1
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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 2024:114357. [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] [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.
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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.
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2
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Crapart CC, Scott ZC, Konno T, Sharma A, Parutto P, Bailey DMD, Westrate LM, Avezov E, Koslover EF. Luminal transport through intact endoplasmic reticulum limits the magnitude of localized Ca 2+ signals. Proc Natl Acad Sci U S A 2024; 121:e2312172121. [PMID: 38502705 PMCID: PMC10990089 DOI: 10.1073/pnas.2312172121] [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: 07/17/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024] Open
Abstract
The endoplasmic reticulum (ER) forms an interconnected network of tubules stretching throughout the cell. Understanding how ER functionality relies on its structural organization is crucial for elucidating cellular vulnerability to ER perturbations, which have been implicated in several neuronal pathologies. One of the key functions of the ER is enabling Ca[Formula: see text] signaling by storing large quantities of this ion and releasing it into the cytoplasm in a spatiotemporally controlled manner. Through a combination of physical modeling and live-cell imaging, we demonstrate that alterations in ER shape significantly impact its ability to support efficient local Ca[Formula: see text] releases, due to hindered transport of luminal content within the ER. Our model reveals that rapid Ca[Formula: see text] release necessitates mobile luminal buffer proteins with moderate binding strength, moving through a well-connected network of ER tubules. These findings provide insight into the functional advantages of normal ER architecture, emphasizing its importance as a kinetically efficient intracellular Ca[Formula: see text] delivery system.
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Affiliation(s)
- Cécile C. Crapart
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | | | - Tasuku Konno
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | - Aman Sharma
- Department of Physics, University of California, San Diego, La Jolla, CA92130
| | - Pierre Parutto
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | - David M. D. Bailey
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | - Laura M. Westrate
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI49546
| | - Edward Avezov
- UK Dementia Research Institute at the University of Cambridge, CambridgeCB2 0AH, United Kingdom
- Department of Clinical Neurosciences, School of Clinical Medicine, The University of Cambridge, CambridgeCB2 0AH, United Kingdom
| | - Elena F. Koslover
- Department of Physics, University of California, San Diego, La Jolla, CA92130
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3
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Song D, Zhang X, Li B, Sun Y, Mei H, Cheng X, Li J, Cheng X, Fang N. Deep Learning-Assisted Automated Multidimensional Single Particle Tracking in Living Cells. NANO LETTERS 2024; 24:3082-3088. [PMID: 38416583 DOI: 10.1021/acs.nanolett.3c04870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
The translational and rotational dynamics of anisotropic optical nanoprobes revealed in single particle tracking (SPT) experiments offer molecular-level information about cellular activities. Here, we report an automated high-speed multidimensional SPT system integrated with a deep learning algorithm for tracking the 3D orientation of anisotropic gold nanoparticle probes in living cells with high localization precision (<10 nm) and temporal resolution (0.9 ms), overcoming the limitations of rotational tracking under low signal-to-noise ratio (S/N) conditions. This method can resolve the azimuth (0°-360°) and polar angles (0°-90°) with errors of less than 2° on the experimental and simulated data under S/N of ∼4. Even when the S/N approaches the limit of 1, this method still maintains better robustness and noise resistance than the conventional pattern matching methods. The usefulness of this multidimensional SPT system has been demonstrated with a study of the motions of cargos transported along the microtubules within living cells.
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Affiliation(s)
- Dongliang Song
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China, 361005
| | - Xin Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China, 361005
| | - Baoyun Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China, 361005
| | - Yuanfang Sun
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China, 361005
| | - Huihui Mei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China, 361005
| | - Xiaojuan Cheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China, 325035
| | - Jieming Li
- Bristol Myers Squibb Company, New Brunswick, New Jersey 08901, United States
| | - Xiaodong Cheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China, 325035
| | - Ning Fang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China, 361005
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4
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Pain C, Tynan C, Botchway SW, Kriechbaumer V. Variable-Angle Epifluorescence Microscopy for Single-Particle Tracking in the Plant ER. Methods Mol Biol 2024; 2772:273-283. [PMID: 38411821 DOI: 10.1007/978-1-0716-3710-4_20] [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
Single-particle tracking (SPT) of biomolecules in the plant endoplasmic reticulum has the potential to inform on the formation of protein-protein complexes, metabolons, and the transport of molecules through both the ER membrane and lumen. Plant cells are particularly challenging for observing and tracking single molecules due to their unique structure, size, and considerable autofluorescence. However, by using variable-angle or highly inclined epifluorescence microscopy (VAEM) and transient expression in tobacco, it is possible to observe single-particle dynamics in the ER. Selecting the appropriate fluorophore, and ensuring the correct fluorophore density in the ER, is essential for successful SPT. By using tuneable fluorophores, which can be photoconverted and photoactivated, it is possible to vary the density of visible fluorophores in the ER dynamically. Here we describe methods to prepare plant samples for VAEM and two methods for determining and analyzing single-particle tracks from VAEM time series.
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Affiliation(s)
- Charlotte Pain
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Christopher Tynan
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
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5
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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.
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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
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6
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Phuyal S, Romani P, Dupont S, Farhan H. Mechanobiology of organelles: illuminating their roles in mechanosensing and mechanotransduction. Trends Cell Biol 2023; 33:1049-1061. [PMID: 37236902 DOI: 10.1016/j.tcb.2023.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023]
Abstract
Mechanobiology studies the mechanisms by which cells sense and respond to physical forces, and the role of these forces in shaping cells and tissues themselves. Mechanosensing can occur at the plasma membrane, which is directly exposed to external forces, but also in the cell's interior, for example, through deformation of the nucleus. Less is known on how the function and morphology of organelles are influenced by alterations in their own mechanical properties, or by external forces. Here, we discuss recent advances on the mechanosensing and mechanotransduction of organelles, including the endoplasmic reticulum (ER), the Golgi apparatus, the endo-lysosmal system, and the mitochondria. We highlight open questions that need to be addressed to gain a broader understanding of the role of organelle mechanobiology.
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Affiliation(s)
- Santosh Phuyal
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Patrizia Romani
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Sirio Dupont
- Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Hesso Farhan
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
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7
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Quiñones-Frías MC, Ocken DM, Rodal A. High-resolution imaging of presynaptic ER networks in Atlastin mutants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555994. [PMID: 37693578 PMCID: PMC10491308 DOI: 10.1101/2023.09.01.555994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The endoplasmic reticulum (ER) is a continuous organelle that extends to the periphery of neurons and regulates many neuronal functions including neurite outgrowth, neurotransmission, and synaptic plasticity. Mutations in proteins that control ER shape are linked to the neurodegenerative disorder Hereditary Spastic Paraplegia (HSP). However, the ultrastructure and dynamics of the neuronal ER have been under-investigated, particularly at presynaptic terminals. Here we developed new super-resolution and live imaging methods in D. melanogaster larval motor neurons to investigate ER structure at presynaptic terminals from wild-type animals, and in null mutants of the HSP gene Atlastin. Previous studies indicated diffuse localization of an ER lumen marker at Atlastin mutant presynaptic terminals, which was attributed to ER fragmentation. By contrast, we found using an ER membrane marker that the ER in Atlastin mutants formed robust networks. Further, our high-resolution imaging results suggest that overexpression of luminal ER proteins in Atlastin mutants causes their progressive displacement to the cytosol at synapses, perhaps due to proteostatic stress and/or changes in ER membrane integrity. Remarkably, these luminal ER proteins remain correctly localized in cell bodies, axons, and other cell types such as body wall muscles, suggesting that ER tubules at synapses have unique structural and functional characteristics. This displacement phenotype has not been reported in numerous studies of Atlastin in non-neuronal cells, emphasizing the importance of conducting experiments in neurons when investigating the mechanisms leading to upper motor neuron dysfunction in HSP.
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Affiliation(s)
| | - Dina M. Ocken
- Department of Biology, Brandeis University, Waltham, MA
| | - Avital Rodal
- Department of Biology, Brandeis University, Waltham, MA
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8
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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.
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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.
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9
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Michalak M. Calreticulin: Endoplasmic reticulum Ca 2+ gatekeeper. J Cell Mol Med 2023; 28:e17839. [PMID: 37424156 PMCID: PMC10902585 DOI: 10.1111/jcmm.17839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
Endoplasmic reticulum (ER) luminal Ca2+ is vital for the function of the ER and regulates many cellular processes. Calreticulin is a highly conserved, ER-resident Ca2+ binding protein and lectin-like chaperone. Over four decades of studying calreticulin demonstrate that this protein plays a crucial role in maintaining Ca2+ supply under different physiological conditions, in managing access to Ca2+ and how Ca2+ is used depending on the environmental events and in making sure that Ca2+ is not misused. Calreticulin plays a role of ER luminal Ca2+ sensor to manage Ca2+ -dependent ER luminal events including maintaining interaction with its partners, Ca2+ handling molecules, substrates and stress sensors. The protein is strategically positioned in the lumen of the ER from where the protein manages access to and distribution of Ca2+ for many cellular Ca2+ -signalling events. The importance of calreticulin Ca2+ pool extends beyond the ER and includes influence of cellular processes involved in many aspects of cellular pathophysiology. Abnormal handling of the ER Ca2+ contributes to many pathologies from heart failure to neurodegeneration and metabolic diseases.
