1
|
Nabi IR, Cardoen B, Khater IM, Gao G, Wong TH, Hamarneh G. AI analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. J Cell Biol 2024; 223:e202311073. [PMID: 38865088 PMCID: PMC11169916 DOI: 10.1083/jcb.202311073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Super-resolution microscopy, or nanoscopy, enables the use of fluorescent-based molecular localization tools to study molecular structure at the nanoscale level in the intact cell, bridging the mesoscale gap to classical structural biology methodologies. Analysis of super-resolution data by artificial intelligence (AI), such as machine learning, offers tremendous potential for the discovery of new biology, that, by definition, is not known and lacks ground truth. Herein, we describe the application of weakly supervised paradigms to super-resolution microscopy and its potential to enable the accelerated exploration of the nanoscale architecture of subcellular macromolecules and organelles.
Collapse
Affiliation(s)
- Ivan R. Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Ben Cardoen
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Ismail M. Khater
- School of Computing Science, Simon Fraser University, Burnaby, Canada
- Department of Electrical and Computer Engineering, Faculty of Engineering and Technology, Birzeit University, Birzeit, Palestine
| | - Guang Gao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Timothy H. Wong
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ghassan Hamarneh
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| |
Collapse
|
2
|
Konno T, Parutto P, Crapart CC, Davì V, Bailey DMD, Awadelkareem MA, Hockings C, Brown AI, Xiang KM, Agrawal A, Chambers JE, Vander Werp MJ, Koning KM, Elfari LM, Steen S, Metzakopian E, Westrate LM, Koslover EF, Avezov E. Endoplasmic reticulum morphology regulation by RTN4 modulates neuronal regeneration by curbing luminal transport. Cell Rep 2024; 43:114357. [PMID: 38955182 DOI: 10.1016/j.celrep.2024.114357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/01/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024] Open
Abstract
Cell functions rely on intracellular transport systems distributing bioactive molecules with high spatiotemporal accuracy. The endoplasmic reticulum (ER) tubular network constitutes a system for delivering luminal solutes, including Ca2+, across the cell periphery. How the ER structure enables this nanofluidic transport system is unclear. Here, we show that ER membrane-localized reticulon 4 (RTN4/Nogo) is sufficient to impose neurite outgrowth inhibition in human cortical neurons while acting as an ER morphoregulator. Improving ER transport visualization methodologies combined with optogenetic Ca2+ dynamics imaging and in silico modeling, we observed that ER luminal transport is modulated by ER tubule narrowing and dilation, proportional to the amount of RTN4. Excess RTN4 limited ER luminal transport and Ca2+ release, while RTN4 elimination reversed the effects. The described morphoregulatory effect of RTN4 defines the capacity of the ER for peripheral Ca2+ delivery for physiological releases and thus may constitute a mechanism for controlling the (re)generation of neurites.
Collapse
Affiliation(s)
- Tasuku Konno
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Pierre Parutto
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Cécile C Crapart
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Valentina Davì
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | | | - Mosab Ali Awadelkareem
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK; Department of Neuroscience Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Colin Hockings
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Aidan I Brown
- Department of Physics, University of California, San Diego, 9500 Gilman Dr. #0374, La Jolla, CA 92093-0374, USA; Department of Physics, Toronto Metropolitan University, Toronto, ON M5B 2K3, Canada
| | | | - Anamika Agrawal
- Department of Physics, University of California, San Diego, 9500 Gilman Dr. #0374, La Jolla, CA 92093-0374, USA
| | - Joseph E Chambers
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Molly J Vander Werp
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI 49546, USA
| | - Katherine M Koning
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI 49546, USA
| | - Louis Mounir Elfari
- Wellcome-MRC Cambridge Stem Cell Institute Advanced Imaging Facility, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Sam Steen
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI 49546, USA
| | - Emmanouil Metzakopian
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Laura M Westrate
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI 49546, USA
| | - Elena F Koslover
- Department of Physics, University of California, San Diego, 9500 Gilman Dr. #0374, La Jolla, CA 92093-0374, USA.
| | - Edward Avezov
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK.
| |
Collapse
|
3
|
Kataoka-Hamai C. Triacylglycerol-droplet-induced bilayer spontaneous curvature in giant unilamellar vesicles. Biophys J 2024; 123:1857-1868. [PMID: 38822522 PMCID: PMC11267425 DOI: 10.1016/j.bpj.2024.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/05/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024] Open
Abstract
This study investigated the incorporation of triacylglycerol droplets in the bilayers of giant unilamellar vesicles (GUVs) using four triacylglycerols and four phosphatidylcholines by confocal laser scanning microscopy. The triacylglycerol droplets were incorporated between the monolayer leaflets of the GUVs. Among the spherical droplets protruding on only one side of the bilayers, the droplets bound to the outer leaflets outnumbered those bound to the inner leaflets. The more frequent droplet binding to the outer leaflet caused transbilayer asymmetry in the droplet surface density. A vesicle consisting of a single-bilayer spherical segment and a double-bilayer spherical segment was also observed. The yield of these vesicles was comparable with or higher than that of the droplet-incorporating GUVs for many of the phosphatidylcholine-triacylglycerol combinations. In a vesicle consisting of single-bilayer and double-bilayer segments, most of the triacylglycerol droplets were localized on the outermost membrane surface along the segment boundary and in the double-bilayer segment. To rationalize the formation of these vesicle structures, we propose that the transbilayer asymmetry in the droplet surface density induces spontaneous curvature of the bilayer, with the bilayer spontaneously bending away from the droplets. Energy calculations performed assuming the existence of spontaneous curvature of the bilayer corroborated the experimentally determined membrane shapes for the vesicles consisting of unilamellar and bilamellar regions.
Collapse
Affiliation(s)
- Chiho Kataoka-Hamai
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan.
| |
Collapse
|
4
|
Sawyer EM, Jensen LE, Meehl JB, Larsen KP, Petito DA, Hurley JH, Voeltz GK. SigmaR1 shapes rough endoplasmic reticulum membrane sheets. Dev Cell 2024:S1534-5807(24)00382-4. [PMID: 38971154 DOI: 10.1016/j.devcel.2024.06.005] [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: 09/25/2023] [Revised: 02/12/2024] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
Rough endoplasmic reticulum (ER) sheets are a fundamental domain of the ER and the gateway into the secretory pathway. Although reticulon proteins stabilize high-curvature ER tubules, it is unclear whether other proteins scaffold the flat membranes of rough ER sheets. Through a proteomics screen using ER sheet-localized RNA-binding proteins as bait, we identify the sigma-1 receptor (SigmaR1) as an ER sheet-shaping factor. High-resolution live cell imaging and electron tomography assign SigmaR1 as an ER sheet-localized factor whose levels determine the amount of rough ER sheets in cells. Structure-guided mutagenesis and in vitro reconstitution on giant unilamellar vesicles further support a mechanism whereby SigmaR1 oligomers use their extended arrays of amphipathic helices to bind and flatten the lumenal leaflet of ER membranes to oppose membrane curvature and stabilize rough ER sheets.
Collapse
Affiliation(s)
- Eric M Sawyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - Liv E Jensen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Janet B Meehl
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - Kevin P Larsen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel A Petito
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gia K Voeltz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute.
| |
Collapse
|
5
|
Bragulat-Teixidor H, Ishihara K, Szücs GM, Otsuka S. The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after mitosis. EMBO Rep 2024; 25:3137-3159. [PMID: 38877171 PMCID: PMC11239909 DOI: 10.1038/s44319-024-00175-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024] Open
Abstract
Junctions between the endoplasmic reticulum (ER) and the outer membrane of the nuclear envelope (NE) physically connect both organelles. These ER-NE junctions are essential for supplying the NE with lipids and proteins synthesized in the ER. However, little is known about the structure of these ER-NE junctions. Here, we systematically study the ultrastructure of ER-NE junctions in cryo-fixed mammalian cells staged in anaphase, telophase, and interphase by correlating live cell imaging with three-dimensional electron microscopy. Our results show that ER-NE junctions in interphase cells have a pronounced hourglass shape with a constricted neck of 7-20 nm width. This morphology is significantly distinct from that of junctions within the ER network, and their morphology emerges as early as telophase. The highly constricted ER-NE junctions are seen in several mammalian cell types, but not in budding yeast. We speculate that the unique and highly constricted ER-NE junctions are regulated via novel mechanisms that contribute to ER-to-NE lipid and protein traffic in higher eukaryotes.
Collapse
Affiliation(s)
- Helena Bragulat-Teixidor
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria.
- Vienna BioCenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria.
| | - Keisuke Ishihara
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gréta Martina Szücs
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria
| | - Shotaro Otsuka
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria.
| |
Collapse
|
6
|
Gong B, Johnston JD, Thiemicke A, de Marco A, Meyer T. Endoplasmic reticulum-plasma membrane contact gradients direct cell migration. Nature 2024; 631:415-423. [PMID: 38867038 PMCID: PMC11236710 DOI: 10.1038/s41586-024-07527-5] [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: 03/22/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Directed cell migration is driven by the front-back polarization of intracellular signalling1-3. Receptor tyrosine kinases and other inputs activate local signals that trigger membrane protrusions at the front2,4-6. Equally important is a long-range inhibitory mechanism that suppresses signalling at the back to prevent the formation of multiple fronts7-9. However, the identity of this mechanism is unknown. Here we report that endoplasmic reticulum-plasma membrane (ER-PM) contact sites are polarized in single and collectively migrating cells. The increased density of these ER-PM contacts at the back provides the ER-resident PTP1B phosphatase more access to PM substrates, which confines receptor signalling to the front and directs cell migration. Polarization of the ER-PM contacts is due to microtubule-regulated polarization of the ER, with more RTN4-rich curved ER at the front and more CLIMP63-rich flattened ER at the back. The resulting ER curvature gradient leads to small and unstable ER-PM contacts only at the front. These contacts flow backwards and grow to large and stable contacts at the back to form the front-back ER-PM contact gradient. Together, our study suggests that the structural polarity mediated by ER-PM contact gradients polarizes cell signalling, directs cell migration and prolongs cell migration.
