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Schodt D, Wester MJ, Fazel M, Mazloom-Farsibaf H, Pallikkuth S, Khan SA, Meddens MBM, Farzam F, Kanagy WK, Rinaldi DA, Jhamba ED, Lidke KA. SMITE (single molecule imaging toolbox extraordinaire), a MATLAB package. Biophys J 2023; 122:275a. [PMID: 36783359 DOI: 10.1016/j.bpj.2022.11.1568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- David Schodt
- Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Michael J Wester
- Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Mohamadreza Fazel
- Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | | | | | - Sajjad A Khan
- Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | | | - Farzin Farzam
- Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - William K Kanagy
- Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Derek A Rinaldi
- Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Elton D Jhamba
- Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Keith A Lidke
- Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
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2
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Schodt DJ, Farzam F, Liu S, Lidke KA. Automated multi-target super-resolution microscopy with trust regions. Biomed Opt Express 2023; 14:429-440. [PMID: 36698655 PMCID: PMC9841995 DOI: 10.1364/boe.477501] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
We describe a dedicated microscope for automated sequential localization microscopy which we term Sequential Super-resolution Microscope (SeqSRM). This microscope automates precise stage stabilization on the order of 5-10 nanometers and data acquisition of all user-selected cells on a coverslip, limiting user interaction to only cell selection and buffer exchanges during sequential relabeling. We additionally demonstrate that nanometer-scale changes to cell morphology affect the fidelity of the resulting multi-target super-resolution overlay reconstructions generated by sequential super-resolution microscopy, and that regions affected by these shifts can be reliably detected and masked out using brightfield images collected periodically throughout the experiment. The SeqSRM enables automated multi-target imaging on multiple user-selected cells without the need for multiple distinct fluorophores and emission channels, while ensuring that the resulting multi-target localization data accurately reflect the relative organization of the underlying targets.
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Affiliation(s)
- David J. Schodt
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87106, USA
- Contributed equally
| | - Farzin Farzam
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87106, USA
- Contributed equally
| | - Sheng Liu
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87106, USA
- Contributed equally
| | - Keith A. Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87106, USA
- Contributed equally
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3
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Sert F, Farzam F, Yalman D, Ozkok S. PD-0665 Geriatric Stage III NSCLC: Which scoring systems could guide us better to predict treatment outcome? Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)02912-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM, Corbett AD, Faklaris O, Lacoste J, Laude A, Nelson G, Nitschke R, Farzam F, Smith CS, Grunwald D, Strambio-De-Castillia C. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Nat Methods 2021; 18:1427-1440. [PMID: 34862501 PMCID: PMC9271325 DOI: 10.1038/s41592-021-01327-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light Microscopy Metadata specifications that extend the OME data model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments.
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Affiliation(s)
- Mathias Hammer
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | | | - Alessandro Rigano
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Ulrike Boehm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - James J Chambers
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
| | | | | | - Jaime A Pimentel
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, OR, USA
| | - Peter Bajcsy
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada
| | | | - Orestis Faklaris
- MRI, BCM, University of Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Alex Laude
- Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Glyn Nelson
- Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Roland Nitschke
- Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany
| | - Farzin Farzam
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA
| | - Carlas S Smith
- Delft Center for Systems and Control and Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | - David Grunwald
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA
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5
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Mazloom-Farsibaf H, Farzam F, Fazel M, Wester MJ, Meddens MBM, Lidke KA. Comparing lifeact and phalloidin for super-resolution imaging of actin in fixed cells. PLoS One 2021; 16:e0246138. [PMID: 33508018 PMCID: PMC7842966 DOI: 10.1371/journal.pone.0246138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/13/2021] [Indexed: 01/14/2023] Open
Abstract
Visualizing actin filaments in fixed cells is of great interest for a variety of topics in cell biology such as cell division, cell movement, and cell signaling. We investigated the possibility of replacing phalloidin, the standard reagent for super-resolution imaging of F-actin in fixed cells, with the actin binding peptide 'lifeact'. We compared the labels for use in single molecule based super-resolution microscopy, where AlexaFluor 647 labeled phalloidin was used in a dSTORM modality and Atto 655 labeled lifeact was used in a single molecule imaging, reversible binding modality. We found that imaging with lifeact had a comparable resolution in reconstructed images and provided several advantages over phalloidin including lower costs, the ability to image multiple regions of interest on a coverslip without degradation, simplified sequential super-resolution imaging, and more continuous labeling of thin filaments.