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Affiliation(s)
- Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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10
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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.
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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
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11
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Groenendyk J, Michalak M. Interplay between calcium and endoplasmic reticulum stress. Cell Calcium 2023; 113:102753. [PMID: 37209448 DOI: 10.1016/j.ceca.2023.102753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/05/2023] [Accepted: 05/06/2023] [Indexed: 05/22/2023]
Abstract
Cellular homeostasis is crucial for the healthy functioning of the organism. Disruption of cellular homeostasis activates endoplasmic reticulum (ER) stress coping responses including the unfolded protein response (UPR). There are three ER resident stress sensors responsible for UPR activation - IRE1α, PERK and ATF6. Ca2+ signaling plays an important role in stress responses including the UPR and the ER is the main Ca2+ storage organelle and a source of Ca2+ for cell signaling. The ER contains many proteins involved in Ca2+ import/export/ storage, Ca2+ movement between different cellular organelles and ER Ca2+ stores refilling. Here we focus on selected aspects of ER Ca2+ homeostasis and its role in activation of the ER stress coping responses.
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Affiliation(s)
- Jody Groenendyk
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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12
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Xiang L, Yan R, Chen K, Li W, Xu K. Single-Molecule Displacement Mapping Unveils Sign-Asymmetric Protein Charge Effects on Intraorganellar Diffusion. NANO LETTERS 2023; 23:1711-1716. [PMID: 36802676 PMCID: PMC10044514 DOI: 10.1021/acs.nanolett.2c04379] [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] [Indexed: 06/18/2023]
Abstract
Using single-molecule displacement/diffusivity mapping (SMdM), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ∼40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, hence a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
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Affiliation(s)
- Limin Xiang
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
- College of Chemistry and Molecular Sciences & TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Rui Yan
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Kun Chen
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Wan Li
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Ke Xu
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
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13
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Xiang L, Yan R, Chen K, Li W, Xu K. Single-molecule displacement mapping unveils sign-asymmetric protein charge effects on intraorganellar diffusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525611. [PMID: 36747807 PMCID: PMC9900983 DOI: 10.1101/2023.01.26.525611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using single-molecule displacement/diffusivity mapping (SM d M), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ~40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, thus a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge, and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
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14
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Parutto P, Heck J, Lu M, Kaminski C, Avezov E, Heine M, Holcman D. High-throughput super-resolution single-particle trajectory analysis reconstructs organelle dynamics and membrane reorganization. CELL REPORTS METHODS 2022; 2:100277. [PMID: 36046627 PMCID: PMC9421586 DOI: 10.1016/j.crmeth.2022.100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/11/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
Abstract
Super-resolution imaging can generate thousands of single-particle trajectories. These data can potentially reconstruct subcellular organization and dynamics, as well as measure disease-linked changes. However, computational methods that can derive quantitative information from such massive datasets are currently lacking. We present data analysis and algorithms that are broadly applicable to reveal local binding and trafficking interactions and organization of dynamic subcellular sites. We applied this analysis to the endoplasmic reticulum and neuronal membrane. The method is based on spatiotemporal segmentation that explores data at multiple levels and detects the architecture and boundaries of high-density regions in areas measuring hundreds of nanometers. By connecting dense regions, we reconstructed the network topology of the endoplasmic reticulum (ER), as well as molecular flow redistribution and the local space explored by trajectories. The presented methods are available as an ImageJ plugin that can be applied to large datasets of overlapping trajectories offering a standard of single-particle trajectory (SPT) metrics.
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Affiliation(s)
- Pierre Parutto
- Group of Data Modeling and Computational Biology, IBENS, Ecole Normale Supérieure, 75005 Paris, France
| | - Jennifer Heck
- Research Group Functional Neurobiology at the Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Meng Lu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Clemens Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Edward Avezov
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
| | - Martin Heine
- Research Group Functional Neurobiology at the Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - David Holcman
- Group of Data Modeling and Computational Biology, IBENS, Ecole Normale Supérieure, 75005 Paris, France
- DAMPT, University of Cambridge, DAMPT and Churchill College, Cambridge CB30DS, UK
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15
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Li W, Kaminski Schierle GS, Lei B, Liu Y, Kaminski CF. Fluorescent Nanoparticles for Super-Resolution Imaging. Chem Rev 2022; 122:12495-12543. [PMID: 35759536 PMCID: PMC9373000 DOI: 10.1021/acs.chemrev.2c00050] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Super-resolution imaging techniques that overcome the diffraction limit of light have gained wide popularity for visualizing cellular structures with nanometric resolution. Following the pace of hardware developments, the availability of new fluorescent probes with superior properties is becoming ever more important. In this context, fluorescent nanoparticles (NPs) have attracted increasing attention as bright and photostable probes that address many shortcomings of traditional fluorescent probes. The use of NPs for super-resolution imaging is a recent development and this provides the focus for the current review. We give an overview of different super-resolution methods and discuss their demands on the properties of fluorescent NPs. We then review in detail the features, strengths, and weaknesses of each NP class to support these applications and provide examples from their utilization in various biological systems. Moreover, we provide an outlook on the future of the field and opportunities in material science for the development of probes for multiplexed subcellular imaging with nanometric resolution.
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Affiliation(s)
- Wei Li
- Key
Laboratory for Biobased Materials and Energy of Ministry of Education,
College of Materials and Energy, South China
Agricultural University, Guangzhou 510642, People’s Republic
of China,Department
of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | | | - Bingfu Lei
- Key
Laboratory for Biobased Materials and Energy of Ministry of Education,
College of Materials and Energy, South China
Agricultural University, Guangzhou 510642, People’s Republic
of China,B. Lei.
| | - Yingliang Liu
- Key
Laboratory for Biobased Materials and Energy of Ministry of Education,
College of Materials and Energy, South China
Agricultural University, Guangzhou 510642, People’s Republic
of China
| | - Clemens F. Kaminski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom,C. F. Kaminski.
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16
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van Krugten J, Danné N, Peterman EJG. A local interplay between diffusion and intraflagellar transport distributes TRPV-channel OCR-2 along C. elegans chemosensory cilia. Commun Biol 2022; 5:720. [PMID: 35858995 PMCID: PMC9300729 DOI: 10.1038/s42003-022-03683-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
To survive, Caenorhabditis elegans depends on sensing soluble chemicals with transmembrane proteins (TPs) in the cilia of its chemosensory neurons. Cilia rely on intraflagellar transport (IFT) to facilitate the distribution of cargo, such as TPs, along the ciliary axoneme. Here, we use fluorescence imaging of living worms and perform single-molecule tracking experiments to elucidate the dynamics underlying the ciliary distribution of the sensory TP OCR-2. Quantitative analysis reveals that the ciliary distribution of OCR-2 depends on an intricate interplay between transport modes that depends on the specific location in the cilium: in dendrite and transition zone, directed transport is predominant. Along the cilium motion is mostly due to normal diffusion together with a small fraction of directed transport, while at the ciliary tip subdiffusion dominates. These insights in the role of IFT and diffusion in ciliary dynamics contribute to a deeper understanding of ciliary signal transduction and chemosensing. Single-molecule tracking of the sensory transmembrane protein OCR-2 in C. elegans reveals an interplay of transport modes during intraflagellar transport in the cilium.
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Affiliation(s)
- Jaap van Krugten
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, 1081 HV, Amsterdam, The Netherlands
| | - Noémie Danné
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, 1081 HV, Amsterdam, The Netherlands.
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17
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Kundu S, Das S, Jaiswal S, Patra A. Molecular to Supramolecular Self-Assembled Luminogens for Tracking the Intracellular Organelle Dynamics. ACS APPLIED BIO MATERIALS 2022; 5:3623-3648. [PMID: 35834795 DOI: 10.1021/acsabm.2c00415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deciphering the dynamics of intracellular organelles has gained immense attention due to their subtle control over diverse, complex biological processes such as cellular metabolism, energy homeostasis, and autophagy. In this context, molecular materials, including small-organic fluorescent probes and their supramolecular self-assembled nano-/microarchitectures, have been employed to explore the diverse intracellular biological events. However, only a handful of fluorescent probes and self-assembled emissive structures have been successfully used to track different organelle's movements, circumventing the issues related to water solubility and long-term photostability. Thus, the water-soluble molecular fluorescent probes and the water-dispersible supramolecular self-assemblies have emerged as promising candidates to explore the trafficking of the organelles under diverse physiological conditions. In this review, we have delineated the recent progress of fluorescent probes and their supramolecular self-assemblies for the elucidation of the dynamics of diverse cellular organelles with a special emphasis on lysosomes, lipid droplets, and mitochondria. Recent advancement in fluorescence lifetime and super-resolution microscopy imaging has also been discussed to investigate the dynamics of organelles. In addition, the fabrication of the next-generation molecular to supramolecular self-assembled luminogens for probing the variation of microenvironments during the trafficking process has been outlined.