Collapse
Affiliation(s)
- Bo Gong
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
| | - Jake D Johnston
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Alexander Thiemicke
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tobias Meyer
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
7
|
Martin-Solana E, Carter SD, Donahue EK, Ning J, Glausier JR, Preisegger MA, Eisenman L, Joseph PN, Bouchet-Marquis C, Wu K, Mobini CL, Frantz AN, Puig S, Hampton CM, Kabbani N, Jensen GJ, Watkins SC, Deisseroth K, Fenno LE, Gold MS, Wills ZP, Burkewitz K, Das S, Freyberg Z. Ribosome-Associated Vesicles promote activity-dependent local translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.598007. [PMID: 38895376 PMCID: PMC11185778 DOI: 10.1101/2024.06.07.598007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Local protein synthesis in axons and dendrites underpins synaptic plasticity. However, the composition of the protein synthesis machinery in distal neuronal processes and the mechanisms for its activity-driven deployment to local translation sites remain unclear. Here, we employed cryo-electron tomography, volume electron microscopy, and live-cell imaging to identify Ribosome-Associated Vesicles (RAVs) as a dynamic platform for moving ribosomes to distal processes. Stimulation via chemically-induced long-term potentiation causes RAV accumulation in distal sites to drive local translation. We also demonstrate activity-driven changes in RAV generation and dynamics in vivo, identifying tubular ER shaping proteins in RAV biogenesis. Together, our work identifies a mechanism for ribosomal delivery to distal sites in neurons to promote activity-dependent local translation.
Collapse
Affiliation(s)
- Eva Martin-Solana
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen D. Carter
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Eric K.F. Donahue
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Jiying Ning
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jill R. Glausier
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Leanna Eisenman
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Paul N. Joseph
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Ken Wu
- Materials and Structural Analysis, Thermo Fisher Scientific, Hillsboro, OR, USA
| | | | - Amber N. Frantz
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephanie Puig
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cheri M. Hampton
- UES, Inc., Dayton, OH, USA
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, USA
| | - Nadine Kabbani
- Interdisciplinary Program in Neuroscience, George Mason University, Fairfax, VA, USA
- School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Grant J. Jensen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Lief E. Fenno
- Departments of Psychiatry and Neuroscience, University of Texas Austin Dell Medical School, Austin, TX, USA
| | - Michael S. Gold
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zachary P. Wills
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kristopher Burkewitz
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Sulagna Das
- Department of Cell Biology, Albert Einstein College of Medicine, NY
- Department of Cell Biology, Emory University, Atlanta, GA, USA
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
8
|
Langley A, Abeling-Wang S, Wagner E, Salogiannis J. Movement of the endoplasmic reticulum is driven by multiple classes of vesicles marked by Rab-GTPases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.592021. [PMID: 38798686 PMCID: PMC11118391 DOI: 10.1101/2024.05.14.592021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Peripheral endoplasmic reticulum (ER) tubules move along microtubules to interact with various organelles through membrane contact sites (MCS). Traditionally, ER moves by either sliding along stable microtubules via molecular motors or attaching to the plus ends of dynamic microtubules through tip attachment complexes (TAC). A recently discovered third process, hitchhiking, involves motile vesicles pulling ER tubules along microtubules. Previous research showed that ER hitchhikes on Rab5- and Rab7-marked endosomes, but it is uncertain if other Rab-vesicles can do the same. In U2OS cells, we screened Rabs for their ability to cotransport with ER tubules and found that ER hitchhikes on post-Golgi vesicles marked by Rab6 (isoforms a and b). Rab6-ER hitchhiking occurs independently of ER-endolysosome contacts and TAC-mediated ER movement. Disrupting either Rab6 or the motility of Rab6-vesicles reduces overall ER movement. Conversely, relocating these vesicles to the cell periphery causes peripheral ER accumulation, indicating that Rab6-vesicle motility is crucial for a subset of ER movements. Proximal post-Golgi vesicles marked by TGN46 are involved in Rab6-ER hitchhiking, while other post-Golgi vesicles (Rabs 8/10/11/13/14) are not essential for ER movement. Our further analysis finds that ER to Golgi vesicles marked by Rab1 are also capable of driving a subset of ER movements. Taken together, our findings suggest that ER hitchhiking on Rab-vesicles is a significant mode of ER movement. SIGNIFICANCE STATEMENT Peripheral endoplasmic reticulum tubules move on microtubules by either attaching to motors (cargo adaptor-mediated), dynamic microtubule-plus ends (tip attachment complexes) or motile vesicles (hitchhiking) but the prevalence of each mode is not clearPost-Golgi vesicles marked by Rab6/TGN46 and ER to Golgi vesicles marked by Rab1 drive ER movementsER hitchhiking on multiple classes of vesicles (endolysosomal, post-Golgi and ER to Golgi) marked by Rabs plays a prominent role in ER movement.
Collapse
|
9
|
Kroll J, Renkawitz J. Principles of organelle positioning in motile and non-motile cells. EMBO Rep 2024; 25:2172-2187. [PMID: 38627564 PMCID: PMC11094012 DOI: 10.1038/s44319-024-00135-4] [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: 11/13/2023] [Revised: 03/15/2024] [Accepted: 04/04/2024] [Indexed: 05/16/2024] Open
Abstract
Cells are equipped with asymmetrically localised and functionally specialised components, including cytoskeletal structures and organelles. Positioning these components to specific intracellular locations in an asymmetric manner is critical for their functionality and affects processes like immune responses, tissue maintenance, muscle functionality, and neurobiology. Here, we provide an overview of strategies to actively move, position, and anchor organelles to specific locations. By conceptualizing the cytoskeletal forces and the organelle-to-cytoskeleton connectivity, we present a framework of active positioning of both membrane-enclosed and membrane-less organelles. Using this framework, we discuss how different principles of force generation and organelle anchorage are utilised by different cells, such as mesenchymal and amoeboid cells, and how the microenvironment influences the plasticity of organelle positioning. Given that motile cells face the challenge of coordinating the positioning of their content with cellular motion, we particularly focus on principles of organelle positioning during migration. In this context, we discuss novel findings on organelle positioning by anchorage-independent mechanisms and their advantages and disadvantages in motile as well as stationary cells.
Collapse
Affiliation(s)
- Janina Kroll
- Biomedical Center, Walter Brendel Center of Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Klinikum der Universität, Ludwig Maximilians Universität München, Munich, Germany
| | - Jörg Renkawitz
- Biomedical Center, Walter Brendel Center of Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Klinikum der Universität, Ludwig Maximilians Universität München, Munich, Germany.
| |
Collapse
|
10
|
Lee CT, Rangamani P. Modeling the mechanochemical feedback for membrane-protein interactions using a continuum mesh model. Methods Enzymol 2024; 701:387-424. [PMID: 39025577 DOI: 10.1016/bs.mie.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The Helfrich free energy is widely used to model the generation of membrane curvature due to different physical and chemical components. The governing equations resulting from the energy minimization procedure are a system of coupled higher order partial differential equations. Simulations of membrane deformation for obtaining quantitative comparisons against experimental observations require computational schemes that will allow us to solve these equations without restrictions to axisymmetric coordinates. Here, we describe one such tool that we developed in our group based on discrete differential geometry to solve these equations along with examples.
Collapse
Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States.
| |
Collapse
|
11
|
Janssen M, Liese S, Al-Izzi SC, Carlson A. Stability of a biomembrane tube covered with proteins. Phys Rev E 2024; 109:044403. [PMID: 38755805 DOI: 10.1103/physreve.109.044403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/29/2024] [Indexed: 05/18/2024]
Abstract
Membrane tubes are essential structural features in cells that facilitate biomaterial transport and inter- and intracellular signaling. The shape of these tubes can be regulated by the proteins that surround and adhere to them. We study the stability of a biomembrane tube coated with proteins by combining linear stability analysis, out-of-equilibrium hydrodynamic calculations, and numerical solutions of a Helfrich-like membrane model. Our analysis demonstrates that both long- and short-wavelength perturbations can destabilize the tubes. Numerical simulations confirm the derived linear stability criteria and yield the nonlinearly perturbed vesicle shapes. Our study highlights the interplay between membrane shape and protein density, where the shape instability concurs with a redistribution of proteins into a banded pattern.
Collapse
Affiliation(s)
- Mathijs Janssen
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, 0315 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
- Norwegian University of Life Sciences, Faculty of Science and Technology, 1433 Ås, Norway
| | - Susanne Liese
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
| | - Sami C Al-Izzi
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, 0315 Oslo, Norway
| | - Andreas Carlson
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, 0315 Oslo, Norway
| |
Collapse
|
12
|
Senftleben ML, Bajor A, Hirata E, Abrahamsson S, Brismar H. Fast volumetric multifocus structured illumination microscopy of subcellular dynamics in living cells. BIOMEDICAL OPTICS EXPRESS 2024; 15:2281-2292. [PMID: 38633103 PMCID: PMC11019691 DOI: 10.1364/boe.516261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/21/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
Studying the nanoscale dynamics of subcellular structures is possible with 2D structured illumination microscopy (SIM). The method allows for acquisition with improved resolution over typical widefield. For 3D samples, the acquisition speed is inherently limited by the need to acquire sequential two-dimensional planes to create a volume. Here, we present a development of multifocus SIM designed to provide high volumetric frame rate by using fast synchronized electro-optical components. We demonstrate the high volumetric imaging capacity of the microscope by recording the dynamics of microtubule and endoplasmatic reticulum in living cells at up to 2.3 super resolution volumes per second for a total volume of 30 × 30 × 1.8 µm3.
