1
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Dutta T, Vlassakis J. Microscale measurements of protein complexes from single cells. Curr Opin Struct Biol 2024; 87:102860. [PMID: 38848654 DOI: 10.1016/j.sbi.2024.102860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024]
Abstract
Proteins execute numerous cell functions in concert with one another in protein-protein interactions (PPI). While essential in each cell, such interactions are not identical from cell to cell. Instead, PPI heterogeneity contributes to cellular phenotypic heterogeneity in health and diseases such as cancer. Understanding cellular phenotypic heterogeneity thus requires measurements of properties of PPIs such as abundance, stoichiometry, and kinetics at the single-cell level. Here, we review recent, exciting progress in single-cell PPI measurements. Novel technology in this area is enabled by microscale and microfluidic approaches that control analyte concentration in timescales needed to outpace PPI disassembly kinetics. We describe microscale innovations, needed technical capabilities, and methods poised to be adapted for single-cell analysis in the near future.
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Affiliation(s)
- Tanushree Dutta
- Department of Bioengineering, Rice University, Houston, TX 77005, USA. https://twitter.com/duttatanu1717
| | - Julea Vlassakis
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
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2
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Moochickal Assainar B, Ragunathan K, Baldridge RD. Direct observation of autoubiquitination for an integral membrane ubiquitin ligase in ERAD. Nat Commun 2024; 15:1340. [PMID: 38351109 PMCID: PMC10864399 DOI: 10.1038/s41467-024-45541-3] [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: 08/02/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
The endoplasmic reticulum associated degradation (ERAD) pathway regulates protein quality control at the endoplasmic reticulum. ERAD of lumenal and membrane proteins requires a conserved E3 ubiquitin ligase, called Hrd1. We do not understand the molecular configurations of Hrd1 that enable autoubiquitination and the subsequent retrotranslocation of misfolded protein substrates from the ER to the cytosol. Here, we have established a generalizable, single-molecule platform that enables high-efficiency labeling, stoichiometry determination, and functional assays for any integral membrane protein. Using this approach, we directly count Hrd1 proteins reconstituted into individual proteoliposomes. We report that Hrd1 assembles in different oligomeric configurations with mostly monomers and dimers detected at limiting dilution. By correlating oligomeric states with ubiquitination in vitro, we conclude that Hrd1 monomers are inefficient in autoubiquitination while dimers efficiently assemble polyubiquitin chains. Therefore, our results reveal the minimal composition of a Hrd1 oligomer that is capable of autoubiquitination. Our methods are broadly applicable to studying other complex membrane protein functions using reconstituted bilayer systems.
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Affiliation(s)
- Basila Moochickal Assainar
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Kaushik Ragunathan
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
| | - Ryan D Baldridge
- Department of Biological Chemistry, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan Medical School, 1150 W Medical Center Drive, Ann Arbor, MI, 48109, USA.
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3
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Khan MR, Yin X, Kang SU, Mitra J, Wang H, Ryu T, Brahmachari S, Karuppagounder SS, Kimura Y, Jhaldiyal A, Kim HH, Gu H, Chen R, Redding-Ochoa J, Troncoso J, Na CH, Ha T, Dawson VL, Dawson TM. Enhanced mTORC1 signaling and protein synthesis in pathologic α-synuclein cellular and animal models of Parkinson's disease. Sci Transl Med 2023; 15:eadd0499. [PMID: 38019930 DOI: 10.1126/scitranslmed.add0499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
Pathologic α-synuclein plays an important role in the pathogenesis of α-synucleinopathies such as Parkinson's disease (PD). Disruption of proteostasis is thought to be central to pathologic α-synuclein toxicity; however, the molecular mechanism of this deregulation is poorly understood. Complementary proteomic approaches in cellular and animal models of PD were used to identify and characterize the pathologic α-synuclein interactome. We report that the highest biological processes that interacted with pathologic α-synuclein in mice included RNA processing and translation initiation. Regulation of catabolic processes that include autophagy were also identified. Pathologic α-synuclein was found to bind with the tuberous sclerosis protein 2 (TSC2) and to trigger the activation of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1), which augmented mRNA translation and protein synthesis, leading to neurodegeneration. Genetic and pharmacologic inhibition of mTOR and protein synthesis rescued the dopamine neuron loss, behavioral deficits, and aberrant biochemical signaling in the α-synuclein preformed fibril mouse model and Drosophila transgenic models of pathologic α-synuclein-induced degeneration. Pathologic α-synuclein furthermore led to a destabilization of the TSC1-TSC2 complex, which plays an important role in mTORC1 activity. Constitutive overexpression of TSC2 rescued motor deficits and neuropathology in α-synuclein flies. Biochemical examination of PD postmortem brain tissues also suggested deregulated mTORC1 signaling. These findings establish a connection between mRNA translation deregulation and mTORC1 pathway activation that is induced by pathologic α-synuclein in cellular and animal models of PD.
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Affiliation(s)
- Mohammed Repon Khan
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Xiling Yin
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Jaba Mitra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hu Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Taekyung Ryu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Saurav Brahmachari
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Senthilkumar S Karuppagounder
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Yasuyoshi Kimura
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aanishaa Jhaldiyal
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun Hee Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hao Gu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Javier Redding-Ochoa
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Juan Troncoso
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chan Hyun Na
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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4
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Merino Urteaga R, Ha T. Mind your tag in single-molecule measurements. CELL REPORTS METHODS 2023; 3:100623. [PMID: 37883922 PMCID: PMC10626269 DOI: 10.1016/j.crmeth.2023.100623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
In this issue of Cell Reports Methods, Molina and colleagues use in vitro single-molecule DNA flow-stretching to demonstrate the severe effects of appending a short lysine-cysteine-lysine (KCK) tag on the Bacillus subtilis ParB protein. This assay could be further utilized to evaluate the impact of other tags on DNA-binding proteins.
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Affiliation(s)
- Raquel Merino Urteaga
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
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5
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Husbands AY, Feller A, Aggarwal V, Dresden CE, Holub AS, Ha T, Timmermans MCP. The START domain potentiates HD-ZIPIII transcriptional activity. THE PLANT CELL 2023; 35:2332-2348. [PMID: 36861320 DOI: 10.1093/plcell/koad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/09/2023] [Accepted: 02/05/2023] [Indexed: 05/30/2023]
Abstract
The CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) transcription factors (TFs) were repeatedly deployed over 725 million years of evolution to regulate central developmental innovations. The START domain of this pivotal class of developmental regulators was recognized over 20 years ago, but its putative ligands and functional contributions remain unknown. Here, we demonstrate that the START domain promotes HD-ZIPIII TF homodimerization and increases transcriptional potency. Effects on transcriptional output can be ported onto heterologous TFs, consistent with principles of evolution via domain capture. We also show the START domain binds several species of phospholipids, and that mutations in conserved residues perturbing ligand binding and/or its downstream conformational readout abolish HD-ZIPIII DNA-binding competence. Our data present a model in which the START domain potentiates transcriptional activity and uses ligand-induced conformational change to render HD-ZIPIII dimers competent to bind DNA. These findings resolve a long-standing mystery in plant development and highlight the flexible and diverse regulatory potential coded within this widely distributed evolutionary module.
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Affiliation(s)
- Aman Y Husbands
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
| | - Antje Feller
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Vasudha Aggarwal
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Courtney E Dresden
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
- Molecular, Cellular, and Developmental Biology (MCDB), The Ohio State University, Columbus, OH 43215, USA
| | - Ashton S Holub
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43215, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
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6
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Djaja NA, Chang MT, Beinart FR, Morris VM, Ganser LR, Myong S. Nucleation and dissolution mechanism underlying amyotrophic lateral sclerosis/frontotemporal lobar dementia-linked fused in sarcoma condensates. iScience 2023; 26:106537. [PMID: 37123224 PMCID: PMC10139993 DOI: 10.1016/j.isci.2023.106537] [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: 10/25/2022] [Revised: 01/17/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Fused in sarcoma (FUS) is a nuclear RNA-binding protein. Mutations in FUS lead to the mislocalization of FUS from the nucleus to the cytosol and formation of pathogenic aggregates in neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD), yet with unknown molecular mechanisms. Using mutant and stress conditions, we visualized FUS localization and aggregate formation in cells. We used single-molecule pull-down (SiMPull) to quantify the native oligomerization states of wildtype (WT) and mutant FUS in cells. We demonstrate that the NLS mutants exhibited the highest oligomerization (>3) followed by other FUS mutants (>2) and WT FUS which is primarily monomeric. Strikingly, the mutant FUS oligomers are extremely stable and resistant to treatment by high salt, hexanediol, RNase, and Karyopherin-β2 and only soluble in GdnHCl and SDS. We propose that the increased oligomerization units of mutant FUS and their high stability may contribute to ALS/FTLD pathogenesis.
