251
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Steiner B, Weber S, Hilbi H. Formation of the Legionella-containing vacuole: phosphoinositide conversion, GTPase modulation and ER dynamics. Int J Med Microbiol 2018; 308:49-57. [DOI: 10.1016/j.ijmm.2017.08.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/06/2017] [Accepted: 08/08/2017] [Indexed: 11/28/2022] Open
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252
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Abstract
Free-flow electrophoresis (FFE) is a technique for separation of proteins, peptides, organelles, and cells. With zone electrophoresis (ZE-FFE), organelles are separated according to surface charge. The ER is the only remaining major cellular compartment in Arabidopsis not to have been isolated using density centrifugation, immune-isolation, or any other method previously applied to purification of plant membranes. By using continuous-flow electrophoresis ER vesicles of similar surface charge, which may have been fragmented during cell lysis, can be focused. A large portion of these vesicles are of sufficiently different surface charge that separation from the majority of Golgi and other contaminants is possible. Here we adapt an earlier ZE-FFE Golgi isolation protocol for the isolation of highly pure ER vesicles and for tracking the migration of peripheral ER vesicles. Isolating ER vesicles of homogenous surface charge allows multi-'omic analyses to be performed on the ER. This facilitates investigations into structure-function relationships within the ER.
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Affiliation(s)
- Harriet T Parsons
- Biochemistry Department, Cambridge University, Cambridge, CB2 1QJ, UK.
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253
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Abstract
Efficient targeting of newly synthesized membrane proteins from the endoplasmic reticulum to the inner nuclear membrane depends on nucleotide hydrolysis. A new study shows that this dependence reflects critical actions of the atlastin family of GTPases in maintaining the morphology of the endoplasmic reticulum network.
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Affiliation(s)
- Craig Blackstone
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Building 35, Room 2A-201, 9000 Rockville Pike, Bethesda MD 20892, USA.
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254
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Georgiades P, Allan VJ, Wright GD, Woodman PG, Udommai P, Chung MA, Waigh TA. The flexibility and dynamics of the tubules in the endoplasmic reticulum. Sci Rep 2017; 7:16474. [PMID: 29184084 PMCID: PMC5705721 DOI: 10.1038/s41598-017-16570-4] [Citation(s) in RCA: 31] [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: 07/25/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
The endoplasmic reticulum (ER) is a single organelle in eukaryotic cells that extends throughout the cell and is involved in a large number of cellular functions. Using a combination of fixed and live cells (human MRC5 lung cells) in diffraction limited and super-resolved fluorescence microscopy (STORM) experiments, we determined that the average persistence length of the ER tubules was 3.03 ± 0.24 μm. Removing the branched network junctions from the analysis caused a slight increase in the average persistence length to 4.71 ± 0.14 μm, and provides the tubule's persistence length with a moderate length scale dependence. The average radius of the tubules was 44.1 ± 3.2 nm. The bending rigidity of the ER tubule membranes was found to be 10.9 ± 1.2 kT (17.0 ± 1.3 kT without branch points). We investigated the dynamic behaviour of ER tubules in live cells, and found that the ER tubules behaved like semi-flexible fibres under tension. The majority of the ER tubules experienced equilibrium transverse fluctuations under tension, whereas a minority number of them had active super-diffusive motions driven by motor proteins. Cells thus actively modulate the dynamics of the ER in a well-defined manner, which is expected in turn to impact on its many functions.
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Affiliation(s)
- Pantelis Georgiades
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK
| | - Victoria J Allan
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK.
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK.
| | - Graham D Wright
- IMB Microscopy Unit, Institute of Medical Biology, A*STAR, 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Republic of Singapore
| | - Philip G Woodman
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
| | - Parinya Udommai
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Manloeng A Chung
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Thomas A Waigh
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK.
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK.
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255
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O'Donnell JP, Byrnes LJ, Cooley RB, Sondermann H. A hereditary spastic paraplegia-associated atlastin variant exhibits defective allosteric coupling in the catalytic core. J Biol Chem 2017; 293:687-700. [PMID: 29180453 DOI: 10.1074/jbc.ra117.000380] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/17/2017] [Indexed: 11/06/2022] Open
Abstract
The dynamin-related GTPase atlastin (ATL) catalyzes membrane fusion of the endoplasmic reticulum and thus establishes a network of branched membrane tubules. When ATL function is compromised, the morphology of the endoplasmic reticulum deteriorates, and these defects can result in neurological disorders such as hereditary spastic paraplegia and hereditary sensory neuropathy. ATLs harness the energy of GTP hydrolysis to initiate a series of conformational changes that enable homodimerization and subsequent membrane fusion. Disease-associated amino acid substitutions cluster in regions adjacent to ATL's catalytic site, but the consequences for the GTPase's molecular mechanism are often poorly understood. Here, we elucidate structural and functional defects of an atypical hereditary spastic paraplegia mutant, ATL1-F151S, that is impaired in its nucleotide-hydrolysis cycle but can still adopt a high-affinity homodimer when bound to a transition-state analog. Crystal structures of mutant proteins yielded models of the monomeric pre- and post-hydrolysis states of ATL. Together, these findings define a mechanism for allosteric coupling in which Phe151 is the central residue in a hydrophobic interaction network connecting the active site to an interdomain interface responsible for nucleotide loading.