Collapse
Affiliation(s)
- Maximilian Lukas Senftleben
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Antone Bajor
- Baskin School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, 95064, CA, USA
| | - Eduardo Hirata
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Sara Abrahamsson
- Baskin School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, 95064, CA, USA
| | - Hjalmar Brismar
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| |
Collapse
|
13
|
Martínez-Andrade JM, Roberson RW, Riquelme M. A bird's-eye view of the endoplasmic reticulum in filamentous fungi. Microbiol Mol Biol Rev 2024; 88:e0002723. [PMID: 38372526 PMCID: PMC10966943 DOI: 10.1128/mmbr.00027-23] [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] [Indexed: 02/20/2024] Open
Abstract
SUMMARYThe endoplasmic reticulum (ER) is one of the most extensive organelles in eukaryotic cells. It performs crucial roles in protein and lipid synthesis and Ca2+ homeostasis. Most information on ER types, functions, organization, and domains comes from studies in uninucleate animal, plant, and yeast cells. In contrast, there is limited information on the multinucleate cells of filamentous fungi, i.e., hyphae. We provide an analytical review of existing literature to categorize different types of ER described in filamentous fungi while emphasizing the research techniques and markers used. Additionally, we identify the knowledge gaps that need to be resolved better to understand the structure-function correlation of ER in filamentous fungi. Finally, advanced technologies that can provide breakthroughs in understanding the ER in filamentous fungi are discussed.
Collapse
Affiliation(s)
- Juan M. Martínez-Andrade
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| | | | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| |
Collapse
|
14
|
Jang W, Haucke V. ER remodeling via lipid metabolism. Trends Cell Biol 2024:S0962-8924(24)00023-0. [PMID: 38395735 DOI: 10.1016/j.tcb.2024.01.011] [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: 11/01/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Unlike most other organelles found in multiple copies, the endoplasmic reticulum (ER) is a unique singular organelle within eukaryotic cells. Despite its continuous membrane structure, encompassing more than half of the cellular endomembrane system, the ER is subdivided into specialized sub-compartments, including morphological, membrane contact site (MCS), and de novo organelle biogenesis domains. In this review, we discuss recent emerging evidence indicating that, in response to nutrient stress, cells undergo a reorganization of these sub-compartmental ER domains through two main mechanisms: non-destructive remodeling of morphological ER domains via regulation of MCS and organelle hitchhiking, and destructive remodeling of specialized domains by ER-phagy. We further highlight and propose a critical role of membrane lipid metabolism in this ER remodeling during starvation.
Collapse
Affiliation(s)
- Wonyul Jang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| |
Collapse
|
15
|
Dora M, Paquin-Lefebvre F, Holcman D. Analyzing Photoactivation with Diffusion Models to Study Transport in the Endoplasmic Reticulum Network. Methods Mol Biol 2024; 2772:407-432. [PMID: 38411832 DOI: 10.1007/978-1-0716-3710-4_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Photoactivation is a paradigm consisting in local molecular fluorescent activation by laser illumination in a chosen region (source) while measuring the concentration at a target region. Data-driven modeling is concerned with the following questions: how from the measurement in these two regions is it possible to infer the properties of molecular propagation? How is it possible to use such responses to infer motions occurring in networks such as the endoplasmic reticulum? In this book chapter, we shall review the data-driven analysis based on diffusion-transport models and numerical simulations to interpret the photoactivation dynamics and extract biophysical parameters. We will discuss modeling approaches to reconstruct local network properties from photoactivation transients.
Collapse
Affiliation(s)
- Matteo Dora
- Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | | | - David Holcman
- Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
- Churchill College, Cambridge University, Cambridge, UK
| |
Collapse
|
16
|
Miner GE, Smith SY, Showalter WK, So CM, Ragusa JV, Powers AE, Zanellati MC, Hsu CH, Marchan MF, Cohen S. Contact-FP: A Dimerization-Dependent Fluorescent Protein Toolkit for Visualizing Membrane Contact Site Dynamics. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241228911. [PMID: 38327561 PMCID: PMC10846013 DOI: 10.1177/25152564241228911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
Membrane contact sites (MCSs) are sites of close apposition between two organelles used to exchange ions, lipids, and information. Cells respond to changing environmental or developmental conditions by modulating the number, extent, or duration of MCSs. Because of their small size and dynamic nature, tools to study the dynamics of MCSs in live cells have been limited. Dimerization-dependent fluorescent proteins (ddFPs) targeted to organelle membranes are an ideal tool for studying MCS dynamics because they reversibly interact to fluoresce specifically at the interface between two organelles. Here, we build on previous work using ddFPs as sensors to visualize the morphology and dynamics of MCSs. We engineered a suite of ddFPs called Contact-FP that targets ddFP monomers to lipid droplets (LDs), the endoplasmic reticulum (ER), mitochondria, peroxisomes, lysosomes, plasma membrane, caveolae, and the cytoplasm. We show that these probes correctly localize to their target organelles. Using LDs as a test case, we demonstrate that Contact-FP pairs specifically localize to the interface between two target organelles. Titration of LD-mitochondria ddFPs revealed that these sensors can be used at high concentrations to drive MCSs or can be titrated down to minimally perturb and visualize endogenous MCSs. We show that Contact-FP probes can be used to: (1) visualize LD-mitochondria MCS dynamics, (2) observe changes in LD-mitochondria MCS dynamics upon overexpression of PLIN5, a known LD-mitochondrial tether, and (3) visualize two MCSs that share one organelle simultaneously (e.g., LD-mitochondria and LD-ER MCSs). Contact-FP probes can be optimized to visualize MCSs between any pair of organelles represented in the toolkit.
Collapse
Affiliation(s)
- Gregory E. Miner
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sidney Y. Smith
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wendy K. Showalter
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christina M. So
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joey V. Ragusa
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alex E. Powers
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maria Clara Zanellati
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chih-Hsuan Hsu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michelle F. Marchan
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
17
|
Parsons HT. Preparation of Highly Enriched ER Membranes Using Free-Flow Electrophoresis. Methods Mol Biol 2024; 2772:115-127. [PMID: 38411809 DOI: 10.1007/978-1-0716-3710-4_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Free-flow electrophoresis (FFE) is a technique for separation of proteins, peptides, organelles, and cells. With zone electrophoresis (ZE-FFE), organelles are separated according to surface charge. The ER is the only remaining major cellular compartment in Arabidopsis not to have been isolated using density centrifugation, immune-isolation, or any other method previously applied to purification of plant membranes. By using continuous-flow electrophoresis, ER vesicles of similar surface charge, which may have been fragmented during cell lysis, can be focused. A large portion of these vesicles are of sufficiently different surface charge that separation from the majority of Golgi and other contaminants is possible. Here we adapt an earlier ZE-FFE Golgi isolation protocol for the isolation of highly pure ER vesicles and for tracking the migration of peripheral ER vesicles. Isolating ER vesicles of homogeneous surface charge allows multi-omic analyses to be performed on the ER. This facilitates investigations into structure-function relationships within the ER.
Collapse
|
18
|
Sung H, Lloyd TE. Disrupted endoplasmic reticulum-mediated autophagosomal biogenesis in a Drosophila model of C9-ALS-FTD. Autophagy 2024; 20:94-113. [PMID: 37599467 PMCID: PMC10761023 DOI: 10.1080/15548627.2023.2249750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023] Open
Abstract
ABBREVIATIONS 3R: UAS construct expressing 3 G4C2 repeats (used as control); 3WJ: three-way junction; 12R: UAS construct expressing leader sequence and 12 G4C2 repeats; 30R: UAS construct expressing 30 G4C2 repeats; 36R: UAS construct expressing 36 G4C2 repeats; 44R: UAS construct expressing leader sequence and 44 G4C2 repeats; ALS: amyotrophic lateral sclerosis; Atg: autophagy related; atl: atlastin; C9-ALS-FTD: ALS or FTD caused by hexanuleotide repeat expansion in C9orf72; ER: endoplasmic reticulum; FTD: frontotemporal dementia; HRE: GGGGCC hexanucleotide repeat expansion; HSP: hereditary spastic paraplegia; Lamp1: lysosomal associated membrane protein 1; MT: microtubule; NMJ: neuromuscular junction; Rab: Ras-associated binding GTPase; RAN: repeat associated non-AUG (RAN) translation; RO-36: UAS construct expression "RNA-only" version of 36 G4C2 repeats in which stop codons in all six reading frames are inserted.; Rtnl1: Reticulon-like 1; SN: segmental nerve; TFEB/Mitf: transcription factor EB/microphthalmia associated transcription factor (Drosophila ortholog of TFEB); TrpA1: transient receptor potential cation channel A1; VAPB: VAMP associated protein B and C; VNC: ventral nerve cord (spinal cord in Drosophila larvae).
Collapse
Affiliation(s)
- Hyun Sung
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Thomas E. Lloyd
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
19
|
Cardoen B, Vandevoorde KR, Gao G, Ortiz-Silva M, Alan P, Liu W, Tiliakou E, Vogl AW, Hamarneh G, Nabi IR. Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts. J Cell Biol 2024; 223:e202206109. [PMID: 37948126 PMCID: PMC10638097 DOI: 10.1083/jcb.202206109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/20/2022] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Identification and morphological analysis of mitochondria-ER contacts (MERCs) by fluorescent microscopy is limited by subpixel resolution interorganelle distances. Here, the membrane contact site (MCS) detection algorithm, MCS-DETECT, reconstructs subpixel resolution MERCs from 3D super-resolution image volumes. MCS-DETECT shows that elongated ribosome-studded riboMERCs, present in HT-1080 but not COS-7 cells, are morphologically distinct from smaller smooth contacts and larger contacts induced by mitochondria-ER linker expression in COS-7 cells. RiboMERC formation is associated with increased mitochondrial potential, reduced in Gp78 knockout HT-1080 cells and induced by Gp78 ubiquitin ligase activity in COS-7 and HeLa cells. Knockdown of riboMERC tether RRBP1 eliminates riboMERCs in both wild-type and Gp78 knockout HT-1080 cells. By MCS-DETECT, Gp78-dependent riboMERCs present complex tubular shapes that intercalate between and contact multiple mitochondria. MCS-DETECT of 3D whole-cell super-resolution image volumes, therefore, identifies novel dual control of tubular riboMERCs, whose formation is dependent on RRBP1 and size modulated by Gp78 E3 ubiquitin ligase activity.
