatively involved in the intracellular trafficking of Notch during eye development in Drosophila.
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Affiliation(s)
- Satoshi Kametaka
- Department of Anatomy and Histology, Fukushima Medical University, 1 Hikarigaoka, Fukushima, Fukushima 960-1295, Japan.
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Le Bras S, Rondanino C, Kriegel-Taki G, Dussert A, Le Borgne R. Genetic identification of intracellular trafficking regulators involved in notch dependent binary cell fate acquisition following asymmetric cell division. J Cell Sci 2012; 125:4886-901. [DOI: 10.1242/jcs.110171] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Notch signaling is involved in numerous cellular processes during development and throughout adult life. Although ligands and receptors are largely expressed in the whole organism, activation of Notch receptors only takes place in a subset of cells and/or tissues and is accurately regulated in time and space. Previous studies have demonstrated that endocytosis and recycling of both ligands and/or receptors are essential for this regulation. However, the precise endocytic routes, compartments and regulators involved in the spatio temporal regulation are largely unknown.
In order to identify Notch signaling intracellular trafficking regulators, we have undertaken a tissue-specific dsRNA genetic screen against candidates potentially involved in endocytosis and recycling within the endolysosomal pathway. dsRNA against 418 genes was induced in Drosophila melanogaster sensory organ lineage in which Notch signaling regulates binary cell fate acquisition. Gain- or loss-of Notch signaling phenotypes were observed in adult sensory organs for 113 of them. Furthermore, 26 genes presented a change in the steady state localization of Notch, Sanpodo, a Notch co-factor, and/or Delta in the pupal lineage. In particular, we identified 20 genes with previously unknown function in Drosophila melanogaster intracellular trafficking. Among them, we identified CG2747 and show that it regulates the localization of clathrin adaptor AP-1 complex, a negative regulator of Notch signaling. All together, our results further demonstrate the essential function of intracellular trafficking in regulating Notch signaling-dependent binary cell fate acquisition and constitute an additional step toward the elucidation of the routes followed by Notch receptor and ligands to signal.
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Maritzen T, Haucke V. Gadkin: A novel link between endosomal vesicles and microtubule tracks. Commun Integr Biol 2011; 3:299-302. [PMID: 20798811 DOI: 10.4161/cib.3.4.11835] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Accepted: 03/21/2010] [Indexed: 12/21/2022] Open
Abstract
Different types of endosomal vesicles show distinct distribution patterns within cells. While early endosomes can be found throughout the cell, recycling endosomal vesicles and tubules tend to cluster near the microtubule organizing center in the perinuclear region in most cell types. The molecular mechanisms underlying the steady-state distribution and dynamics of various types of endosomal vesicles has long remained enigmatic. However, during the past decade it has become evident that microtubule-based motor proteins of the kinesin family play a pivotal role in the positioning of endosomes. Early endosomes were shown to cluster in the perinuclear area in the absence of KIF16B,1 KIF3A is required for the steady-state distribution of late endosomes/lysosomes,2 and KIF13A directs M6PR-containing vesicles from the TGN to the plasma membrane3 to name only a few examples. In the case of Tf-containing recycling endosomes antibody-injection experiments implicated kinesin-1, a heteromer comprised of KIF5 heavy and KLC light chains, as a motor for their transport towards the cell periphery.4 Indeed, KIF5B knockdown experiments confirmed that kinesin-1 is necessary to maintain the peripheral pool of recycling endosomes.5 But how is kinesin-1 linked to endosomal vesicles? Work from our own laboratory has identified the AP-1-binding protein Gadkin as a molecular link between AP-1-mediated traffic and kinesin-1-based transport along microtubules.5 This work as well as hypothetical models for kinesin-dependent endosomal membrane traffic will be discussed here.
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Exit from the trans-Golgi network: from molecules to mechanisms. Curr Opin Cell Biol 2011; 23:443-51. [PMID: 21550789 DOI: 10.1016/j.ceb.2011.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/07/2011] [Accepted: 03/22/2011] [Indexed: 11/23/2022]
Abstract
The trans-Golgi network is a major sorting platform of the secretory pathway from which proteins and lipids, both newly synthesized and retrieved from endocytic compartments, are targeted to different destinations. These sorting processes occur during the formation of pleomorphic tubular-vesicular carriers. The past years have provided insights into basic mechanisms coordinating the spatial and temporal organization of machineries necessary for the segregation of membrane components into distinct microdomains, for the bending, elongation, and fission of corresponding membranes, thus revealing a complex interplay of protein-protein and protein-lipid interactions.