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Affiliation(s)
- John P O'Donnell
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Laura J Byrnes
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Richard B Cooley
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
| | - Holger Sondermann
- From the Department of Molecular Medicine, Cornell University, Ithaca, New York 14853
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256
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Luarte A, Cornejo VH, Bertin F, Gallardo J, Couve A. The axonal endoplasmic reticulum: One organelle-many functions in development, maintenance, and plasticity. Dev Neurobiol 2017; 78:181-208. [PMID: 29134778 DOI: 10.1002/dneu.22560] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/02/2017] [Accepted: 11/07/2017] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is highly conserved in eukaryotes and neurons. Indeed, the localization of the organelle in axons has been known for nearly half a century. However, the relevance of the axonal ER is only beginning to emerge. In this review, we discuss the structure of the ER in axons, examining the role of ER-shaping proteins and highlighting reticulons. We analyze the multiple functions of the ER and their potential contribution to axonal physiology. First, we examine the emerging roles of the axonal ER in lipid synthesis, protein translation, processing, quality control, and secretory trafficking of transmembrane proteins. We also review the impact of the ER on calcium dynamics, focusing on intracellular mechanisms and functions. We describe the interactions between the ER and endosomes, mitochondria, and synaptic vesicles. Finally, we analyze available proteomic data of axonal preparations to reveal the dynamic functionality of the ER in axons during development. We suggest that the dynamic proteome and a validated axonal interactome, together with state-of-the-art methodologies, may provide interesting research avenues in axon physiology that may extend to pathology and regeneration. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 78: 181-208, 2018.
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Affiliation(s)
- Alejandro Luarte
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Víctor Hugo Cornejo
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Francisca Bertin
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Javiera Gallardo
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Andrés Couve
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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257
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Affiliation(s)
- Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Albert-Einstein Straße 9, 07745 Jena, Germany
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, 07745 Jena, Germany
| | - Thomas Huser
- Biomolecular
Photonics, Department of Physics, University of Bielefeld, Universitätsstraße
25, 33615 Bielefeld, Germany
- Department
of Internal Medicine and NSF Center for Biophotonics, University of California, Davis, Sacramento, California 95817, United States
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258
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Han Y, Li M, Qiu F, Zhang M, Zhang YH. Cell-permeable organic fluorescent probes for live-cell long-term super-resolution imaging reveal lysosome-mitochondrion interactions. Nat Commun 2017; 8:1307. [PMID: 29101340 PMCID: PMC5670236 DOI: 10.1038/s41467-017-01503-6] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 09/22/2017] [Indexed: 01/10/2023] Open
Abstract
Characterizing the long-term nanometer-scale interactions between lysosomes and mitochondria in live cells is essential for understanding their functions but remains challenging due to limitations of the existing fluorescent probes. Here, we develop cell-permeable organic fluorescent probes for lysosomes with excellent specificity and high photostability. We also use an existing Atto 647N dye with high brightness and excellent photostability to achieve specific labeling of mitochondria in live cells. Using these probes, we obtain dual-color structured illumination microscopy (SIM) images of dynamic physical lysosome-mitochondrion interactions in live cells at an ~90-nm resolution over a long time course of ~13 min. We successfully record the consecutive dynamic processes of lysosomal fusion and fission, as well as four types of physical lysosome-mitochondrion interactions by super-resolution imaging. Our probes provide an avenue for understanding the functions and the dynamic interplay of lysosomes and mitochondria in live cells. Studying interactions between lysosomes and mitochondria in living cells is difficult due to the limitations of existing probes. Here, the authors develop new cell-permeable fluorescent probes to image the dynamics of lysosomes and their physical interactions with mitochondria using super-resolution microscopy.
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Affiliation(s)
- Yubing Han
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Meihua Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Fengwu Qiu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Meng Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China. .,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
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259
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Lang S, Pfeffer S, Lee PH, Cavalié A, Helms V, Förster F, Zimmermann R. An Update on Sec61 Channel Functions, Mechanisms, and Related Diseases. Front Physiol 2017; 8:887. [PMID: 29163222 PMCID: PMC5672155 DOI: 10.3389/fphys.2017.00887] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/19/2017] [Indexed: 12/18/2022] Open
Abstract
The membrane of the endoplasmic reticulum (ER) of nucleated human cells harbors the protein translocon, which facilitates membrane integration or translocation of almost every newly synthesized polypeptide targeted to organelles of the endo- and exocytotic pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins and complexes that are permanently or transiently associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, modification of precursor polypeptides in transit through the Sec61 complex, and Sec61 channel gating, i.e., dynamic regulation of the pore forming subunit to mediate precursor transport and calcium efflux. Recently, cryoelectron tomography of translocons in native ER membrane vesicles, derived from human cell lines or patient fibroblasts, and even intact cells has given unprecedented insights into the architecture and dynamics of the native translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion, and translocation of newly synthesized polypeptides as well as the putative physiological roles of the Sec61 channel as a passive ER calcium leak channel. Furthermore, the structural insights into the Sec61 channel are incorporated into an overview and update on Sec61 channel-related diseases—the Sec61 channelopathies—and novel therapeutic concepts for their treatment.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Homburg, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Po-Hsien Lee
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Adolfo Cavalié
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, Homburg, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Homburg, Germany
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260
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Hoffmann PC, Kukulski W. Perspective on architecture and assembly of membrane contact sites. Biol Cell 2017; 109:400-408. [PMID: 28960356 DOI: 10.1111/boc.201700031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 01/25/2023]
Abstract
Membrane contact sites (MCS) are platforms of physical contact between different organelles. They are formed through interactions involving lipids and proteins, and function in processes such as calcium and lipid exchange, metabolism and organelle biogenesis. In this article, we discuss emerging questions regarding the architecture, organisation and assembly of MCS, such as: What is the contribution of different components to the interaction between organelles? How is the specific composition of different types of membrane contacts sites established and maintained? How are proteins and lipids spatially organised at MCS and how does that influence their function? How dynamic are MCS on the molecular and ultrastructural level? We highlight current state of research and point out experimental approaches that promise to contribute to a spatiomechanistic understanding of MCS functions.