Collapse
Affiliation(s)
- Ben Cardoen
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Kurt R. Vandevoorde
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Guang Gao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Milene Ortiz-Silva
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Parsa Alan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - William Liu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ellie Tiliakou
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - A. Wayne Vogl
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ghassan Hamarneh
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Ivan R. Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| |
Collapse
|
20
|
Ci Y, Han K, Kong J, Huang S, Yang Y, Qin C, Shi L. Flavivirus Concentrates Host ER in Main Replication Compartments to Facilitate Replication. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2305093. [PMID: 37888856 PMCID: PMC10754076 DOI: 10.1002/advs.202305093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Indexed: 10/28/2023]
Abstract
Flavivirus remodels the host endoplasmic reticulum (ER) to generate replication compartments (RCs) as the fundamental structures to accommodate viral replication. Here, a centralized replication mode of flavivirus is reported, i.e., flavivirus concentrates host ER in perinuclear main replication compartments (MRCs) for efficient replication. Superresolution live-cell imaging demonstrated that flavivirus MRCs formed via a series of events, including multisite ER clustering, growth and merging of ER clusters, directional movement, and convergence in the perinuclear region. The dynamic activities of viral RCs are driven by nonstructural (NS) proteins and are independent of microtubules and actin. Moreover, disrupting MRCs formation by small molecule compounds inhibited flavivirus replication. Overall, the findings reveal unprecedented insight into dynamic ER reorganization by flavivirus and identify a new inhibition strategy.
Collapse
Affiliation(s)
- Yali Ci
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Kai Han
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Jie Kong
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Shuhan Huang
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Yang Yang
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| | - Cheng‐Feng Qin
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijing100071China
| | - Lei Shi
- State Key Laboratory of Common Mechanism Research for Major DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
- Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical CollegeBeijing100005China
| |
Collapse
|
21
|
Laine RF, Heil HS, Coelho S, Nixon-Abell J, Jimenez A, Wiesner T, Martínez D, Galgani T, Régnier L, Stubb A, Follain G, Webster S, Goyette J, Dauphin A, Salles A, Culley S, Jacquemet G, Hajj B, Leterrier C, Henriques R. High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation. Nat Methods 2023; 20:1949-1956. [PMID: 37957430 PMCID: PMC10703683 DOI: 10.1038/s41592-023-02057-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Live-cell super-resolution microscopy enables the imaging of biological structure dynamics below the diffraction limit. Here we present enhanced super-resolution radial fluctuations (eSRRF), substantially improving image fidelity and resolution compared to the original SRRF method. eSRRF incorporates automated parameter optimization based on the data itself, giving insight into the trade-off between resolution and fidelity. We demonstrate eSRRF across a range of imaging modalities and biological systems. Notably, we extend eSRRF to three dimensions by combining it with multifocus microscopy. This realizes live-cell volumetric super-resolution imaging with an acquisition speed of ~1 volume per second. eSRRF provides an accessible super-resolution approach, maximizing information extraction across varied experimental conditions while minimizing artifacts. Its optimal parameter prediction strategy is generalizable, moving toward unbiased and optimized analyses in super-resolution microscopy.
Collapse
Affiliation(s)
- Romain F Laine
- Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
- Micrographia Bio, Translation and Innovation Hub, London, UK
| | - Hannah S Heil
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Simao Coelho
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Jonathon Nixon-Abell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Cambridge Institute for Medical Research, Cambridge Univeristy, Cambridge, UK
| | - Angélique Jimenez
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Theresa Wiesner
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Damián Martínez
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Tommaso Galgani
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France
- Revvity Signals, Tres Cantos, Madrid, Spain
| | - Louise Régnier
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France
| | - Aki Stubb
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Munster, Germany
| | - Gautier Follain
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Samantha Webster
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Aurelien Dauphin
- Unite Genetique et Biologie du Développement U934, PICT-IBiSA, Institut Curie, INSERM, CNRS, PSL Research University, Paris, France
| | - Audrey Salles
- Institut Pasteur, Université Paris Cité, Unit of Technology and Service Photonic BioImaging (UTechS PBI), C2RT, Paris, France
| | - Siân Culley
- Laboratory for Molecular Cell Biology, University College London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku, Finland
| | - Bassam Hajj
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France.
| | | | - Ricardo Henriques
- Laboratory for Molecular Cell Biology, University College London, London, UK.
- The Francis Crick Institute, London, UK.
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal.
| |
Collapse
|
22
|
Saguy A, Alalouf O, Opatovski N, Jang S, Heilemann M, Shechtman Y. DBlink: dynamic localization microscopy in super spatiotemporal resolution via deep learning. Nat Methods 2023; 20:1939-1948. [PMID: 37500760 DOI: 10.1038/s41592-023-01966-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Single-molecule localization microscopy (SMLM) has revolutionized biological imaging, improving the spatial resolution of traditional microscopes by an order of magnitude. However, SMLM techniques require long acquisition times, typically a few minutes, to yield a single super-resolved image, because they depend on accumulation of many localizations over thousands of recorded frames. Hence, the capability of SMLM to observe dynamics at high temporal resolution has always been limited. In this work, we present DBlink, a deep-learning-based method for super spatiotemporal resolution reconstruction from SMLM data. The input to DBlink is a recorded video of SMLM data and the output is a super spatiotemporal resolution video reconstruction. We use a convolutional neural network combined with a bidirectional long short-term memory network architecture, designed for capturing long-term dependencies between different input frames. We demonstrate DBlink performance on simulated filaments and mitochondria-like structures, on experimental SMLM data under controlled motion conditions and on live-cell dynamic SMLM. DBlink's spatiotemporal interpolation constitutes an important advance in super-resolution imaging of dynamic processes in live cells.
Collapse
Affiliation(s)
- Alon Saguy
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Onit Alalouf
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nadav Opatovski
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Soohyen Jang
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
- Institute of Physical and Theoretical Chemistry, IMPRS on Cellular Biophysics, Goethe-University Frankfurt, Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
- Institute of Physical and Theoretical Chemistry, IMPRS on Cellular Biophysics, Goethe-University Frankfurt, Frankfurt, Germany
| | - Yoav Shechtman
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
23
|
Xu X, Qiu K, Tian Z, Aryal C, Rowan F, Chen R, Sun Y, Diao J. Probing the dynamic crosstalk of lysosomes and mitochondria with structured illumination microscopy. Trends Analyt Chem 2023; 169:117370. [PMID: 37928815 PMCID: PMC10621629 DOI: 10.1016/j.trac.2023.117370] [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] [Indexed: 11/07/2023]
Abstract
Structured illumination microscopy (SIM) is a super-resolution technology for imaging living cells and has been used for studying the dynamics of lysosomes and mitochondria. Recently, new probes and analyzing methods have been developed for SIM imaging, enabling the quantitative analysis of these subcellular structures and their interactions. This review provides an overview of the working principle and advances of SIM, as well as the organelle-targeting principles and types of fluorescence probes, including small molecules, metal complexes, nanoparticles, and fluorescent proteins. Additionally, quantitative methods based on organelle morphology and distribution are outlined. Finally, the review provides an outlook on the current challenges and future directions for improving the combination of SIM imaging and image analysis to further advance the study of organelles. We hope that this review will be useful for researchers working in the field of organelle research and help to facilitate the development of SIM imaging and analysis techniques.
Collapse
Affiliation(s)
- Xiuqiong Xu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kangqiang Qiu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Chinta Aryal
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Fiona Rowan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Rui Chen
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Yujie Sun
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| |
Collapse
|
24
|
Li J, Gui Q, Liang FX, Sall J, Zhang Q, Duan Y, Dhabaria A, Askenazi M, Ueberheide B, Stapleford KA, Pagano M. The REEP5/TRAM1 complex binds SARS-CoV-2 NSP3 and promotes virus replication. J Virol 2023; 97:e0050723. [PMID: 37768083 PMCID: PMC10617467 DOI: 10.1128/jvi.00507-23] [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: 04/04/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Generation of virus-host protein-protein interactions (PPIs) maps may provide clues to uncover SARS-CoV-2-hijacked cellular processes. However, these PPIs maps were created by expressing each viral protein singularly, which does not reflect the life situation in which certain viral proteins synergistically interact with host proteins. Our results reveal the host-viral protein-protein interactome of SARS-CoV-2 NSP3, NSP4, and NSP6 expressed individually or in combination. Furthermore, REEP5/TRAM1 complex interacts with NSP3 at ROs and promotes viral replication. The significance of our research is identifying virus-host interactions that may be targeted for therapeutic intervention.