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Affiliation(s)
- Hanieh Mazloom-Farsibaf
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Farzin Farzam
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Mohamadreza Fazel
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Michael J Wester
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Marjolein B M Meddens
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
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6
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Schodt DJ, Farzam F, Lidke KA. High-Throughput Automated Sequential Superresolution Imaging of Membrane Proteins. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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7
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Kumar S, Gu Y, Abudu YP, Bruun JA, Jain A, Farzam F, Mudd M, Anonsen JH, Rusten TE, Kasof G, Ktistakis N, Lidke KA, Johansen T, Deretic V. Phosphorylation of Syntaxin 17 by TBK1 Controls Autophagy Initiation. Dev Cell 2019; 49:130-144.e6. [PMID: 30827897 DOI: 10.1016/j.devcel.2019.01.027] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/16/2018] [Accepted: 01/30/2019] [Indexed: 01/07/2023]
Abstract
Syntaxin 17 (Stx17) has been implicated in autophagosome-lysosome fusion. Here, we report that Stx17 functions in assembly of protein complexes during autophagy initiation. Stx17 is phosphorylated by TBK1 whereby phospho-Stx17 controls the formation of the ATG13+FIP200+ mammalian pre-autophagosomal structure (mPAS) in response to induction of autophagy. TBK1 phosphorylates Stx17 at S202. During autophagy induction, Stx17pS202 transfers from the Golgi, where its steady-state pools localize, to the ATG13+FIP200+ mPAS. Stx17pS202 was in complexes with ATG13 and FIP200, whereas its non-phosphorylatable mutant Stx17S202A was not. Stx17 or TBK1 knockouts blocked ATG13 and FIP200 puncta formation. Stx17 or TBK1 knockouts reduced the formation of ATG13 protein complexes with FIP200 and ULK1. Endogenous Stx17pS202 colocalized with LC3B following induction of autophagy. Stx17 knockout diminished LC3 response and reduced sequestration of the prototypical bulk autophagy cargo lactate dehydrogenase. We conclude that Stx17 is a TBK1 substrate and that together they orchestrate assembly of mPAS.
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Affiliation(s)
- Suresh Kumar
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Yuexi Gu
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Yakubu Princely Abudu
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, The Arctic University of Norway, Tromsø 9037, Norway
| | - Jack-Ansgar Bruun
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, The Arctic University of Norway, Tromsø 9037, Norway
| | - Ashish Jain
- Department of Molecular Cell Biology, Centre for Cancer Biomedicine, University of Oslo and Institute for Cancer Research, The Norwegian Radium Hospital, Oslo 0379, Norway
| | - Farzin Farzam
- Departments of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA
| | - Michal Mudd
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jan Haug Anonsen
- Department of Biosciences IBV Mass Spectrometry and Proteomics Unit, University of Oslo, Oslo 0371, Norway
| | - Tor Erik Rusten
- Department of Molecular Cell Biology, Centre for Cancer Biomedicine, University of Oslo and Institute for Cancer Research, The Norwegian Radium Hospital, Oslo 0379, Norway
| | - Gary Kasof
- Cell Signaling Technology, Danvers, MA 01923, USA
| | | | - Keith A Lidke
- Departments of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø, The Arctic University of Norway, Tromsø 9037, Norway
| | - Vojo Deretic
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
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Abstract
Single-molecule resolution imaging has become an important tool in the study of cell biology. Aptamer-based approaches (e.g., MS2 and PP7) allow for detection of single RNA molecules in living cells and have been used to study various aspects of mRNA metabolism, including mRNP nuclear export. Here we outline an imaging protocol for the study of interactions between mRNPs and nuclear pore complexes (NPCs) in the yeast S. cerevisiae, including mRNP export. We describe in detail the steps that allow for high-resolution live-cell mRNP imaging and measurement of mRNP interactions with NPCs using simultaneous two-color imaging. Our protocol discusses yeast strain construction, choice of marker proteins to label the nuclear pore complex, as well as imaging conditions that allow high signal-to-noise data acquisition. Moreover, we describe various aspects of postacquisition image analysis for single molecule tracking and image registration allowing for the characterization of mRNP-NPC interactions.
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Affiliation(s)
- Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Farzin Farzam
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pierre Bensidoun
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA.