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Affiliation(s)
- Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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261
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Danial JSH, García-Sáez AJ. Improving certainty in single molecule imaging. Curr Opin Struct Biol 2017; 46:24-30. [DOI: 10.1016/j.sbi.2017.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/06/2017] [Accepted: 04/16/2017] [Indexed: 11/30/2022]
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262
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Abstract
Lipid membrane nanotubes are abundant in living cells, even though tubules are energetically less stable than sheet-like structures. According to membrane elastic theory, the tubular endoplasmic reticulum (ER), with its high area-to-volume ratio, appears to be particularly unstable. We explore how tubular membrane structures can nevertheless be induced and why they persist. In Monte Carlo simulations of a fluid-elastic membrane model subject to thermal fluctuations and without constraints on symmetry, we find that a steady increase in the area-to-volume ratio readily induces tubular structures. In simulations mimicking the ER wrapped around the cell nucleus, tubules emerge naturally as the membrane area increases. Once formed, a high energy barrier separates tubules from the thermodynamically favored sheet-like membrane structures. Remarkably, this barrier persists even at large area-to-volume ratios, protecting tubules against shape transformations despite enormous driving forces toward sheet-like structures. Molecular dynamics simulations of a molecular membrane model confirm the metastability of tubular structures. Volume reduction by osmotic regulation and membrane area growth by lipid production and by fusion of small vesicles emerge as powerful factors in the induction and stabilization of tubular membrane structures.
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Affiliation(s)
- Amir Houshang Bahrami
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt , 60438 Frankfurt am Main, Germany
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263
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Knorr RL, Mizushima N, Dimova R. Fusion and scission of membranes: Ubiquitous topological transformations in cells. Traffic 2017; 18:758-761. [DOI: 10.1111/tra.12509] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Roland L. Knorr
- Max Planck Institute of Colloids and Interfaces; Science Park Golm; Potsdam Germany
| | - Noboru Mizushima
- Graduate School and Faculty of Medicine; The University of Tokyo; Tokyo Japan
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces; Science Park Golm; Potsdam Germany
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264
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Abstract
Fluorescence nanoscopy uniquely combines minimally invasive optical access to the internal nanoscale structure and dynamics of cells and tissues with molecular detection specificity. While the basic physical principles of 'super-resolution' imaging were discovered in the 1990s, with initial experimental demonstrations following in 2000, the broad application of super-resolution imaging to address cell-biological questions has only more recently emerged. Nanoscopy approaches have begun to facilitate discoveries in cell biology and to add new knowledge. One current direction for method improvement is the ambition to quantitatively account for each molecule under investigation and assess true molecular colocalization patterns via multi-colour analyses. In pursuing this goal, the labelling of individual molecules to enable their visualization has emerged as a central challenge. Extending nanoscale imaging into (sliced) tissue and whole-animal contexts is a further goal. In this Review we describe the successes to date and discuss current obstacles and possibilities for further development.
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265
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Improved split fluorescent proteins for endogenous protein labeling. Nat Commun 2017; 8:370. [PMID: 28851864 PMCID: PMC5575300 DOI: 10.1038/s41467-017-00494-8] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/30/2017] [Indexed: 12/22/2022] Open
Abstract
Self-complementing split fluorescent proteins (FPs) have been widely used for protein labeling, visualization of subcellular protein localization, and detection of cell–cell contact. To expand this toolset, we have developed a screening strategy for the direct engineering of self-complementing split FPs. Via this strategy, we have generated a yellow–green split-mNeonGreen21–10/11 that improves the ratio of complemented signal to the background of FP1–10-expressing cells compared to the commonly used split GFP1–10/11; as well as a 10-fold brighter red-colored split-sfCherry21–10/11. Based on split sfCherry2, we have engineered a photoactivatable variant that enables single-molecule localization-based super-resolution microscopy. We have demonstrated dual-color endogenous protein tagging with sfCherry211 and GFP11, revealing that endoplasmic reticulum translocon complex Sec61B has reduced abundance in certain peripheral tubules. These new split FPs not only offer multiple colors for imaging interaction networks of endogenous proteins, but also hold the potential to provide orthogonal handles for biochemical isolation of native protein complexes. Split fluorescent proteins (FPs) have been widely used to visualise proteins in cells. Here the authors develop a screen for engineering new split FPs, and report a yellow-green split-mNeonGreen2 with reduced background, a red split-sfCherry2 for multicolour labeling, and its photoactivatable variant for super-resolution use.