Collapse
Affiliation(s)
- Jie Li
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Qi Gui
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Feng-Xia Liang
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Joseph Sall
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Yatong Duan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- William A. Shine Great Neck South High School, Lake Success, New York, USA
| | - Avantika Dhabaria
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Biomedical Hosting LLC, Arlington, Massachusetts, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, New York, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, New York, USA
| |
Collapse
|
25
|
Kim N, Kim TH, Kim C, Lee JE, Kang MG, Shin S, Jung M, Kim JS, Mun JY, Rhee HW, Park SY, Shin Y, Yoo JY. Intrinsically disordered region-mediated condensation of IFN-inducible SCOTIN/SHISA-5 inhibits ER-to-Golgi vesicle transport. Dev Cell 2023; 58:1950-1966.e8. [PMID: 37816329 DOI: 10.1016/j.devcel.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023]
Abstract
Newly synthesized proteins in the endoplasmic reticulum (ER) are sorted by coat protein complex II (COPII) at the ER exit site en route to the Golgi. Under cellular stresses, COPII proteins become targets of regulation to control the transport. Here, we show that the COPII outer coat proteins Sec31 and Sec13 are selectively sequestered into the biomolecular condensate of SCOTIN/SHISA-5, which interferes with COPII vesicle formation and inhibits ER-to-Golgi transport. SCOTIN is an ER transmembrane protein with a cytosolic intrinsically disordered region (IDR), which is required and essential for the formation of condensates. Upon IFN-γ stimulation, which is a cellular condition that induces SCOTIN expression and condensation, ER-to-Golgi transport was inhibited in a SCOTIN-dependent manner. Furthermore, cancer-associated mutations of SCOTIN perturb its ability to form condensates and control transport. Together, we propose that SCOTIN impedes the ER-to-Golgi transport through its ability to form biomolecular condensates at the ER membrane.
Collapse
Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
| | - Tae-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jee-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sanghee Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
| |
Collapse
|
26
|
Fuentes LA, Marin Z, Tyson J, Baddeley D, Bewersdorf J. The nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ. J Cell Biol 2023; 222:e202301112. [PMID: 37516910 PMCID: PMC10373298 DOI: 10.1083/jcb.202301112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/31/2023] [Accepted: 07/06/2023] [Indexed: 07/31/2023] Open
Abstract
The endoplasmic reticulum's (ER's) structure is directly linked to the many functions of the ER, but its formation is not fully understood. We investigate how the ER-membrane curving protein reticulon 4 (Rtn4) localizes to and organizes in the membrane and how that affects the local ER structure. We show a strong correlation between the local Rtn4 density and the local ER membrane curvature. Our data further reveal that the typical ER tubule possesses an elliptical cross-section with Rtn4 enriched at either end of the major axis. Rtn4 oligomers are linear shaped, contain about five copies of the protein, and preferentially orient parallel to the tubule axis. Our observations support a mechanism in which oligomerization leads to an increase of the local Rtn4 concentration with each molecule, increasing membrane curvature through a hairpin wedging mechanism. This quantitative analysis of Rtn4 and its effects on the ER membrane result in a new model of tubule shape as it relates to Rtn4.
Collapse
Affiliation(s)
- Lukas A. Fuentes
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zach Marin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Jonathan Tyson
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| |
Collapse
|
27
|
Zalejski J, Sun J, Sharma A. Unravelling the Mystery inside Cells by Using Single-Molecule Fluorescence Imaging. J Imaging 2023; 9:192. [PMID: 37754956 PMCID: PMC10532472 DOI: 10.3390/jimaging9090192] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Live-cell imaging is a powerful technique to study the dynamics and mechanics of various biological molecules like proteins, organelles, DNA, and RNA. With the rapid evolution of optical microscopy, our understanding of how these molecules are implicated in the cells' most critical physiological roles deepens. In this review, we focus on how spatiotemporal nanoscale live-cell imaging at the single molecule level allows for profound contributions towards new discoveries in life science. This review will start by summarizing how single-molecule tracking has been used to analyze membrane dynamics, receptor-ligand interactions, protein-protein interactions, inner- and extra-cellular transport, gene expression/transcription, and whole organelle tracking. We then move on to how current authors are trying to improve single-molecule tracking and overcome current limitations by offering new ways of labeling proteins of interest, multi-channel/color detection, improvements in time-lapse imaging, and new methods and programs to analyze the colocalization and movement of targets. We later discuss how single-molecule tracking can be a beneficial tool used for medical diagnosis. Finally, we wrap up with the limitations and future perspectives of single-molecule tracking and total internal reflection microscopy.
Collapse
Affiliation(s)
| | | | - Ashutosh Sharma
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA; (J.Z.); (J.S.)
| |
Collapse
|
28
|
Chang BJ, Shepherd D, Fiolka R. Projective oblique plane structured illumination microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552447. [PMID: 37609312 PMCID: PMC10441343 DOI: 10.1101/2023.08.08.552447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Structured illumination microscopy (SIM) can double the spatial resolution of a fluorescence microscope and video rate live cell imaging in a two-dimensional format has been demonstrated. However, rapid implementations of 2D SIM typically only cover a narrow slice of the sample immediately at the coverslip, with most of the cellular volume out of reach. Here we implement oblique plane structured illumination microscopy (OPSIM) in a projection format to rapidly image an entire cell in a 2D SIM framework. As no mechanical scanning of the sample or objective is involved, this technique has the potential for rapid projection imaging with doubled resolution. We characterize the spatial resolution with fluorescent nanospheres, compare projection and 3D imaging using OPSIM and image mitochondria and ER dynamics across an entire cell at up to 2.7 Hz. To our knowledge, this represents the fastest whole cell SIM imaging to date.
Collapse
Affiliation(s)
- Bo-Jui Chang
- Lyda Hill Department for Bioinformatics, UT Southwestern Medical Center, 6000 Harry Hines BLVD, Dallas, TX 75390, USA
| | - Douglas Shepherd
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ 82587, USA
| | | |
Collapse
|
29
|
Scott ZC, Koning K, Vanderwerp M, Cohen L, Westrate LM, Koslover EF. Endoplasmic reticulum network heterogeneity guides diffusive transport and kinetics. Biophys J 2023; 122:3191-3205. [PMID: 37401053 PMCID: PMC10432226 DOI: 10.1016/j.bpj.2023.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/17/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
The endoplasmic reticulum (ER) is a dynamic network of interconnected sheets and tubules that orchestrates the distribution of lipids, ions, and proteins throughout the cell. The impact of its complex, dynamic morphology on its function as an intracellular transport hub remains poorly understood. To elucidate the functional consequences of ER network structure and dynamics, we quantify how the heterogeneity of the peripheral ER in COS7 cells affects diffusive protein transport. In vivo imaging of photoactivated ER membrane proteins demonstrates their nonuniform spreading to adjacent regions, in a manner consistent with simulations of diffusing particles on extracted network structures. Using a minimal network model to represent tubule rearrangements, we demonstrate that ER network dynamics are sufficiently slow to have little effect on diffusive protein transport. Furthermore, stochastic simulations reveal a novel consequence of ER network heterogeneity: the existence of "hot spots" where sparse diffusive reactants are more likely to find one another. ER exit sites, specialized domains regulating cargo export from the ER, are shown to be disproportionately located in highly accessible regions, further from the outer boundary of the cell. Combining in vivo experiments with analytic calculations, quantitative image analysis, and computational modeling, we demonstrate how structure guides diffusive protein transport and reactions in the ER.
Collapse
Affiliation(s)
| | - Katherine Koning
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, Michigan
| | - Molly Vanderwerp
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, Michigan
| | | | - Laura M Westrate
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, Michigan
| | - Elena F Koslover
- Department of Physics, University of California, San Diego, La Jolla, California.
| |
Collapse
|
30
|
Miner GE, So CM, Edwards W, Ragusa JV, Wine JT, Wong Gutierrez D, Airola MV, Herring LE, Coleman RA, Klett EL, Cohen S. PLIN5 interacts with FATP4 at membrane contact sites to promote lipid droplet-to-mitochondria fatty acid transport. Dev Cell 2023; 58:1250-1265.e6. [PMID: 37290445 PMCID: PMC10525032 DOI: 10.1016/j.devcel.2023.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 01/19/2023] [Accepted: 05/16/2023] [Indexed: 06/10/2023]
Abstract
Cells adjust their metabolism by remodeling membrane contact sites that channel metabolites to different fates. Lipid droplet (LD)-mitochondria contacts change in response to fasting, cold exposure, and exercise. However, their function and mechanism of formation have remained controversial. We focused on perilipin 5 (PLIN5), an LD protein that tethers mitochondria, to probe the function and regulation of LD-mitochondria contacts. We demonstrate that efficient LD-to-mitochondria fatty acid (FA) trafficking and ß-oxidation during starvation of myoblasts are promoted by phosphorylation of PLIN5 and require an intact PLIN5 mitochondrial tethering domain. Using human and murine cells, we further identified the acyl-CoA synthetase, FATP4 (ACSVL4), as a mitochondrial interactor of PLIN5. The C-terminal domains of PLIN5 and FATP4 constitute a minimal protein interaction capable of inducing organelle contacts. Our work suggests that starvation leads to phosphorylation of PLIN5, lipolysis, and subsequent channeling of FAs from LDs to FATP4 on mitochondria for conversion to fatty-acyl-CoAs and subsequent oxidation.
Collapse
Affiliation(s)
- Gregory E Miner
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christina M So
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Whitney Edwards
- Department of Biology and Genetics, McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joey V Ragusa
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan T Wine
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Daniel Wong Gutierrez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael V Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Laura E Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rosalind A Coleman
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eric L Klett
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
31
|
Chen X, Zhong S, Hou Y, Cao R, Wang W, Li D, Dai Q, Kim D, Xi P. Superresolution structured illumination microscopy reconstruction algorithms: a review. LIGHT, SCIENCE & APPLICATIONS 2023; 12:172. [PMID: 37433801 DOI: 10.1038/s41377-023-01204-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023]
Abstract
Structured illumination microscopy (SIM) has become the standard for next-generation wide-field microscopy, offering ultrahigh imaging speed, superresolution, a large field-of-view, and long-term imaging. Over the past decade, SIM hardware and software have flourished, leading to successful applications in various biological questions. However, unlocking the full potential of SIM system hardware requires the development of advanced reconstruction algorithms. Here, we introduce the basic theory of two SIM algorithms, namely, optical sectioning SIM (OS-SIM) and superresolution SIM (SR-SIM), and summarize their implementation modalities. We then provide a brief overview of existing OS-SIM processing algorithms and review the development of SR-SIM reconstruction algorithms, focusing primarily on 2D-SIM, 3D-SIM, and blind-SIM. To showcase the state-of-the-art development of SIM systems and assist users in selecting a commercial SIM system for a specific application, we compare the features of representative off-the-shelf SIM systems. Finally, we provide perspectives on the potential future developments of SIM.