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Affiliation(s)
- Nathalie A. Djaja
- Program in Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Matthew T. Chang
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Freya R. Beinart
- Department of Biology, Kenyon College, 106 College Park Dr, Gambler, OH 43022, USA
| | - Vivian M. Morris
- Lymphoid Malignancy Branch, National Cancer Institute, National Institutes of Health, Building 10, Bethesda, MD 20814, USA
| | - Laura R. Ganser
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Sua Myong
- Program in Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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7
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Serey-Gaut M, Cortes M, Makrythanasis P, Suri M, Taylor AMR, Sullivan JA, Asleh AN, Mitra J, Dar MA, McNamara A, Shashi V, Dugan S, Song X, Rosenfeld JA, Cabrol C, Iwaszkiewicz J, Zoete V, Pehlivan D, Akdemir ZC, Roeder ER, Littlejohn RO, Dibra HK, Byrd PJ, Stewart GS, Geckinli BB, Posey J, Westman R, Jungbluth C, Eason J, Sachdev R, Evans CA, Lemire G, VanNoy GE, O'Donnell-Luria A, Mau-Them FT, Juven A, Piard J, Nixon CY, Zhu Y, Ha T, Buckley MF, Thauvin C, Essien Umanah GK, Van Maldergem L, Lupski JR, Roscioli T, Dawson VL, Dawson TM, Antonarakis SE. Bi-allelic TTI1 variants cause an autosomal-recessive neurodevelopmental disorder with microcephaly. Am J Hum Genet 2023; 110:499-515. [PMID: 36724785 PMCID: PMC10027477 DOI: 10.1016/j.ajhg.2023.01.006] [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: 09/19/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Telomere maintenance 2 (TELO2), Tel2 interacting protein 2 (TTI2), and Tel2 interacting protein 1 (TTI1) are the three components of the conserved Triple T (TTT) complex that modulates activity of phosphatidylinositol 3-kinase-related protein kinases (PIKKs), including mTOR, ATM, and ATR, by regulating the assembly of mTOR complex 1 (mTORC1). The TTT complex is essential for the expression, maturation, and stability of ATM and ATR in response to DNA damage. TELO2- and TTI2-related bi-allelic autosomal-recessive (AR) encephalopathies have been described in individuals with moderate to severe intellectual disability (ID), short stature, postnatal microcephaly, and a movement disorder (in the case of variants within TELO2). We present clinical, genomic, and functional data from 11 individuals in 9 unrelated families with bi-allelic variants in TTI1. All present with ID, and most with microcephaly, short stature, and a movement disorder. Functional studies performed in HEK293T cell lines and fibroblasts and lymphoblastoid cells derived from 4 unrelated individuals showed impairment of the TTT complex and of mTOR pathway activity which is improved by treatment with Rapamycin. Our data delineate a TTI1-related neurodevelopmental disorder and expand the group of disorders related to the TTT complex.
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Affiliation(s)
- Margaux Serey-Gaut
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France.
| | - Marisol Cortes
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Periklis Makrythanasis
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland; Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Mohnish Suri
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Alexander M R Taylor
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Ayat N Asleh
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jaba Mitra
- Department of Biophysics and Biophysical Chemistry, Biophysics and Biomedical Engineering, JHU Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Mohamad A Dar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amy McNamara
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Sarah Dugan
- Providence Medical Group Genetic Clinics, Spokane, WA, USA
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christelle Cabrol
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research Lausanne Branch, University of Lausanne, Lausanne, Switzerland
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; EA481 Integrative and Cognitive Neuroscience Research Unit, University of Franche-Comte, Besancon, France
| | - Zeynep Coban Akdemir
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; University Texas Health Science Center, Houston, TX 77030, USA
| | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca Okashah Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harpreet K Dibra
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Philip J Byrd
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Bilgen B Geckinli
- Department of Medical Genetics, Marmara University School of Medicine, Istanbul 34722, Turkey
| | - Jennifer Posey
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Westman
- Providence Medical Group Genetic Clinics, Spokane, WA, USA
| | | | - Jacqueline Eason
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia
| | - Gabrielle Lemire
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Grace E VanNoy
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne O'Donnell-Luria
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Frédéric Tran Mau-Them
- UF6254 Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Aurélien Juven
- UF6254 Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Juliette Piard
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Cheng Yee Nixon
- Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia
| | - Ying Zhu
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Biophysics and Biomedical Engineering, JHU Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Christel Thauvin
- INSERM UMR1231 GAD, Bourgogne Franche-Comté University, Dijon, France; Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, Dijon, France
| | - George K Essien Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lionel Van Maldergem
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France; Clinical Investigation Center 1431, National Institute of Health and Medical Research (INSERM), CHU, Besancon, France; EA481 Integrative and Cognitive Neuroscience Research Unit, University of Franche-Comte, Besancon, France
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stylianos E Antonarakis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland; Medigenome, Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland.
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8
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Ma G, Zhang P, Zhou X, Wan Z, Wang S. Label-Free Single-Molecule Pulldown for the Detection of Released Cellular Protein Complexes. ACS CENTRAL SCIENCE 2022; 8:1272-1281. [PMID: 36188347 PMCID: PMC9523780 DOI: 10.1021/acscentsci.2c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 06/16/2023]
Abstract
Precise and sensitive detection of intracellular proteins and complexes is key to the understanding of signaling pathways and cell functions. Here, we present a label-free single-molecule pulldown (LFSMP) technique for the imaging of released cellular protein and protein complexes with single-molecule sensitivity and low sample consumption down to a few cells per mm2. LFSMP is based on plasmonic scattering imaging and thus can directly image the surface-captured molecules without labels and quantify the binding kinetics. In this paper, we demonstrate the detection principle for LFSMP, study the phosphorylation of protein complexes involved in a signaling pathway, and investigate how kinetic analysis can be used to improve the pulldown specificity. We wish our technique can contribute to uncovering the molecular mechanisms in cells with single-molecule resolution.
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Affiliation(s)
- Guangzhong Ma
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
| | - Pengfei Zhang
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
| | - Xinyu Zhou
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Zijian Wan
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Shaopeng Wang
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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9
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Umanah GKE, Abalde-Atristain L, Khan MR, Mitra J, Dar MA, Chang M, Tangella K, McNamara A, Bennett S, Chen R, Aggarwal V, Cortes M, Worley PF, Ha T, Dawson TM, Dawson VL. AAA + ATPase Thorase inhibits mTOR signaling through the disassembly of the mTOR complex 1. Nat Commun 2022; 13:4836. [PMID: 35977929 PMCID: PMC9385847 DOI: 10.1038/s41467-022-32365-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) signals through the mTOR complex 1 (mTORC1) and the mTOR complex 2 to maintain cellular and organismal homeostasis. Failure to finely tune mTOR activity results in metabolic dysregulation and disease. While there is substantial understanding of the molecular events leading mTORC1 activation at the lysosome, remarkably little is known about what terminates mTORC1 signaling. Here, we show that the AAA + ATPase Thorase directly binds mTOR, thereby orchestrating the disassembly and inactivation of mTORC1. Thorase disrupts the association of mTOR to Raptor at the mitochondria-lysosome interface and this action is sensitive to amino acids. Lack of Thorase causes accumulation of mTOR-Raptor complexes and altered mTORC1 disassembly/re-assembly dynamics upon changes in amino acid availability. The resulting excessive mTORC1 can be counteracted with rapamycin in vitro and in vivo. Collectively, we reveal Thorase as a key component of the mTOR pathway that disassembles and thus inhibits mTORC1.
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Affiliation(s)
- George K E Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Leire Abalde-Atristain
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Vollum Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Mohammed Repon Khan
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jaba Mitra
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Mohamad Aasif Dar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Melissa Chang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kavya Tangella
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Amy McNamara
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Samuel Bennett
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rong Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Vasudha Aggarwal
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Marisol Cortes
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Paul F Worley
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Taekjip Ha
- Departments of Biophysics and Biophysical Chemistry, Biophysics and Biomedical Engineering, JHU Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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10
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Luciano AK, Korobkina E, Lyons SP, Haley JA, Fluharty S, Jung SM, Kettenbach AN, Guertin DA. Proximity labeling of endogenous RICTOR identifies mTOR Complex 2 regulation by ADP ribosylation factor ARF1. J Biol Chem 2022; 298:102379. [PMID: 35973513 PMCID: PMC9513271 DOI: 10.1016/j.jbc.2022.102379] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/22/2022] [Accepted: 08/09/2022] [Indexed: 01/08/2023] Open
Abstract
Mechanistic target of rapamycin (mTOR) complex 2 (mTORC2) regulates metabolism, cell proliferation, and cell survival. mTORC2 activity is stimulated by growth factors, and it phosphorylates the hydrophobic motif site of the AGC kinases AKT, SGK, and PKC. However, the proteins that interact with mTORC2 to control its activity and localization remain poorly defined. To identify mTORC2-interacting proteins in living cells, we tagged endogenous RICTOR, an essential mTORC2 subunit, with the modified BirA biotin ligase BioID2 and performed live-cell proximity labeling. We identified 215 RICTOR-proximal proteins, including proteins with known mTORC2 pathway interactions, and 135 proteins (63%) not previously linked to mTORC2 signaling, including nuclear and cytoplasmic proteins. Our imaging and cell fractionation experiments suggest nearly 30% of RICTOR is in the nucleus, hinting at potential nuclear functions. We also identified 29 interactors containing RICTOR-dependent, insulin-stimulated phosphorylation sites, thus providing insight into mTORC2-dependent insulin signaling dynamics. Finally, we identify the endogenous ADP ribosylation factor 1 (ARF1) GTPase as an mTORC2-interacting protein. Through gain-of-function and loss-of-function studies, we provide functional evidence that ARF1 may negatively regulate mTORC2. In summary, we present a new method of studying endogenous mTORC2, a resource of RICTOR/mTORC2 protein interactions in living cells, and a potential mechanism of mTORC2 regulation by the ARF1 GTPase.