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266
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Steiner B, Swart AL, Welin A, Weber S, Personnic N, Kaech A, Freyre C, Ziegler U, Klemm RW, Hilbi H. ER remodeling by the large GTPase atlastin promotes vacuolar growth of Legionella pneumophila. EMBO Rep 2017; 18:1817-1836. [PMID: 28835546 DOI: 10.15252/embr.201743903] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/13/2017] [Accepted: 07/25/2017] [Indexed: 01/31/2023] Open
Abstract
The pathogenic bacterium Legionella pneumophila replicates in host cells within a distinct ER-associated compartment termed the Legionella-containing vacuole (LCV). How the dynamic ER network contributes to pathogen proliferation within the nascent LCV remains elusive. A proteomic analysis of purified LCVs identified the ER tubule-resident large GTPase atlastin3 (Atl3, yeast Sey1p) and the reticulon protein Rtn4 as conserved LCV host components. Here, we report that Sey1/Atl3 and Rtn4 localize to early LCVs and are critical for pathogen vacuole formation. Sey1 overproduction promotes intracellular growth of L. pneumophila, whereas a catalytically inactive, dominant-negative GTPase mutant protein, or Atl3 depletion, restricts pathogen replication and impairs LCV maturation. Sey1 is not required for initial recruitment of ER to PtdIns(4)P-positive LCVs but for subsequent pathogen vacuole expansion. GTP (but not GDP) catalyzes the Sey1-dependent aggregation of purified, ER-positive LCVs in vitro Thus, Sey1/Atl3-dependent ER remodeling contributes to LCV maturation and intracellular replication of L. pneumophila.
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Affiliation(s)
- Bernhard Steiner
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Anna Leoni Swart
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Amanda Welin
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Stephen Weber
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Nicolas Personnic
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zürich, Zürich, Switzerland
| | - Christophe Freyre
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Urs Ziegler
- Center for Microscopy and Image Analysis, University of Zürich, Zürich, Switzerland
| | - Robin W Klemm
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
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267
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Abstract
Lipid droplets (LDs) are ubiquitous organelles that store neutral lipids for energy or membrane synthesis and act as hubs for metabolic processes. Cells generate LDs de novo, converting cells to emulsions with LDs constituting the dispersed oil phase in the aqueous cytoplasm. Here we review our current view of LD biogenesis. We present a model of LD formation from the ER in distinct steps and highlight the biology of proteins that govern this biophysical process. Areas of incomplete knowledge are identified, as are connections with physiology and diseases linked to alterations in LD biology.
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Affiliation(s)
- Tobias C Walther
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115; , .,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142.,Howard Hughes Medical Institute, Boston, Massachusetts 02115
| | - Jeeyun Chung
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115; , .,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Robert V Farese
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115; , .,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142
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268
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Long time-lapse nanoscopy with spontaneously blinking membrane probes. Nat Biotechnol 2017; 35:773-780. [PMID: 28671662 PMCID: PMC5609855 DOI: 10.1038/nbt.3876] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/13/2017] [Indexed: 01/14/2023]
Abstract
Imaging cellular structures and organelles in living cells by long time-lapse super-resolution microscopy is challenging, as it requires dense labeling, bright and highly photostable dyes, and non-toxic conditions. We introduce a set of high-density, environment-sensitive (HIDE) membrane probes, based on the membrane-permeable silicon-rhodamine dye HMSiR, that assemble in situ and enable long time-lapse, live-cell nanoscopy of discrete cellular structures and organelles with high spatiotemporal resolution. HIDE-enabled nanoscopy movies span tens of minutes, whereas movies obtained with labeled proteins span tens of seconds. Our data reveal 2D dynamics of the mitochondria, plasma membrane and filopodia, and the 2D and 3D dynamics of the endoplasmic reticulum, in living cells. HIDE probes also facilitate acquisition of live-cell, two-color, super-resolution images, expanding the utility of nanoscopy to visualize dynamic processes and structures in living cells.