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Antrobus R, Borner GHH. Improved elution conditions for native co-immunoprecipitation. PLoS One 2011; 6:e18218. [PMID: 21448433 PMCID: PMC3063181 DOI: 10.1371/journal.pone.0018218] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 02/28/2011] [Indexed: 11/23/2022] Open
Abstract
Background Native immunoprecipitation followed by protein A-mediated recovery of the immuno-complex is a powerful tool to study protein-protein interactions. A limitation of this technique is the concomitant recovery of large amounts of immunoglobulin, which interferes with down-stream applications such as mass spectrometric analysis and Western blotting. Here we report a detergent-based “soft” elution protocol that allows effective recovery of immunoprecipitated antigen and binding partners, yet avoids elution of the bulk of the immunoglobulin. Methodology/Principal Findings We assessed the performance of the soft elution protocol using immunoprecipitation of Adaptor protein complex 1 (AP-1) and associated proteins as a test case. Relative to conventional elution conditions, the novel protocol substantially improved the sensitivity of mass spectrometric identification of immunoprecipitated proteins from unfractionated solution digests. Averaging over three independent experiments, Mascot scores of identified AP-1 binding partners were increased by 39%. Conversely, the estimated amount of recovered immunoglobulin was reduced by 44%. We tested the protocol with five further antibodies derived from rabbit, mouse and goat. In each case we observed a significant reduction of co-eluting immunoglobulin. Conclusions/Significance The soft elution protocol presented here shows superior performance compared to standard elution conditions for subsequent protein identification by mass spectrometry from solution digests. The method was developed for rabbit polyclonal antibodies, but also performed well with the tested goat and mouse antibodies. Hence we expect the soft elution protocol to be widely applicable.
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Affiliation(s)
- Robin Antrobus
- Cambridge Institute for Medical Research, Wellcome Trust, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Georg H. H. Borner
- Cambridge Institute for Medical Research, Wellcome Trust, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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Maritzen T, Schmidt MR, Kukhtina V, Higman VA, Strauss H, Volkmer R, Oschkinat H, Dotti CG, Haucke V. A novel subtype of AP-1-binding motif within the palmitoylated trans-Golgi network/endosomal accessory protein Gadkin/gamma-BAR. J Biol Chem 2009; 285:4074-4086. [PMID: 19965873 DOI: 10.1074/jbc.m109.049197] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Membrane traffic between the trans-Golgi network (TGN) and endosomes is mediated in part by the assembly of clathrin-AP-1 adaptor complex-coated vesicles. This process involves multiple accessory proteins that directly bind to the ear domain of AP-1gamma via degenerate peptide motifs that conform to the consensus sequence diameterG(P/D/E)(diameter/L/M) (with diameter being a large hydrophobic amino acid). Recently, gamma-BAR (hereafter referred to as Gadkin for reasons explained below) has been identified as a novel AP-1 recruitment factor involved in AP-1-dependent endosomal trafficking of lysosomal enzymes. How precisely Gadkin interacts with membranes and with AP-1gamma has remained unclear. Here we show that Gadkin is an S-palmitoylated peripheral membrane protein that lacks stable tertiary structure. S-Palmitoylation is required for the recruitment of Gadkin to TGN/endosomal membranes but not for binding to AP-1. Furthermore, we identify a novel subtype of AP-1-binding motif within Gadkin that specifically associates with the gamma1-adaptin ear domain. Mutational inactivation of this novel type of motif, either alone or in combination with three more conventional AP-1gamma binding peptides, causes Gadkin to mislocalize to the plasma membrane and interferes with its ability to render AP-1 brefeldin A-resistant, indicating its physiological importance. Our studies thus unravel the molecular basis for Gadkin-mediated AP-1 recruitment to TGN/endosomal membranes and identify a novel subtype of the AP-1-binding motif.