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Affiliation(s)
- Subhankar Kundu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Subhadeep Das
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Shilpi Jaiswal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Abhijit Patra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
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18
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Melo EP, Konno T, Farace I, Awadelkareem MA, Skov LR, Teodoro F, Sancho TP, Paton AW, Paton JC, Fares M, Paulo PMR, Zhang X, Avezov E. Stress-induced protein disaggregation in the endoplasmic reticulum catalysed by BiP. Nat Commun 2022; 13:2501. [PMID: 35523806 PMCID: PMC9076838 DOI: 10.1038/s41467-022-30238-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 04/20/2022] [Indexed: 01/31/2023] Open
Abstract
Protein synthesis is supported by cellular machineries that ensure polypeptides fold to their native conformation, whilst eliminating misfolded, aggregation prone species. Protein aggregation underlies pathologies including neurodegeneration. Aggregates’ formation is antagonised by molecular chaperones, with cytoplasmic machinery resolving insoluble protein aggregates. However, it is unknown whether an analogous disaggregation system exists in the Endoplasmic Reticulum (ER) where ~30% of the proteome is synthesised. Here we show that the ER of a variety of mammalian cell types, including neurons, is endowed with the capability to resolve protein aggregates under stress. Utilising a purpose-developed protein aggregation probing system with a sub-organellar resolution, we observe steady-state aggregate accumulation in the ER. Pharmacological induction of ER stress does not augment aggregates, but rather stimulate their clearance within hours. We show that this dissagregation activity is catalysed by the stress-responsive ER molecular chaperone – BiP. This work reveals a hitherto unknow, non-redundant strand of the proteostasis-restorative ER stress response. Aggregation of misfolded proteins underlie dementias. Here, the authors show that stressed cells activate an innate mechanism to resolve aggregates of defective proteins in the endoplasmic reticulum, where a third of cellular proteins are produced.
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Affiliation(s)
- Eduardo Pinho Melo
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK. .,CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Faro, Portugal.
| | - Tasuku Konno
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Ilaria Farace
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Mosab Ali Awadelkareem
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Lise R Skov
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Fernando Teodoro
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Teresa P Sancho
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Fares
- Department of Chemistry, The Pennsylvania State University, University Park, State College, PA, USA
| | - Pedro M R Paulo
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, Lisboa, Portugal
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, State College, PA, USA
| | - Edward Avezov
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge, UK.
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19
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Chambers JE, Zubkov N, Kubánková M, Nixon-Abell J, Mela I, Abreu S, Schwiening M, Lavarda G, López-Duarte I, Dickens JA, Torres T, Kaminski CF, Holt LJ, Avezov E, Huntington JA, George-Hyslop PS, Kuimova MK, Marciniak SJ. Z-α 1-antitrypsin polymers impose molecular filtration in the endoplasmic reticulum after undergoing phase transition to a solid state. SCIENCE ADVANCES 2022; 8:eabm2094. [PMID: 35394846 PMCID: PMC8993113 DOI: 10.1126/sciadv.abm2094] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/16/2022] [Indexed: 05/06/2023]
Abstract
Misfolding of secretory proteins in the endoplasmic reticulum (ER) features in many human diseases. In α1-antitrypsin deficiency, the pathogenic Z variant aberrantly assembles into polymers in the hepatocyte ER, leading to cirrhosis. We show that α1-antitrypsin polymers undergo a liquid:solid phase transition, forming a protein matrix that retards mobility of ER proteins by size-dependent molecular filtration. The Z-α1-antitrypsin phase transition is promoted during ER stress by an ATF6-mediated unfolded protein response. Furthermore, the ER chaperone calreticulin promotes Z-α1-antitrypsin solidification and increases protein matrix stiffness. Single-particle tracking reveals that solidification initiates in cells with normal ER morphology, previously assumed to represent a healthy pool. We show that Z-α1-antitrypsin-induced hypersensitivity to ER stress can be explained by immobilization of ER chaperones within the polymer matrix. This previously unidentified mechanism of ER dysfunction provides a template for understanding a diverse group of related proteinopathies and identifies ER chaperones as potential therapeutic targets.
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Affiliation(s)
- 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
| | - Nikita Zubkov
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Markéta Kubánková
- Department of Chemistry, Imperial College London, Wood Lane, London W12 0BZ, UK
| | - Jonathon Nixon-Abell
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
| | - Susana Abreu
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Max Schwiening
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Giulia Lavarda
- Departamento de Química Orgánica and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Ismael López-Duarte
- Departamento de Química Orgánica and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jennifer A. Dickens
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Tomás Torres
- Departamento de Química Orgánica and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- IMDEA Nanociencia, Campus de Cantoblanco, Madrid 28049, Spain
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
| | - Liam J. Holt
- Institute for Systems Genetics, New York University Grossman School of Medicine, 435 E 30th St, New York, NY 10016, USA
| | - Edward Avezov
- Department of Clinical Neurosciences and UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - James A. Huntington
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine (Neurology), Temerty Faculty of Medicine, University of Toronto, University Health Network, Toronto, ON M5T 0S8, Canada
- Taub Institute For Research on Alzheimer’s Disease and the Ageing Brain, Department of Neurology, Columbia University Irvine Medical Center, 630 West 1/68 Street, New York, NY 10032, USA
| | - Marina K. Kuimova
- Department of Chemistry, Imperial College London, Wood Lane, London W12 0BZ, UK
| | - Stefan J. Marciniak
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
- Royal Papworth Hospital, Cambridge CB2 0AY, UK
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20
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Abstract
Transport of intracellular components relies on a variety of active and passive mechanisms, ranging from the diffusive spreading of small molecules over short distances to motor-driven motion across long distances. The cell-scale behavior of these mechanisms is fundamentally dependent on the morphology of the underlying cellular structures. Diffusion-limited reaction times can be qualitatively altered by the presence of occluding barriers or by confinement in complex architectures, such as those of reticulated organelles. Motor-driven transport is modulated by the architecture of cytoskeletal filaments that serve as transport highways. In this review, we discuss the impact of geometry on intracellular transport processes that fulfill a broad range of functional objectives, including delivery, distribution, and sorting of cellular components. By unraveling the interplay between morphology and transport efficiency, we aim to elucidate key structure-function relationships that govern the architecture of transport systems at the cellular scale. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Anamika Agrawal
- Department of Physics, University of California, San Diego, La Jolla, California, USA;
| | - Zubenelgenubi C Scott
- Department of Physics, University of California, San Diego, La Jolla, California, USA;
| | - Elena F Koslover
- Department of Physics, University of California, San Diego, La Jolla, California, USA;
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21
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Direct imaging of intraflagellar-transport turnarounds reveals that motors detach, diffuse, and reattach to opposite-direction trains. Proc Natl Acad Sci U S A 2021; 118:2115089118. [PMID: 34732580 PMCID: PMC8609318 DOI: 10.1073/pnas.2115089118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 12/16/2022] Open
Abstract
Primary cilia are important organelles that exist in almost all eukaryotic cells. Intraflagellar transport (IFT) is a motor-protein–driven bidirectional intracellular transport mechanism in cilia. Previous studies have shown that motors in Caenorhabditis elegans chemosensory cilia undergo rapid turnarounds to effectively work together in driving orderly IFT. The mechanism of motor turnarounds has, however, remained unclear. Here, using a combination of advanced fluorescence imaging and single-molecule analysis, we directly show that the individual turnarounds are due to motors switching between opposite-direction IFT trains. Furthermore, we show that switching events consist of motors detaching from a train, diffusing to another one followed by attachment. This directly demonstrates that motors switch trains by diffusion, which clarifies the mechanism of motor turnarounds. Intraflagellar transport (IFT), a bidirectional intracellular transport mechanism in cilia, relies on the cooperation of kinesin-2 and IFT-dynein motors. In Caenorhabditis elegans chemosensory cilia, motors undergo rapid turnarounds to effectively work together in driving IFT. Here, we push the envelope of fluorescence imaging to obtain insight into the underlying mechanism of motor turnarounds. We developed an alternating dual-color imaging system that allows simultaneous single-molecule imaging of kinesin-II turnarounds and ensemble imaging of IFT trains. This approach allowed direct visualization of motor detachment and reattachment during turnarounds and accordingly demonstrated that the turnarounds are actually single-motor switching between opposite-direction IFT trains rather than the behaviors of motors moving independently of IFT trains. We further improved the time resolution of single-motor imaging up to 30 ms to zoom into motor turnarounds, revealing diffusion during motor turnarounds, which unveils the mechanism of motor switching trains: detach–diffuse–attach. The subsequent single-molecule analysis of turnarounds unveiled location-dependent diffusion coefficients and diffusion times for both kinesin-2 and IFT-dynein motors. From correlating the diffusion times with IFT train frequencies, we estimated that kinesins tend to attach to the next train passing in the opposite direction. IFT-dynein, however, diffuses longer and lets one or two trains pass before attaching. This might be a direct consequence of the lower diffusion coefficient of the larger IFT-dynein. Our results provide important insights into how motors can cooperate to drive intracellular transport.