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269
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Yalçın B, Zhao L, Stofanko M, O'Sullivan NC, Kang ZH, Roost A, Thomas MR, Zaessinger S, Blard O, Patto AL, Sohail A, Baena V, Terasaki M, O'Kane CJ. Modeling of axonal endoplasmic reticulum network by spastic paraplegia proteins. eLife 2017; 6. [PMID: 28742022 PMCID: PMC5576921 DOI: 10.7554/elife.23882] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 07/24/2017] [Indexed: 01/17/2023] Open
Abstract
Axons contain a smooth tubular endoplasmic reticulum (ER) network that is thought to be continuous with ER throughout the neuron; the mechanisms that form this axonal network are unknown. Mutations affecting reticulon or REEP proteins, with intramembrane hairpin domains that model ER membranes, cause an axon degenerative disease, hereditary spastic paraplegia (HSP). We show that Drosophila axons have a dynamic axonal ER network, which these proteins help to model. Loss of HSP hairpin proteins causes ER sheet expansion, partial loss of ER from distal motor axons, and occasional discontinuities in axonal ER. Ultrastructural analysis reveals an extensive ER network in axons, which shows larger and fewer tubules in larvae that lack reticulon and REEP proteins, consistent with loss of membrane curvature. Therefore HSP hairpin-containing proteins are required for shaping and continuity of axonal ER, thus suggesting roles for ER modeling in axon maintenance and function. DOI:http://dx.doi.org/10.7554/eLife.23882.001 The way we move – from simple motions like reaching out to grab something, to playing the piano or dancing – is coordinated in our brain. These processes involve many regions and steps, in which nerve cells transport signals along projections known as axons. Axons rely on sophisticated ‘engineering’ to work properly over long distances and are vulnerable to diseases that disrupt their engineering. For example, in genetic diseases called ‘hereditary spastic paraplegias’, damages to the ‘distal’ end of axons – the end furthest from the nerve cell body – cause paralysis of the lower body. Axons have several internal structures that make sure everything works properly. One of these structures is the endoplasmic reticulum, which is a network of tubular membranes that runs lengthwise along the axon. It is known that spastic paraplegias are sometimes caused by mutations affecting proteins that help to build and shape the endoplasmic reticulum, for example, the proteins of the reticulon and REEP families. However, until now it was not known how the ER forms its network in the axons and if this is influenced by these proteins. To see whether reticulons and REEPs affect the shape of the endoplasmic reticulum, Yalçιn et al. used healthy fruit fly larvae, and genetically modified ones that lacked the proteins. The results show that in healthy flies, the tubular network runs continuously along the axons. When either reticulon or REEP proteins were removed, the distal axons contained less endoplasmic reticulum. In mutant fly larvae that lacked both protein families, the endoplasmic reticulum was more interrupted and contained more gaps than in normal larvae. Using high-magnification electron microscopy confirmed these findings, and showed that the tubules of the endoplasmic reticulum in mutant axons were larger, but fewer. A next step will be to test whether these mutations also affect how the axons work and communicate over long distances. A better knowledge of the role of the endoplasmic reticulum in axons will help us to understand how damages to it could affect hereditary spastic paraplegias and other degenerative conditions. DOI:http://dx.doi.org/10.7554/eLife.23882.002
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Affiliation(s)
- Belgin Yalçın
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lu Zhao
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Martin Stofanko
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Niamh C O'Sullivan
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Zi Han Kang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Annika Roost
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Matthew R Thomas
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Sophie Zaessinger
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Olivier Blard
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Alex L Patto
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Anood Sohail
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Valentina Baena
- Department of Cell Biology, University of Connecticut Health Center, Farmington, United States
| | - Mark Terasaki
- Department of Cell Biology, University of Connecticut Health Center, Farmington, United States
| | - Cahir J O'Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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270
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Sezgin E. Super-resolution optical microscopy for studying membrane structure and dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:273001. [PMID: 28481213 PMCID: PMC5952331 DOI: 10.1088/1361-648x/aa7185] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.
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Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX39DS, United Kingdom
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271
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Schoen I, Aires L, Ries J, Vogel V. Nanoscale invaginations of the nuclear envelope: Shedding new light on wormholes with elusive function. Nucleus 2017; 8:506-514. [PMID: 28686487 DOI: 10.1080/19491034.2017.1337621] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Recent advances in fluorescence microscopy have opened up new possibilities to investigate chromosomal and nuclear 3D organization on the nanoscale. We here discuss their potential for elucidating topographical details of the nuclear lamina. Single molecule localization microscopy (SMLM) in combination with immunostainings of lamina proteins readily reveals tube-like invaginations with a diameter of 100-500 nm. Although these invaginations have been established as a frequent and general feature of interphase nuclei across different cell types, their formation mechanism and function have remained largely elusive. We critically review the current state of research, propose possible connections to lamina associated domains (LADs), and revisit the discussion about the potential role of these invaginations for accelerating mRNA nuclear export. Illustrative studies using 3D super-resolution imaging are shown and will be instrumental to decipher the physiological role of these nanoscale invaginations.