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Affiliation(s)
- Tanja Maritzen
- From the Institute of Chemistry and Biochemistry, Department of Membrane Biochemistry, Freie Universität and Charité-Universitätsmedizin Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Michael R Schmidt
- From the Institute of Chemistry and Biochemistry, Department of Membrane Biochemistry, Freie Universität and Charité-Universitätsmedizin Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Viktoria Kukhtina
- From the Institute of Chemistry and Biochemistry, Department of Membrane Biochemistry, Freie Universität and Charité-Universitätsmedizin Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Victoria A Higman
- the Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Holger Strauss
- the Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Rudolf Volkmer
- the Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Hartmut Oschkinat
- the Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Carlos G Dotti
- the Vlanders Institute for Biotechnology, Molecular & Developmental Genetics Program and Department of Human Genetics, University of Leuven Medical School, Herestraat 49, 3000 Leuven, Belgium, and
| | - Volker Haucke
- From the Institute of Chemistry and Biochemistry, Department of Membrane Biochemistry, Freie Universität and Charité-Universitätsmedizin Berlin, Takustrasse 6, 14195 Berlin, Germany; the Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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Regulation of endosomal membrane traffic by a Gadkin/AP-1/kinesin KIF5 complex. Proc Natl Acad Sci U S A 2009; 106:15344-9. [PMID: 19706427 DOI: 10.1073/pnas.0904268106] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Endosomes and endosomal vesicles (EVs) rapidly move along cytoskeletal filaments allowing them to exchange proteins and lipids between different endosomal compartments, lysosomes, the trans-Golgi network (TGN), and the plasma membrane. The precise mechanisms that connect membrane traffic between the TGN and perinuclear endosomal compartments with motor-protein driven transport have largely remained elusive. Here we show that Gadkin (also termed gamma-BAR), a peripheral membrane protein localized to the TGN and to TGN-derived EVs, directly associates with the clathrin adaptor AP-1 and with the motor protein kinesin KIF5, thereby potentially regulating EV dynamics. Gadkin overexpression induced the dispersion of transferrin (Tf)- and Rab4-positive EVs to the cell periphery, whereas KIF5B-depleted cells displayed a perinuclear concentration. Functional experiments suggest that the role of Gadkin as a regulator of endosomal membrane traffic critically depends on complex formation with both AP-1 and KIF5. Our data thus provide a direct molecular link between TGN-derived EVs and the microtubule-based cytoskeleton.
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Sorting of lysosomal proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1793:605-14. [PMID: 19046998 DOI: 10.1016/j.bbamcr.2008.10.016] [Citation(s) in RCA: 573] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 10/07/2008] [Accepted: 10/30/2008] [Indexed: 11/24/2022]
Abstract
Lysosomes are composed of soluble and transmembrane proteins that are targeted to lysosomes in a signal-dependent manner. The majority of soluble acid hydrolases are modified with mannose 6-phosphate (M6P) residues, allowing their recognition by M6P receptors in the Golgi complex and ensuing transport to the endosomal/lysosomal system. Other soluble enzymes and non-enzymatic proteins are transported to lysosomes in an M6P-independent manner mediated by alternative receptors such as the lysosomal integral membrane protein LIMP-2 or sortilin. Sorting of cargo receptors and lysosomal transmembrane proteins requires sorting signals present in their cytosolic domains. These signals include dileucine-based motifs, DXXLL or [DE]XXXL[LI], and tyrosine-based motifs, YXXØ, which interact with components of clathrin coats such as GGAs or adaptor protein complexes. In addition, phosphorylation and lipid modifications regulate signal recognition and trafficking of lysosomal membrane proteins. The complex interaction of both luminal and cytosolic signals with recognition proteins guarantees the specific and directed transport of proteins to lysosomes.
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Lui-Roberts WWY, Ferraro F, Nightingale TD, Cutler DF. Aftiphilin and gamma-synergin are required for secretagogue sensitivity of Weibel-Palade bodies in endothelial cells. Mol Biol Cell 2008; 19:5072-81. [PMID: 18815278 DOI: 10.1091/mbc.e08-03-0301] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Formation of secretory organelles requires the coupling of cargo selection to targeting into the correct exocytic pathway. Although the assembly of regulated secretory granules is driven in part by selective aggregation and retention of content, we recently reported that adaptor protein-1 (AP-1) recruitment of clathrin is essential to the initial formation of Weibel-Palade bodies (WPBs) at the trans-Golgi network. A selective co-aggregation process might include recruitment of components required for targeting to the regulated secretory pathway. However, we find that acquisition of the regulated secretory phenotype by WPBs in endothelial cells is coupled to but can be separated from formation of the distinctive granule core by ablation of the AP-1 effectors aftiphilin and gamma-synergin. Their depletion by small interfering RNA leads to WPBs that fail to respond to secretagogue and release their content in an unregulated manner. We find that these non-responsive WPBs have density, markers of maturation, and highly multimerized von Willebrand factor similar to those of wild-type granules. Thus, by also recruiting aftiphilin/gamma-synergin in addition to clathrin, AP-1 coordinates formation of WPBs with their acquisition of a regulated secretory phenotype.