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22
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Intertwined and Finely Balanced: Endoplasmic Reticulum Morphology, Dynamics, Function, and Diseases. Cells 2021; 10:cells10092341. [PMID: 34571990 PMCID: PMC8472773 DOI: 10.3390/cells10092341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) is an organelle that is responsible for many essential subcellular processes. Interconnected narrow tubules at the periphery and thicker sheet-like regions in the perinuclear region are linked to the nuclear envelope. It is becoming apparent that the complex morphology and dynamics of the ER are linked to its function. Mutations in the proteins involved in regulating ER structure and movement are implicated in many diseases including neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis (ALS). The ER is also hijacked by pathogens to promote their replication. Bacteria such as Legionella pneumophila and Chlamydia trachomatis, as well as the Zika virus, bind to ER morphology and dynamics-regulating proteins to exploit the functions of the ER to their advantage. This review covers our understanding of ER morphology, including the functional subdomains and membrane contact sites that the organelle forms. We also focus on ER dynamics and the current efforts to quantify ER motion and discuss the diseases related to ER morphology and dynamics.
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23
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Perkins HT, Allan VJ, Waigh TA. Network organisation and the dynamics of tubules in the endoplasmic reticulum. Sci Rep 2021; 11:16230. [PMID: 34376706 PMCID: PMC8355327 DOI: 10.1038/s41598-021-94901-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) is a eukaryotic subcellular organelle composed of tubules and sheet-like areas of membrane connected at junctions. The tubule network is highly dynamic and undergoes rapid and continual rearrangement. There are currently few tools to evaluate network organisation and dynamics. We quantified ER network organisation in Vero and MRC5 cells, and developed an analysis workflow for dynamics of established tubules in live cells. The persistence length, tubule length, junction coordination number and angles of the network were quantified. Hallmarks of imbalances in ER tension, indications of interactions with microtubules and other subcellular organelles, and active dynamics were observed. Clear differences in dynamic behaviour were observed for established tubules at different positions within the cell using itemset mining. We found that tubules with activity-driven fluctuations were more likely to be located away from the cell periphery and a population of peripheral tubules with no signs of active motion was found.
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Affiliation(s)
- Hannah T Perkins
- Biological Physics, Department of Physics and Astronomy, Schuster Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Michael Smith Building, The University of Manchester, Dover Street, Manchester, M13 9PT, UK
| | - Victoria J Allan
- Division of Molecular and Cellular Function, School of Biological Sciences, Michael Smith Building, The University of Manchester, Dover Street, Manchester, M13 9PT, UK.
| | - Thomas A Waigh
- Biological Physics, Department of Physics and Astronomy, Schuster Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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24
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Scott ZC, Brown AI, Mogre SS, Westrate LM, Koslover EF. Diffusive search and trajectories on tubular networks: a propagator approach. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:80. [PMID: 34143351 PMCID: PMC8213674 DOI: 10.1140/epje/s10189-021-00083-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/25/2021] [Indexed: 05/11/2023]
Abstract
Several organelles in eukaryotic cells, including mitochondria and the endoplasmic reticulum, form interconnected tubule networks extending throughout the cell. These tubular networks host many biochemical pathways that rely on proteins diffusively searching through the network to encounter binding partners or localized target regions. Predicting the behavior of such pathways requires a quantitative understanding of how confinement to a reticulated structure modulates reaction kinetics. In this work, we develop both exact analytical methods to compute mean first passage times and efficient kinetic Monte Carlo algorithms to simulate trajectories of particles diffusing in a tubular network. Our approach leverages exact propagator functions for the distribution of transition times between network nodes and allows large simulation time steps determined by the network structure. The methodology is applied to both synthetic planar networks and organelle network structures, demonstrating key general features such as the heterogeneity of search times in different network regions and the functional advantage of broadly distributing target sites throughout the network. The proposed algorithms pave the way for future exploration of the interrelationship between tubular network structure and biomolecular reaction kinetics.
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Affiliation(s)
- Zubenelgenubi C Scott
- Department of Physics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aidan I Brown
- Department of Physics, Ryerson University, Toronto, Canada
| | - Saurabh S Mogre
- Department of Physics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - 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, La Jolla, CA, 92093, USA.
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25
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Ivchenkov DV, Kuzmin PI, Galimzyanov TR, Shnyrova AV, Bashkirov PV, Frolov VA. Nonlinear material and ionic transport through membrane nanotubes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183677. [PMID: 34118214 DOI: 10.1016/j.bbamem.2021.183677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022]
Abstract
Membrane nanotubes (NTs) and their networks play an important role in intracellular membrane transport and intercellular communications. The transport characteristics of the NT lumen resemble those of conventional solid-state nanopores. However, unlike the rigid pores, the soft membrane wall of the NT can be deformed by forces driving the transport through the NT lumen. This intrinsic coupling between the NT geometry and transport properties remains poorly explored. Using synchronized fluorescence microscopy and conductance measurements, we revealed that the NT shape was changed by both electric and hydrostatic forces driving the ionic and solute fluxes through the NT lumen. Far from the shape instability, the strength of the force effect is determined by the lateral membrane tension and is scaled with membrane elasticity so that the NT can be operated as a linear elastic sensor. Near shape instabilities, the transport forces triggered large-scale shape transformations, both stochastic and periodic. The periodic oscillations were coupled to a vesicle passage along the NT axis, resembling peristaltic transport. The oscillations were parametrically controlled by the electric field, making NT a highly nonlinear nanofluidic circuitry element with biological and technological implications.
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Affiliation(s)
- D V Ivchenkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia; Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Institutskiy lane 9, Dolgoprudnyy, Moskow region 141700, Russia
| | - P I Kuzmin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - T R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - A V Shnyrova
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, barrio Sarriena s/n, 48940 Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country, barrio Sarriena s/n, 48940 Leioa, Spain
| | - P V Bashkirov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia; Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Institutskiy lane 9, Dolgoprudnyy, Moskow region 141700, Russia.
| | - V A Frolov
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, barrio Sarriena s/n, 48940 Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country, barrio Sarriena s/n, 48940 Leioa, Spain; Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 6 solairua, 48013 Bilbao, Spain.
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26
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Lin Y, Andersson SB. Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images. PLoS One 2021; 16:e0243115. [PMID: 34019541 PMCID: PMC8139521 DOI: 10.1371/journal.pone.0243115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/03/2021] [Indexed: 11/19/2022] Open
Abstract
Single Particle Tracking (SPT) is a well known class of tools for studying the dynamics of biological macromolecules moving inside living cells. In this paper, we focus on the problem of localization and parameter estimation given a sequence of segmented images. In the standard paradigm, the location of the emitter inside each frame of a sequence of camera images is estimated using, for example, Gaussian fitting (GF), and these locations are linked to provide an estimate of the trajectory. Trajectories are then analyzed by using Mean Square Displacement (MSD) or Maximum Likelihood Estimation (MLE) techniques to determine motion parameters such as diffusion coefficients. However, the problems of localization and parameter estimation are clearly coupled. Motivated by this, we have created an Expectation Maximization (EM) based framework for simultaneous localization and parameter estimation. We demonstrate this framework through two representative methods, namely, Sequential Monte Carlo combined with Expectation Maximization (SMC-EM) and Unscented Kalman Filter combined with Expectation Maximization (U-EM). Using diffusion in two-dimensions as a prototypical example, we conduct quantitative investigations on localization and parameter estimation performance across a wide range of signal to background ratios and diffusion coefficients and compare our methods to the standard techniques based on GF-MSD/MLE. To demonstrate the flexibility of the EM based framework, we do comparisons using two different camera models, an ideal camera with Poisson distributed shot noise but no readout noise, and a camera with both shot noise and the pixel-dependent readout noise that is common to scientific complementary metal-oxide semiconductor (sCMOS) camera. Our results indicate our EM based methods outperform the standard techniques, especially at low signal levels. While U-EM and SMC-EM have similar accuracy, U-EM is significantly more computationally efficient, though the use of the Unscented Kalman Filter limits U-EM to lower diffusion rates.
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Affiliation(s)
- Ye Lin
- Division of Systems Engineering, Boston University, Boston, MA, United States of America
| | - Sean B. Andersson
- Division of Systems Engineering, Boston University, Boston, MA, United States of America
- Department of Mechanical Engineering, Boston University, Boston, MA, United States of America
- * E-mail:
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27
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Kerselidou D, Dohai BS, Nelson DR, Daakour S, De Cock N, Hassoun ZAO, Kim DK, Olivet J, El Assal DC, Jaiswal A, Alzahmi A, Saha D, Pain C, Matthijssens F, Lemaitre P, Herfs M, Chapuis J, Ghesquiere B, Vertommen D, Kriechbaumer V, Knoops K, Lopez-Iglesias C, van Zandvoort M, Lambert JC, Hanson J, Desmet C, Thiry M, Lauersen KJ, Vidal M, Van Vlierberghe P, Dequiedt F, Salehi-Ashtiani K, Twizere JC. Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. SCIENCE ADVANCES 2021; 7:7/19/eabe8349. [PMID: 33962942 PMCID: PMC8104865 DOI: 10.1126/sciadv.abe8349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/18/2021] [Indexed: 05/28/2023]
Abstract
The endoplasmic reticulum (ER) is a central eukaryotic organelle with a tubular network made of hairpin proteins linked by hydrolysis of guanosine triphosphate nucleotides. Among posttranslational modifications initiated at the ER level, glycosylation is the most common reaction. However, our understanding of the impact of glycosylation on the ER structure remains unclear. Here, we show that exostosin-1 (EXT1) glycosyltransferase, an enzyme involved in N-glycosylation, is a key regulator of ER morphology and dynamics. We have integrated multiomics and superresolution imaging to characterize the broad effect of EXT1 inactivation, including the ER shape-dynamics-function relationships in mammalian cells. We have observed that inactivating EXT1 induces cell enlargement and enhances metabolic switches such as protein secretion. In particular, suppressing EXT1 in mouse thymocytes causes developmental dysfunctions associated with the ER network extension. Last, our data illuminate the physical and functional aspects of the ER proteome-glycome-lipidome structure axis, with implications in biotechnology and medicine.