Collapse
Affiliation(s)
- Xin Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Suyi Zhong
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Yiwei Hou
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Ruijie Cao
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Wenyi Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multidimension & Multiscale Computational Photography, Tsinghua University, Beijing, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, China
| | - Donghyun Kim
- School of Electrical and Electronic Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Korea
| | - Peng Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China.
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China.
| |
Collapse
|
32
|
Chukrallah LG, Potgieter S, Chueh L, Snyder EM. Two RNA binding proteins, ADAD2 and RNF17, interact to form a heterogeneous population of novel meiotic germ cell granules with developmentally dependent organelle association. PLoS Genet 2023; 19:e1010519. [PMID: 37428816 PMCID: PMC10359003 DOI: 10.1371/journal.pgen.1010519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/20/2023] [Accepted: 06/17/2023] [Indexed: 07/12/2023] Open
Abstract
Mammalian male germ cell differentiation relies on complex RNA biogenesis events, many of which occur in non-membrane bound organelles termed RNA germ cell granules that are rich in RNA binding proteins (RBPs). Though known to be required for male germ cell differentiation, we understand little of the relationships between the numerous granule subtypes. ADAD2, a testis specific RBP, is required for normal male fertility and forms a poorly characterized granule in meiotic germ cells. This work aimed to understand the role of ADAD2 granules in male germ cell differentiation by clearly defining their molecular composition and relationship to other granules. Biochemical analyses identified RNF17, a testis specific RBP that forms meiotic male germ cell granules, as an ADAD2-interacting protein. Phenotypic analysis of Adad2 and Rnf17 mutants identified a rare post-meiotic chromatin defect, suggesting shared biological roles. ADAD2 and RNF17 were found to be dependent on one another for granularization and together form a previously unstudied set of germ cell granules. Based on co-localization studies with well-characterized granule RBPs and organelle-specific markers, a subset of the ADAD2-RNF17 granules are found to be associated with the intermitochondrial cement and piRNA biogenesis. In contrast, a second, morphologically distinct population of ADAD2-RNF17 granules co-localized with the translation regulators NANOS1 and PUM1, along with the molecular chaperone PDI. These large granules form a unique funnel-shaped structure that displays distinct protein subdomains and is tightly associated with the endoplasmic reticulum. Developmental studies suggest the different granule populations represent different phases of a granule maturation process. Lastly, a double Adad2-Rnf17 mutant model suggests the interaction between ADAD2 and RNF17, as opposed to loss of either, is the likely driver of the Adad2 and Rnf17 mutant phenotypes. These findings shed light on the relationship between germ cell granule pools and define new genetic approaches to their study.
Collapse
Affiliation(s)
- Lauren G. Chukrallah
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sarah Potgieter
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Lisa Chueh
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Elizabeth M. Snyder
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| |
Collapse
|
33
|
Yun H, Jung M, Lee H, Jung S, Kim T, Kim N, Park SY, Kim WJ, Mun JY, Yoo JY. Homotypic SCOTIN assemblies form ER-endosome membrane contacts and regulate endosome dynamics. EMBO Rep 2023:e56538. [PMID: 37377038 PMCID: PMC10398665 DOI: 10.15252/embr.202256538] [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: 11/23/2022] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
The ER regulates the spatiotemporal organization of endolysosomal systems by membrane contact. In addition to tethering via heterotypic interactions on both organelles, we present a novel ER-endosome tethering mechanism mediated by homotypic interactions. The single-pass transmembrane protein SCOTIN is detected in the membrane of the ER and endosomes. In SCOTIN-knockout (KO) cells, the ER-late endosome contacts are reduced, and the perinuclear positioning of endosomes is disturbed. The cytosolic proline-rich domain (PRD) of SCOTIN forms homotypic assemblies in vitro and is necessary for ER-endosome membrane tethering in cells. A region of 28 amino acids spanning 150-177 within the SCOTIN PRD is essential to elicit membrane tethering and endosomal dynamics, as verified by reconstitution in SCOTIN-KO cells. The assembly of SCOTIN (PRD) is sufficient to mediate membrane tethering, as purified SCOTIN (PRD), but not SCOTIN (PRDΔ150-177), brings two different liposomes closer in vitro. Using organelle-specific targeting of a chimeric PRD domain shows that only the presence on both organellar membranes enables the ER-endosome membrane contact, indicating that the assembly of SCOTIN on heterologous membranes mediates organelle tethering.
Collapse
Affiliation(s)
- Hyeri Yun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hojin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Taehyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Won Jong Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| |
Collapse
|
34
|
Lipowsky R, Pramanik S, Benk AS, Tarnawski M, Spatz JP, Dimova R. Elucidating the Morphology of the Endoplasmic Reticulum: Puzzles and Perspectives. ACS NANO 2023. [PMID: 37377213 DOI: 10.1021/acsnano.3c01338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Artificial or synthetic organelles are a key challenge for bottom-up synthetic biology. So far, synthetic organelles have typically been based on spherical membrane compartments, used to spatially confine selected chemical reactions. In vivo, these compartments are often far from being spherical and can exhibit rather complex architectures. A particularly fascinating example is provided by the endoplasmic reticulum (ER), which extends throughout the whole cell by forming a continuous network of membrane nanotubes connected by three-way junctions. The nanotubes have a typical diameter of between 50 and 100 nm. In spite of much experimental progress, several fundamental aspects of the ER morphology remain elusive. A long-standing puzzle is the straight appearance of the tubules in the light microscope, which form irregular polygons with contact angles close to 120°. Another puzzling aspect is the nanoscopic shapes of the tubules and junctions, for which very different images have been obtained by electron microcopy and structured illumination microscopy. Furthermore, both the formation and maintenance of the reticular networks require GTP and GTP-hydrolyzing membrane proteins. In fact, the networks are destroyed by the fragmentation of nanotubes when the supply of GTP is interrupted. Here, it is argued that all of these puzzling observations are intimately related to each other and to the dimerization of two membrane proteins anchored to the same membrane. So far, the functional significance of this dimerization process remained elusive and, thus, seemed to waste a lot of GTP. However, this process can generate an effective membrane tension that stabilizes the irregular polygonal geometry of the reticular networks and prevents the fragmentation of their tubules, thereby maintaining the integrity of the ER. By incorporating the GTP-hydrolyzing membrane proteins into giant unilamellar vesicles, the effective membrane tension will become accessible to systematic experimental studies.
Collapse
Affiliation(s)
- Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Shreya Pramanik
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Amelie S Benk
- Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | | | - Joachim P Spatz
- Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| |
Collapse
|
35
|
Kasberg W, Luong P, Hanna MG, Minushkin K, Tsao A, Shankar R, Block S, Audhya A. The Sar1 GTPase is dispensable for COPII-dependent cargo export from the ER. Cell Rep 2023; 42:112635. [PMID: 37300835 PMCID: PMC10592460 DOI: 10.1016/j.celrep.2023.112635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/21/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Coat protein complex II (COPII) plays an integral role in the packaging of secretory cargoes within membrane-enclosed transport carriers that leave the endoplasmic reticulum (ER) from discrete subdomains. Lipid bilayer remodeling necessary for this process is driven initially by membrane penetration mediated by the Sar1 GTPase and further stabilized by assembly of a multilayered complex of several COPII proteins. However, the relative contributions of these distinct factors to transport carrier formation and protein trafficking remain unclear. Here, we demonstrate that anterograde cargo transport from the ER continues in the absence of Sar1, although the efficiency of this process is dramatically reduced. Specifically, secretory cargoes are retained nearly five times longer at ER subdomains when Sar1 is depleted, but they ultimately remain capable of being translocated to the perinuclear region of cells. Taken together, our findings highlight alternative mechanisms by which COPII promotes transport carrier biogenesis.
Collapse
Affiliation(s)
- William Kasberg
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Peter Luong
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Michael G Hanna
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Kayla Minushkin
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Annabelle Tsao
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Raakhee Shankar
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Samuel Block
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.
| |
Collapse
|
36
|
Wen K, Gao Z, Liu R, Fang X, Ma Y, Zheng J, An S, Kozacki T, Gao P. Structured illumination phase and fluorescence microscopy for bioimaging. APPLIED OPTICS 2023; 62:4871-4879. [PMID: 37707263 DOI: 10.1364/ao.486718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/14/2023] [Indexed: 09/15/2023]
Abstract
This study presents a dual-modality microscopic imaging approach that combines quantitative phase microscopy and fluorescence microscopy based on structured illumination (SI) to provide structural and functional information for the same sample. As the first imaging modality, structured illumination digital holographic microscopy (SI-DHM) is implemented along the transmission beam path. SI-DHM acts as a label-free, noninvasive approach and provides high-contrast and quantitative phase images utilizing the refractive index contrast of the inner structures of samples against the background. As the second imaging modality, structured illumination (fluorescence) microscopy (SIM) is constructed along the reflection beam path. SIM utilizes fluorescent labeling and provides super-resolution images for specific functional structures of samples. We first experimentally demonstrated phase imaging of SI-DHM on rice leaves and fluorescence (SIM) imaging on mouse kidney sections. Then, we demonstrated dual-modality imaging of biological samples, using DHM to acquire the overall cell morphology and SIM to obtain specific functional structures. These results prove that the proposed technique is of great importance in biomedical studies, such as providing insight into cell physiology by visualizing and quantifying subcellular structures.