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Affiliation(s)
- Winnie W Y Lui-Roberts
- MRC Laboratory of Molecular Cell Biology, Cell Biology Unit and Department of Cell and Developmental Biology, University College London, London WC1E 6BT, United Kingdom
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Chi S, Cao H, Chen J, McNiven MA. Eps15 mediates vesicle trafficking from the trans-Golgi network via an interaction with the clathrin adaptor AP-1. Mol Biol Cell 2008; 19:3564-75. [PMID: 18524853 PMCID: PMC2488291 DOI: 10.1091/mbc.e07-10-0997] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 05/21/2008] [Accepted: 05/22/2008] [Indexed: 11/11/2022] Open
Abstract
Eps15 (EGFR pathway substrate clone 15) is well known for its role in clathrin-coated vesicle formation at the plasma membrane through interactions with other clathrin adaptor proteins such as AP-2. Interestingly, we observed that in addition to its plasma membrane localization, Eps15 is also present at the trans-Golgi network (TGN). Therefore, we predicted that Eps15 might associate with clathrin adaptor proteins at the TGN and thereby mediate the formation of Golgi-derived vesicles. Indeed, we have found that Eps15 and the TGN clathrin adaptor AP-1 coimmunoprecipitate from rat liver Golgi fractions. Furthermore, we have identified a 14-amino acid motif near the AP-2-binding domain of Eps15 that is required for binding to AP-1, but not AP-2. Disruption of the Eps15-AP-1 interaction via siRNA knockdown of AP-1 or expression of mutant Eps15 protein, which lacks a 14-amino acid motif representing the AP-1 binding site of Eps15, significantly reduced the exit of secretory proteins from the TGN. Together, these findings indicate that Eps15 plays an important role in clathrin-coated vesicle formation not only at the plasma membrane but also at the TGN during the secretory process.
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Affiliation(s)
- Susan Chi
- Mayo Clinic College of Medicine, Department of Biochemistry and Molecular Biology, and the Miles and Shirley Fiterman Center for Digestive Diseases, Rochester, MN 55905
| | - Hong Cao
- Mayo Clinic College of Medicine, Department of Biochemistry and Molecular Biology, and the Miles and Shirley Fiterman Center for Digestive Diseases, Rochester, MN 55905
| | - Jing Chen
- Mayo Clinic College of Medicine, Department of Biochemistry and Molecular Biology, and the Miles and Shirley Fiterman Center for Digestive Diseases, Rochester, MN 55905
| | - Mark A. McNiven
- Mayo Clinic College of Medicine, Department of Biochemistry and Molecular Biology, and the Miles and Shirley Fiterman Center for Digestive Diseases, Rochester, MN 55905
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Park JJ, Loh YP. How peptide hormone vesicles are transported to the secretion site for exocytosis. Mol Endocrinol 2008; 22:2583-95. [PMID: 18669645 DOI: 10.1210/me.2008-0209] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Post-Golgi transport of peptide hormone-containing vesicles from the site of genesis at the trans-Golgi network to the release site at the plasma membrane is essential for activity-dependent hormone secretion to mediate various endocrinological functions. It is known that these vesicles are transported on microtubules to the proximity of the release site, and they are then loaded onto an actin/myosin system for distal transport through the actin cortex to just below the plasma membrane. The vesicles are then tethered to the plasma membrane, and a subpopulation of them are docked and primed to become the readily releasable pool. Cytoplasmic tails of vesicular transmembrane proteins, as well as many cytosolic proteins including adaptor proteins, motor proteins, and guanosine triphosphatases, are involved in vesicle budding, the anchoring of the vesicles, and the facilitation of movement along the transport systems. In addition, a set of cytosolic proteins is also necessary for tethering/docking of the vesicles to the plasma membrane. Many of these proteins have been identified from different types of (neuro)endocrine cells. Here, we summarize the proteins known to be involved in the mechanisms of sorting various cargo proteins into regulated secretory pathway hormone-containing vesicles, movement of these vesicles along microtubules and actin filaments, and their eventual tethering/docking to the plasma membrane for hormone secretion.