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Affiliation(s)
- Amelia K Luciano
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Ekaterina Korobkina
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Scott P Lyons
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - John A Haley
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Shelagh Fluharty
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Su Myung Jung
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - David A Guertin
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605.
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11
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Volta V, Pérez-Baos S, de la Parra C, Katsara O, Ernlund A, Dornbaum S, Schneider RJ. A DAP5/eIF3d alternate mRNA translation mechanism promotes differentiation and immune suppression by human regulatory T cells. Nat Commun 2021; 12:6979. [PMID: 34848685 PMCID: PMC8632918 DOI: 10.1038/s41467-021-27087-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
Regulatory T cells (Treg cells) inhibit effector T cells and maintain immune system homeostasis. Treg cell maturation in peripheral sites requires inhibition of protein kinase mTORC1 and TGF-beta-1 (TGF-beta). While Treg cell maturation requires protein synthesis, mTORC1 inhibition downregulates it, leaving unanswered how Treg cells achieve essential mRNA translation for development and immune suppression activity. Using human CD4+ T cells differentiated in culture and genome-wide transcription and translation profiling, here we report that TGF-beta transcriptionally reprograms naive T cells to express Treg cell differentiation and immune suppression mRNAs, while mTORC1 inhibition impairs translation of T cell mRNAs but not those induced by TGF-beta. Rather than canonical mTORC1/eIF4E/eIF4G translation, Treg cell mRNAs utilize the eIF4G homolog DAP5 and initiation factor eIF3d in a non-canonical translation mechanism that requires cap-dependent binding by eIF3d directed by Treg cell mRNA 5' noncoding regions. Silencing DAP5 in isolated human naive CD4+ T cells impairs their differentiation into Treg cells. Treg cell differentiation is mediated by mTORC1 downregulation and TGF-beta transcriptional reprogramming that establishes a DAP5/eIF3d-selective mechanism of mRNA translation.
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Affiliation(s)
- Viviana Volta
- Synthis LLC, 430 East 29th Street, Launch Labs, Alexandria Center for Life Sciences, New York, NY, 10016, USA
| | - Sandra Pérez-Baos
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Columba de la Parra
- Department of Chemistry, Herbert H. Lehman College, City University of New York, The Graduate Center, Biochemistry Ph.D. Program, City University of New York, New York, NY, 10016, USA
| | - Olga Katsara
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Amanda Ernlund
- Johns Hopkins Applied Physics Lab, 11000 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Sophie Dornbaum
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Robert J Schneider
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, 10016, USA.
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, 10016, USA.
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY, 10016, USA.
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12
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Swain O, Romano SK, Miryala R, Tsai J, Parikh V, Umanah GKE. SARS-CoV-2 Neuronal Invasion and Complications: Potential Mechanisms and Therapeutic Approaches. J Neurosci 2021; 41:5338-5349. [PMID: 34162747 PMCID: PMC8221594 DOI: 10.1523/jneurosci.3188-20.2021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/12/2021] [Accepted: 05/02/2021] [Indexed: 12/15/2022] Open
Abstract
Clinical reports suggest that the coronavirus disease-19 (COVID-19) pandemic caused by severe acute respiratory syndrome (SARS)-coronavirus-2 (CoV-2) has not only taken millions of lives, but has also created a major crisis of neurologic complications that persist even after recovery from the disease. Autopsies of patients confirm the presence of the coronaviruses in the CNS, especially in the brain. The invasion and transmission of SARS-CoV-2 in the CNS is not clearly defined, but, because the endocytic pathway has become an important target for the development of therapeutic strategies for COVID-19, it is necessary to understand endocytic processes in the CNS. In addition, mitochondria and mechanistic target of rapamycin (mTOR) signaling pathways play a critical role in the antiviral immune response, and may also be critical for endocytic activity. Furthermore, dysfunctions of mitochondria and mTOR signaling pathways have been associated with some high-risk conditions such as diabetes and immunodeficiency for developing severe complications observed in COVID-19 patients. However, the role of these pathways in SARS-CoV-2 infection and spread are largely unknown. In this review, we discuss the potential mechanisms of SARS-CoV-2 entry into the CNS and how mitochondria and mTOR pathways might regulate endocytic vesicle-mitochondria interactions and dynamics during SARS-CoV-2 infection. The mechanisms that plausibly account for severe neurologic complications with COVID-19 and potential treatments with Food and Drug Administration-approved drugs targeting mitochondria and the mTOR pathways are also addressed.
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Affiliation(s)
- Olivia Swain
- Neuroscience Department, Krieger School of Arts and Sciences, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Sofia K Romano
- Neuroscience Department, Krieger School of Arts and Sciences, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Ritika Miryala
- Neuroscience Department, Krieger School of Arts and Sciences, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Jocelyn Tsai
- Neuroscience Department, Krieger School of Arts and Sciences, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Vinnie Parikh
- Neuroscience Department, Krieger School of Arts and Sciences, The Johns Hopkins University, Baltimore, Maryland 21205
| | - George K E Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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13
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Su B, Zhang X, Li L, Abbas S, Yu M, Cui Y, Baluška F, Hwang I, Shan X, Lin J. Dynamic spatial reorganization of BSK1 complexes in the plasma membrane underpins signal-specific activation for growth and immunity. MOLECULAR PLANT 2021; 14:588-603. [PMID: 33524551 DOI: 10.1016/j.molp.2021.01.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 05/25/2023]
Abstract
Growth and immunity are opposing processes that compete for cellular resources, and proper resource allocation is crucial for plant survival. BSK1 plays a key role in the regulation of both growth and immunity by associating with BRI1 and FLS2, respectively. However, it remains unclear how two antagonistic signals co-opt BSK1 to induce signal-specific activation. Here we show that the dynamic spatial reorganization of BSK1 within the plasma membrane underlies the mechanism of signal-specific activation for growth or immunity. Resting BSK1 localizes to membrane rafts as complexes. Unlike BSK1-associated FLS2 and BRI1, flg22 or exogenous brassinosteroid (BR) treatment did not decrease BSK1 levels at the plasma membrane (PM) but rather induced BSK1 multimerization and dissociation from FLS2/BSK1 or BRI1/BSK1, respectively. Moreover, flg22-activated BSK1 translocated from membrane rafts to non-membrane-raft regions, whereas BR-activated BSK1 remained in membrane rafts. When applied together with flg22, BR suppressed various flg22-induced BSK1 activities such as BSK1 dissociation from FLS2/BSK1, BSK1 interaction with MAPKKK5, and BSK translocation together with MAPKKK5. Taken together, this study provides a unique insight into how the precise control of BSK1 spatiotemporal organization regulates the signaling specificity to balance plant growth and immunity.
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Affiliation(s)
- Bodan Su
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xi Zhang
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Li Li
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Sammar Abbas
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Meng Yu
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yaning Cui
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, 53115, Germany
| | - Inhwan Hwang
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China; Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Xiaoyi Shan
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China.
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14
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Flesch J, Bettenhausen M, Kazmierczak M, Klesse WM, Skibitzki O, Psathaki OE, Kurre R, Capellini G, Guha S, Schroeder T, Witzigmann B, You C, Piehler J. Three-Dimensional Interfacing of Cells with Hierarchical Silicon Nano/Microstructures for Midinfrared Interrogation of In Situ Captured Proteins. ACS APPLIED MATERIALS & INTERFACES 2021; 13:8049-8059. [PMID: 33570931 DOI: 10.1021/acsami.0c22421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Label-free optical detection of biomolecules is currently limited by a lack of specificity rather than sensitivity. To exploit the much more characteristic refractive index dispersion in the mid-infrared (IR) regime, we have engineered three-dimensional IR-resonant silicon micropillar arrays (Si-MPAs) for protein sensing. By exploiting the unique hierarchical nano- and microstructured design of these Si-MPAs attained by CMOS-compatible silicon-based microfabrication processes, we achieved an optimized interrogation of surface protein binding. Based on spatially resolved surface functionalization, we demonstrate controlled three-dimensional interfacing of mammalian cells with Si-MPAs. Spatially controlled surface functionalization for site-specific protein immobilization enabled efficient targeting of soluble and membrane proteins into sensing hotspots directly from cells cultured on Si-MPAs. Protein binding to Si-MPA hotspots at submonolayer level was unambiguously detected by conventional Fourier transform IR spectroscopy. The compatibility with cost-effective CMOS-based microfabrication techniques readily allows integration of this novel IR transducer into fully fledged bioanalytical microdevices for selective and sensitive protein sensing.