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9
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Pallikkuth S, Martin C, Farzam F, Edwards JS, Lakin MR, Lidke DS, Lidke KA. Sequential super-resolution imaging using DNA strand displacement. PLoS One 2018; 13:e0203291. [PMID: 30169528 PMCID: PMC6118358 DOI: 10.1371/journal.pone.0203291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022] Open
Abstract
Sequential labeling and imaging in fluorescence microscopy allows the imaging of multiple structures in the same cell using a single fluorophore species. In super-resolution applications, the optimal dye suited to the method can be chosen, the optical setup can be simpler and there are no chromatic aberrations between images of different structures. We describe a method based on DNA strand displacement that can be used to quickly and easily perform the labeling and removal of the fluorophores during each sequence. Site-specific tags are conjugated with unique and orthogonal single stranded DNA. Labeling for a particular structure is achieved by hybridization of antibody-bound DNA with a complimentary dye-labeled strand. After imaging, the dye is removed using toehold-mediated strand displacement, in which an invader strand competes off the dye-labeled strand than can be subsequently washed away. Labeling and removal of each DNA-species requires only a few minutes. We demonstrate the concept using sequential dSTORM super-resolution for multiplex imaging of subcellular structures.
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Affiliation(s)
- Sandeep Pallikkuth
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Cheyenne Martin
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Farzin Farzam
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Jeremy S. Edwards
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Matthew R. Lakin
- Department of Computer Science, University of New Mexico, Albuquerque, New Mexico, United States of America
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Diane S. Lidke
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Keith A. Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- * E-mail:
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10
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Kumar S, Jain A, Farzam F, Jia J, Gu Y, Choi SW, Mudd MH, Claude-Taupin A, Wester MJ, Lidke KA, Rusten TE, Deretic V. Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins. J Cell Biol 2018; 217:997-1013. [PMID: 29420192 PMCID: PMC5839791 DOI: 10.1083/jcb.201708039] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/12/2017] [Accepted: 12/22/2017] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a conserved eukaryotic process with metabolic, immune, and general homeostatic functions in mammalian cells. Mammalian autophagosomes fuse with lysosomes in a SNARE-driven process that includes syntaxin 17 (Stx17). How Stx17 translocates to autophagosomes is unknown. In this study, we show that the mechanism of Stx17 recruitment to autophagosomes in human cells entails the small guanosine triphosphatase IRGM. Stx17 directly interacts with IRGM, and efficient Stx17 recruitment to autophagosomes requires IRGM. Both IRGM and Stx17 directly interact with mammalian Atg8 proteins, thus being guided to autophagosomes. We also show that Stx17 is significant in defense against infectious agents and that Stx17-IRGM interaction is targeted by an HIV virulence factor Nef.
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Affiliation(s)
- Suresh Kumar
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Ashish Jain
- Department of Molecular Cell Biology, Centre for Cancer Biomedicine, University of Oslo and Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Farzin Farzam
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM
| | - Jingyue Jia
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Yuexi Gu
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Seong Won Choi
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Michal H Mudd
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Aurore Claude-Taupin
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Michael J Wester
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM
| | - Tor-Erik Rusten
- Department of Molecular Cell Biology, Centre for Cancer Biomedicine, University of Oslo and Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Vojo Deretic
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM .,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
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11
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Lidke DS, Martin C, Farzam F, Edwards JS, Lakin M, Pallikkuth S, Lidke KA. Multi-Structure Super-Resolution Imaging using DNA Strand Displacement. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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12
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Kimura T, Jia J, Claude-Taupin A, Kumar S, Choi SW, Gu Y, Mudd M, Dupont N, Jiang S, Peters R, Farzam F, Jain A, Lidke KA, Adams CM, Johansen T, Deretic V. Cellular and molecular mechanism for secretory autophagy. Autophagy 2017; 13:1084-1085. [PMID: 28368721 DOI: 10.1080/15548627.2017.1307486] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Macroautophagy/autophagy plays a role in unconventional secretion of leaderless cytosolic proteins. Whether and how secretory autophagy diverges from conventional degradative autophagy is unclear. We have shown that the prototypical secretory autophagy cargo IL1B/IL-1β (interleukin 1 β) is recognized by TRIM16, and that this first to be identified secretory autophagy receptor interacts with the R-SNARE SEC22B to jointly deliver cargo to the MAP1LC3B-II-positive sequestration membranes. Cargo secretion is unaffected by knockdowns of STX17, a SNARE catalyzing autophagosome-lysosome fusion as a prelude to cargo degradation. Instead, SEC22B in combination with plasma membrane syntaxins completes cargo secretion. Thus, secretory autophagy diverges from degradative autophagy by using specialized receptors and a dedicated SNARE machinery to bypass fusion with lysosomes.