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Affiliation(s)
- Despoina Kerselidou
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Bushra Saeed Dohai
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - David R Nelson
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Nicolas De Cock
- TERRA Teaching and Research Centre, University of Liege, Liege, Belgium
| | - Zahra Al Oula Hassoun
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Dae-Kyum Kim
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Julien Olivet
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - Diana C El Assal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ashish Jaiswal
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Deeya Saha
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Charlotte Pain
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Filip Matthijssens
- Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pierre Lemaitre
- GIGA-I3 Unit, GIGA Institute, University of Liege, Liege, Belgium
| | - Michael Herfs
- GIGA-Cancer Unit, GIGA Institute, University of Liege, Liege, Belgium
| | - Julien Chapuis
- Laboratory of Excellence Distalz, INSERM Unit 1167, Pasteur Institute of Lille, Lille, France
| | - Bart Ghesquiere
- Metabolomics Expertise Center, Center for Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Didier Vertommen
- de Duve Institute, Catholic University of Louvain, Brussels, Belgium
| | - Verena Kriechbaumer
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Kèvin Knoops
- Microscopy CORE Lab, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Carmen Lopez-Iglesias
- Microscopy CORE Lab, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Marc van Zandvoort
- Department of Cell Biology, School for Cardiovascular Diseases (CARIM), School for Nutrition and Translational Research in Metabolism (NUTRIM), School for Mental health and Neuroscience (MHeNS), and School for Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, Netherlands
| | - Jean-Charles Lambert
- Laboratory of Excellence Distalz, INSERM Unit 1167, Pasteur Institute of Lille, Lille, France
| | - Julien Hanson
- GIGA-Molecular Pharmacology, University of Liege, Liege, Belgium
| | | | - Marc Thiry
- Laboratory of cell and tissue Biology, GIGA-Neurosciences, University of Liege, Liege, Belgium
| | - Kyle J Lauersen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Franck Dequiedt
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium.
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium.
- TERRA Teaching and Research Centre, University of Liege, Liege, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
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28
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Christensen CN, Ward EN, Lu M, Lio P, Kaminski CF. ML-SIM: universal reconstruction of structured illumination microscopy images using transfer learning. BIOMEDICAL OPTICS EXPRESS 2021; 12:2720-2733. [PMID: 34123499 PMCID: PMC8176814 DOI: 10.1364/boe.414680] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 05/20/2023]
Abstract
Structured illumination microscopy (SIM) has become an important technique for optical super-resolution imaging because it allows a doubling of image resolution at speeds compatible with live-cell imaging. However, the reconstruction of SIM images is often slow, prone to artefacts, and requires multiple parameter adjustments to reflect different hardware or experimental conditions. Here, we introduce a versatile reconstruction method, ML-SIM, which makes use of transfer learning to obtain a parameter-free model that generalises beyond the task of reconstructing data recorded by a specific imaging system for a specific sample type. We demonstrate the generality of the model and the high quality of the obtained reconstructions by application of ML-SIM on raw data obtained for multiple sample types acquired on distinct SIM microscopes. ML-SIM is an end-to-end deep residual neural network that is trained on an auxiliary domain consisting of simulated images, but is transferable to the target task of reconstructing experimental SIM images. By generating the training data to reflect challenging imaging conditions encountered in real systems, ML-SIM becomes robust to noise and irregularities in the illumination patterns of the raw SIM input frames. Since ML-SIM does not require the acquisition of experimental training data, the method can be efficiently adapted to any specific experimental SIM implementation. We compare the reconstruction quality enabled by ML-SIM with current state-of-the-art SIM reconstruction methods and demonstrate advantages in terms of generality and robustness to noise for both simulated and experimental inputs, thus making ML-SIM a useful alternative to traditional methods for challenging imaging conditions. Additionally, reconstruction of a SIM stack is accomplished in less than 200 ms on a modern graphics processing unit, enabling future applications for real-time imaging. Source code and ready-to-use software for the method are available at http://ML-SIM.github.io.
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Affiliation(s)
- Charles N. Christensen
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Laser Analytics Group, Philippa Fawcett Dr, Cambridge, UK
- University of Cambridge, Department of Computer Science and Technology, Artificial Intelligence Group, JJ Thomson Ave, Cambridge, UK
| | - Edward N. Ward
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Laser Analytics Group, Philippa Fawcett Dr, Cambridge, UK
| | - Meng Lu
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Laser Analytics Group, Philippa Fawcett Dr, Cambridge, UK
| | - Pietro Lio
- University of Cambridge, Department of Computer Science and Technology, Artificial Intelligence Group, JJ Thomson Ave, Cambridge, UK
| | - Clemens F. Kaminski
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Laser Analytics Group, Philippa Fawcett Dr, Cambridge, UK
- Corresponding author:
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29
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Lujan P, Angulo-Capel J, Chabanon M, Campelo F. Interorganelle communication and membrane shaping in the early secretory pathway. Curr Opin Cell Biol 2021; 71:95-102. [PMID: 33711785 DOI: 10.1016/j.ceb.2021.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/25/2021] [Accepted: 01/30/2021] [Indexed: 01/02/2023]
Abstract
Biomolecules in the secretory pathway use membrane trafficking for reaching their final intracellular destination or for secretion outside the cell. This highly dynamic and multipartite process involves different organelles that communicate to one another while maintaining their identity, shape, and function. Recent studies unraveled new mechanisms of interorganelle communication that help organize the early secretory pathway. We highlight how the spatial proximity between endoplasmic reticulum (ER) exit sites and early Golgi elements provides novel means of ER-Golgi communication for ER export. We also review recent findings on how membrane contact sites between the ER and the trans-Golgi membranes can sustain anterograde traffic out of the Golgi complex.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Jessica Angulo-Capel
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Morgan Chabanon
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain; Universitat Politècnica de Catalunya-BarcelonaTech, E-08034, Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain.
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30
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Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues. Nat Protoc 2021; 16:1600-1628. [PMID: 33627844 DOI: 10.1038/s41596-020-00471-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/24/2020] [Indexed: 01/31/2023]
Abstract
Super-resolution microscopy techniques have pushed the limit of optical imaging to unprecedented spatial resolutions. However, one of the frontiers in nanoscopy is its application to intact living organisms. Here we describe the implementation and application of super-resolution single-particle tracking photoactivated localization microscopy (sptPALM) to probe single-molecule dynamics of membrane proteins in live roots of the model plant Arabidopsis thaliana. We first discuss the advantages and limitations of sptPALM for studying the diffusion properties of membrane proteins and compare this to fluorescence recovery after photobleaching (FRAP) and fluorescence correlation spectroscopy (FCS). We describe the technical details for handling and imaging the samples for sptPALM, with a particular emphasis on the specificity of imaging plant cells, such as their thick cell walls or high degree of autofluorescence. We then provide a practical guide from data collection to image analyses. In particular, we introduce our sptPALM_viewer software and describe how to install and use it for analyzing sptPALM experiments. Finally, we report an R statistical analysis pipeline to analyze and compare sptPALM experiments. Altogether, this protocol should enable plant researchers to perform sptPALM using a benchmarked reproducible protocol. Routinely, the procedure takes 3-4 h of imaging followed by 3-4 d of image processing and data analysis.
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31
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Cremer T, Neefjes J, Berlin I. The journey of Ca 2+ through the cell - pulsing through the network of ER membrane contact sites. J Cell Sci 2020; 133:133/24/jcs249136. [PMID: 33376155 DOI: 10.1242/jcs.249136] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Calcium is the third most abundant metal on earth, and the fundaments of its homeostasis date back to pre-eukaryotic life forms. In higher organisms, Ca2+ serves as a cofactor for a wide array of (enzymatic) interactions in diverse cellular contexts and constitutes the most important signaling entity in excitable cells. To enable responsive behavior, cytosolic Ca2+ concentrations are kept low through sequestration into organellar stores, particularly the endoplasmic reticulum (ER), but also mitochondria and lysosomes. Specific triggers are then used to instigate a local release of Ca2+ on demand. Here, communication between organelles comes into play, which is accomplished through intimate yet dynamic contacts, termed membrane contact sites (MCSs). The field of MCS biology in relation to cellular Ca2+ homeostasis has exploded in recent years. Taking advantage of this new wealth of knowledge, in this Review, we invite the reader on a journey of Ca2+ flux through the ER and its associated MCSs. New mechanistic insights and technological advances inform the narrative on Ca2+ acquisition and mobilization at these sites of communication between organelles, and guide the discussion of their consequences for cellular physiology.