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Affiliation(s)
- Julia Flesch
- Department of Biology, University of Osnabrück, Osnabrück 49076, Germany
| | - Maximilian Bettenhausen
- Department of Electrical Engineering/Computer Science and CINSaT, University of Kassel, Kassel 34121, Germany
| | - Marcin Kazmierczak
- IHP-Leibniz-Institut für Innovative Mikroelektronik, Frankfurt (Oder) 15236, Germany
| | - Wolfgang M Klesse
- IHP-Leibniz-Institut für Innovative Mikroelektronik, Frankfurt (Oder) 15236, Germany
| | - Oliver Skibitzki
- IHP-Leibniz-Institut für Innovative Mikroelektronik, Frankfurt (Oder) 15236, Germany
| | - Olympia E Psathaki
- Department of Biology, University of Osnabrück, Osnabrück 49076, Germany
- Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück 49076, Germany
| | - Rainer Kurre
- Department of Biology, University of Osnabrück, Osnabrück 49076, Germany
- Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück 49076, Germany
| | - Giovanni Capellini
- IHP-Leibniz-Institut für Innovative Mikroelektronik, Frankfurt (Oder) 15236, Germany
- Dipartimento di Scienze, Università Roma Tre, Roma 00146, Italy
| | - Subhajit Guha
- IHP-Leibniz-Institut für Innovative Mikroelektronik, Frankfurt (Oder) 15236, Germany
| | - Thomas Schroeder
- Leibniz-Institut für Kristallzüchtung (IKZ), Berlin 12489, Germany
| | - Bernd Witzigmann
- Department of Electrical Engineering/Computer Science and CINSaT, University of Kassel, Kassel 34121, Germany
| | - Changjiang You
- Department of Biology, University of Osnabrück, Osnabrück 49076, Germany
- Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück 49076, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Osnabrück 49076, Germany
- Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück 49076, Germany
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15
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mTORC2 Assembly Is Regulated by USP9X-Mediated Deubiquitination of RICTOR. Cell Rep 2020; 33:108564. [PMID: 33378666 DOI: 10.1016/j.celrep.2020.108564] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/14/2020] [Accepted: 12/07/2020] [Indexed: 11/23/2022] Open
Abstract
The mechanistic target of rapamycin complex 2 (mTORC2) controls cell metabolism and survival in response to environmental inputs. Dysregulation of mTORC2 signaling has been linked to diverse human diseases, including cancer and metabolic disorders, highlighting the importance of a tightly controlled mTORC2. While mTORC2 assembly is a critical determinant of its activity, the factors regulating this event are not well understood, and it is unclear whether this process is regulated by growth factors. Here, we present data, from human cell lines and mice, describing a mechanism by which growth factors regulate ubiquitin-specific protease 9X (USP9X) deubiquitinase to stimulate mTORC2 assembly and activity. USP9X removes Lys63-linked ubiquitin from RICTOR to promote its interaction with mTOR, thereby facilitating mTORC2 signaling. As mTORC2 is central for cellular homeostasis, understanding the mechanisms regulating mTORC2 activation toward its downstream targets is vital for our understanding of physiological processes and for developing new therapeutic strategies in pathology.
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16
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Unraveling the multifaceted nature of the nuclear function of mTOR. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118907. [PMID: 33189783 DOI: 10.1016/j.bbamcr.2020.118907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/02/2020] [Accepted: 11/08/2020] [Indexed: 01/25/2023]
Abstract
Positioned at the axis between the cell and its environment, mTOR directs a wide range of cellular activity in response to nutrients, growth factors, and stress. Our understanding of the role of mTOR is evolving beyond the spatial confines of the cytosol, and its role in the nucleus becoming ever more apparent. In this review, we will address various studies that explore the role of nuclear mTOR (nmTOR) in specific cellular programs and how these pathways influence one another. To understand the emerging roles of nuclear mTOR, we discuss data and propose plausible mechanisms to offer novel ideas, hypotheses, and future research directions.
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17
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Teh AH, Yeap KH, Hisano T. Insights into DEPTOR regulation from in silico analysis of DEPTOR complexes. J Struct Biol 2020; 212:107602. [PMID: 32798656 DOI: 10.1016/j.jsb.2020.107602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/21/2020] [Accepted: 08/11/2020] [Indexed: 01/25/2023]
Abstract
DEPTOR is an inhibitor of the mTOR kinase which controls cell growth. DEPTOR consists of two DEP domains and a PDZ domain connected by an unstructured linker, and its stability is tightly regulated through post-translational modifications of its linker region that contains the 286SSGYFS291 degron. Based on the mTORC1 complex, our modelling suggests a possible spatial arrangement of DEPTOR which is characterised to form a dimer. Our model shows that the two PDZ domains of a DEPTOR dimer bind separately to the dimeric mTOR's FAT domains ~130 Å apart, while each of the two extended linkers is sufficiently long to span from the FAT domain to the kinase domain of mTOR and beyond to join a shared dimer of the DEP domains. This places the linker's S299 closest to the kinase's catalytic site, indicating that phosphorylation would start with it and successively upstream towards DEPTOR's degron. The CK1α kinase is reportedly responsible for the phosphorylation of the degron, and our docking analysis further reveals that CK1α contains sites to bind DEPTOR's pS286, pS287 and pT295, which may act as priming phosphates for the phosphorylation of the degron's S291. DEPTOR's linker can also be ubiquitylated by the UbcH5A-SCFβ-TrCP complex without its PDZ dissociating from mTOR according to the modelling. As the catalytic cleft of mTOR's kinase is restricted, interactions between the kinase's unstructured segment surrounding the cleft and DEPTOR's linker, which may involve S293 and S299, may be critical to controlling DEPTOR's access to the catalytic cleft and hence its phosphorylation by mTOR in a manner dependent on mTOR's activation.
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Affiliation(s)
- Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Penang, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, 11800 Penang, Malaysia.
| | - Kean-Heng Yeap
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Penang, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Tamao Hisano
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, 11800 Penang, Malaysia; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
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18
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Tran T, Mitra J, Ha T, Kavran JM. Increasing kinase domain proximity promotes MST2 autophosphorylation during Hippo signaling. J Biol Chem 2020; 295:16166-16179. [PMID: 32994222 DOI: 10.1074/jbc.ra120.015723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/22/2020] [Indexed: 01/20/2023] Open
Abstract
The Hippo pathway plays an important role in developmental biology, mediating organ size by controlling cell proliferation through the activity of a core kinase cassette. Multiple upstream events activate the pathway, but how each controls this core kinase cassette is not fully understood. Activation of the core kinase cassette begins with phosphorylation of the kinase MST1/2 (also known as STK3/4). Here, using a combination of in vitro biochemistry and cell-based assays, including chemically induced dimerization and single-molecule pulldown, we revealed that increasing the proximity of adjacent kinase domains, rather than formation of a specific protein assembly, is sufficient to trigger autophosphorylation. We validate this mechanism in cells and demonstrate that multiple events associated with the active pathway, including SARAH domain-mediated homodimerization, membrane recruitment, and complex formation with the effector protein SAV1, each increase the kinase domain proximity and autophosphorylation of MST2. Together, our results reveal that multiple and distinct upstream signals each utilize the same common molecular mechanism to stimulate MST2 autophosphorylation. This mechanism is likely conserved among MST2 homologs. Our work also highlights potential differences in Hippo signal propagation between each activating event owing to differences in the dynamics and regulation of each protein ensemble that triggers MST2 autophosphorylation and possible redundancy in activation.
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Affiliation(s)
- Thao Tran
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jaba Mitra
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA; T. C. Jenkins Department of Biophysics, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA; Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Jennifer M Kavran
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.