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Affiliation(s)
- Ingmar Schoen
- a ETH Zurich, Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology , Zurich , Switzerland
| | - Lina Aires
- a ETH Zurich, Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology , Zurich , Switzerland
| | - Jonas Ries
- b European Molecular Biology Laboratory, Cell Biology and Biophysics Unit , Heidelberg , Germany
| | - Viola Vogel
- a ETH Zurich, Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology , Zurich , Switzerland
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272
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Dhanvantari S. Secretory Granules Tell (Almost) All in Enteroendocrine Cells. Endocrinology 2017; 158:2068-2070. [PMID: 28881871 DOI: 10.1210/en.2017-00459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/15/2017] [Indexed: 11/19/2022]
Affiliation(s)
- Savita Dhanvantari
- Lawson Health Research Institute and Western University, London, Ontario N6A 4V2, Canada
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273
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Grumati P, Morozzi G, Hölper S, Mari M, Harwardt MLI, Yan R, Müller S, Reggiori F, Heilemann M, Dikic I. Full length RTN3 regulates turnover of tubular endoplasmic reticulum via selective autophagy. eLife 2017; 6. [PMID: 28617241 PMCID: PMC5517149 DOI: 10.7554/elife.25555] [Citation(s) in RCA: 289] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/14/2017] [Indexed: 12/21/2022] Open
Abstract
The turnover of endoplasmic reticulum (ER) ensures the correct biological activity of its distinct domains. In mammalian cells, the ER is degraded via a selective autophagy pathway (ER-phagy), mediated by two specific receptors: FAM134B, responsible for the turnover of ER sheets and SEC62 that regulates ER recovery following stress. Here, we identified reticulon 3 (RTN3) as a specific receptor for the degradation of ER tubules. Oligomerization of the long isoform of RTN3 is sufficient to trigger fragmentation of ER tubules. The long N-terminal region of RTN3 contains several newly identified LC3-interacting regions (LIR). Binding to LC3s/GABARAPs is essential for the fragmentation of ER tubules and their delivery to lysosomes. RTN3-mediated ER-phagy requires conventional autophagy components, but is independent of FAM134B. None of the other reticulon family members have the ability to induce fragmentation of ER tubules during starvation. Therefore, we assign a unique function to RTN3 during autophagy. DOI:http://dx.doi.org/10.7554/eLife.25555.001
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Affiliation(s)
- Paolo Grumati
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
| | - Giulio Morozzi
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
| | - Soraya Hölper
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
| | - Muriel Mari
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Marie-Lena Ie Harwardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Riqiang Yan
- Department of Neurosciences, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Stefan Müller
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
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274
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Timing and Reset Mechanism of GTP Hydrolysis-Driven Conformational Changes of Atlastin. Structure 2017; 25:997-1010.e4. [PMID: 28602821 DOI: 10.1016/j.str.2017.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/12/2017] [Accepted: 05/10/2017] [Indexed: 01/09/2023]
Abstract
The endoplasmic reticulum (ER) forms a branched, dynamic membrane tubule network that is vital for cellular function. Branching arises from membrane fusion facilitated by the GTPase atlastin (ATL). Many metazoan genomes encode for three ATL isoforms that appear to fulfill partially redundant function despite differences in their intrinsic GTPase activity and localization within the ER; however, the underlying mechanistic differences between the isoforms are poorly understood. Here, we identify discrete temporal steps in the catalytic cycle for the two most dissimilar isoforms, ATL1 and ATL3, revealing an overall conserved progression of molecular events from nucleotide binding and hydrolysis to ATL dimerization and phosphate release. A crystal structure of ATL3 suggests a mechanism for the displacement of the catalytic Mg2+ ion following guanosine triphosphate (GTP) hydrolysis. Together, the data extend the mechanistic framework for how GTP hydrolysis drives conformational changes in ATL and how the cycle is reset for subsequent rounds of catalysis.
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275
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Chang CL, Chen YJ, Liou J. ER-plasma membrane junctions: Why and how do we study them? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1494-1506. [PMID: 28554772 DOI: 10.1016/j.bbamcr.2017.05.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/09/2017] [Accepted: 05/17/2017] [Indexed: 12/17/2022]
Abstract
Endoplasmic reticulum (ER)-plasma membrane (PM) junctions are membrane microdomains important for communication between the ER and the PM. ER-PM junctions were first reported in muscle cells in 1957, but mostly ignored in non-excitable cells due to their scarcity and lack of functional significance. In 2005, the discovery of stromal interaction molecule 1 (STIM1) mediating a universal Ca2+ feedback mechanism at ER-PM junctions in mammalian cells led to a resurgence of research interests toward ER-PM junctions. In the past decade, several major advancements have been made in this emerging topic in cell biology, including the generation of tools for labeling ER-PM junctions and the unraveling of mechanisms underlying regulation and functions of ER-PM junctions. This review summarizes early studies, recently developed tools, and current advances in the characterization and understanding of ER-PM junctions. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann.
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Affiliation(s)
- Chi-Lun Chang
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Ju Chen
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jen Liou
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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276
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Aouacheria A, Baghdiguian S, Lamb HM, Huska JD, Pineda FJ, Hardwick JM. Connecting mitochondrial dynamics and life-or-death events via Bcl-2 family proteins. Neurochem Int 2017; 109:141-161. [PMID: 28461171 DOI: 10.1016/j.neuint.2017.04.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/17/2017] [Indexed: 12/12/2022]
Abstract
The morphology of a population of mitochondria is the result of several interacting dynamical phenomena, including fission, fusion, movement, elimination and biogenesis. Each of these phenomena is controlled by underlying molecular machinery, and when defective can cause disease. New understanding of the relationships between form and function of mitochondria in health and disease is beginning to be unraveled on several fronts. Studies in mammals and model organisms have revealed that mitochondrial morphology, dynamics and function appear to be subject to regulation by the same proteins that regulate apoptotic cell death. One protein family that influences mitochondrial dynamics in both healthy and dying cells is the Bcl-2 protein family. Connecting mitochondrial dynamics with life-death pathway forks may arise from the intersection of Bcl-2 family proteins with the proteins and lipids that determine mitochondrial shape and function. Bcl-2 family proteins also have multifaceted influences on cells and mitochondria, including calcium handling, autophagy and energetics, as well as the subcellular localization of mitochondrial organelles to neuronal synapses. The remarkable range of physical or functional interactions by Bcl-2 family proteins is challenging to assimilate into a cohesive understanding. Most of their effects may be distinct from their direct roles in apoptotic cell death and are particularly apparent in the nervous system. Dual roles in mitochondrial dynamics and cell death extend beyond BCL-2 family proteins. In this review, we discuss many processes that govern mitochondrial structure and function in health and disease, and how Bcl-2 family proteins integrate into some of these processes.