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Affiliation(s)
- Tom Cremer
- Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
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32
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Lu M, van Tartwijk FW, Lin JQ, Nijenhuis W, Parutto P, Fantham M, Christensen CN, Avezov E, Holt CE, Tunnacliffe A, Holcman D, Kapitein L, Schierle GSK, Kaminski CF. The structure and global distribution of the endoplasmic reticulum network are actively regulated by lysosomes. SCIENCE ADVANCES 2020; 6:eabc7209. [PMID: 33328230 PMCID: PMC7744115 DOI: 10.1126/sciadv.abc7209] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/27/2020] [Indexed: 06/12/2023]
Abstract
The endoplasmic reticulum (ER) comprises morphologically and functionally distinct domains: sheets and interconnected tubules. These domains undergo dynamic reshaping in response to changes in the cellular environment. However, the mechanisms behind this rapid remodeling are largely unknown. Here, we report that ER remodeling is actively driven by lysosomes, following lysosome repositioning in response to changes in nutritional status: The anchorage of lysosomes to ER growth tips is critical for ER tubule elongation and connection. We validate this causal link via the chemo- and optogenetically driven repositioning of lysosomes, which leads to both a redistribution of the ER tubules and a change of its global morphology. Therefore, lysosomes sense metabolic change in the cell and regulate ER tubule distribution accordingly. Dysfunction in this mechanism during axonal extension may lead to axonal growth defects. Our results demonstrate a critical role of lysosome-regulated ER dynamics and reshaping in nutrient responses and neuronal development.
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Affiliation(s)
- Meng Lu
- Cambridge Infinitus Research Centre, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Julie Qiaojin Lin
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
| | - Wilco Nijenhuis
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Pierre Parutto
- Group of Computational Biology and Applied Mathematics, Institut de Biologie de l'École Normale Supérieure-PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Marcus Fantham
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Charles N Christensen
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Edward Avezov
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
| | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Alan Tunnacliffe
- Cambridge Infinitus Research Centre, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institut de Biologie de l'École Normale Supérieure-PSL, 46 rue d'Ulm, 75005 Paris, France
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK
| | - Lukas Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Gabriele S Kaminski Schierle
- Cambridge Infinitus Research Centre, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Clemens F Kaminski
- Cambridge Infinitus Research Centre, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK.
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK
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33
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Kriechbaumer V, Brandizzi F. The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions. J Microsc 2020; 280:122-133. [PMID: 32426862 PMCID: PMC10895883 DOI: 10.1111/jmi.12909] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review, we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.
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Affiliation(s)
- V Kriechbaumer
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, U.K
| | - F Brandizzi
- MSU-DOE Plant Research Laboratory, Department of Plant Biology, Michigan State University, East Lansing, Michigan, U.S.A
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34
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Al-Izzi SC, Sens P, Turner MS, Komura S. Dynamics of passive and active membrane tubes. SOFT MATTER 2020; 16:9319-9330. [PMID: 32935733 DOI: 10.1039/d0sm01290d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Utilising Onsager's variational formulation, we derive dynamical equations for the relaxation of a fluid membrane tube in the limit of small deformation, allowing for a contrast of solvent viscosity across the membrane and variations in surface tension due to membrane incompressibility. We compute the relaxation rates, recovering known results in the case of purely axis-symmetric perturbations and making new predictions for higher order (azimuthal) m-modes. We analyse the long and short wavelength limits of these modes by making use of various asymptotic arguments. We incorporate stochastic terms to our dynamical equations suitable to describe both passive thermal forces and non-equilibrium active forces. We derive expressions for the fluctuation amplitudes, an effective temperature associated with active fluctuations, and the power spectral density for both the thermal and active fluctuations. We discuss an experimental assay that might enable measurement of these fluctuations to infer the properties of the active noise. Finally we discuss our results in the context of active membranes more generally and give an overview of some open questions in the field.
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Affiliation(s)
- Sami C Al-Izzi
- School of Physics & EMBL-Australia node in Single Molecule Science, University of New South Wales, Sydney, Australia and Department of Mathematics, University of Warwick, Coventry CV4 7AL, UK and Institut Curie, PSL Research University, CNRS, Physical Chemistry Curie, F-75005, Paris, France and Sorbonne Université, CNRS, UMR 168, F-75005, Paris, France
| | - Pierre Sens
- Institut Curie, PSL Research University, CNRS, Physical Chemistry Curie, F-75005, Paris, France and Sorbonne Université, CNRS, UMR 168, F-75005, Paris, France
| | - Matthew S Turner
- Department of Physics & Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, UK and Department of Chemical Engineering, University of Kyoto, Kyoto 615-8510, Japan
| | - Shigeyuki Komura
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan.
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35
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S Mogre S, Brown AI, Koslover EF. Getting around the cell: physical transport in the intracellular world. Phys Biol 2020; 17:061003. [PMID: 32663814 DOI: 10.1088/1478-3975/aba5e5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.
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Affiliation(s)
- Saurabh S Mogre
- Department of Physics, University of California, San Diego, San Diego, California 92093, United States of America
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36
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Qin B, Yuan X, Jiang M, Yin H, Luo Z, Zhang J, Zhu C, Li X, Shi Y, Luo L, Du Y, You J. Targeting DNA to the endoplasmic reticulum efficiently enhances gene delivery and therapy. NANOSCALE 2020; 12:18249-18262. [PMID: 32857088 DOI: 10.1039/d0nr03156a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Gene therapy mediated by non-viral carriers is gaining an increasing popularity due to its high biosafety and the convenience of production on a large scale, yet inefficient gene delivery is a limiting obstacle. Few gene vectors can avoid the endosome-lysosome route, and as a result, their DNA payloads are easily decomposed during transfection. Herein, a peptide (pardaxin, PAR)-modified cationic liposome (PAR-Lipo) targeting the endoplasmic reticulum (ER) was developed for improving the gene delivery efficiency. Interestingly, compared to non-PAR-modified cationic liposomes (Non-Lipos) and Lipofectamine 2000 (Lipo 2000, a commercial genetic vector), PAR-Lipos showed remarkably higher gene delivery efficiency in vitro and better antitumor efficacy in vivo. It was demonstrated that PAR-Lipos could be accumulated into the ER via a non-lysosome intracellular route after cellular internalization, which induced the retention of the DNA payload in the ER close to the nucleus, while Non-Lipos, like most conventional cationic carriers, mainly presented lysosomal retention after their endocytosis. The unique intracellular transport behavior of PAR-Lipos can enhance the protection of the DNA payload, prolong their residence time in the cell, and promote their entry into the nucleus relying on the intimate relationship between the ER and nuclear membrane, which is the explanation for the enhanced gene-therapy effect mediated by PAR-Lipos. Our research may provide alternative means of efficiently delivering genes in cells.
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Affiliation(s)
- Bing Qin
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, P. R. China.
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37
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Oliva MK, Pérez-Moreno JJ, O’Shaughnessy J, Wardill TJ, O’Kane CJ. Endoplasmic Reticulum Lumenal Indicators in Drosophila Reveal Effects of HSP-Related Mutations on Endoplasmic Reticulum Calcium Dynamics. Front Neurosci 2020; 14:816. [PMID: 32903680 PMCID: PMC7438849 DOI: 10.3389/fnins.2020.00816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/10/2020] [Indexed: 12/02/2022] Open
Abstract
Genes for endoplasmic reticulum (ER)-shaping proteins are among the most commonly mutated in hereditary spastic paraplegia (HSP). Mutation of these genes in model organisms can lead to disruption of the ER network. To investigate how the physiological roles of the ER might be affected by such disruption, we developed tools to interrogate its Ca2+ signaling function. We generated GAL4-driven Ca2+ sensors targeted to the ER lumen, to record ER Ca2+ fluxes in identified Drosophila neurons. Using GAL4 lines specific for Type Ib or Type Is larval motor neurons, we compared the responses of different lumenal indicators to electrical stimulation, in axons and presynaptic terminals. The most effective sensor, ER-GCaMP6-210, had a Ca2+ affinity close to the expected ER lumenal concentration. Repetitive nerve stimulation generally showed a transient increase of lumenal Ca2+ in both the axon and presynaptic terminals. Mutants lacking neuronal reticulon and REEP proteins, homologs of human HSP proteins, showed a larger ER lumenal evoked response compared to wild type; we propose mechanisms by which this phenotype could lead to neuronal dysfunction or degeneration. Our lines are useful additions to a Drosophila Ca2+ imaging toolkit, to explore the physiological roles of ER, and its pathophysiological roles in HSP and in axon degeneration more broadly.