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19
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Chadha R, Meador-Woodruff JH. Downregulated AKT-mTOR signaling pathway proteins in dorsolateral prefrontal cortex in Schizophrenia. Neuropsychopharmacology 2020; 45:1059-1067. [PMID: 31952070 PMCID: PMC7162985 DOI: 10.1038/s41386-020-0614-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 11/09/2022]
Abstract
Abnormal neurotransmission is central to schizophrenia (SZ). Alterations across multiple neurotransmitter systems in SZ suggest that this illness may be associated with dysregulation of core intracellular processes such as signaling pathways that underlie the regulation and integration of these systems. The AKT-mTOR signaling cascade has been implicated in SZ by gene association, postmortem brain and animal studies. AKT and mTOR are serine/threonine kinases which play important roles in cell growth, proliferation, survival, and differentiation. Both AKT and mTOR require phosphorylation at specific sites for their complete activation. mTOR forms two functionally distinct multiprotein complexes, mTOR Complex 1 (mTORC1) and Complex 2 (mTORC2). mTORC1 mediates ribosome biogenesis, protein translation, and autophagy, whereas mTORC2 contributes to actin dynamics. Altered protein synthesis and actin dynamics can lead to an abnormal neuronal morphology resulting in deficits in learning and memory. Currently, there is a lack of direct evidence to support the hypothesis of disrupted mTOR signaling in SZ, and we have addressed this by characterizing this signaling pathway in SZ brain. We found a reduction in AKT and mTOR protein expression and/or phosphorylation state in dorsolateral prefrontal cortex (DLPFC) from 22 pairs of SZ and matched comparison subjects. We also found reduced protein expression of GβL, a subunit protein common to both mTOR complexes. We further investigated mTOR complex-specific subunit composition and phosphorylation state, and found abnormal mTOR expression in both complexes in SZ DLPFC. These findings provide evidence that proteins associated with the AKT-mTOR signaling cascade are downregulated in SZ DLPFC.
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Affiliation(s)
- Radhika Chadha
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, 1719 6th Avenue South, Birmingham, AL, 35294-0021, USA.
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, 1719 6th Avenue South, Birmingham, AL, 35294-0021, USA
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20
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Chen C, Ulbrich MH. Zinc-Finger-Mediated Labeling Reveals the Stoichiometry of Membrane Proteins. ACS NANO 2020; 14:4134-4140. [PMID: 32208669 DOI: 10.1021/acsnano.9b08865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Characterizing interactions of proteins is pivotal for understanding their function. Recently, single-molecule imaging-based methods have proven useful for directly testing the stoichiometry of multi-subunit protein complexes. A limiting factor is the labeling of proteins with multiple spectrally discernible tags and low background. Here, we describe the use of zinc-finger (ZF)-mediated protein labeling for single-molecule imaging studies in living cells. A DNA-binding ZF is fused to the protein of interest and labeled by a DNA probe carrying the specific ZF binding sequence and an organic dye. Nonspecific binding is minimized by injecting the DNA/dye conjugate into the cell. With a reproducible labeling efficiency of 20%, we developed an approach to deduce the multiplicity of the subunits in a protein complex from the overall degree of labeling. We were able to confirm the fixed 2:2 assembly of the NMDA receptor in a three-color single-molecule imaging setup and reject alternative stoichiometries. Due to the modular design and small size of ZF proteins, this approach will allow the analysis of more complicated protein interaction patterns to understand the assembly rules for large protein complexes.
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Affiliation(s)
- Changsheng Chen
- School of Life Sciences, Co-innovation Center of Neuroregeneration, Key Laboratory of Neurogeneration of Jiangsu and MOE, Nantong University, 226019 Jiangsu, China
- Internal Medicine IV, Department of Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Maximilian H Ulbrich
- Internal Medicine IV, Department of Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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21
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Cairns L, Patterson A, Weingartner KA, Koehler TJ, DeAngelis DR, Tripp KW, Bothner B, Kavran JM. Biophysical characterization of SARAH domain-mediated multimerization of Hippo pathway complexes in Drosophila. J Biol Chem 2020; 295:6202-6213. [PMID: 32213597 DOI: 10.1074/jbc.ra120.012679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/23/2020] [Indexed: 11/06/2022] Open
Abstract
Hippo pathway signaling limits cell growth and proliferation and maintains the stem-cell niche. These cellular events result from the coordinated activity of a core kinase cassette that is regulated, in part, by interactions involving Hippo, Salvador, and dRassF. These interactions are mediated by a conserved coiled-coil domain, termed SARAH, in each of these proteins. SARAH domain-mediated homodimerization of Hippo kinase leads to autophosphorylation and activation. Paradoxically, SARAH domain-mediated heterodimerization between Hippo and Salvador enhances Hippo kinase activity in cells, whereas complex formation with dRassF inhibits it. To better understand the mechanism by which each complex distinctly modulates Hippo kinase and pathway activity, here we biophysically characterized the entire suite of SARAH domain-mediated complexes. We purified the three SARAH domains from Drosophila melanogaster and performed an unbiased pulldown assay to identify all possible interactions, revealing that isolated SARAH domains are sufficient to recapitulate the cellular assemblies and that Hippo is a universal binding partner. Additionally, we found that the Salvador SARAH domain homodimerizes and demonstrate that this interaction is conserved in Salvador's mammalian homolog. Using native MS, we show that each of these complexes is dimeric in solution. We also measured the stability of each SARAH domain complex, finding that despite similarities at both the sequence and structural levels, SARAH domain complexes differ in stability. The identity, stoichiometry, and stability of these interactions characterized here comprehensively reveal the nature of SARAH domain-mediated complex formation and provide mechanistic insights into how SARAH domain-mediated interactions influence Hippo pathway activity.
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Affiliation(s)
- Leah Cairns
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, 59717
| | - Kyler A Weingartner
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215
| | - T J Koehler
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215
| | - Daniel R DeAngelis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215
| | - Katherine W Tripp
- The T. C. Jenkins Department of Biophysics, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland, 201218
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, 59717
| | - Jennifer M Kavran
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 20215; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 20215; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, 20215.
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22
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Sanders SS, De Simone FI, Thomas GM. mTORC1 Signaling Is Palmitoylation-Dependent in Hippocampal Neurons and Non-neuronal Cells and Involves Dynamic Palmitoylation of LAMTOR1 and mTOR. Front Cell Neurosci 2019; 13:115. [PMID: 31001086 PMCID: PMC6454084 DOI: 10.3389/fncel.2019.00115] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/08/2019] [Indexed: 11/13/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) Complex 1 (mTORC1) controls growth and proliferation of non-neuronal cells, while during neuronal development mTORC1 responds to glutamate and neurotrophins to promote neuronal migration and dendritic arborization. Recent studies reveal that mTORC1 signaling complexes are assembled on lysosomal membranes, but how mTORC1 membrane targeting is regulated is not fully clear. Our examination of palmitoyl-proteomic databases and additional bioinformatic analyses revealed that several mTORC1 proteins are predicted to undergo covalent modification with the lipid palmitate. This process, palmitoylation, can dynamically target proteins to specific membranes but its roles in mTORC1 signaling are not well described. Strikingly, we found that acute pharmacological inhibition of palmitoylation prevents amino acid-dependent mTORC1 activation in HEK293T cells and brain-derived neurotrophic factor (BDNF)-dependent mTORC1 activation in hippocampal neurons. We sought to define the molecular basis for this finding and found that the mTORC1 proteins LAMTOR1 and mTOR itself are directly palmitoylated, while several other mTORC1 proteins are not palmitoylated, despite strong bioinformatic prediction. Interestingly, palmitoylation of LAMTOR1, whose anchoring on lysosomal membranes is important for mTORC1 signaling, was rapidly increased prior to mTORC1 activation. In contrast, mTOR palmitoylation was decreased by stimuli that activate mTORC1. These findings reveal that specific key components of the mTOR pathway are dynamically palmitoylated, suggesting that palmitoylation is not merely permissive for mTOR activation but is instead actively involved in mTORC1-dependent signaling.
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Affiliation(s)
- Shaun S Sanders
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Francesca I De Simone
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Gareth M Thomas
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States.,Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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23
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Croop B, Han KY. Facile single-molecule pull-down assay for analysis of endogenous proteins. Phys Biol 2019; 16:035002. [PMID: 30769341 DOI: 10.1088/1478-3975/ab0792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The single-molecule pull-down (SiMPull) assay analyzes molecular complexes in physiological conditions from cell or tissue lysates. Currently the approach requires a lengthy sample preparation process, which has largely prevented the widespread adoption of this technique in bioanalysis. Here, we present a simplified SiMPull assay based upon dichlorodimethylsilane-Tween-20 passivation and F(ab) fragment labeling. Our passivation is a much shorter process than the standard polyethylene glycol passivation used in most single-molecule studies. The use of F(ab) fragments for indirect fluorescent labeling rather than divalent F(ab')2 or whole IgG antibodies allows for the pre-incubation of the detection antibodies, reducing the sample preparation time for single-molecule immunoprecipitation samples. We examine the applicability of our approach to recombinant proteins and endogenous proteins from mammalian cell lysates.