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Affiliation(s)
- Abdel Aouacheria
- Institute of Evolutionary Sciences of Montpellier (ISEM), CNRS UMR 5554, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Stephen Baghdiguian
- Institute of Evolutionary Sciences of Montpellier (ISEM), CNRS UMR 5554, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Heather M Lamb
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA
| | - Jason D Huska
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA
| | - Fernando J Pineda
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins University, Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA
| | - J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA.
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277
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Minde D, Dunker AK, Lilley KS. Time, space, and disorder in the expanding proteome universe. Proteomics 2017; 17:1600399. [PMID: 28145059 PMCID: PMC5573936 DOI: 10.1002/pmic.201600399] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 12/31/2022]
Abstract
Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms.
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Affiliation(s)
- David‐Paul Minde
- Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - A. Keith Dunker
- Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisINUSA
| | - Kathryn S. Lilley
- Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
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278
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Wilts BD, Apeleo Zubiri B, Klatt MA, Butz B, Fischer MG, Kelly ST, Spiecker E, Steiner U, Schröder-Turk GE. Butterfly gyroid nanostructures as a time-frozen glimpse of intracellular membrane development. SCIENCE ADVANCES 2017; 3:e1603119. [PMID: 28508050 PMCID: PMC5406134 DOI: 10.1126/sciadv.1603119] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/23/2017] [Indexed: 05/05/2023]
Abstract
The formation of the biophotonic gyroid material in butterfly wing scales is an exceptional feat of evolutionary engineering of functional nanostructures. It is hypothesized that this nanostructure forms by chitin polymerization inside a convoluted membrane of corresponding shape in the endoplasmic reticulum. However, this dynamic formation process, including whether membrane folding and chitin expression are simultaneous or sequential processes, cannot yet be elucidated by in vivo imaging. We report an unusual hierarchical ultrastructure in the butterfly Thecla opisena that, as a solid material, allows high-resolution three-dimensional microscopy. Rather than the conventional polycrystalline space-filling arrangement, a gyroid occurs in isolated facetted crystallites with a pronounced size gradient. When interpreted as a sequence of time-frozen snapshots of the morphogenesis, this arrangement provides insight into the formation mechanisms of the nanoporous gyroid material as well as of the intracellular organelle membrane that acts as the template.
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Affiliation(s)
- Bodo D. Wilts
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Benjamin Apeleo Zubiri
- Institute of Micro- and Nanostructure Research and Center for Nanoanalysis and Electron Microscopy, Department of Materials Science and Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 6, D-91058 Erlangen, Germany
| | - Michael A. Klatt
- Institute of Stochastics, Karlsruhe Institute of Technology, Englerstraße 2, D-76131 Karlsruhe, Germany
| | - Benjamin Butz
- Institute of Micro- and Nanostructure Research and Center for Nanoanalysis and Electron Microscopy, Department of Materials Science and Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 6, D-91058 Erlangen, Germany
| | - Michael G. Fischer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Stephen T. Kelly
- Carl Zeiss X-Ray Microscopy, 4385 Hopyard Road, Pleasanton, CA 94588, USA
| | - Erdmann Spiecker
- Institute of Micro- and Nanostructure Research and Center for Nanoanalysis and Electron Microscopy, Department of Materials Science and Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 6, D-91058 Erlangen, Germany
| | - Ullrich Steiner
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Gerd E. Schröder-Turk
- School of Engineering and Information Technology, Mathematics and Statistics, Murdoch University, Murdoch, 90 South Street, Western Australia 6150, Australia
- Department of Applied Mathematics, Research School of Physics and Engineering, 60 Mills Road, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Institute of Theoretical Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 7B, D-91058 Erlangen, Germany
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279
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Deciphering the molecular architecture of membrane contact sites by cryo-electron tomography. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1507-1512. [PMID: 28330771 DOI: 10.1016/j.bbamcr.2017.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/13/2017] [Accepted: 03/17/2017] [Indexed: 01/16/2023]
Abstract
At membrane contact sites (MCS) two cellular membranes form tight appositions that play critical roles in fundamental phenomena such as lipid metabolism or Ca2+ homeostasis. The interest for these structures has surged in recent years, bringing about the characterization of a plethora of MCS-resident molecules. How those molecules are structurally organized at MCS remains enigmatic, limiting our understanding of MCS function. Whereas such molecular detail is obscured by conventional electron microscopy sample preparation, cryo-electron tomography (cryo-ET) allows high resolution imaging of cellular landscapes in close-to-native conditions. Here we briefly review the fundamentals of cryo-ET and how recent developments in this technique are beginning to unveil the molecular architecture of MCS. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann.