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Affiliation(s)
- Joshua J Park
- Section on Cellular Neurobiology, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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Ishizaki R, Shin HW, Mitsuhashi H, Nakayama K. Redundant roles of BIG2 and BIG1, guanine-nucleotide exchange factors for ADP-ribosylation factors in membrane traffic between the trans-Golgi network and endosomes. Mol Biol Cell 2008; 19:2650-60. [PMID: 18417613 DOI: 10.1091/mbc.e07-10-1067] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BIG2 and BIG1 are closely related guanine-nucleotide exchange factors (GEFs) for ADP-ribosylation factors (ARFs) and are involved in the regulation of membrane traffic through activating ARFs and recruiting coat protein complexes, such as the COPI complex and the AP-1 clathrin adaptor complex. Although both ARF-GEFs are associated mainly with the trans-Golgi network (TGN) and BIG2 is also associated with recycling endosomes, it is unclear whether BIG2 and BIG1 share some roles in membrane traffic. We here show that knockdown of both BIG2 and BIG1 by RNAi causes mislocalization of a subset of proteins associated with the TGN and recycling endosomes and blocks retrograde transport of furin from late endosomes to the TGN. Similar mislocalization and protein transport block, including furin, were observed in cells depleted of AP-1. Taken together with previous reports, these observations indicate that BIG2 and BIG1 play redundant roles in trafficking between the TGN and endosomes that involves the AP-1 complex.
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Affiliation(s)
- Ray Ishizaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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Medigeshi GR, Krikunova M, Radhakrishnan K, Wenzel D, Klingauf J, Schu P. AP-1 Membrane–Cytoplasm Recycling Regulated by μ1A-Adaptin. Traffic 2008; 9:121-32. [DOI: 10.1111/j.1600-0854.2007.00672.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chibalina MV, Seaman MNJ, Miller CC, Kendrick-Jones J, Buss F. Myosin VI and its interacting protein LMTK2 regulate tubule formation and transport to the endocytic recycling compartment. J Cell Sci 2007; 120:4278-88. [PMID: 18029400 DOI: 10.1242/jcs.014217] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Myosin VI is an actin-based retrograde motor protein that plays a crucial role in both endocytic and secretory membrane trafficking pathways. Myosin VI's targeting to and function in these intracellular pathways is mediated by a number of specific binding partners. In this paper we have identified a new myosin-VI-binding partner, lemur tyrosine kinase 2 (LMTK2), which is the first transmembrane protein and kinase that directly binds to myosin VI. LMTK2 binds to the WWY site in the C-terminal myosin VI tail, the same site as the endocytic adaptor protein Dab2. When either myosin VI or LMTK2 is depleted by siRNAs, the transferrin receptor (TfR) is trapped in swollen endosomes and tubule formation in the endocytic recycling pathway is dramatically reduced, showing that both proteins are required for the transport of cargo, such as the TfR, from early endosomes to the endocytic recycling compartment.
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Affiliation(s)
- Margarita V Chibalina
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
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43
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Borner GHH, Rana AA, Forster R, Harbour M, Smith JC, Robinson MS. CVAK104 is a novel regulator of clathrin-mediated SNARE sorting. Traffic 2007; 8:893-903. [PMID: 17587408 PMCID: PMC2239300 DOI: 10.1111/j.1600-0854.2007.00576.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clathrin-coated vesicles (CCVs) mediate transport between the plasma membrane, endosomes and the trans Golgi network. Using comparative proteomics, we have identified coated-vesicle-associated kinase of 104 kDa (CVAK104) as a candidate accessory protein for CCV-mediated trafficking. Here, we demonstrate that the protein colocalizes with clathrin and adaptor protein-1 (AP-1), and that it is associated with a transferrin-positive endosomal compartment. Consistent with these observations, clathrin as well as the cargo adaptors AP-1 and epsinR can be coimmunoprecipitated with CVAK104. Small interfering RNA (siRNA) knockdown of CVAK104 in HeLa cells results in selective loss of the SNARE proteins syntaxin 8 and vti1b from CCVs. Morpholino-mediated knockdown of CVAK104 in Xenopus tropicalis causes severe developmental defects, including a bent body axis and ventral oedema. Thus, CVAK104 is an evolutionarily conserved protein involved in SNARE sorting that is essential for normal embryonic development.