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Affiliation(s)
- Benjamin Croop
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, United States of America
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24
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Ahmed AR, Owens RJ, Stubbs CD, Parker AW, Hitchman R, Yadav RB, Dumoux M, Hawes C, Botchway SW. Direct imaging of the recruitment and phosphorylation of S6K1 in the mTORC1 pathway in living cells. Sci Rep 2019; 9:3408. [PMID: 30833605 PMCID: PMC6399282 DOI: 10.1038/s41598-019-39410-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
Knowledge of protein signalling pathways in the working cell is seen as a primary route to identifying and developing targeted medicines. In recent years there has been a growing awareness of the importance of the mTOR pathway, making it an attractive target for therapeutic intervention in several diseases. Within this pathway we have focused on S6 kinase 1 (S6K1), the downstream phosphorylation substrate of mTORC1, and specifically identify its juxtaposition with mTORC1. When S6K1 is co-expressed with raptor we show that S6K1 is translocated from the nucleus to the cytoplasm. By developing a novel biosensor we demonstrate in real-time, that phosphorylation and de-phosphorylation of S6K1 occurs mainly in the cytoplasm of living cells. Furthermore, we show that the scaffold protein raptor, that typically recruits mTOR substrates, is not always involved in S6K1 phosphorylation. Overall, we demonstrate how FRET-FLIM imaging technology can be used to show localisation of S6K1 phosphorylation in living cells and hence a key site of action of inhibitors targeting mTOR phosphorylation.
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Affiliation(s)
- Abdullah R Ahmed
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0FA, UK
| | - Raymond J Owens
- Protein Production UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0FA, UK.,The Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Christopher D Stubbs
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0FA, UK
| | - Anthony W Parker
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0FA, UK
| | - Richard Hitchman
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Rahul B Yadav
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Maud Dumoux
- Protein Production UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0FA, UK.,Diamond Light Source, Harwell Campus, Didcot, OX11 0DE, UK
| | - Chris Hawes
- Oxford Brookes University, Headington Campus, Oxford, OX3 0BP, UK
| | - Stanley W Botchway
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0FA, UK.
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25
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Croop B, Zhang C, Lim Y, Gelfand RM, Han KY. Recent advancement of light-based single-molecule approaches for studying biomolecules. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1445. [PMID: 30724484 DOI: 10.1002/wsbm.1445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/01/2018] [Accepted: 01/08/2019] [Indexed: 12/27/2022]
Abstract
Recent advances in single-molecule techniques have led to new discoveries in analytical chemistry, biophysics, and medicine. Understanding the structure and behavior of single biomolecules provides a wealth of information compared to studying large ensembles. However, developing single-molecule techniques is challenging and requires advances in optics, engineering, biology, and chemistry. In this paper, we will review the state of the art in single-molecule applications with a focus over the last few years of development. The advancements covered will mainly include light-based in vitro methods, and we will discuss the fundamentals of each with a focus on the platforms themselves. We will also summarize their limitations and current and future applications to the wider biological and chemical fields. This article is categorized under: Laboratory Methods and Technologies > Imaging Laboratory Methods and Technologies > Macromolecular Interactions, Methods Analytical and Computational Methods > Analytical Methods.
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Affiliation(s)
- Benjamin Croop
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Chenyi Zhang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Youngbin Lim
- Department of Bioengineering, Stanford University, Stanford, California
| | - Ryan M Gelfand
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
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26
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Goodman CA. Role of mTORC1 in mechanically induced increases in translation and skeletal muscle mass. J Appl Physiol (1985) 2019; 127:581-590. [PMID: 30676865 DOI: 10.1152/japplphysiol.01011.2018] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Skeletal muscle mass is, in part, regulated by the rate of mRNA translation (i.e., protein synthesis). The conserved serine/threonine kinase, mTOR (the mammalian/mechanistic target of rapamycin), found in the multiprotein complex, mTOR complex 1 (mTORC1), is a major positive regulator of protein synthesis. The purpose of this review is to describe some of the critical steps in translation initiation, mTORC1 and its potential direct and indirect roles in regulating translation, and evidence that mTORC1 regulates protein synthesis and muscle mass, with a particular focus on basal conditions and the response to mechanical stimuli. Current evidence suggests that for acute contraction models of mechanical stimuli, there is an emerging pattern suggesting that there is an early increase in protein synthesis governed by a rapamycin-sensitive mTORC1-dependent mechanism, while at later poststimulation time points, the mechanism may change to a rapamycin-insensitive mTORC1-dependent or even an mTORC1-independent mechanism. Furthermore, evidence suggests that mTORC1 appears to be absolutely necessary for muscle fiber hypertrophy induced by chronic mechanical loading but may only play a partial role in the hypertrophy induced by more intermittent types of acute resistance exercise, with the possibility of mTORC1-independent mechanisms also playing a role. Despite the progress that has been made, many questions about the activation of mTORC1, and its downstream targets, remain to be answered. Further research will hopefully provide novel insights into the regulation of skeletal muscle mTORC1 that may eventually be translated into novel exercise programing and/or targeted pharmacological therapies aimed at preventing muscle wasting and/or increasing muscle mass.
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Affiliation(s)
- Craig A Goodman
- Institute of Health and Sport; Victoria University, Melbourne, Australia.,Australian Institute for Musculoskeletal Science (AIMSS), Victoria University, St. Albans, Victoria, Australia
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27
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Identification and targeting of novel CDK9 complexes in acute myeloid leukemia. Blood 2018; 133:1171-1185. [PMID: 30587525 DOI: 10.1182/blood-2018-08-870089] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/07/2018] [Indexed: 01/09/2023] Open
Abstract
Aberrant activation of mTOR signaling in acute myeloid leukemia (AML) results in a survival advantage that promotes the malignant phenotype. To improve our understanding of factors that contribute to mammalian target of rapamycin (mTOR) signaling activation and identify novel therapeutic targets, we searched for unique interactors of mTOR complexes through proteomics analyses. We identify cyclin dependent kinase 9 (CDK9) as a novel binding partner of the mTOR complex scaffold protein, mLST8. Our studies demonstrate that CDK9 is present in distinct mTOR-like (CTOR) complexes in the cytoplasm and nucleus. In the nucleus, CDK9 binds to RAPTOR and mLST8, forming CTORC1, to promote transcription of genes important for leukemogenesis. In the cytoplasm, CDK9 binds to RICTOR, SIN1, and mLST8, forming CTORC2, and controls messenger RNA (mRNA) translation through phosphorylation of LARP1 and rpS6. Pharmacological targeting of CTORC complexes results in suppression of growth of primitive human AML progenitors in vitro and elicits strong antileukemic responses in AML xenografts in vivo.
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28
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Abstract
G protein-coupled receptors (GPCRs) transduce pleiotropic intracellular signals in a broad range of physiological responses and disease states. Activated GPCRs can undergo agonist-induced phosphorylation by G protein receptor kinases (GRKs) and second messenger-dependent protein kinases such as protein kinase A (PKA). Here, we characterize spatially segregated subpopulations of β2-adrenergic receptor (β2AR) undergoing selective phosphorylation by GRKs or PKA in a single cell. GRKs primarily label monomeric β2ARs that undergo endocytosis, whereas PKA modifies dimeric β2ARs that remain at the cell surface. In hippocampal neurons, PKA-phosphorylated β2ARs are enriched in dendrites, whereas GRK-phosphorylated β2ARs accumulate in soma, being excluded from dendrites in a neuron maturation-dependent manner. Moreover, we show that PKA-phosphorylated β2ARs are necessary to augment the activity of L-type calcium channel. Collectively, these findings provide evidence that functionally distinct subpopulations of this prototypical GPCR exist in a single cell. β2-adrenergic receptor (β2AR) can be phosphorylated by G protein receptor kinases and second messenger-dependent kinases. Here, the authors demonstrate that these phosphorylation events are specific to functionally distinct and spatially segregated subpopulations of β2AR that co-exist in a single cell.
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29
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Je G, Croop B, Basu S, Tang J, Han KY, Kim YS. Endogenous Alpha-Synuclein Protein Analysis from Human Brain Tissues Using Single-Molecule Pull-Down Assay. Anal Chem 2017; 89:13044-13048. [PMID: 29172450 DOI: 10.1021/acs.analchem.7b04335] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Alpha-synuclein (α-SYN) is a central molecule in Parkinson's disease pathogenesis. Despite several studies, the molecular nature of endogenous α-SYN especially in human brain samples is still not well understood due to the lack of reliable methods and the limited amount of biospecimens. Here, we introduce α-SYN single-molecule pull-down (α-SYN SiMPull) assay combined with in vivo protein crosslinking to count individual α-SYN protein and assess its native oligomerization states from biological samples including human postmortem brains. This powerful single-molecule assay can be highly useful in diagnostic applications using various specimens for neurodegenerative diseases including Alzheimer's disease and Parkinson's disease.