Collapse
|
37
|
Xie Y, Zhang Y, Wang Y, Feng Y. Mechanism and Modulation of SidE Family Proteins in the Pathogenesis of Legionella pneumophila. Pathogens 2023; 12:pathogens12040629. [PMID: 37111515 PMCID: PMC10143409 DOI: 10.3390/pathogens12040629] [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: 02/19/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Legionella pneumophila is the causative agent of Legionnaires' disease, causing fever and lung infection, with a death rate up to 15% in severe cases. In the process of infection, Legionella pneumophila secretes over 330 effectors into host cell via the Dot/Icm type IV secretion system to modulate multiple host cellular physiological processes, thereby changing the environment of the host cell and promoting the growth and propagation of the bacterium. Among these effector proteins, SidE family proteins from Legionella pneumophila catalyze a non-canonical ubiquitination reaction, which combines mono-ADP-ribosylation and phosphodiesterase activities together to attach ubiquitin onto substrates. Meanwhile, the activity of SidE family proteins is also under multiple modulations by other effectors. Herein we summarize the key insights into recent studies in this area, emphasizing the tight link between the modular structure of SidE family proteins and the pathogen virulence as well as the fundamental mechanism and modulation network for further extensive research.
Collapse
Affiliation(s)
- Yongchao Xie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| |
Collapse
|
38
|
Küppers M, Albrecht D, Kashkanova AD, Lühr J, Sandoghdar V. Confocal interferometric scattering microscopy reveals 3D nanoscopic structure and dynamics in live cells. Nat Commun 2023; 14:1962. [PMID: 37029107 PMCID: PMC10081331 DOI: 10.1038/s41467-023-37497-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023] Open
Abstract
Bright-field light microscopy and related phase-sensitive techniques play an important role in life sciences because they provide facile and label-free insights into biological specimens. However, lack of three-dimensional imaging and low sensitivity to nanoscopic features hamper their application in many high-end quantitative studies. Here, we demonstrate that interferometric scattering (iSCAT) microscopy operated in the confocal mode provides unique label-free solutions for live-cell studies. We reveal the nanometric topography of the nuclear envelope, quantify the dynamics of the endoplasmic reticulum, detect single microtubules, and map nanoscopic diffusion of clathrin-coated pits undergoing endocytosis. Furthermore, we introduce the combination of confocal and wide-field iSCAT modalities for simultaneous imaging of cellular structures and high-speed tracking of nanoscopic entities such as single SARS-CoV-2 virions. We benchmark our findings against simultaneously acquired fluorescence images. Confocal iSCAT can be readily implemented as an additional contrast mechanism in existing laser scanning microscopes. The method is ideally suited for live studies on primary cells that face labeling challenges and for very long measurements beyond photobleaching times.
Collapse
Affiliation(s)
- Michelle Küppers
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - David Albrecht
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Anna D Kashkanova
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Jennifer Lühr
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany.
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058, Erlangen, Germany.
| |
Collapse
|
39
|
Wang P, Duckney P, Gao E, Hussey PJ, Kriechbaumer V, Li C, Zang J, Zhang T. Keep in contact: multiple roles of endoplasmic reticulum-membrane contact sites and the organelle interaction network in plants. THE NEW PHYTOLOGIST 2023; 238:482-499. [PMID: 36651025 DOI: 10.1111/nph.18745] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Functional regulation and structural maintenance of the different organelles in plants contribute directly to plant development, reproduction and stress responses. To ensure these activities take place effectively, cells have evolved an interconnected network amongst various subcellular compartments, regulating rapid signal transduction and the exchange of biomaterial. Many proteins that regulate membrane connections have recently been identified in plants, and this is the first step in elucidating both the mechanism and function of these connections. Amongst all organelles, the endoplasmic reticulum is the key structure, which likely links most of the different subcellular compartments through membrane contact sites (MCS) and the ER-PM contact sites (EPCS) have been the most intensely studied in plants. However, the molecular composition and function of plant MCS are being found to be different from other eukaryotic systems. In this article, we will summarise the most recent advances in this field and discuss the mechanism and biological relevance of these essential links in plants.
Collapse
Affiliation(s)
- Pengwei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Patrick Duckney
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Erlin Gao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Patrick J Hussey
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Chengyang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jingze Zang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Tong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| |
Collapse
|
40
|
Lu M, Christensen CN, Weber JM, Konno T, Läubli NF, Scherer KM, Avezov E, Lio P, Lapkin AA, Kaminski Schierle GS, Kaminski CF. ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology. Nat Methods 2023; 20:569-579. [PMID: 36997816 DOI: 10.1038/s41592-023-01815-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 02/10/2023] [Indexed: 04/01/2023]
Abstract
The ability to quantify structural changes of the endoplasmic reticulum (ER) is crucial for understanding the structure and function of this organelle. However, the rapid movement and complex topology of ER networks make this challenging. Here, we construct a state-of-the-art semantic segmentation method that we call ERnet for the automatic classification of sheet and tubular ER domains inside individual cells. Data are skeletonized and represented by connectivity graphs, enabling precise and efficient quantification of network connectivity. ERnet generates metrics on topology and integrity of ER structures and quantifies structural change in response to genetic or metabolic manipulation. We validate ERnet using data obtained by various ER-imaging methods from different cell types as well as ground truth images of synthetic ER structures. ERnet can be deployed in an automatic high-throughput and unbiased fashion and identifies subtle changes in ER phenotypes that may inform on disease progression and response to therapy.
Collapse
Affiliation(s)
- Meng Lu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Cambridge Infinitus Research Centre, University of Cambridge, Cambridge, UK
| | - Charles N Christensen
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Artificial Intelligence Group, Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | - Jana M Weber
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Delft Bioinformatics Lab, Intelligent Systems Department, Delft University of Technology, Delft, the Netherlands
| | - Tasuku Konno
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Nino F Läubli
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Katharina M Scherer
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Edward Avezov
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Pietro Lio
- Artificial Intelligence Group, Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | - Alexei A Lapkin
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Cambridge Infinitus Research Centre, University of Cambridge, Cambridge, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.
- Cambridge Infinitus Research Centre, University of Cambridge, Cambridge, UK.
| |
Collapse
|
41
|
Fang X, Wen K, An S, Zheng J, Li J, Zalevsky Z, Gao P. Reconstruction algorithm using 2N+1 raw images for structured illumination microscopy. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2023; 40:765-773. [PMID: 37132974 DOI: 10.1364/josaa.483884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This paper presents a structured illumination microscopy (SIM) reconstruction algorithm that allows the reconstruction of super-resolved images with 2N + 1 raw intensity images, with N being the number of structured illumination directions used. The intensity images are recorded after using a 2D grating for the projection fringe and a spatial light modulator to select two orthogonal fringe orientations and perform phase shifting. Super-resolution images can be reconstructed from the five intensity images, enhancing the imaging speed and reducing the photobleaching by 17%, compared to conventional two-direction and three-step phase-shifting SIM. We believe the proposed technique will be further developed and widely applied in many fields.
Collapse
|
42
|
Sun N, Jia Y, Bai S, Li Q, Dai L, Li J. The power of super-resolution microscopy in modern biomedical science. Adv Colloid Interface Sci 2023; 314:102880. [PMID: 36965225 DOI: 10.1016/j.cis.2023.102880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Super-resolution microscopy (SRM) technology that breaks the diffraction limit has revolutionized the field of cell biology since its appearance, which enables researchers to visualize cellular structures with nanometric resolution, multiple colors and single-molecule sensitivity. With the flourishing development of hardware and the availability of novel fluorescent probes, the impact of SRM has already gone beyond cell biology and extended to nanomedicine, material science and nanotechnology, and remarkably boosted important breakthroughs in these fields. In this review, we will mainly highlight the power of SRM in modern biomedical science, discussing how these SRM techniques revolutionize the way we understand cell structures, biomaterials assembly and how assembled biomaterials interact with cellular organelles, and finally their promotion to the clinical pre-diagnosis. Moreover, we also provide an outlook on the current technical challenges and future improvement direction of SRM. We hope this review can provide useful information, inspire new ideas and propel the development both from the perspective of SRM techniques and from the perspective of SRM's applications.
Collapse
Affiliation(s)
- Nan Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Qi Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences, Beijing 100190, China
| | - Luru Dai
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049.
| |
Collapse
|
43
|
Han K, Huang S, Kong J, Yang Y, Shi L, Ci Y. A novel fluorescent endoplasmic reticulum marker for super-resolution imaging in live cells. FEBS Lett 2023; 597:693-701. [PMID: 36694281 DOI: 10.1002/1873-3468.14581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/26/2023]
Abstract
Endoplasmic reticulum (ER) is a highly complicated and dynamic organelle that actively changes its shape and communicates with other organelles. Visualization of ER in live cells is of great importance to understand cellular activities. Here, we designed a novel ER marker, RR-mNeonGreen, which comprised an N-terminal ER retention signal, a bright fluorescent protein (mNeonGreen), and a C-terminal transmembrane region. Colocalization of RR-mNeonGreen with mCherry-KDEL verified that RR-mNeonGreen perfectly labeled the ER. RR-mNeonGreen showed better continuity of ER tubules when imaged by super-resolution microscopy. Moreover, RR-mNeonGreen is competent for live-cell imaging of ER dynamics and tracing of the interaction between ER and mitochondria at high spatiotemporal resolution. In summary, RR-mNeonGreen is a novel ER marker for super-resolution live-cell imaging with multiple merits.