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Affiliation(s)
- Megan K. Oliva
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Trevor J. Wardill
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Cahir J. O’Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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38
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Dora M, Holcman D. Active flow network generates molecular transport by packets: case of the endoplasmic reticulum. Proc Biol Sci 2020; 287:20200493. [PMID: 32605515 DOI: 10.1098/rspb.2020.0493] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biological networks are characterized by their connectivity and topology but also by their ability to transport materials. In the case of random transportation, the efficacy is measured by the time it takes to travel between two nodes of the network. We study here the consequences of a unidirectional transport mechanism occurring in the endoplasmic reticulum (ER) network, a structure present in the cell cytoplasm. This unidirectional transport mechanism is an active-waiting transportation, where molecules have to wait a random time before being transported from one node to the next one. We develop here a general theory of transport in an active network and find an unusual network transportation, where molecules group together in redundant packets instead of being disperse. Finally, the mean time to travel between two nodes of the ER is of the order of 20 min, but is reduced to 30 s when we consider the fastest particles because it uses optimal paths. To conclude, the present theory shows that unidirectional transport is an efficient and robust mechanism for fast molecular redistribution inside the ER.
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Affiliation(s)
- M Dora
- Group of Computational Biology, IBENS, Ecole Normale Supérieure-PSL, Paris, France
| | - D Holcman
- Group of Computational Biology, IBENS, Ecole Normale Supérieure-PSL, Paris, France.,DAMPT, University of Cambridge and Churchill College, CB30DS Cambridge, UK
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39
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Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020; 287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
| | | | | | - Alexej Kedrov
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
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40
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Caldas LA, Azevedo RC, da Silva JL, de Souza W. Microscopy analysis of Zika virus morphogenesis in mammalian cells. Sci Rep 2020; 10:8370. [PMID: 32433502 PMCID: PMC7239924 DOI: 10.1038/s41598-020-65409-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
Zika virus (ZIKV) is an arbovirus that recently emerged in the Americas as an important pathogen mainly because of its expanded pathogenesis, and elevated tropism for neuronal cells, transposition across the placental barrier, and replication in reproductive tract cells. Thus, transmission modes are eventually independent of an invertebrate vector, which is an atypical behavior for the flavivirus genus and indicates the need to study the replication of this virus in different cell types. Although ZIKV became a target for public health programs, the interaction of this flavivirus with the infected cell is still poorly understood. Herein, we analyzed the main stages of virus morphogenesis in mammalian cells, from establishment of the viroplasm-like zone to viral release from infected cells, using super-resolution fluorescence microscopy and electron microscopy. In addition, we compared this with other host cell types and other members of the Flaviviridae family that present a similar dynamic.
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Affiliation(s)
- Lucio Ayres Caldas
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro. Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, subsolo, CEP:21941902, Cidade Universitária, Rio de Janeiro, RJ, Brazil. .,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem. Avenida Carlos Chagas Filho 373. Centro de Ciências da Saúde (CCS), Bloco M, Unidade 3, Cidade Universitária, CEP:21941902, Rio de Janeiro, RJ, Brazil.
| | - Renata Campos Azevedo
- Laboratório de Interação Vírus-Célula, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro. Av. Carlos Chagas Filho 373, Prédio CCS, Bloco I, subsolo, CEP:21941902, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Jerson Lima da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Laboratório de Termodinâmica de Proteínas e Estruturas Virais Gregório Weber, Universidade Federal do Rio de Janeiro. Av. Carlos Chagas Filho 373, Prédio CCS, Bloco E, sala 10, Cidade Universitária, CEP:21941902, Rio de Janeiro, RJ, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro. Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, subsolo, CEP:21941902, Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem. Avenida Carlos Chagas Filho 373. Centro de Ciências da Saúde (CCS), Bloco M, Unidade 3, Cidade Universitária, CEP:21941902, Rio de Janeiro, RJ, Brazil
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41
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Alam SMD, Tsukamoto Y, Ogawa M, Senoo Y, Ikeda K, Tashima Y, Takeuchi H, Okajima T. N-Glycans on EGF domain-specific O-GlcNAc transferase (EOGT) facilitate EOGT maturation and peripheral endoplasmic reticulum localization. J Biol Chem 2020; 295:8560-8574. [PMID: 32376684 DOI: 10.1074/jbc.ra119.012280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/30/2020] [Indexed: 02/03/2023] Open
Abstract
Epidermal growth factor (EGF) domain-specific O-GlcNAc transferase (EOGT) is an endoplasmic reticulum (ER)-resident protein that modifies EGF repeats of Notch receptors and thereby regulates Delta-like ligand-mediated Notch signaling. Several EOGT mutations that may affect putative N-glycosylation consensus sites are recorded in the cancer database, but the presence and function of N-glycans in EOGT have not yet been characterized. Here, we identified N-glycosylation sites in mouse EOGT and elucidated their molecular functions. Three predicted N-glycosylation consensus sequences on EOGT are highly conserved among mammalian species. Within these sites, we found that Asn-263 and Asn-354, but not Asn-493, are modified with N-glycans. Lectin blotting, endoglycosidase H digestion, and MS analysis revealed that both residues are modified with oligomannose N-glycans. Loss of an individual N-glycan on EOGT did not affect its endoplasmic reticulum (ER) localization, enzyme activity, and ability to O-GlcNAcylate Notch1 in HEK293T cells. However, simultaneous substitution of both N-glycosylation sites affected both EOGT maturation and expression levels without an apparent change in enzymatic activity, suggesting that N-glycosylation at a single site is sufficient for EOGT maturation and expression. Accordingly, a decrease in O-GlcNAc stoichiometry was observed in Notch1 co-expressed with an N263Q/N354Q variant compared with WT EOGT. Moreover, the N263Q/N354Q variant exhibited altered subcellular distribution within the ER in HEK293T cells, indicating that N-glycosylation of EOGT is required for its ER localization at the cell periphery. These results suggest critical roles of N-glycans in sustaining O-GlcNAc transferase function both by maintaining EOGT levels and by ensuring its proper subcellular localization in the ER.
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Affiliation(s)
- Sayad Md Didarul Alam
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yohei Tsukamoto
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mitsutaka Ogawa
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuya Senoo
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazutaka Ikeda
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,RIKEN, Center for Integrative Medical Sciences, Suehiro-cho, Tsurumi, Yokohama, Japan
| | - Yuko Tashima
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideyuki Takeuchi
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Okajima
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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42
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Miller RC, Aplin CP, Kay TM, Leighton R, Libal C, Simonet R, Cembran A, Heikal AA, Boersma AJ, Sheets ED. FRET Analysis of Ionic Strength Sensors in the Hofmeister Series of Salt Solutions Using Fluorescence Lifetime Measurements. J Phys Chem B 2020; 124:3447-3458. [PMID: 32267692 DOI: 10.1021/acs.jpcb.9b10498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Living cells are complex, crowded, and dynamic and continually respond to environmental and intracellular stimuli. They also have heterogeneous ionic strength with compartmentalized variations in both intracellular concentrations and types of ions. These challenges would benefit from the development of quantitative, noninvasive approaches for mapping the heterogeneous ionic strength fluctuations in living cells. Here, we investigated a class of recently developed ionic strength sensors that consists of mCerulean3 (a cyan fluorescent protein) and mCitrine (a yellow fluorescent protein) tethered via a linker made of two charged α-helices and a flexible loop. The two helices are designed to bear opposite charges, which is hypothesized to increase the ionic screening and therefore a larger intermolecular distance. In these protein constructs, mCerulean3 and mCitrine act as a donor-acceptor pair undergoing Förster resonance energy transfer (FRET) that is dependent on both the linker amino acids and the environmental ionic strength. Using time-resolved fluorescence of the donor (mCerulean3), we determined the sensitivity of the energy transfer efficiencies and the donor-acceptor distances of these sensors at variable concentrations of the Hofmeister series of salts (KCl, LiCl, NaCl, NaBr, NaI, Na2SO4). As controls, similar measurements were carried out on the FRET-incapable, enzymatically cleaved counterparts of these sensors as well as a construct designed with two electrostatically neutral α-helices (E6G2). Our results show that the energy transfer efficiencies of these sensors are sensitive to both the linker amino acid sequence and the environmental ionic strength, whereas the sensitivity of these sensors to the identity of the dissolved ions of the Hofmeister series of salts seems limited. We also developed a theoretical framework to explain the observed trends as a function of the ionic strength in terms of the Debye screening of the electrostatic interaction between the two charged α-helices in the linker region. These controlled solution studies represent an important step toward the development of rationally designed FRET-based environmental sensors while offering different models for calculating the energy transfer efficiency using time-resolved fluorescence that is compatible with future in vivo studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
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Carter SD, Hampton CM, Langlois R, Melero R, Farino ZJ, Calderon MJ, Li W, Wallace CT, Tran NH, Grassucci RA, Siegmund SE, Pemberton J, Morgenstern TJ, Eisenman L, Aguilar JI, Greenberg NL, Levy ES, Yi E, Mitchell WG, Rice WJ, Wigge C, Pilli J, George EW, Aslanoglou D, Courel M, Freyberg RJ, Javitch JA, Wills ZP, Area-Gomez E, Shiva S, Bartolini F, Volchuk A, Murray SA, Aridor M, Fish KN, Walter P, Balla T, Fass D, Wolf SG, Watkins SC, Carazo JM, Jensen GJ, Frank J, Freyberg Z. Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells. SCIENCE ADVANCES 2020; 6:eaay9572. [PMID: 32270040 PMCID: PMC7112762 DOI: 10.1126/sciadv.aay9572] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/13/2020] [Indexed: 05/21/2023]
Abstract
The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo-electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic β-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells.