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Affiliation(s)
| | - Amer A Rana
- Gurdon Institute, University of CambridgeCambridge CB2 1QN, UK
| | | | | | - James C Smith
- Gurdon Institute, University of CambridgeCambridge CB2 1QN, UK
| | - Margaret S Robinson
- CIMR, University of CambridgeCambridge CB2 0XY, UK
- Corresponding author: Margaret S. Robinson,
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Mardones GA, Burgos PV, Brooks DA, Parkinson-Lawrence E, Mattera R, Bonifacino JS. The trans-Golgi network accessory protein p56 promotes long-range movement of GGA/clathrin-containing transport carriers and lysosomal enzyme sorting. Mol Biol Cell 2007; 18:3486-501. [PMID: 17596511 PMCID: PMC1951763 DOI: 10.1091/mbc.e07-02-0190] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The sorting of acid hydrolase precursors at the trans-Golgi network (TGN) is mediated by binding to mannose 6-phosphate receptors (MPRs) and subsequent capture of the hydrolase-MPR complexes into clathrin-coated vesicles or transport carriers (TCs) destined for delivery to endosomes. This capture depends on the function of three monomeric clathrin adaptors named GGAs. The GGAs comprise a C-terminal "ear" domain that binds a specific set of accessory proteins. Herein we show that one of these accessory proteins, p56, colocalizes and physically interacts with the three GGAs at the TGN. Moreover, overexpression of the GGAs enhances the association of p56 with the TGN, and RNA interference (RNAi)-mediated depletion of the GGAs decreases the TGN association and total levels of p56. RNAi-mediated depletion of p56 or the GGAs causes various degrees of missorting of the precursor of the acid hydrolase, cathepsin D. In the case of p56 depletion, this missorting correlates with decreased mobility of GGA-containing TCs. Transfection with an RNAi-resistant p56 construct, but not with a p56 construct lacking the GGA-ear-interacting motif, restores the mobility of the TCs. We conclude that p56 tightly cooperates with the GGAs in the sorting of cathepsin D to lysosomes, probably by enabling the movement of GGA-containing TCs.
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Affiliation(s)
- Gonzalo A. Mardones
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Patricia V. Burgos
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Doug A. Brooks
- Sansom Institute, University of South Australia, Adelaide, SA 5001, Australia; and
- Lysosomal Diseases Research Unit, Department of Genetic Medicine, Children Youth and Women's Health Service, North Adelaide, SA 5006, Australia
| | - Emma Parkinson-Lawrence
- Sansom Institute, University of South Australia, Adelaide, SA 5001, Australia; and
- Lysosomal Diseases Research Unit, Department of Genetic Medicine, Children Youth and Women's Health Service, North Adelaide, SA 5006, Australia
| | - Rafael Mattera
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Juan S. Bonifacino
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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45
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Kametaka S, Moriyama K, Burgos PV, Eisenberg E, Greene LE, Mattera R, Bonifacino JS. Canonical interaction of cyclin G associated kinase with adaptor protein 1 regulates lysosomal enzyme sorting. Mol Biol Cell 2007; 18:2991-3001. [PMID: 17538018 PMCID: PMC1949374 DOI: 10.1091/mbc.e06-12-1162] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The adaptor protein 1 (AP1) complex is a heterotetramer that participates in cargo sorting into clathrin-coated vesicles at the trans-Golgi network (TGN) and endosomes. The gamma subunit of AP1 possesses a C-terminal "ear" domain that recruits a cohort of accessory proteins through recognition of a shared canonical motif, PsiG[PDE][PsiLM] (where Psi is an aromatic residue). The physiological relevance of these ear-motif interactions, however, remains to be demonstrated. Here we report that the cyclin G-associated kinase (GAK) has two sequences fitting this motif, FGPL and FGEF, which mediate binding to the AP1-gamma-ear domain in vitro. Mutation of both gamma-ear-binding sequences or depletion of AP1-gamma by RNA interference (RNAi) decreases the association of GAK with the TGN in vivo. Depletion of GAK by RNAi impairs the sorting of the acid hydrolase, cathepsin D, to lysosomes. Importantly, expression of RNAi-resistant GAK restores the lysosomal sorting of cathepsin D in cells depleted of endogenous GAK, whereas expression of a similar construct bearing mutations in both gamma-ear-binding sequences fails to correct the sorting defect. Thus, interactions between the PsiG[PDE][PsiLM]-motif sequences in GAK and the AP1-gamma-ear domain are critical for the recruitment of GAK to the TGN and the function of GAK in lysosomal enzyme sorting.