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Affiliation(s)
- Goun Je
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
| | - Benjamin Croop
- CREOL, The College of Optics and Photonics, University of Central Florida , Orlando Florida 32816, United States
| | - Sambuddha Basu
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
| | - Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida , Orlando Florida 32816, United States
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida , Orlando Florida 32816, United States
| | - Yoon-Seong Kim
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
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30
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The Role of Mammalian Target of Rapamycin (mTOR) in Insulin Signaling. Nutrients 2017; 9:nu9111176. [PMID: 29077002 PMCID: PMC5707648 DOI: 10.3390/nu9111176] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 12/15/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) is a serine/threonine kinase that controls a wide spectrum of cellular processes, including cell growth, differentiation, and metabolism. mTOR forms two distinct multiprotein complexes known as mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), which are characterized by the presence of raptor and rictor, respectively. mTOR controls insulin signaling by regulating several downstream components such as growth factor receptor-bound protein 10 (Grb10), insulin receptor substrate (IRS-1), F-box/WD repeat-containing protein 8 (Fbw8), and insulin like growth factor 1 receptor/insulin receptor (IGF-IR/IR). In addition, mTORC1 and mTORC2 regulate each other through a feedback loop to control cell growth. This review outlines the current understanding of mTOR regulation in insulin signaling in the context of whole body metabolism.
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31
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Mihailovic MK, Chen A, Gonzalez-Rivera JC, Contreras LM. Defective Ribonucleoproteins, Mistakes in RNA Processing, and Diseases. Biochemistry 2017; 56:1367-1382. [PMID: 28206738 DOI: 10.1021/acs.biochem.6b01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribonucleoproteins (RNPs) are vital to many cellular events. To this end, many neurodegenerative diseases and cancers have been linked to RNP malfunction, particularly as this relates to defective processing of cellular RNA. The connection of RNPs and diseases has also propagated a shift of focus onto RNA targeting from traditional protein targeting treatments. However, therapeutic development in this area has been limited by incomplete molecular insight into the specific contributions of RNPs to disease. This review outlines the role of several RNPs in diseases, focusing on molecular defects in processes that affect proper RNA handling in the cell. This work also evaluates the contributions of recently developed methods to understanding RNP association and function. We review progress in this area by focusing on molecular malfunctions of RNPs associated with the onset and progression of several neurodegenerative diseases and cancer and conclude with a brief discussion of RNA-based therapeutic efforts.
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Affiliation(s)
- Mia K Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Juan C Gonzalez-Rivera
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
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32
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Single-molecule fluorescence microscopy of native macromolecular complexes. Curr Opin Struct Biol 2016; 41:225-232. [PMID: 27662375 DOI: 10.1016/j.sbi.2016.09.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 12/11/2022]
Abstract
Macromolecular complexes consisting of proteins, lipids, and/or nucleic acids are ubiquitous in biological processes. Their composition, stoichiometry, order of assembly, and conformations can be heterogeneous or can change dynamically, making single-molecule studies best suited to measure these properties accurately. Recent single-molecule pull-down and other related approaches have combined the principles of conventional co-immunoprecipitation assay with single-molecule fluorescence microscopy to probe native macromolecular complexes. In this review, we present the advances in single-molecule pull-down methods and biological systems that have been investigated in such semi vivo manner.
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33
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Husbands AY, Aggarwal V, Ha T, Timmermans MCP. In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes. THE PLANT CELL 2016; 28:1783-94. [PMID: 27385814 PMCID: PMC5006705 DOI: 10.1105/tpc.16.00289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/03/2016] [Indexed: 05/12/2023]
Abstract
Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies.
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Affiliation(s)
- Aman Y Husbands
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Vasudha Aggarwal
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205 Howard Hughes Medical Institute, Baltimore, Maryland 21205
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
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34
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Choi S, Kim H, Kim SY, Yang EG. Probing protein complexes inside living cells using a silicon nanowire-based pull-down assay. NANOSCALE 2016; 8:11380-11384. [PMID: 27198202 DOI: 10.1039/c6nr00171h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Most proteins perform their functions as interacting complexes. Here we propose a novel method for capturing an intracellular protein and its interacting partner out of living cells by utilizing intracellular access of antibody modified vertical silicon nanowire arrays whose surface is covered with a polyethylene glycol layer to prevent strong cell adhesion. Such a feature facilitates the removal of cells by simple washing, enabling subsequent detection of a pulled-down protein and its interacting partner, and further assessment of a drug-induced change in the interacting complex. Our new SiNW-based tool is thus suitable for authentication of protein networks inside living cells.
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Affiliation(s)
- Sojoong Choi
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Hyunju Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - So Yeon Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Department of Biomedical Engineering, Korea University of Science and Technology (UST), KIST campus, Seoul 02792, Republic of Korea
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Department of Biological Chemistry, Korea University of Science and Technology (UST), KIST campus, Seoul 02792, Republic of Korea
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35
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Fareh M, Loeff L, Szczepaniak M, Haagsma AC, Yeom KH, Joo C. Single-molecule pull-down for investigating protein-nucleic acid interactions. Methods 2016; 105:99-108. [PMID: 27017911 DOI: 10.1016/j.ymeth.2016.03.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/26/2016] [Accepted: 03/24/2016] [Indexed: 12/30/2022] Open
Abstract
The genome and transcriptome are constantly modified by proteins in the cell. Recent advances in single-molecule techniques allow for high spatial and temporal observations of these interactions between proteins and nucleic acids. However, due to the difficulty of obtaining functional protein complexes, it remains challenging to study the interactions between macromolecular protein complexes and nucleic acids. Here, we combined single-molecule fluorescence with various protein complex pull-down techniques to determine the function and stoichiometry of ribonucleoprotein complexes. Through the use of three examples of protein complexes from eukaryotic cells (Drosha, Dicer, and TUT4 protein complexes), we provide step-by-step guidance for using novel single-molecule techniques. Our single-molecule methods provide sub-second and nanometer resolution and can be applied to other nucleoprotein complexes that are essential for cellular processes.
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Affiliation(s)
- Mohamed Fareh
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Luuk Loeff
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Malwina Szczepaniak
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Anna C Haagsma
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Kyu-Hyeon Yeom
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands.
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36
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Kim K, Qiang L, Hayden MS, Sparling DP, Purcell NH, Pajvani UB. mTORC1-independent Raptor prevents hepatic steatosis by stabilizing PHLPP2. Nat Commun 2016; 7:10255. [PMID: 26743335 PMCID: PMC4729872 DOI: 10.1038/ncomms10255] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/23/2015] [Indexed: 01/08/2023] Open
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1), defined by the presence of Raptor, is an evolutionarily conserved and nutrient-sensitive regulator of cellular growth and other metabolic processes. To date, all known functions of Raptor involve its scaffolding mTOR kinase with substrate. Here we report that mTORC1-independent ('free') Raptor negatively regulates hepatic Akt activity and lipogenesis. Free Raptor levels in liver decline with age and in obesity; restoration of free Raptor levels reduces liver triglyceride content, through reduced β-TrCP-mediated degradation of the Akt phosphatase, PHLPP2. Commensurately, forced PHLPP2 expression ameliorates hepatic steatosis in diet-induced obese mice. These data suggest that the balance of free and mTORC1-associated Raptor governs hepatic lipid accumulation, and uncover the potentially therapeutic role of PHLPP2 activators in non-alcoholic fatty liver disease.
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Affiliation(s)
- KyeongJin Kim
- Department of Medicine, Columbia University, New York, New York 10032, USA
| | - Li Qiang
- Department of Medicine, Columbia University, New York, New York 10032, USA
| | - Matthew S Hayden
- Department of Dermatology, Columbia University, New York, New York 10032, USA.,Department of Microbiology &Immunology, Columbia University, New York, New York 10032, USA
| | - David P Sparling
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Nicole H Purcell
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA
| | - Utpal B Pajvani
- Department of Medicine, Columbia University, New York, New York 10032, USA
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37
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Pinto A, Mace Y, Drouet F, Bony E, Boidot R, Draoui N, Lobysheva I, Corbet C, Polet F, Martherus R, Deraedt Q, Rodríguez J, Lamy C, Schicke O, Delvaux D, Louis C, Kiss R, Kriegsheim AV, Dessy C, Elias B, Quetin-Leclercq J, Riant O, Feron O. A new ER-specific photosensitizer unravels (1)O2-driven protein oxidation and inhibition of deubiquitinases as a generic mechanism for cancer PDT. Oncogene 2015; 35:3976-85. [PMID: 26686091 DOI: 10.1038/onc.2015.474] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 10/29/2015] [Accepted: 11/17/2015] [Indexed: 12/19/2022]
Abstract
Photosensitizers (PS) are ideally devoid of any activity in the absence of photoactivation, and rely on molecular oxygen for the formation of singlet oxygen ((1)O2) to produce cellular damage. Off-targets and tumor hypoxia therefore represent obstacles for the use of PS for cancer photodynamic therapy. Herein, we describe the characterization of OR141, a benzophenazine compound identified through a phenotypic screening for its capacity to be strictly activated by light and to kill a large variety of tumor cells under both normoxia and hypoxia. This new class of PS unraveled an unsuspected common mechanism of action for PS that involves the combined inhibition of the mammalian target of rapamycin (mTOR) signaling pathway and proteasomal deubiquitinases (DUBs) USP14 and UCH37. Oxidation of mTOR and other endoplasmic reticulum (ER)-associated proteins drives the early formation of high molecular weight (MW) complexes of multimeric proteins, the concomitant blockade of DUBs preventing their degradation and precipitating cell death. Furthermore, we validated the antitumor effects of OR141 in vivo and documented its highly selective accumulation in the ER, further increasing the ER stress resulting from (1)O2 generation upon light activation.