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Affiliation(s)
- Stephen D. Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cheri M. Hampton
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Robert Langlois
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Roberto Melero
- Biocomputing Unit, Centro Nacional de Biotecnología–CSIC, Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Zachary J. Farino
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michael J. Calderon
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Callen T. Wallace
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ngoc Han Tran
- HHMI, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert A. Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stephanie E. Siegmund
- Department of Cellular, Molecular and Biophysical Studies, Columbia University Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Joshua Pemberton
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Travis J. Morgenstern
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Leanna Eisenman
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jenny I. Aguilar
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Nili L. Greenberg
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Elana S. Levy
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Edward Yi
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - William G. Mitchell
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | | | | | - Jyotsna Pilli
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Emily W. George
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Despoina Aslanoglou
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maïté Courel
- CNRS-UMR7622, Institut de Biologie Paris-Seine, Université Pierre & Marie Curie, 75252 Paris, France
| | - Robin J. Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jonathan A. Javitch
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Zachary P. Wills
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Allen Volchuk
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sandra A. Murray
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Meir Aridor
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kenneth N. Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Peter Walter
- HHMI, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon G. Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - José María Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología–CSIC, Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Grant J. Jensen
- HHMI, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Pain C, Kriechbaumer V. Defining the dance: quantification and classification of endoplasmic reticulum dynamics. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1757-1762. [PMID: 31811712 PMCID: PMC7094074 DOI: 10.1093/jxb/erz543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The availability of quantification methods for subcellular organelle dynamic analysis has increased rapidly over the last 20 years. The application of these techniques to contiguous subcellular structures that exhibit dynamic remodelling over a range of scales and orientations is challenging, as quantification of 'movement' rarely corresponds to traditional, qualitative classifications of types of organelle movement. The plant endoplasmic reticulum represents a particular challenge for dynamic quantification as it itself is an entirely contiguous organelle that is in a constant state of flux and gross remodelling, controlled by the actinomyosin cytoskeleton.
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Affiliation(s)
- Charlotte Pain
- Oxford Brookes University, Faculty of Health and Life Sciences, Gipsy Lane, Plant Cell Biology, Oxford, UK
| | - Verena Kriechbaumer
- Oxford Brookes University, Faculty of Health and Life Sciences, Gipsy Lane, Plant Cell Biology, Oxford, UK
- Correspondence:
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45
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Impact of global structure on diffusive exploration of organelle networks. Sci Rep 2020; 10:4984. [PMID: 32188905 PMCID: PMC7080787 DOI: 10.1038/s41598-020-61598-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/25/2020] [Indexed: 01/08/2023] Open
Abstract
We investigate diffusive search on planar networks, motivated by tubular organelle networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time on a spatial network is used to characterize the typical search time as a function of network connectivity. We find that global structural properties — the total edge length and number of loops — are sufficient to largely determine network exploration times for a variety of both synthetic planar networks and organelle morphologies extracted from living cells. For synthetic networks on a lattice, we predict the search time dependence on these global structural parameters by connecting with percolation theory, providing a bridge from irregular real-world networks to a simpler physical model. The dependence of search time on global network structural properties suggests that network architecture can be designed for efficient search without controlling the precise arrangement of connections. Specifically, increasing the number of loops substantially decreases search times, pointing to a potential physical mechanism for regulating reaction rates within organelle network structures.
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46
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Heine M, Holcman D. Asymmetry Between Pre- and Postsynaptic Transient Nanodomains Shapes Neuronal Communication. Trends Neurosci 2020; 43:182-196. [DOI: 10.1016/j.tins.2020.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 10/25/2022]
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47
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Laurent F, Floderer C, Favard C, Muriaux D, Masson JB, Vestergaard CL. Mapping spatio-temporal dynamics of single biomolecules in living cells. Phys Biol 2019; 17:015003. [PMID: 31765328 DOI: 10.1088/1478-3975/ab5167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We present a Bayesian framework for inferring spatio-temporal maps of diffusivity and potential fields from recorded trajectories of single molecules inside living cells. The framework naturally lets us regularise the high-dimensional inference problem using prior distributions in order to obtain robust results. To overcome the computational complexity of inferring thousands of map parameters from large single particle tracking datasets, we developed a stochastic optimisation method based on local mini-batches and parsimonious gradient calculation. We quantified the gain in convergence speed on numerical simulations, and we demonstrated for the first time temporal regularisation and aligned values of the inferred potential fields across multiple time segments. As a proof-of-concept, we mapped the dynamics of HIV-1 Gag proteins involved in the formation of virus-like particles (VLPs) on the plasma membrane of live T cells at high spatial and temporal resolutions. We focused on transient aggregation events lasting only on tenth of the time required for full VLP formation. The framework and optimisation methods are implemented in the TRamWAy open-source software platform for analysing single biomolecule dynamics.
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Affiliation(s)
- François Laurent
- Decision and Bayesian Computation, Department of Computational Biology, Department of Neuroscience, CNRS USR 3756, CNRS UMR 3571, Institut Pasteur, 25 rue du Docteur Roux, Paris, 75015, France. Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
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49
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Gao G, Zhu C, Liu E, Nabi IR. Reticulon and CLIMP-63 regulate nanodomain organization of peripheral ER tubules. PLoS Biol 2019; 17:e3000355. [PMID: 31469817 PMCID: PMC6742417 DOI: 10.1371/journal.pbio.3000355] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 09/12/2019] [Accepted: 07/26/2019] [Indexed: 11/18/2022] Open
Abstract
The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle composed of smooth peripheral tubules and rough, ribosome-studded central ER sheets whose morphology is determined, in part, by the ER-shaping proteins, reticulon (RTN) and cytoskeleton-linking membrane protein 63 (CLIMP-63), respectively. Here, stimulated emission depletion (STED) super-resolution microscopy shows that reticulon4a (RTN4a) and CLIMP-63 also regulate the organization and dynamics of peripheral ER tubule nanodomains. STED imaging shows that lumenal ER monomeric oxidizing environment-optimized green fluorescent protein (ERmoxGFP), membrane Sec61βGFP, knock-in calreticulin-GFP, and antibody-labeled ER-resident proteins calnexin and derlin-1 are all localized to periodic puncta along the length of peripheral ER tubules that are not readily observable by diffraction limited confocal microscopy. RTN4a segregates away from and restricts lumenal blob length, while CLIMP-63 associates with and increases lumenal blob length. RTN4a and CLIMP-63 also regulate the nanodomain distribution of ER-resident proteins, being required for the preferential segregation of calnexin and derlin-1 puncta away from lumenal ERmoxGFP blobs. High-speed (40 ms/frame) live cell STED imaging shows that RTN4a and CLIMP-63 regulate dynamic nanoscale lumenal compartmentalization along peripheral ER tubules. RTN4a enhances and CLIMP-63 disrupts the local accumulation of lumenal ERmoxGFP at spatially defined sites along ER tubules. The ER-shaping proteins RTN and CLIMP-63 therefore regulate lumenal ER nanodomain heterogeneity, interaction with ER-resident proteins, and dynamics in peripheral ER tubules.
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Affiliation(s)
- Guang Gao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Chengjia Zhu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Emma Liu
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ivan R. Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- * E-mail:
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Shukron O, Seeber A, Amitai A, Holcman D. Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics. Trends Genet 2019; 35:685-705. [PMID: 31371030 DOI: 10.1016/j.tig.2019.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/12/2019] [Accepted: 06/26/2019] [Indexed: 12/16/2022]
Abstract
Chromatin organization remains complex and far from understood. In this article, we review recent statistical methods of extracting biophysical parameters from in vivo single-particle trajectories of loci to reconstruct chromatin reorganization in response to cellular stress such as DNA damage. We look at methods for analyzing both single locus and multiple loci tracked simultaneously and explain how to quantify and describe chromatin motion using a combination of extractable parameters. These parameters can be converted into information about chromatin dynamics and function. Furthermore, we discuss how the timescale of recurrent encounter between loci can be extracted and interpreted. We also discuss the effect of sampling rate on the estimated parameters. Finally, we review a polymer method to reconstruct chromatin structure using crosslinkers between chromatin sites. We list and refer to some software packages that are now publicly available to simulate polymer motion. To conclude, chromatin organization and dynamics can be reconstructed from locus trajectories and predicted based on polymer models.
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Affiliation(s)
- O Shukron
- Group of Data Modeling, Computational Biology and Predictive Medicine, Institut de Biologie, CNRS/INSERM/PSL Ecole Normale Supérieure, Paris, 75005, France
| | - A Seeber
- Center for Advanced Imaging, Northwest Building, 52 Oxford St, Suite 147, Harvard University, Cambridge, MA, 02138, USA
| | - A Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - D Holcman
- Group of Data Modeling, Computational Biology and Predictive Medicine, Institut de Biologie, CNRS/INSERM/PSL Ecole Normale Supérieure, Paris, 75005, France.
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