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Affiliation(s)
- Tomonori Kimura
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Jingyue Jia
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Aurore Claude-Taupin
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Suresh Kumar
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Seong Won Choi
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Yuexi Gu
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Michal Mudd
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Nicolas Dupont
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Shanya Jiang
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Ryan Peters
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
| | - Farzin Farzam
- b Department of Physics and Astronomy , University of New Mexico Northeast , Albuquerque , NM , USA
| | - Ashish Jain
- c Molecular Cancer Research Group , Institute of Medical Biology, University of Tromsø-The Arctic University of Norway , Tromsø , Norway
| | - Keith A Lidke
- b Department of Physics and Astronomy , University of New Mexico Northeast , Albuquerque , NM , USA
| | - Christopher M Adams
- d Stanford University Mass Spectrometry , Stanford University , Stanford , CA , USA
| | - Terje Johansen
- c Molecular Cancer Research Group , Institute of Medical Biology, University of Tromsø-The Arctic University of Norway , Tromsø , Norway
| | - Vojo Deretic
- a Department of Molecular Genetics and Microbiology , University of New Mexico Health Sciences Center, Northeast , Albuquerque , NM , USA
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13
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Kimura T, Jia J, Kumar S, Choi SW, Gu Y, Mudd M, Dupont N, Jiang S, Peters R, Farzam F, Jain A, Lidke KA, Adams CM, Johansen T, Deretic V. Dedicated SNAREs and specialized TRIM cargo receptors mediate secretory autophagy. EMBO J 2016; 36:42-60. [PMID: 27932448 DOI: 10.15252/embj.201695081] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/25/2016] [Accepted: 11/01/2016] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a process delivering cytoplasmic components to lysosomes for degradation. Autophagy may, however, play a role in unconventional secretion of leaderless cytosolic proteins. How secretory autophagy diverges from degradative autophagy remains unclear. Here we show that in response to lysosomal damage, the prototypical cytosolic secretory autophagy cargo IL-1β is recognized by specialized secretory autophagy cargo receptor TRIM16 and that this receptor interacts with the R-SNARE Sec22b to recruit cargo to the LC3-II+ sequestration membranes. Cargo secretion is unaffected by downregulation of syntaxin 17, a SNARE promoting autophagosome-lysosome fusion and cargo degradation. Instead, Sec22b in combination with plasma membrane syntaxin 3 and syntaxin 4 as well as SNAP-23 and SNAP-29 completes cargo secretion. Thus, secretory autophagy utilizes a specialized cytosolic cargo receptor and a dedicated SNARE system. Other unconventionally secreted cargo, such as ferritin, is secreted via the same pathway.
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Affiliation(s)
- Tomonori Kimura
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jingyue Jia
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Suresh Kumar
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Seong Won Choi
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Yuexi Gu
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Michal Mudd
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Nicolas Dupont
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Shanya Jiang
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ryan Peters
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Farzin Farzam
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Ashish Jain
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Christopher M Adams
- Stanford University Mass Spectrometry, Stanford University, Stanford, CA, USA
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Vojo Deretic
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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Abstract
BACKGROUND Subinhibitory concentrations of antibiotics, which can occur in vivo, have been demonstrated to alter the production of bacterial virulence factors, including the capsule, or the interaction between microorganism and phagocyte by affecting surface hydrophobicity. METHODS Using a microtiter assay system, the effect of subinhibitory concentrations of amikacin, gentamicin, cephalothin and doxycycline on the surface hydrophobicity and production of acidic polysaccharide by Vibrio vulnificus (8 human isolates, 8 environmental isolates) was determined. RESULTS All four drugs, in a dose-dependent manner, caused alterations in adherence to polystyrene, a measure of surface hydrophobicity, and the production of acidic polysaccharides, as determined by Alcian blue staining. CONCLUSION The changes in capsule production and surface hydrophobicity measured in response to sub-MICs of antibiotics appear to be independent variables.
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Affiliation(s)
- F Farzam
- Department of Microbiology, University of Southwestern Louisiana, Lafayette, La., USA
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