Collapse
Affiliation(s)
- Kai Han
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Shuhan Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Jie Kong
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Lei Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yali Ci
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| |
Collapse
|
44
|
Zheng Y, Ye Z, Xiao Y. Subtle Structural Translation Magically Modulates the Super-Resolution Imaging of Self-Blinking Rhodamines. Anal Chem 2023; 95:4172-4179. [PMID: 36787420 DOI: 10.1021/acs.analchem.2c05298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The evolution of super-resolution imaging techniques is benefited from the ongoing competition for optimal rhodamine fluorophores. Yet, it seems blind to construct the desired rhodamine molecule matching the imaging need without the knowledge on imaging impact of even the minimum structural translation. Herein, we have designed a pair of self-blinking sulforhodamines (STMR and SRhB) with the bare distinction of methyl or ethyl substituents and engineered them with Halo protein ligands. Although the two possess similar spectral properties (λab, λfl, ϕ, etc.), they demonstrated unique single-molecule characteristics preferring to individual imaging applications. Experimentally, STMR with high emissive rates was qualified for imaging structures with rapid dynamics (endoplasmic reticulum, and mitochondria), and SRhB with prolonged on-times and photostability was suited for relatively "static" nuclei and microtubules. Using this new knowledge, the mitochondrial morphology during apoptosis and ferroptosis was first super-resolved by STMR. Our study highlights the significance of even the smallest structural modification to the modulation of super-resolution imaging performance and would provide insights for future fluorophore design.
Collapse
Affiliation(s)
- Ying Zheng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Zhiwei Ye
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| |
Collapse
|
45
|
Berlin I, Sapmaz A, Stévenin V, Neefjes J. Ubiquitin and its relatives as wizards of the endolysosomal system. J Cell Sci 2023; 136:288517. [PMID: 36825571 PMCID: PMC10022685 DOI: 10.1242/jcs.260101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The endolysosomal system comprises a dynamic constellation of vesicles working together to sense and interpret environmental cues and facilitate homeostasis. Integrating extracellular information with the internal affairs of the cell requires endosomes and lysosomes to be proficient in decision-making: fusion or fission; recycling or degradation; fast transport or contacts with other organelles. To effectively discriminate between these options, the endolysosomal system employs complex regulatory strategies that crucially rely on reversible post-translational modifications (PTMs) with ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. The cycle of conjugation, recognition and removal of different Ub- and Ubl-modified states informs cellular protein stability and behavior at spatial and temporal resolution and is thus well suited to finetune macromolecular complex assembly and function on endolysosomal membranes. Here, we discuss how ubiquitylation (also known as ubiquitination) and its biochemical relatives orchestrate endocytic traffic and designate cargo fate, influence membrane identity transitions and support formation of membrane contact sites (MCSs). Finally, we explore the opportunistic hijacking of Ub and Ubl modification cascades by intracellular bacteria that remodel host trafficking pathways to invade and prosper inside cells.
Collapse
Affiliation(s)
- Ilana Berlin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Virginie Stévenin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Jacques Neefjes
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| |
Collapse
|
46
|
Arruda AP, Parlakgül G. Endoplasmic Reticulum Architecture and Inter-Organelle Communication in Metabolic Health and Disease. Cold Spring Harb Perspect Biol 2023; 15:cshperspect.a041261. [PMID: 35940911 PMCID: PMC9899651 DOI: 10.1101/cshperspect.a041261] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The endoplasmic reticulum (ER) is a key organelle involved in the regulation of lipid and glucose metabolism, proteostasis, Ca2+ signaling, and detoxification. The structural organization of the ER is very dynamic and complex, with distinct subdomains such as the nuclear envelope and the peripheral ER organized into ER sheets and tubules. ER also forms physical contact sites with all other cellular organelles and with the plasma membrane. Both form and function of the ER are highly adaptive, with a potent capacity to respond to transient changes in environmental cues such as nutritional fluctuations. However, under obesity-induced chronic stress, the ER fails to adapt, leading to ER dysfunction and the development of metabolic pathologies such as insulin resistance and fatty liver disease. Here, we discuss how the remodeling of ER structure and contact sites with other organelles results in diversification of metabolic function and how perturbations to this structural flexibility by chronic overnutrition contribute to ER dysfunction and metabolic pathologies in obesity.
Collapse
Affiliation(s)
- Ana Paula Arruda
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California 94720, USA.,Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Güneş Parlakgül
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California 94720, USA.,Sabri Ülker Center for Metabolic Research and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| |
Collapse
|
47
|
Fuentes LA, Marin Z, Tyson J, Baddeley D, Bewersdorf J. The nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525608. [PMID: 36747764 PMCID: PMC9900957 DOI: 10.1101/2023.01.26.525608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
UNLABELLED The endoplasmic reticulum’s (ER) structure is directly linked to the many functions of the ER but its formation is not fully understood. We investigate how the ER-membrane curving protein reticulon 4 (Rtn4) localizes to and organizes in the membrane and how that affects local ER structure. We show a strong correlation between the local Rtn4 density and the local ER membrane curvature. Our data further reveal that the typical ER tubule possesses an elliptical cross-section with Rtn4 enriched at either end of the major axis. Rtn4 oligomers are linear-shaped, contain about five copies of the protein, and preferentially orient parallel to the tubule axis. Our observations support a mechanism in which oligomerization leads to an increase of the local Rtn4 concentration with each molecule increasing membrane curvature through a hairpin wedging mechanism. This quantitative analysis of Rtn4 and its effects on the ER membrane result in a new model of tubule shape as it relates to Rtn4. SUMMARY Rtn4 forms linear-shaped oligomers that contain an average of five Rtn4 proteins, localize to the sides of elliptical tubules, prefer orientations near parallel to the tubule axis, and increase local curvature of the ER membrane by increasing local Rtn4 density.
Collapse
Affiliation(s)
- Lukas A. Fuentes
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zach Marin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Jonathan Tyson
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| |
Collapse
|
48
|
Melnyk A, Lang S, Sicking M, Zimmermann R, Jung M. Co-chaperones of the Human Endoplasmic Reticulum: An Update. Subcell Biochem 2023; 101:247-291. [PMID: 36520310 DOI: 10.1007/978-3-031-14740-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In mammalian cells, the rough endoplasmic reticulum (ER) plays central roles in the biogenesis of extracellular plus organellar proteins and in various signal transduction pathways. For these reasons, the ER comprises molecular chaperones, which are involved in import, folding, assembly, export, plus degradation of polypeptides, and signal transduction components, such as calcium channels, calcium pumps, and UPR transducers plus adenine nucleotide carriers/exchangers in the ER membrane. The calcium- and ATP-dependent ER lumenal Hsp70, termed immunoglobulin heavy-chain-binding protein or BiP, is the central player in all these activities and involves up to nine different Hsp40-type co-chaperones, i.e., ER membrane integrated as well as ER lumenal J-domain proteins, termed ERj or ERdj proteins, two nucleotide exchange factors or NEFs (Grp170 and Sil1), and NEF-antagonists, such as MANF. Here we summarize the current knowledge on the ER-resident BiP/ERj chaperone network and focus on the interaction of BiP with the polypeptide-conducting and calcium-permeable Sec61 channel of the ER membrane as an example for BiP action and how its functional cycle is linked to ER protein import and various calcium-dependent signal transduction pathways.
Collapse
Affiliation(s)
- Armin Melnyk
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Sven Lang
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Mark Sicking
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany.
| | - Martin Jung
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| |
Collapse
|
49
|
Kozlov MM, Taraska JW. Generation of nanoscopic membrane curvature for membrane trafficking. Nat Rev Mol Cell Biol 2023; 24:63-78. [PMID: 35918535 DOI: 10.1038/s41580-022-00511-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Curved membranes are key features of intracellular organelles, and their generation involves dynamic protein complexes. Here we describe the fundamental mechanisms such as the hydrophobic insertion, scaffolding and crowding mechanisms these proteins use to produce membrane curvatures and complex shapes required to form intracellular organelles and vesicular structures involved in endocytosis and secretion. For each mechanism, we discuss its cellular functions as well as the underlying physical principles and the specific membrane properties required for the mechanism to be feasible. We propose that the integration of individual mechanisms into a highly controlled, robust process of curvature generation often relies on the assembly of proteins into coats. How cells unify and organize the curvature-generating factors at the nanoscale is presented for three ubiquitous coats central for membrane trafficking in eukaryotes: clathrin-coated pits, caveolae, and COPI and COPII coats. The emerging theme is that these coats arrange and coordinate curvature-generating factors in time and space to dynamically shape membranes to accomplish membrane trafficking within cells.
Collapse
Affiliation(s)
- Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
50
|
Jang W, Puchkov D, Samsó P, Liang Y, Nadler-Holly M, Sigrist SJ, Kintscher U, Liu F, Mamchaoui K, Mouly V, Haucke V. Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function. Science 2022; 378:eabq5209. [PMID: 36520888 DOI: 10.1126/science.abq5209] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cells respond to fluctuating nutrient supply by adaptive changes in organelle dynamics and in metabolism. How such changes are orchestrated on a cell-wide scale is unknown. We show that endosomal signaling lipid turnover by MTM1, a phosphatidylinositol 3-phosphate [PI(3)P] 3-phosphatase mutated in X-linked centronuclear myopathy in humans, controls mitochondrial morphology and function by reshaping the endoplasmic reticulum (ER). Starvation-induced endosomal recruitment of MTM1 impairs PI(3)P-dependent contact formation between tubular ER membranes and early endosomes, resulting in the conversion of ER tubules into sheets, the inhibition of mitochondrial fission, and sustained oxidative metabolism. Our results unravel an important role for early endosomal lipid signaling in controlling ER shape and, thereby, mitochondrial form and function to enable cells to adapt to fluctuating nutrient environments.
Collapse
Affiliation(s)
- Wonyul Jang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Paula Samsó
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - YongTian Liang
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michal Nadler-Holly
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Stephan J Sigrist
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Kamel Mamchaoui
- Centre de Recherche en Myologie, Institut de Myologie, Inserm, Sorbonne Université, 75013 Paris, France
| | - Vincent Mouly
- Centre de Recherche en Myologie, Institut de Myologie, Inserm, Sorbonne Université, 75013 Paris, France
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.,Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| |
Collapse
|