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Affiliation(s)
- A Pinto
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - Y Mace
- Institute of Condensed Matter and Nanosciences Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - F Drouet
- Institute of Condensed Matter and Nanosciences Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - E Bony
- Pharmacognosy Research Group (GNOS), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - R Boidot
- Institute of Condensed Matter and Nanosciences Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - N Draoui
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - I Lobysheva
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - C Corbet
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - F Polet
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - R Martherus
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - Q Deraedt
- Institute of Condensed Matter and Nanosciences Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - J Rodríguez
- Systems Biology Ireland, Conway Institute, Belfield, Dublin 4, Ireland
| | - C Lamy
- Institute of Condensed Matter and Nanosciences Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - O Schicke
- Institute of Condensed Matter and Nanosciences Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - D Delvaux
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - C Louis
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - R Kiss
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - A V Kriegsheim
- Systems Biology Ireland, Conway Institute, Belfield, Dublin 4, Ireland
| | - C Dessy
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
| | - B Elias
- Institute of Condensed Matter and Nanosciences Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - J Quetin-Leclercq
- Pharmacognosy Research Group (GNOS), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - O Riant
- Institute of Condensed Matter and Nanosciences Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - O Feron
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, Brussels, Belgium
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38
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Liko D, Hall MN. mTOR in health and in sickness. J Mol Med (Berl) 2015; 93:1061-73. [DOI: 10.1007/s00109-015-1326-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/14/2015] [Accepted: 07/22/2015] [Indexed: 01/12/2023]
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39
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Liu P, Gan W, Chin YR, Ogura K, Guo J, Zhang J, Wang B, Blenis J, Cantley LC, Toker A, Su B, Wei W. PtdIns(3,4,5)P3-Dependent Activation of the mTORC2 Kinase Complex. Cancer Discov 2015; 5:1194-209. [PMID: 26293922 DOI: 10.1158/2159-8290.cd-15-0460] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 08/18/2015] [Indexed: 12/15/2022]
Abstract
UNLABELLED mTOR serves as a central regulator of cell growth and metabolism by forming two distinct complexes, mTORC1 and mTORC2. Although mechanisms of mTORC1 activation by growth factors and amino acids have been extensively studied, the upstream regulatory mechanisms leading to mTORC2 activation remain largely elusive. Here, we report that the pleckstrin homology (PH) domain of SIN1, an essential and unique component of mTORC2, interacts with the mTOR kinase domain to suppress mTOR activity. More importantly, PtdIns(3,4,5)P3, but not other PtdInsPn species, interacts with SIN1-PH to release its inhibition on the mTOR kinase domain, thereby triggering mTORC2 activation. Mutating critical SIN1 residues that mediate PtdIns(3,4,5)P3 interaction inactivates mTORC2, whereas mTORC2 activity is pathologically increased by patient-derived mutations in the SIN1-PH domain, promoting cell growth and tumor formation. Together, our study unravels a PI3K-dependent mechanism for mTORC2 activation, allowing mTORC2 to activate AKT in a manner that is regulated temporally and spatially by PtdIns(3,4,5)P3. SIGNIFICANCE The SIN1-PH domain interacts with the mTOR kinase domain to suppress mTOR activity, and PtdIns(3,4,5)P3 binds the SIN1-PH domain to release its inhibition on the mTOR kinase domain, leading to mTORC2 activation. Cancer patient-derived SIN1-PH domain mutations gain oncogenicity by loss of suppressing mTOR activity as a means to facilitate tumorigenesis.
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Affiliation(s)
- Pengda Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Wenjian Gan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Y Rebecca Chin
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Kohei Ogura
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Bin Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - John Blenis
- Cancer Center at Weill Cornell Medical College and New York-Presbyterian Hospital, New York, New York
| | - Lewis C Cantley
- Cancer Center at Weill Cornell Medical College and New York-Presbyterian Hospital, New York, New York
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Bing Su
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China. Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University, New Haven, Connecticut.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
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40
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Zhou P, Zhang N, Nussinov R, Ma B. Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. J Comput Biol 2015; 22:876-86. [PMID: 26176550 DOI: 10.1089/cmb.2015.0103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mammalian target of rapamycin (mTOR) complexes play a pivotal role in the cell. Raptor and Rictor proteins interact with mTOR to form two distinct complexes, mTORC1 and mTORC2, respectively. While the domain structure of Raptor is known, current bioinformatics tools failed to classify the domains in Rictor. Here we focus on identifying specific domains in Rictor by searching for conserved regions. We scanned the pdb structural database and constructed three protein domain datasets. Next we carried out multiple pairwise sequence alignments of the proteins in the domain dataset. By analyzing the z-scores of Rictor sequence similarity to protein sequences in the dataset, we assigned the structural and functional domains of Rictor. We found that, like Raptor, Rictor also has HEAT and WD40 domains, which could be the common motif binding to mTORC. Rictor may also have pleckstrin homology domains, which mediate cellular localization and transmit signals to downstream targets, as well as a domain that is homologous to 50S protein L17 and human 39S protein L17. This putative ribosome binding domain could mediate mTORC2-ribosome interaction.
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Affiliation(s)
- Ping Zhou
- 1 Research Center of Basic Medical Sciences and Cancer Institute and Hospital, Tianjin Medical University , Tianjin, China
| | - Ning Zhang
- 1 Research Center of Basic Medical Sciences and Cancer Institute and Hospital, Tianjin Medical University , Tianjin, China
| | - Ruth Nussinov
- 2 Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute , Frederick, Maryland.,3 Department of Human Genetics and Molecular Medicine, Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University , Tel Aviv, Israel
| | - Buyong Ma
- 2 Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute , Frederick, Maryland
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41
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Gaubitz C, Oliveira TM, Prouteau M, Leitner A, Karuppasamy M, Konstantinidou G, Rispal D, Eltschinger S, Robinson GC, Thore S, Aebersold R, Schaffitzel C, Loewith R. Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2. Mol Cell 2015; 58:977-88. [PMID: 26028537 DOI: 10.1016/j.molcel.2015.04.031] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 03/31/2015] [Accepted: 04/22/2015] [Indexed: 10/23/2022]
Abstract
Target of Rapamycin (TOR) plays central roles in the regulation of eukaryote growth as the hub of two essential multiprotein complexes: TORC1, which is rapamycin-sensitive, and the lesser characterized TORC2, which is not. TORC2 is a key regulator of lipid biosynthesis and Akt-mediated survival signaling. In spite of its importance, its structure and the molecular basis of its rapamycin insensitivity are unknown. Using crosslinking-mass spectrometry and electron microscopy, we determined the architecture of TORC2. TORC2 displays a rhomboid shape with pseudo-2-fold symmetry and a prominent central cavity. Our data indicate that the C-terminal part of Avo3, a subunit unique to TORC2, is close to the FKBP12-rapamycin-binding domain of Tor2. Removal of this sequence generated a FKBP12-rapamycin-sensitive TORC2 variant, which provides a powerful tool for deciphering TORC2 function in vivo. Using this variant, we demonstrate a role for TORC2 in G2/M cell-cycle progression.
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Affiliation(s)
- Christl Gaubitz
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Taiana M Oliveira
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; Fondation ARC, 9 rue Guy Môquet, BP 90003, 04803 Villejuif Cedex, France
| | - Manoel Prouteau
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Manikandan Karuppasamy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Georgia Konstantinidou
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Delphine Rispal
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Sandra Eltschinger
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Graham C Robinson
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Stéphane Thore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland; University of Bordeaux, European Institute for Chemistry and Biology, ARNA Laboratory, F-33607 Pessac, France; Institut National de la Santé Et de la Recherche Médicale, INSERM-U869, ARNA Laboratory, F-33000, Bordeaux, France
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom.
| | - Robbie Loewith
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland; National Centre of Competence in Research "Chemical Biology," University of Geneva, Geneva CH-1211, Switzerland.
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42
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Wedeking T, Löchte S, Richter CP, Bhagawati M, Piehler J, You C. Single Cell GFP-Trap Reveals Stoichiometry and Dynamics of Cytosolic Protein Complexes. NANO LETTERS 2015; 15:3610-3615. [PMID: 25901412 DOI: 10.1021/acs.nanolett.5b01153] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We developed in situ single cell pull-down (SiCPull) of GFP-tagged protein complexes based on micropatterned functionalized surface architectures. Cells cultured on these supports are lysed by mild detergents and protein complexes captured to the surface are probed in situ by total internal reflection fluorescence microscopy. Using SiCPull, we quantitatively mapped the lifetimes of various signal transducer and activator of transcription complexes by monitoring dissociation from the surface and defined their stoichiometry on the single molecule level.
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Affiliation(s)
- Tim Wedeking
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | | | - Maniraj Bhagawati
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Changjiang You
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
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