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Affiliation(s)
- Satoshi Kametaka
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, and
| | - Kengo Moriyama
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, and
| | - Patricia V. Burgos
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, and
| | - Evan Eisenberg
- Laboratory of Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lois E. Greene
- Laboratory of Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Rafael Mattera
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, and
| | - Juan S. Bonifacino
- *Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, and
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46
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Desmond JC, Raynaud S, Tung E, Hofmann WK, Haferlach T, Koeffler HP. Discovery of epigenetically silenced genes in acute myeloid leukemias. Leukemia 2007; 21:1026-34. [PMID: 17330099 DOI: 10.1038/sj.leu.2404611] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The demethylating 5-aza-2'deoxycytidine (DAC) and the histone deacetylase inhibitor (HDACi) suberoyl anilide bishydroxamide (SAHA) possess potent antitumorigenic properties in myeloid disorders. However, the transcriptome alterations mediated by these drugs are poorly understood. We analyzed the transcriptional effects of DAC and SAHA in the AML cell line KG-1. Microarray analyses revealed 76 genes expressed in normal CD34+ cells, absent in KG-1 cells but whose expression was induced after drug treatment. A total of 39 of these genes harbored CpG islands in their promoters. We examined the expression level of these genes in 120 AML patient samples representing diverse karyotpyes. Gas2l1, tfIIs, ehd3, enolase 2, mx1, dral, astml and pxdn were diminished across all AML karyotypes examined. Ehd3 was methylated in 63% of AML patients examined. This methylation was lost upon complete remission, and not observed in normal CD34+ cells. CD34+ cells expressed ehd3 at approximately 10-fold higher levels than AML samples. Another highlighted gene, alpha-catenin, is located at q31 of chromosome 5. Analyses of 29 5q- AML/myelodysplastic syndrome (MDS) samples revealed marked decreases in expression of alpha-catenin, compared to non-5q- MDS samples (6.6+/-9-fold). However, no methylation was detected, suggesting indirect effects of these drugs on the expression of alpha-catenin.
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Affiliation(s)
- J C Desmond
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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47
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Fernández GE, Payne GS. Laa1p, a conserved AP-1 accessory protein important for AP-1 localization in yeast. Mol Biol Cell 2006; 17:3304-17. [PMID: 16687571 PMCID: PMC1483057 DOI: 10.1091/mbc.e06-02-0096] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
AP-1 and Gga adaptors participate in clathrin-mediated protein transport between the trans-Golgi network and endosomes. Both adaptors contain homologous domains that act to recruit accessory proteins involved in clathrin-coated vesicle formation, but the spectrum of known adaptor-binding partners is limited. This study describes an evolutionarily conserved protein of Saccharomyces cerevisiae, Laa1p (Yjl207cp), that interacts and functions specifically with AP-1. Deletion of LAA1, when combined with a conditional mutation in clathrin heavy chain or deletion of GGA genes, accentuated growth defects and increased disruption of clathrin-dependent alpha-factor maturation and transport of carboxypeptidase Y to the vacuole. In contrast, such genetic interactions were not observed between deletions of LAA1 and AP-1 subunit genes. Laa1p preferentially interacted with AP-1 compared with Gga proteins by glutathione S-transferase-fusion affinity binding and coimmunoprecipitations. Localization of AP-1 and Laa1p, but not Gga proteins, was highly sensitive to brefeldin A, an inhibitor of ADP-ribosylation factor (Arf) activation. Importantly, deletion of LAA1 caused mislocalization of AP-1, especially in cells at high density (postdiauxic shift), but it did not affect Gga protein distribution. Our results identify Laa1p as a new determinant of AP-1 localization, suggesting a model in which Laa1p and Arf cooperate to direct stable association of AP-1 with appropriate intracellular membranes.