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280
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Curchoe CL, Manor U. Actin Cytoskeleton-Mediated Constriction of Membrane Organelles via Endoplasmic Reticulum Scaffolding. ACS Biomater Sci Eng 2017; 3:2727-2732. [PMID: 29250592 DOI: 10.1021/acsbiomaterials.6b00802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intracellular organelles constantly undergo fission to facilitate turnover, transport, and functional changes. The cytoskeleton has long been understood to play a role in these events, and recent work strongly suggests that several conserved molecular players cooperate with the cytoskeleton to mediate the fission process. Membrane curvature-inducing, membrane scission proteins, and force-inducing cytoskeletal proteins all cooperate to drive the fission process. Recent work suggests that the endoplasmic reticulum serves as the linchpin that orchestrates and spatially organizes fission via these curvature-inducing, scission, and force-producing molecules. This all leads us to postulate a "universal theory" of organelle fission with distinct biophysical and biochemical features mediated by a finite number of physical and molecular constraints. This new physical paradigm deserves special attention from those who wish to model these processes, since previous theoretical and experimental attempts to elucidate these fission mechanisms have not included the organizing factor of the endoplasmic reticulum. Here we review the basic concepts of this new model for organelle fission, and explore the implications thereof. Previous studies that didn't include this component can now be interpreted in light of these new data and serve as a useful guide for understanding how this process happens in vivo. Thus, this review provides direction for future modeling and experimental efforts to better understand how these complex systems and processes are regulated in both healthy and diseased biological systems.
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Affiliation(s)
- Carol Lynn Curchoe
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd., La Jolla, CA 92037
| | - Uri Manor
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd., La Jolla, CA 92037
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281
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Lambert TJ, Waters JC. Navigating challenges in the application of superresolution microscopy. J Cell Biol 2017; 216:53-63. [PMID: 27920217 PMCID: PMC5223610 DOI: 10.1083/jcb.201610011] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 11/22/2022] Open
Abstract
In 2014, the Nobel Prize in Chemistry was awarded to three scientists who have made groundbreaking contributions to the field of superresolution (SR) microscopy (SRM). The first commercial SR microscope came to market a decade earlier, and many other commercial options have followed. As commercialization has lowered the barrier to using SRM and the awarding of the Nobel Prize has drawn attention to these methods, biologists have begun adopting SRM to address a wide range of questions in many types of specimens. There is no shortage of reviews on the fundamental principles of SRM and the remarkable achievements made with these methods. We approach SRM from another direction: we focus on the current practical limitations and compromises that must be made when designing an SRM experiment. We provide information and resources to help biologists navigate through common pitfalls in SRM specimen preparation and optimization of image acquisition as well as errors and artifacts that may compromise the reproducibility of SRM data.
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Affiliation(s)
- Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Jennifer C Waters
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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282
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Stepanek L, Pigino G. Millisecond time resolution correlative light and electron microscopy for dynamic cellular processes. Methods Cell Biol 2017; 140:1-20. [DOI: 10.1016/bs.mcb.2017.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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283
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Organelle Communication at Membrane Contact Sites (MCS): From Curiosity to Center Stage in Cell Biology and Biomedical Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 997:1-12. [DOI: 10.1007/978-981-10-4567-7_1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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284
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Kotewicz KM, Ramabhadran V, Sjoblom N, Vogel JP, Haenssler E, Zhang M, Behringer J, Scheck RA, Isberg RR. A Single Legionella Effector Catalyzes a Multistep Ubiquitination Pathway to Rearrange Tubular Endoplasmic Reticulum for Replication. Cell Host Microbe 2016; 21:169-181. [PMID: 28041930 DOI: 10.1016/j.chom.2016.12.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 02/07/2023]
Abstract
Intracellular pathogens manipulate host organelles to support replication within cells. For Legionella pneumophila, the bacterium translocates proteins that establish an endoplasmic reticulum (ER)-associated replication compartment. We show here that the bacterial Sde proteins target host reticulon 4 (Rtn4) to control tubular ER dynamics, resulting in tubule rearrangements as well as alterations in Rtn4 associated with the replication compartment. These rearrangements are triggered via Sde-promoted ubiquitin transfer to Rtn4, occurring almost immediately after bacterial uptake. Ubiquitin transfer requires two sequential enzymatic activities from a single Sde polypeptide: an ADP-ribosyltransferase and a nucleotidase/phosphohydrolase. The ADP-ribosylated moiety of ubiquitin is a substrate for the nucleotidase/phosphohydrolase, resulting in either transfer of ubiquitin to Rtn4 or phosphoribosylation of ubiquitin in the absence of a ubiquitination target. Therefore, a single bacterial protein drives a multistep biochemical pathway to control ubiquitination and tubular ER function independently of the host ubiquitin machinery.
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Affiliation(s)
- Kristin M Kotewicz
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Vinay Ramabhadran
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA; Howard Hughes Medical Institute, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Nicole Sjoblom
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA 02155, USA
| | - Joseph P Vogel
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eva Haenssler
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Mengyun Zhang
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Jessica Behringer
- Program in Genetics, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Rebecca A Scheck
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA 02155, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA; Howard Hughes Medical Institute, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA.
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