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Affiliation(s)
- G. Esteban Fernández
- Department of Biological Chemistry, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095
| | - Gregory S. Payne
- Department of Biological Chemistry, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095
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48
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Harasaki K, Lubben NB, Harbour M, Taylor MJ, Robinson MS. Sorting of major cargo glycoproteins into clathrin-coated vesicles. Traffic 2006; 6:1014-26. [PMID: 16190982 DOI: 10.1111/j.1600-0854.2005.00341.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The AP-1 and AP-2 complexes are the most abundant adaptors in clathrin-coated vesicles (CCVs), but clathrin-mediated trafficking can still occur in the absence of any detectable AP-1 or AP-2. To find out whether adaptor abundance reflects cargo abundance, we used lectin pulldowns to identify the major membrane glycoproteins in CCVs from human placenta and rat liver. Both preparations contained three prominent high molecular-weight proteins: the cation-independent mannose 6-phosphate receptor (CIMPR), carboxypeptidase D (CPD) and low-density lipoprotein receptor-related protein 1 (LRP1). To investigate how these proteins are sorted, we constructed and stably transfected CD8 chimeras into HeLa cells. CD8-CIMPR localized mainly to early/tubular endosomes, CD8-CPD to the trans Golgi network and CD8-LRP1 to late/multivesicular endosomes. All three constructs redistributed to the plasma membrane when clathrin was depleted by siRNA. CD8-CIMPR was also strongly affected by AP-2 depletion. CD8-CPD was moderately affected by AP-2 depletion but strongly affected by depleting AP-1 and AP-2 together. CD8-LRP1 was only slightly affected by AP-2 depletion; however, mutating an NPXY motif in the LRP1 tail caused it to become AP-2 dependent. These results indicate that all three proteins have AP-dependent sorting signals, which may help to explain the relative abundance of AP complexes in CCVs. However, the relatively low abundance of cargo proteins in CCV preparations suggests either that some of the APs may be empty or that the preparations may be dominated by empty coats.
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Affiliation(s)
- Kouki Harasaki
- University of Cambridge, Department of Clinical Biochemistry, Cambridge Institute for Medical Research, Cambridge CB2 2XY, UK
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49
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Naslavsky N, Rahajeng J, Sharma M, Jovic M, Caplan S. Interactions between EHD proteins and Rab11-FIP2: a role for EHD3 in early endosomal transport. Mol Biol Cell 2005; 17:163-77. [PMID: 16251358 PMCID: PMC1345656 DOI: 10.1091/mbc.e05-05-0466] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Eps15 homology domain (EHD) 1 enables membrane recycling by controlling the exit of internalized molecules from the endocytic recycling compartment (ERC) en route to the plasma membrane, similar to the role described for Rab11. However, no physical or functional connection between Rab11 and EHD-family proteins has been demonstrated yet, and the mode by which they coordinate their regulatory activity remains unknown. Here, we demonstrate that EHD1 and EHD3 (the closest EHD1 paralog), bind to the Rab11-effector Rab11-FIP2 via EH-NPF interactions. The EHD/Rab11-FIP2 associations are affected by the ability of the EHD proteins to bind nucleotides, and Rab11-FIP2 is recruited to EHD-containing membranes. These results are consistent with a coordinated role for EHD1 and Rab11-FIP2 in regulating exit from the ERC. However, because no function has been attributed to EHD3, the significance of its interaction with Rab11-FIP2 remained unclear. Surprisingly, loss of EHD3 expression prevented the delivery of internalized transferrin and early endosomal proteins to the ERC, an effect differing from that described upon EHD1 knockdown. Moreover, the subcellular localization of Rab11-FIP2 and endogenous Rab11 were altered upon EHD3 knockdown, with both proteins absent from the ERC and retained in the cell periphery. The results presented herein promote a coordinated role for EHD proteins and Rab11-FIP2 in mediating endocytic recycling and provide evidence for the function of EHD3 in early endosome to ERC transport.
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Affiliation(s)
- Naava Naslavsky
- Department of Biochemistry and Molecular Biology and Eppley Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
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50
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Perret E, Lakkaraju A, Deborde S, Schreiner R, Rodriguez-Boulan E. Evolving endosomes: how many varieties and why? Curr Opin Cell Biol 2005; 17:423-34. [PMID: 15975780 DOI: 10.1016/j.ceb.2005.06.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Accepted: 06/08/2005] [Indexed: 01/02/2023]
Abstract
The cell biologist's insight into endosomal diversity, in terms of both form and function, has increased dramatically in the past few years. This understanding has been promoted by the availability of powerful new techniques that allow imaging of both cargo and machinery in the endocytic process in real time, and by our ability to inhibit components of this machinery by RNA interference. The emerging picture from these studies is of a highly complex, dynamic and adaptable endosomal system that interacts at various points with the secretory system of the cell.
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Affiliation(s)
- Emilie Perret
- Margaret Dyson Vision Research Institute, LC-300, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
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